ORCID Profile
0000-0002-5124-4721
Current Organisation
Macquarie University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Plant Cell and Molecular Biology | Proteomics and Intermolecular Interactions (excl. Medical Proteomics) | Plant Biology | Plant Physiology |
ANZSRC Socio-Economic Objective (SEO)
Plant Production and Plant Primary Products not elsewhere classified | Expanding Knowledge in the Biological Sciences
Related Links
Publications
Proteomics Reveals New Salt Responsive Proteins Associated with Rice Plasma Membrane
Publisher: Informa UK Limited
Date: 23-09-2007
DOI: 10.1271/BBB.70027
Insight into Physiological, Molecular, and Proteomic Changes Associated with Phytoplasma Infection in Crop Plants
Publisher: Springer International Publishing
Date: 2016
Human Proteome Project and Human Pluripotent Stem Cells: Odd Bedfellows or a Perfect Match?
Publisher: American Chemical Society (ACS)
Date: 30-10-2020
Insect Pest Proteomics and Its Potential Application in Pest Control Management
Publisher: Springer International Publishing
Date: 2016
An efficient and easy-to-use cryopreservation protocol for human ES and iPS cells
Publisher: Springer Science and Business Media LLC
Date: 03-2010
Abstract: Here we describe a simple and efficient human embryonic stem (ES) and induced pluripotent stem (iPS) cells cryopreservation protocol. This protocol involves the use of Rho-associated kinase (ROCK) inhibitor, Y-27632, for the feeder-free dissociated cells. The addition of ROCK inhibitor to both pre- and post-thaw culture media enhanced the cloning efficiency. The presence of Y-27632 in Matrigel further increased the cloning efficiency. As compared with other available protocols for human ES and iPS cells cryopreservation, our protocol differs in the technical simplicity, high cloning efficiency and post-thawing passaging. We believe that this protocol could be a generally applicable and robust platform for feeder-free cryopreservation and the expansion of present and future applications of human ES and iPS cells. The treatment with ROCK inhibitor, cell harvesting and the freezing-thawing process usually takes about 2 h excluding overnight incubation at -80 degrees C.
ISL1 Protein Transduction Promotes Cardiomyocyte Differentiation from Human Embryonic Stem Cells
Publisher: Public Library of Science (PLoS)
Date: 30-01-2013
The quest of cell surface markers for stem cell therapy
Publisher: Springer Science and Business Media LLC
Date: 24-07-2020
Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla
Publisher: MDPI AG
Date: 06-12-2022
Abstract: The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al3+ during different stages of flower development. F3′5′H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al3+-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.
The comparative analysis of phenotypic and whole transcriptome gene expression data of ascites susceptible versus ascites resistant chickens
Publisher: Springer Science and Business Media LLC
Date: 05-12-2018
DOI: 10.1007/S11033-018-4534-8
Abstract: Ascites syndrome (AS) is a metabolic disorder that mainly occurs at later ages of meat-type chickens. Despite many research, there is no consensus about the origin of this syndrome. Our main purpose were to investigate the syndrome using both phenotypic and RNA-Seq data to elucidate the most causative factors predisposing the birds to AS. Phenotypic data analysis showed that AS indicator traits (AITs) were moderate to high heritable. Inexistence of consistent direct genetic correlation between AITs and growth related traits, indicated that neither faster growth rate nor heavier body weight is the most causative factor affecting the susceptibility of broilers to AS. However, respiratory capacity was revealed to be the most probable factor predisposing the birds to AS, as both lung weight and lung percentage were negatively correlated with AITs. Transcriptomic data analysis revealed 125 differentially expressed genes (DEGs) between the ascitic and healthy groups. Up-regulated genes in ascitic group enriched mainly in gas transport biological process, while down-regulated genes involved in defense response to bacteria, biological adhesion, cell adhesion, killing of cells of another organism and cell ision. Genetic association of the DEGs with human cardiovascular diseases suggested excessive heart problems of the ascitic chicks. Heart is, probably, the first tissue suffering from the incompetence of small respiratory system of the AS-susceptible chickens. In other word, tissue hypoxia, that causes free radicals to concentrate in heart cells, may be the commencement of events that finally result to heart failure, suffocation and death of chicks due to the AS.
The Stabilizing Mechanism of Immobilized Metagenomic Xylanases on Bio-Based Hydrogels to Improve Utilization Performance: Computational and Functional Perspectives
Publisher: American Chemical Society (ACS)
Date: 28-07-2020
A Proteomics Approach to Discover Drought Tolerance Proteins in Wheat Pollen Grain at Meiosis Stage
Publisher: Bentham Science Publishers Ltd.
Date: 13-12-2016
A Fresh Look at the Male-specific Region of the Human Y Chromosome
Publisher: American Chemical Society (ACS)
Date: 20-12-2012
DOI: 10.1021/PR300864K
Abstract: The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically map the entire human proteome with the intent to enhance our understanding of human biology at the cellular level. This project attempts simultaneously to establish a sound basis for the development of diagnostic, prognostic, therapeutic, and preventive medical applications. In Iran, current efforts focus on mapping the proteome of the human Y chromosome. The male-specific region of the Y chromosome (MSY) is unique in many aspects and comprises 95% of the chromosome's length. The MSY continually retains its haploid state and is full of repeated sequences. It is responsible for important biological roles such as sex determination and male fertility. Here, we present the most recent update of MSY protein-encoding genes and their association with various traits and diseases including sex determination and reversal, spermatogenesis and male infertility, cancers such as prostate cancers, sex-specific effects on the brain and behavior, and graft-versus-host disease. We also present information available from RNA sequencing, protein-protein interaction, post-translational modification of MSY protein-coding genes and their implications in biological systems. An overview of Human Y chromosome Proteome Project is presented and a systematic approach is suggested to ensure that at least one of each predicted protein-coding gene's major representative proteins will be characterized in the context of its major anatomical sites of expression, its abundance, and its functional relevance in a biological and/or medical context. There are many technical and biological issues that will need to be overcome in order to accomplish the full scale mapping.
Physiology and proteome responses of two contrasting rice mutants and their wild type parent under salt stress conditions at the vegetative stage
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.JPLPH.2013.07.014
Abstract: Salinity is one of the major environmental limiting factors that affects growth and productivity of rice (Oryza sativa L.) worldwide. Rice is among the most sensitive crops to salinity, especially at early vegetative stages. In order to get a better understanding of molecular pathways affected in rice mutants showing contrasting responses to salinity, we exploited the power of 2-DE based proteomics to explore the proteome changes associated with salt stress response. Our physiological observations showed that standard evaluation system (SES) scores, Na+ and K+ concentrations in shoots and Na+/K+ ratio were significantly different in contrasting mutants under salt stress condition. Proteomics analysis showed that, out of 854 protein spots which were reproducibly detected, 67 protein spots showed significant responses to salt stress. The tandem mass spectrometry analysis of these significantly differentially accumulated proteins resulted in identification of 34 unique proteins. These proteins are involved in various molecular processes including defense to oxidative stresses, metabolisms, photosynthesis, protein synthesis and processing, signal transduction. Several of the identified proteins were emerged as key participants in salt stress tolerance. The possible implication of salt responsive proteins in plant adaptation to salt stress is discussed.
Non-coding RNA: Chief architects of drought-resilient roots
Publisher: Elsevier BV
Date: 09-2022
The dynamics of the bacterial communities developed in maize silage
Publisher: Wiley
Date: 11-07-2017
Key Genes and Biochemical Networks in Various Brain Regions Affected in Alzheimer’s Disease
Publisher: MDPI AG
Date: 14-03-2022
Abstract: Alzheimer’s disease (AD) is one of the most complicated progressive neurodegenerative brain disorders, affecting millions of people around the world. Ageing remains one of the strongest risk factors associated with the disease and the increasing trend of the ageing population globally has significantly increased the pressure on healthcare systems worldwide. The pathogenesis of AD is being extensively investigated, yet several unknown key components remain. Therefore, we aimed to extract new knowledge from existing data. Ten gene expression datasets from different brain regions including the hippoc us, cerebellum, entorhinal, frontal and temporal cortices of 820 AD cases and 626 healthy controls were analyzed using the robust rank aggregation (RRA) method. Our results returned 1713 robust differentially expressed genes (DEGs) between five brain regions of AD cases and healthy controls. Subsequent analysis revealed pathways that were altered in each brain region, of which the GABAergic synapse pathway and the retrograde endocannabinoid signaling pathway were shared between all AD affected brain regions except the cerebellum, which is relatively less sensitive to the effects of AD. Furthermore, we obtained common robust DEGs between these two pathways and predicted three miRNAs as potential candidates targeting these genes hsa-mir-17-5p, hsa-mir-106a-5p and hsa-mir-373-3p. Three transcription factors (TFs) were also identified as the potential upstream regulators of the robust DEGs ELK-1, GATA1 and GATA2. Our results provide the foundation for further research investigating the role of these pathways in AD pathogenesis, and potential application of these miRNAs and TFs as therapeutic and diagnostic targets.
Application of carboxymethyl cellulose-g-poly(acrylic acid-co-acrylamide) hydrogel sponges for improvement of efficiency, reusability and thermal stability of a recombinant xylanase
Publisher: Elsevier BV
Date: 11-2019
Efficient saccharification of ionic liquid-pretreated rice straw in a one-pot system using novel metagenomics derived cellulases
Publisher: Elsevier BV
Date: 02-2022
DOI: 10.1016/J.BIORTECH.2021.126536
Abstract: Ionic liquids (ILs)-resistant cellulase enzymes can facilitate the saccharification of IL- pretreated biomass in a one-pot wash-free method. Using a bioinformatics approach, two cellulases, Persicel7 and Persicel8, with convincing evidence for ionic liquid tolerance were identified. Subsequently, these enzymes were heterologously expressed and biochemically characterized. Persicel7 and Persicel8 exhibited endo-β-1, 4-glucanase activity and were resistant to inhibitors and several organic solvents. Their activity in 10% (v/v) 1-ethyl-3-methylimidazolium chloride and 1-butyl-3-methylimidazolium chloride were 130% higher compared with IL-free control. The half-life of cellulases was improved up to 11-fold when incubated with 20% (v/v) solution of ion liquids. In addition, a one-pot IL-pretreatment and enzymatic saccharification of rice straw enhanced the saccharification rate by 33% compared to the untreated reaction. The Persicel7 and Persicel8 unique properties make them attractive candidates for industrial applications, particularly hydrolyzing ion liquid activated biomass in a one-pot system.
Shotgun Proteomic Analysis of the Mexican Lime Tree Infected with “CandidatusPhytoplasma aurantifolia”
Publisher: American Chemical Society (ACS)
Date: 07-01-2013
DOI: 10.1021/PR300865T
Abstract: Infection of Mexican lime trees (Citrus aurantifolia L.) with the specialized bacterium "CandidatusPhytoplasma aurantifolia" causes witches' broom disease. Witches' broom disease has the potential to cause significant economic losses throughout western Asia and North Africa. We used label-free quantitative shotgun proteomics to study changes in the proteome of Mexican lime trees in response to infection by "Ca. Phytoplasma aurantifolia". Of 990 proteins present in five replicates of healthy and infected plants, the abundances of 448 proteins changed significantly in response to phytoplasma infection. Of these, 274 proteins were less abundant in infected plants than in healthy plants, and 174 proteins were more abundant in infected plants than in healthy plants. These 448 proteins were involved in stress response, metabolism, growth and development, signal transduction, photosynthesis, cell cycle, and cell wall organization. Our results suggest that proteomic changes in response to infection by phytoplasmas might support phytoplasma nutrition by promoting alterations in the host's sugar metabolism, cell wall biosynthesis, and expression of defense-related proteins. Regulation of defense-related pathways suggests that defense compounds are induced in interactions with susceptible as well as resistant hosts, with the main differences between the two interactions being the speed and intensity of the response.
Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol and ethanol under aerobic conditions
Publisher: Springer Science and Business Media LLC
Date: 04-01-2016
DOI: 10.1038/SREP18408
Abstract: The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50 and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp. and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated.
Enzymatically triggered delignification through a novel stable laccase: A mixed in-silico /in-vitro exploration of a complex environmental microbiota
Publisher: Elsevier BV
Date: 06-2022
DOI: 10.1016/J.IJBIOMAC.2022.05.039
Abstract: Laccases have been broadly applied as a multitasking biocatalyst in various industries, but their applications tend to be limited by easy deactivation, lack of adequate stability, and susceptibility under complex conditions. Identifying stable laccase as a green-biocatalyst is crucial for developing cost-effective biorefining processes. In this direction, we attempted in-silico screening a stable metagenome-derived laccase (PersiLac1) from tannery wastewater in a complex environment. The laccase exhibited high thermostability, retaining 53.19% activity after 180 min at 70 °C, and it was stable in a wide range of pH (4.0-9.0). After 33 days of storage at 50°C, pH 6.0, the enzyme retained 71.65% of its activity. Various metal ions, inhibitors, and organic solvents showed that PersiLac1 has a stable structure. The stable PersiLac1 could successfully remove lignin and phenolic from quinoa husk and rice straw. In the separate hydrolysis and fermentation process (SHF) after 72 h, hydrolysis was obtained 100% and 73.4% for quinoa husk and rice straw, and fermentation by the S. cerevisiae was be produced 41.46 g/L and 27.75g/L ethanol, respectively. Results signified that the novel lignin-degrading enzyme was confirmed to have great potential for industrial application as a green-biocatalyst based on enzymatically triggered to delignification and detoxify lignocellulosic biomass.
A proteomic approach to analyzing drought- and salt-responsiveness in rice
Publisher: Elsevier BV
Date: 07-2002
Proteomic analysis of wheat contrasting genotypes reveals the interplay between primary metabolic and regulatory pathways in anthers under drought stress
Publisher: Elsevier BV
Date: 08-2020
The novel homologue of the human α‐glucosidase inhibited by the non‐germinated and germinated quinoa protein hydrolysates after in vitro gastrointestinal digestion
Publisher: Hindawi Limited
Date: 16-12-2021
DOI: 10.1111/JFBC.14030
Abstract: Quinoa (Chenopodium quinoa Willd) is a potential source of protein with ideal amino acid profiles which its bioactive compounds can be improved during germination and gastrointestinal digestion. The present investigation studies the impact of germination for 24 hr and simulated gastrointestinal digestion on α-glucosidase inhibitory activity of the quinoa protein and bioactive peptides against the novel homologue of human α-glucosidase, PersiAlpha-GL1. The sprouted quinoa after gastroduodenal digestion was the most effective α-glucosidase inhibitor showing 81.10% α-glucosidase inhibition at concentration 4 mg/ml with the half inhibition rate (IC
Proteome analysis of human embryonic stem cells organelles
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.JPROT.2017.04.017
Abstract: As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.
Proteomic and metabolomic analysis of desiccation tolerance in wheat young seedlings
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.PLAPHY.2019.11.017
Abstract: Young wheat seedlings are desiccation tolerant and have the capacity to withstand long dehydration period. In this study, we characterized the proteome and metabolome of wheat seedlings during desiccation and after recovery. Functional classification of differentially identified proteins revealed dynamic changes in the number and abundance of proteins observed during stress and recovery. Desiccation resulted in a decline in the abundance of proteins associated with photosynthesis and carbohydrate reserves, along with an increase in the presence of proteins associated with stress and defense response, such as peroxiredoxins and antioxidant enzymes. Following recovery, the abundance of stress-responsive proteins returned either partially or completely to their baseline level, confirming their importance to the seedling's desiccation response. Furthermore, proteins involved in carbohydrate metabolism, as well as fructose-bisphosphate aldolase and fructokinase-2 and phosphorylated metabolites as the substrate or the end-product, showed the inverse pattern during desiccation and after re-watering. This may reflect the fact that plants maintained energy supply during stress to protect seedlings from further damage, and for use in subsequent recovery after rewatering period. This study provides novel insights into the molecular mechanisms underlying the desiccation tolerance of wheat seedlings, and paves the way for more detailed molecular analysis of this remarkable phenomenon.
Quantitative proteomics analysis highlights the role of redox hemostasis and energy metabolism in human embryonic stem cell differentiation to neural cells
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.JPROT.2014.02.002
Abstract: Neural differentiation of human embryonic stem cells (hESCs) is a unique opportunity for in vitro analyses of neurogenesis in humans. Extrinsic cues through neural plate formation are well described in the hESCs although intracellular mechanisms underlying neural development are largely unknown. Proteome analysis of hESC differentiation to neural cells will help to further define molecular mechanisms involved in neurogenesis in humans. Using a two-dimensional differential gel electrophoresis (2D-DIGE) system, we analyzed the proteome of hESC differentiation to neurons at three stages, early neural differentiation, neural ectoderm and mature neurons. Out of 137 differentially accumulated protein spots, 118 spots were identified using MALDI-TOF/TOF and LC MS/MS. We observed that proteins involved in redox hemostasis, vitamin and energy metabolism and ubiquitin dependent proteolysis were more abundant in differentiated cells, whereas the abundance of proteins associated with RNA processing and protein folding was higher in hESCs. Higher abundance of proteins involved in maintaining cellular redox state suggests the importance of redox hemostasis in neural differentiation. Furthermore, our results support the concept of a coupling mechanism between neuronal activity and glucose utilization. The protein network analysis showed that the majority of the interacting proteins were associated with the cell cycle and cellular proliferation. These results enhanced our understanding of the molecular dynamics that underlie neural commitment and differentiation. In highlighting the role of redox and unique metabolic properties of neuronal cells, the present findings add insight to our understanding of hESC differentiation to neurons. The abundance of fourteen proteins involved in maintaining cellular redox state, including 10 members of peroxiredoxin (Prdx) family, mainly increased during differentiation, thus highlighting a link of neural differentiation to redox. Our results revealed markedly higher expression of genes encoding enzymes involved in the glycolysis and amino acid synthesis during differentiation. Protein network analysis predicted a number of critical mediators in hESC differentiation. These proteins included TP53, CTNNB1, SMARCA4, TNF, TERT, E2F1, MYC, RB1, and AR.
Proteome analysis of brain in murine experimental autoimmune encephalomyelitis
Publisher: Wiley
Date: 27-07-2010
Abstract: Multiple sclerosis is considered a prototype inflammatory autoimmune disorder of the CNS. Experimental autoimmune encephalomyelitis (EAE) induced by myelin oligodendrocyte glycoprotein is one of the best-characterized animal models of multiple sclerosis. Comprehensive understanding of gene expression in EAE can help identify genes that are important in drug response and pathogenesis. We applied a 2-DE-based proteomics approach to analyze the protein expression pattern of the brain in healthy and EAE s les. Of more than 1000 protein spots we analyzed, 70 showed reproducible and significant changes in EAE compared to controls. Of these, 42 protein spots could be identified using MALDI TOF-TOF-MS. They included mitochondrial and structural proteins as well as proteins involved in ionic and neurotransmitter release, blood barriers, apoptosis, and signal transduction. The possible role of these proteins in the responses of mice to animal models of multiple sclerosis is discussed.
Biological and molecular variability of Zucchini yellow mosaic virus in Iran
Publisher: Wiley
Date: 11-11-2008
DOI: 10.1111/J.1439-0434.2008.01430.X
Abstract: Zucchini yellow mosaic v irus (ZYMV family Potyviridae , genus Potyvirus ) causes high yield losses to cucurbits in many parts of the world. The virus was detected for the first time in Iran in 1988, but the isolates have not been characterized. To study the genetic and biological ersity among Iranian ZYMV isolates, a set of twelve isolates, obtained during an extensive survey conducted from 2003 to 2006 in the major cucurbit‐growing areas, were characterized. An experimental host range study of these isolates (referred as Iran‐1 to Iran‐12) revealed some variation in their biological properties. The nucleotide sequences of the genomic portion spanning the C‐terminal part of NIb and N‐terminal part of coat protein (CP) coding region were determined and compared with other available sequences. The identity among Iranian ZYMV isolates at the amino acid level reached 95.6–100%. The Iranian ZYMV isolates did not form a compact cluster in the phylogenetic tree, and the phylogenetic analyses and the estimation of genetic distance indicate that the Iranian ZYMV group consists of several independent introductions that evolved separately.
Identification and characterization of a novel thermostable xylanase from camel rumen metagenome
Publisher: Elsevier BV
Date: 04-2019
DOI: 10.1016/J.IJBIOMAC.2018.12.041
Abstract: Metagenomics has emerged to isolate novel enzymes from the uncultured microbiota in the environment. In this study, the metagenomic data obtained from camel rumen was considered as the potential source of microbial xylanase enzymes with proper activity in extreme conditions. The metagenomic data were assembled and contigs were used for in-silico identification of candidate thermostable enzyme. A novel thermostable xylanase enzyme, named PersiXyn1, with 1146 bp full-length gene which encodes a 381 amino acid protein was identified. Using the DNA template extracted from camel rumen metagenomic s les, the candidate enzyme genes were cloned and expressed in proper E. coli strains. The phylogenetic analysis showed the evolutionary position of PersiXyn1 among the known thermostable xylanases. The results of the CD analysis and determining the secondary structure of the enzyme, confirmed the presence of a high percentage of β-sheets as an important characteristic of thermophilic xylanases. The PersiXyn1 was active at a broad range of pH (6-11) and temperature (25-90 °C). The optimum pH and temperature were 8 and 40 °C respectively, and the enzyme maintained 80% of its maximum activity in the pH 8 and temperature 40 °C for 1 h. The Scanning electron microscope (SEM) micrograph of enzyme treated pulp clearly showed that the effective use of enzymes in fiber separation may reduce the cost of carton paper production. The novelty of this enzyme lies in the fact that it is highly active and stable in a broad range of pH and temperature. This study highlights the potential importance of camel microbiome for discovering novel thermostable enzymes with applications in agriculture and industries.
Disease-Corrected Hepatocyte-Like Cells from Familial Hypercholesterolemia-Induced Pluripotent Stem Cells
Publisher: Springer Science and Business Media LLC
Date: 18-12-2012
DOI: 10.1007/S12033-012-9635-3
Abstract: The generation of human induced pluripotent stem cells (hiPSCs) from an in idual patient provides a unique tool for disease modeling, drug discovery, and cell replacement therapies. Patient-specific pluripotent stem cells can be expanded in vitro and are thus suitable for genetic manipulations. To date, several genetic liver disorders have been modeled using patient-specific hiPSCs. Here, we present the generation of corrected hepatocyte-like cells (HLCs) from hiPSCs of a familial hypercholesterolemia (FH) patient with a homozygous mutation in the low-density lipoprotein receptor (LDLR) gene. We generated hiPSCs from a patient with FH with the mutated gene encoding a truncated non-functional receptor. In order to deliver normal LDLR to the defective cells, we used a plasmid vector carrying the normal receptor ORF to genetically transform the hiPSCs. The transformed cells were expanded and directed toward HLCs. Undifferentiated defective hiPSCs and HLCs differentiated from the defective hiPSCs did not have the ability to uptake labeled low-density lipoprotein (LDL) particles. The differentiated transformed hiPSCs showed LDL-uptake ability and the correction of disease phenotype as well as expressions of hepatocyte-specific markers. The functionality of differentiated cells was also confirmed by indo-cyanine green (ICG) uptake assay, PAS staining, inducible cyp450 activity, and oil red staining. These data suggest that hiPSC technology can be used for generation of disease-corrected, patient-specific HLCs with potential value for disease modeling and drug discovery as well as cell therapy applications in future.
Advanced glycation end-products produced systemically and by macrophages: A common contributor to inflammation and degenerative diseases
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.PHARMTHERA.2017.02.030
Abstract: Advanced glycation end products (AGEs) and their receptor have been implicated in the progressions of many intractable diseases, such as diabetes and atherosclerosis, and are also critical for pathologic changes in chronic degenerative diseases, such as Alzheimer's disease, Parkinson's disease, and alcoholic brain damage. Recently activated macrophages were found to be a source of AGEs, and the most abundant form of AGEs, AGE-albumin excreted by macrophages has been implicated in these diseases and to act through common pathways. AGEs inhibition has been shown to prevent the pathogenesis of AGEs-related diseases in human, and therapeutic advances have resulted in several agents that prevent their adverse effects. Recently, anti-inflammatory molecules that inhibit AGEs have been shown to be good candidates for ameliorating diabetic complications as well as degenerative diseases. This review was undertaken to present, discuss, and clarify current understanding regarding AGEs formation in association with macrophages, different diseases, therapeutic and diagnostic strategy and links with RAGE inhibition.
Comparison of biologically distinct isolates of Citrus tristeza virus from Iran using major coat protein sequences
Publisher: Springer Science and Business Media LLC
Date: 2005
DOI: 10.1071/AP05079
An orthogonal comparison of the proteome of human embryonic stem cells with that of human induced pluripotent stem cells of different genetic background
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2MB25018G
Abstract: Induced pluripotent stem cells (iPSCs) provide an invaluable resource for drug or toxicology screening, medical research and patient-specific cell therapy. However, the potential applications of iPSCs are largely dependent on the degree of similarity between iPSCs and embryonic stem cells (ESCs). In the present study, we analyzed the proteome of human ESCs and hiPSCs with different genetic background. We carried out an orthogonal contrast analysis of the proteome pattern of two human ESC lines (Royan H5 and Royan H6) and two hiPSC lines from a normal in idual, three hiPSC lines from a normal in idual with Bombay blood group phenotype, and two hiPSC lines from a patient with tyrosinemia. Forty-nine protein spots showed statistically significant differences between two human ESC lines and seven human iPSCs. Mass spectrometry analysis resulted in the identification of 48 proteins belonging to different biological processes, including cytoskeleton organization, energy and metabolic processes, protein synthesis and processing, signal transduction, cell growth and proliferation, cellular trafficking, transcription, calcium binding and immune response. Our results showed that hESCs and hiPSCs had subtle differences at the proteome level thus warranting more detailed and systematic examinations of these cells.
Draft Genome Sequence of Nesterenkonia sp. Strain F, Isolated From Aran-Bidgol Salt Lake in Iran
Publisher: American Society for Microbiology
Date: 10-2011
DOI: 10.1128/JB.05808-11
Abstract: The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp. strain F consists of a 2,812,133-bp chromosome. This study is the first to report the shotgun-sequenced draft genome of a member of the genus Nesterenkonia .
Stable cellulase immobilized on graphene oxide@CMC-g-poly(AMPS-co-AAm) hydrogel for enhanced enzymatic hydrolysis of lignocellulosic biomass
Publisher: Elsevier BV
Date: 02-2020
DOI: 10.1016/J.CARBPOL.2019.115661
Abstract: This study indicated tailoring efficient polymer-enzyme bioconjugates with superb stability and activity for practical utilization of cellulase enzyme in hydrolyzing lignocellulosic biomass. To this goal, a dual crosslinking (DC) strategy was presented to synthesize novel 3D networks of carboxymethyl cellulose grafted copolymers of 2-acrylamido-2methyl propane sulfonate and acrylamide (CMC-g-poly(AMPS-co-AAm)) hydrogels. Graphene oxide (GO) nano-sheets were utilized as nano-filler and physical cross-linker making H-bondings between polymeric chains to prepare GO@CMC-g-poly(AMPS-co-AAm) networks. The GO content effects on the performance of as-synthesized architectures in conjugation to a model enzyme (PersiCel1) were examined. PersiCel1 immobilization on the GO reinforced hydrogels resulted in noticeable retaining near 60 % of its maximum activity at 90 °C, along with the remarkable enhancement of its specific activity and storage stability. Compared with the free PersiCel1, the immobilized enzyme on the GO containing hydrogels showed 154.8 % increase in conversion of alkalin-treated sugar beet pulp, while the PersiCel1/neat-Hydrogel indicated an increment of 66.7 %, under the same conditions.
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen
Publisher: Springer Science and Business Media LLC
Date: 12-2020
In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia
Publisher: Public Library of Science (PLoS)
Date: 07-2015
A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features
Publisher: Public Library of Science (PLoS)
Date: 22-10-2018
Molecular analysis of a stress-induced cDNA encoding the translation initiation factor, eIF1, from the salt-tolerant wild relative of rice, Porteresia coarctata
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/FP03233
Abstract: The analysis of plant response to stress is an important route to the discovery of genes conferring stress tolerance. Protein synthesis is very sensitive to salt stress and proteins involved in this process may be an important determinant of salt tolerance. The halophytic plant, Porteresia coarctata Tateoka, is a close relative of Oryza sativa L., and has the ability to withstand sudden changes in the soil salinity. The translation initiation factor 1 (PceIF1) cDNA was isolated from the leaves of P. coarctata that had been subjected to a high-salt treatment (150 mm NaCl). An expression study showed that the abundance of eIF1 transcripts increased to a maximum level 5 d after stress induction and then decreased to levels similar to leaves of control (unsalinised) plants. This gene was also up-regulated in exogenous abscisic acid (ABA) and mannitol treatments, suggesting that its induction is related to the water deficit effect of high salt. Our studies showed that expression levels of eIF1 transcripts might form a convenient indicator for monitoring a stress-responsive mechanism that operates in the leaves of P. coarctata.
Cold acclimation proteome analysis reveals close link between the up-regulation of low-temperature associated proteins and vernalization fulfillment
Publisher: American Chemical Society (ACS)
Date: 06-10-2010
DOI: 10.1021/PR100475R
Abstract: Low-temperature (LT) stress is one of the major limiting factors in cereal production in cold high-altitude mountainous areas of Iran where cereals are exposed to variable periods of temperatures in the vernalization range during the autumn season. Cereals regulate their development through adaptive mechanisms that are responsive to low but nonfreezing temperatures. We exploited a proteomic approach to determine the interrelationship between vernalization fulfillment and expression of low-temperature (LT)-induced protein in most hardy Norstar and semi-hardy Azar2 wheat (Triticum aestivum L. em. Thell). These cultivars were subjected to 12 h of cold acclimating temperature (2 °C) over a period of 0-89 days. LT tolerance, as measured by LT50, and vernalization fulfillment, as estimated from final leaf number (FLN), was determined at intervals throughout the acclimation period. A significant decrease in FLN associated with LT treatment indicated that Norstar and Azar2 had vernalization responses. Azar2 achieved its vernalization fulfillment and maximum LT tolerance (∼ -8 °C) by 28 days of acclimation. However, Norstar had a longer vernalization requirement (between 35 and 42 days) and reached vernalization fulfillment and maximum LT tolerance (∼ -18.7 °C) about the same time as vernalization fulfillment. We applied a two-dimensional electrophoresis-based proteomics approach to analyze changes in the leaf proteome of two genotypes, Norstar and Azar2, during cold acclimation. Using MALDI-TOF/TOF mass spectrometry, 66 LT-associated proteins could significantly be identified. These proteins were categorized into cold-regulated proteins, antifreezing proteins, oxidative stress defense, photosynthesis, chloroplast post-transcriptional regulation, metabolisms, and protein synthesis. A close association between the vernalization fulfillment and the start of a decline in the protein accumulation of hardy Norstar with a long vernalization requirement and semi-hardy Azar2 with a short vernalization requirement was observed. This finding supported the hypothesis that developmental trait which was regulated by vernalization had a regulatory influence over LT proteome response and highlight a close link between the up-regulation of LT-associated proteins and vernalization fulfillment at the molecular level in wheat.
Epigenetic analysis of human embryonic carcinoma cells during retinoic acid-induced neural differentiation
Publisher: Canadian Science Publishing
Date: 06-2010
DOI: 10.1139/O09-181
Abstract: Differentiation of stem cells from a pluripotent to a committed state involves global changes in genome expression patterns, critically determined by chromatin structure and interactions of chromatin-binding proteins. The dynamics of chromatin structure are tightly regulated by multiple epigenetic mechanisms such as histone modifications and the incorporation of histone variants. In the current work, we induced neural differentiation of a human embryonal carcinoma stem cell line, NTERA2/NT2, by retinoic acid (RA) treatment, primarily according to two different methods of adherent cell culture (rosette formation) and suspension cell culture (EB formation) conditions, and histone modifications and variations were compared through these processes. Western blot analysis of histone extracts showed significant changes in the acetylation and methylation patterns of histone H3, and expression level of the histone variant H2A.Z, after RA treatment in both protocols. Using chromatin immunoprecipitation (ChIP) coupled with real-time PCR, it was shown that these epigenetic changes occurred on the regulatory regions of 4 marker genes (Oct4, Nanog, Nestin, and Pax6) in a culture condition dependent manner. This report demonstrates the dynamic interplay of histone modification and variation in regulating the gene expression profile, during stem cell differentiation and under different culture conditions.
Bi-functionalized aminoguanidine-PEGylated periodic mesoporous organosilica nanoparticles
Publisher: Springer Science and Business Media LLC
Date: 31-03-2021
DOI: 10.1186/S12951-021-00838-Z
Abstract: There is a great interest in the efficient intracellular delivery of Cas9-sgRNA ribonucleoprotein complex (RNP) and its possible applications for in vivo CRISPR-based gene editing. In this study, a nanoporous mediated gene-editing approach has been successfully performed using a bi-functionalized aminoguanidine-PEGylated periodic mesoporous organosilica (PMO) nanoparticles (RNP@AGu@PEG 1500 -PMO) as a potent and biocompatible nanocarrier for RNP delivery. The bi-functionalized MSN-based nanomaterials have been fully characterized using electron microscopy (TEM and SEM), nitrogen adsorption measurements, thermogravimetric analysis (TGA), X-ray powder diffraction (XRD), Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR), and dynamic light scattering (DLS). The results confirm that AGu@PEG 1500 -PMO can be applied for gene-editing with an efficiency of about 40% as measured by GFP gene knockdown of HT1080-GFP cells with no notable change in the morphology of the cells. Due to the high stability and biocompatibility, simple synthesis, and cost-effectiveness, the developed bi-functionalized PMO-based nano-network introduces a tailored nanocarrier that has remarkable potential as a promising trajectory for biomedical and RNP delivery applications.
Comparative proteomic analysis of mouse embryonic stem cells and neonatal-derived cardiomyocytes
Publisher: Elsevier BV
Date: 10-2006
DOI: 10.1016/J.BBRC.2006.08.151
Abstract: Pluripotent embryonic stem cells (ESCs) spontaneously differentiate via embryo-like aggregates into cardiomyocytes. A thorough understanding of the molecular conditions in ESCs is necessary before other potential applications of these cells such as cell therapy can be materialized. We applied two dimensional electrophoresis to analyze and compare the proteome profiling of spontaneous mouse ESC-derived cardiomyocytes (ESC-DCs), undifferentiated mouse ESCs, and neonatal-derived cardiomyocytes (N-DCs). Ninety-five percent of the proteins detected on the ESC-DCs and N-DCs could be precisely paired with one other, whereas only twenty percent of the ESC proteins could be reliably matched with those on the ESC-DCs and N-DCSs, suggesting a striking similarity between them. Having identified sixty proteins in the said three cell types, we sought to provide possible explanations for their differential expression patterns and discuss their relevance to cell biology. This study provides a new insight into the gene expression pattern of differentiated cardiomyocytes and is further evidence for a close relation between ESC-DCs and N-DCSs.
Drought responsive microRNAs in two barley cultivars differing in their level of sensitivity to drought stress
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.PLAPHY.2017.06.007
Abstract: MicroRNAs (miRNAs) are known to be involved in the regulation of gene expression, including that of genes involved in the response to stress. Here, a comparison has been drawn between the miRNA profiles of a drought susceptible, 'Morocco 9-75', and a drought tolerant, 'Yousef', barley cultivars. Leaf water content, shoot dry matter and chlorophyll content decreased in 'Morocco 9-75' more considerably compared with 'Yousef' under drought stress. Furthermore, lower stomatal conductance and higher leaf temperature were observed in 'Morocco 9-75' compared with 'Yousef'. Based on the criteria set for differential abundance, 118 of conserved and novel miRNAs were identified as being responsive to soil water status. Although drought stress resulted in an altered abundance of more miRNAs in 'Morocco 9-75' than in 'Yousef', drought stress was generally associated with an increased miRNA abundance in 'Yousef' and a decreased abundance in 'Morocco 9-75'. An in silico analysis identified 645 genes as putative targets for the drought-responsive miRNAs in 'Yousef' and 3735 in 'Morocco 9-75'. Gene ontology analysis showed that drought stress was associated with the altered abundance of miRNAs targeting growth, development, the juvenile to adult transition and hormone signaling. Some miRNAs which became more abundant in 'Yousef' are thought to target genes intimately involved in development and stress adaptation. In 'Morocco 9-75', drought stress induced changes in the abundance of miRNAs associated with genes affecting growth, development, the juvenile to adult transition and ABA signaling. The data imply that miRNAs may affect the tolerance/sensitivity of barley to drought stress by modulating the expression of a wide set of genes and induction of some physiological changes.
Root Growth and Water Extraction Response of Doubled-Haploid Rice Lines to Drought and Rewatering during the Vegetative Stage
Publisher: Informa UK Limited
Date: 2005
DOI: 10.1626/PPS.8.497
Identification of Mouse Embryonic Stem Cell-Associated Proteins
Publisher: American Chemical Society (ACS)
Date: 30-11-2007
DOI: 10.1021/PR700560T
Abstract: Over the past few years, there has been a growing interest in discovering the molecular mechanisms controlling embryonic stem cells' (ESCs) proliferation and differentiation. Proteome analysis has proven to be an effective approach to comprehensively unravel the regulatory network of differentiation. We applied a two-dimensional electrophoresis based proteomic approach followed by mass spectrometry to analyze the proteome of two mouse ESC lines, Royan B1 and D3, at 0, 6, and 16 days after differentiation initiation. Out of 97 ESC-associated proteins commonly expressed in two ESC lines, 72 proteins were identified using MALDI TOF-TOF mass spectrometry analysis. The expression pattern of four down-regulated proteins including Hspd1, Hspa8, beta-Actin, and Tpt1 were further confirmed by Western blot and immunofluorescence analyses in Royan B1 and D3 as well as two other mouse ESC lines, Royan C1 and Royan C4. Differential mRNA expression analysis of 20 genes using quantitative real-time reverse transcription PCR revealed a low correlation between mRNA and protein levels during differentiation. We also observed that the mRNA level of Tpt1 increased significantly in differentiating cells, whereas its protein level decreased. Several novel ESC-associated proteins have been presented in this study which warrants further investigation with respect to the etiology of stemness.
DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation
Publisher: American Chemical Society (ACS)
Date: 22-07-2015
DOI: 10.1021/ACS.JPROTEOME.5B00512
Abstract: Although it is apparent that chromosome complement mediates sexually dimorphic expression patterns of some proteins that lead to functional differences, there has been insufficient evidence following the manipulation of the male-specific region of the Y chromosome (MSY) gene expression during neural development. In this study, we profiled the expression of 23 MSY genes and 15 of their X-linked homologues during neural cell differentiation of NTERA-2 human embryonal carcinoma cell line (NT2) cells in three different developmental stages using qRT-PCR, Western blotting, and immunofluorescence. The expression level of 12 Y-linked genes significantly increased over neural differentiation, including RBMY1, EIF1AY, DDX3Y, HSFY1, BPY2, PCDH11Y, UTY, RPS4Y1, USP9Y, SRY, PRY, and ZFY. We showed that siRNA-mediated knockdown of DDX3Y, a DEAD box RNA helicase enzyme, in neural progenitor cells impaired cell cycle progression and increased apoptosis, consequently interrupting differentiation. Label-free quantitative shotgun proteomics based on a spectral counting approach was then used to characterize the proteomic profile of the cells after DDX3Y knockdown. Among 917 reproducibly identified proteins detected, 71 proteins were differentially expressed following DDX3Y siRNA treatment compared with mock treated cells. Functional grouping indicated that these proteins were involved in cell cycle, RNA splicing, and apoptosis, among other biological functions. Our results suggest that MSY genes may play an important role in neural differentiation and demonstrate that DDX3Y could play a multifunctional role in neural cell development, probably in a sexually dimorphic manner.
Highly Efficient Computationally Derived Novel Metagenome α-Amylase With Robust Stability Under Extreme Denaturing Conditions
Publisher: Frontiers Media SA
Date: 30-08-2021
DOI: 10.3389/FMICB.2021.713125
Abstract: α-Amylases are among the very critical enzymes used for different industrial purposes. Most α-amylases cannot accomplish the requirement of industrial conditions and easily lose their activity in harsh environments. In this study, a novel α-amylase named PersiAmy1 has been identified through the multistage in silico screening pipeline from the rumen metagenomic data. The long-term storage of PersiAmy1 in low and high temperatures demonstrated 82.13 and 71.01% activities after 36 days of incubation at 4 and 50°C, respectively. The stable α-amylase retained 61.09% of its activity after 180 min of incubation at 90°C and was highly stable in a broad pH range, showing 60.48 and 86.05% activities at pH 4.0 and pH 9.0 after 180 min of incubation, respectively. Also, the enzyme could resist the high-salinity condition and demonstrated 88.81% activity in the presence of 5 M NaCl. PersiAmy1 showed more than 74% activity in the presence of various metal ions. The addition of the detergents, surfactants, and organic solvents did not affect the α-amylase activity considerably. Substrate spectrum analysis showed that PersiAmy1 could act on a wide array of substrates. PersiAmy1 showed high stability in inhibitors and superb activity in downstream conditions, thus useful in detergent and baking industries. Investigating the applicability in detergent formulation, PersiAmy1 showed more than 69% activity after incubation with commercial detergents at different temperatures (30–50°C) and retained more than 56% activity after incubation with commercial detergents for 3 h at 10°C. Furthermore, the results of the wash performance analysis exhibited a good stain removal at 10°C. The power of PersiAmy1 in the bread industry revealed soft, chewable crumbs with improved volume and porosity compared with control. This study highlights the intense power of robust novel PersiAmy1 as a functional bio-additive in many industrial applications.
Editorial: A Systems View of Plant Cellular Communication
Publisher: Frontiers Media SA
Date: 21-03-2022
In-silico discovery of bifunctional enzymes with enhanced lignocellulose hydrolysis from microbiota big data
Publisher: Elsevier BV
Date: 04-2021
Efficient bioconversion of lignocellulosic waste by a novel computationally screened hyperthermostable enzyme from a specialized microbiota
Publisher: Elsevier BV
Date: 03-2023
The suitability of some blood gas and biochemical parameters as diagnostic tools or early indicators of ascites syndrome in broiler sire lines
Publisher: Wiley
Date: 26-11-2015
DOI: 10.1111/JPN.12395
Abstract: In recent few years, there have been some attempts to find a reliable indicator trait as a selection criterion against susceptibility to ascites syndrome (AS). Blood parameters were of great interest as they could be measured in live animals without implementing an ascites-inducing challenge (AIC). In this work, the suitability of some blood parameters was evaluated for diagnosing AS-susceptible chicks in later steps of the disease in trial 1 as well as their early predictive ability in trial 2. In the first trial, one hundred 1-day-old chicks from two pure broiler lines namely S1 and S2 and, in the second trial, 226 1-day-old chicks from line S2 were subjected to AIC. Saline drinking water (1200 mg/l) and lower-than-standard ambient temperatures were the implemented AICs in trials 1 and 2 respectively. The blood parameters including pH, partial pressure of O2 (pO2 ), partial pressure of CO2 (pCO2 ), bicarbonate ion concentration (BIC), percentage of haematocrit (HCT) and saturated haemoglobin (SaO2 ) were measured twice per each bird at days 28 and 35 in trial 1 and once in trial 2 at day 21. The results of the first trial revealed that in line S2 some of the blood parameters differed significantly between the ascitic and non-ascitic groups following exposure to AIC. In this line, the incidence of AS was accompanied by a lower pO2 , SaO2 and BIC, while with higher pCO2 and HCT values. In the second trial, however, although almost all of the parameters showed meaningful differences between the ascitic and non-ascitic broilers, only mean difference of BIC parameter was statistically significant. The general conclusion of this study is that the blood parameters can somewhat have diagnostic ability in the condition in which the AIC is already present, whereas the results did not approve their usefulness as early predictors of AS.
Root endophytic fungus Serendipita indica modulates barley leaf blade proteome by increasing the abundance of photosynthetic proteins in response to salinity
Publisher: Oxford University Press (OUP)
Date: 04-2021
DOI: 10.1111/JAM.15063
Proteomics study reveals the molecular mechanisms underlying cryotolerance induced by mild sublethal stress in human sperm
Publisher: Springer Science and Business Media LLC
Date: 03-11-2021
DOI: 10.1007/S00441-021-03537-1
Abstract: The preconditioning of human sperm with sublethal nitrosative stress before cryopreservation can potentially improve the thawed sperm quality. However, the underlying mechanisms behind this protective strategy are not entirely understood. We compared the cryosurvival of human sperm exposed to 0.01 μM nitric oxide (NO) throughout the cryopreservation and used multiplexed quantitative proteomics approach to identify changes in the proteome profile of preconditioned sperm cells. Semen s les were obtained from 30 normospermia donors and then each s le was ided into three equal parts: fresh (F), frozen-control (C), and frozen exposed to nitric oxide (NO). The sperm undergoing mild sublethal stress showed higher values for motility and viability compared to the frozen control sperm. Moreover, out of 2912 identified proteins, 248 proteins were detected as differentially abundant proteins (DAPs) between cryopreserved groups and fresh group (F) (p < 0.05). Gene ontology (GO) analysis of differentially abundant proteins indicated that the abundance of proteins associated with glycolysis, gluconeogenesis, and fertilization processes was reduced while oxidative phosphorylation pathway was increased in abundance in cryopreserved sperm compared to the fresh sperm. Moreover, redox protein such as thioredoxin 17 was increased in abundance in the NO group compared to the control freezing group. Therefore, the pre-conditioning of sperm prior to cryopreservation may play an important role in maintaining the redox balance in mitochondria of sperm after freezing. Overall, our results indicate that arylsulfatase A (ARSA), serine protease 37 (PRSS37), and sperm surface protein (SP17) may potentially serve as protein biomarkers associated with screening the fertilization potential of the thawed sperm.
Abstract book of the 31stESHRE Annual Meeting, Lisbon, Portugal, 14–17 June 2015
Publisher: Oxford University Press (OUP)
Date: 06-2015
Inhibition of TGFβ Signaling Promotes Ground State Pluripotency
Publisher: Springer Science and Business Media LLC
Date: 15-09-2013
DOI: 10.1007/S12015-013-9473-0
Abstract: Embryonic stem (ES) cells are considered to exist in a ground state if shielded from differentiation triggers. Here we show that FGF4 and TGFβ signaling pathway inhibitors, designated R2i, not only provide the ground state pluripotency in production and maintenance of naïve ES cells from blastocysts of different mouse strains, but also maintain ES cells with higher genomic integrity following long-term cultivation compared with the chemical inhibition of the FGF4 and GSK3 pathways, known as 2i. Global transcriptome analysis of the ES cells highlights augmented BMP4 signaling pathway. The crucial role of the BMP4 pathway in maintaining the R2i ground state pluripotency is demonstrated by BMP4 receptor suppression, resulting in differentiation and cell death. In conclusion, by inhibiting TGFβ and FGF signaling pathways, we introduce a novel defined approach to efficiently establish the ground state pluripotency.
Shotgun Proteomic Analysis of Long-distance Drought Signaling in Rice Roots
Publisher: American Chemical Society (ACS)
Date: 02-12-2011
DOI: 10.1021/PR2008779
Abstract: Rice (Oryza sativa L. cv. IR64) was grown in split-root systems to analyze long-distance drought signaling within root systems. This in turn underpins how root systems in heterogeneous soils adapt to drought. The approach was to compare four root tissues: (1) fully watered (2) fully droughted and split-root systems where (3) one-half was watered and (4) the other half was droughted. This was specifically aimed at identifying how droughted root tissues altered the proteome of adjacent wet roots by hormone signals and how wet roots reciprocally affected dry roots hydraulically. Quantitative label-free shotgun proteomic analysis of four different root tissues resulted in identification of 1487 nonredundant proteins, with nearly 900 proteins present in triplicate in each treatment. Drought caused surprising changes in expression, most notably in partially droughted roots where 38% of proteins were altered in level compared to adjacent watered roots. Specific functional groups changed consistently in drought. Pathogenesis-related proteins were generally up-regulated in response to drought and heat-shock proteins were totally absent in roots of fully watered plants. Proteins involved in transport and oxidation-reduction reactions were also highly dependent upon drought signals, with the former largely absent in roots receiving a drought signal while oxidation-reduction proteins were strongly present during drought. Finally, two functionally contrasting protein families were compared to validate our approach, showing that nine tubulins were strongly reduced in droughted roots while six chitinases were up-regulated, even when the signal arrived remotely from adjacent droughted roots.
Proteomic analysis of rice leaves during drought stress and recovery
Publisher: Wiley
Date: 09-2002
DOI: 10.1002/1615-9861(200209)2:9<1131::AID-PROT1131>3.0.CO;2-1
A New Efficient Protocol for Directed Differentiation of Retinal Pigmented Epithelial Cells from Normal and Retinal Disease Induced Pluripotent Stem Cells
Publisher: Mary Ann Liebert Inc
Date: 10-08-2012
Abstract: We describe a new, efficient protocol that involves the serial addition of noggin, basic fibroblast growth factor (bFGF), retinoic acid, and sonic hedgehog (Shh) for the differentiation of human induced pluripotent stem cells (hiPSC) to retinal pigmented epithelium (RPE) in a serum- and feeder-free adherent condition. hiPSC-RPE cells exhibited RPE morphology and specific molecular markers. Additionally, several hiPSC lines were generated from retinal-specific patients with Leber's congenital amaurosis, Usher syndrome, two patients with retinitis pigmentosa, and a patient with Leber's hereditary optic neuropathy. The RPE cells generated from these disease-specific hiPSCs expressed specific markers by the same RPE lineage-directed differentiation protocol. These findings indicate a new short-term, simple, and efficient protocol for differentiation of hiPSCs to RPE cells. Such specific retinal disease-specific hiPSCs offer an unprecedented opportunity to recapitulate normal and pathologic formation of human retinal cells in vitro, thereby enabling pharmaceutical screening, and potentially autologous cell replacement therapies for retinal diseases.
Age-dependent changes of hindgut microbiota succession and metabolic function of Mongolian cattle in the semi-arid rangelands
Publisher: Frontiers Media SA
Date: 22-07-2022
DOI: 10.3389/FMICB.2022.957341
Abstract: Dietary changes have significant effects on gut microbiota and host health. Weaning is an important stage of dietary change in ruminants. The gastrointestinal tract (GIT) microbiota of calf in the early life undergo some changes, and the plasticity of the calf is beneficial to cope with these changes and challenges. However, the complex development of hindgut microorganisms in post-weaning ruminants is not fully understood. In this study, we used 16S rRNA sequencing and untargeted metabolomic analysis to determine the cecal and colonic bacterial community and associated metabolome of Mongolian cattle at age of the 5th (at weaning), 18th, and 36th months. Moreover, the maturation patterns of the hindgut bacterial community and the dynamic changes of metabolites were also explored. Sequencing results showed that Firmicutes and Bacteroidetes were the dominant phyla in the cecum and colon. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that were stage-specific in the cecum and colon. The relative abundance of Ruminococcaceae, a microbial family related to fiber degradation, gradually increased with age in the cecum, while the relative abundance of Bacteroides and Alistipes , which are related to immunity, gradually increased in the colon. The differential metabolites in the cecum and colon were mainly enriched in steroid hormone biosynthesis, primary bile acid biosynthesis, and arachidonic acid metabolism between different ages of Mongolian cattle after weaning. Consequently, this dual omics analysis provided important information on the changes in microbial and metabolite interactions in Mongolian cattle after weaning. The microorganisms and metabolites in the cecum and colon further enhanced the abiotic stress resistance of Mongolian cattle to the harsh environment. The information obtained in this study is of great significance for future strategies of cecum and colon microbiota regulation of post-weaning Mongolian cattle in the harsh Mongolian Plateau ecosystem.
Simultaneous hydrolysis of various protein-rich industrial wastes by a naturally evolved protease from tannery wastewater microbiota
Publisher: Elsevier BV
Date: 04-2022
DOI: 10.1016/J.SCITOTENV.2021.152796
Abstract: Elimination of protein-rich waste materials is one of the vital environmental protection requirements. Using of non-naturally occurring chemicals for their remediation properties can potentially induce new pollutants. Therefore, enzymes encoded in the genomes of microorganisms evolved in the same environment can be considered suitable alternatives to chemicals. Identification of efficient proteases that can hydrolyze recalcitrant, protein-rich wastes produced by various industrial processes has been widely welcomed as an eco-friendly waste management strategy. In this direction, we attempted to screen a thermo-halo-alkali-stable metagenome-derived protease (PersiProtease1) from tannery wastewater. The PersiProtease1 exhibited high pH stability over a wide range and at 1 h in pH 11.0 maintained 87.59% activity. The enzyme possessed high thermal stability while retaining 76.64% activity after 1 h at 90 °C. Moreover, 65.34% of the initial activity of the enzyme remained in the presence of 6 M NaCl, showing tolerance against high salinity. The presence of various metal ions, inhibitors, and organic solvents did not remarkably inhibit the activity of the discovered protease. The PersiProtease1 was extracted from the tannery wastewater microbiota and efficiently applied for biodegradation of real s le tannery wastewater protein, chicken feathers, whey protein, dehairing sheepskins, and waste X-ray films. PersiProtease1 proved its enormous potential in simultaneous biodegradation of solid and liquid protein-rich industrial wastes based on the results.
Cold-induced physiological and biochemical responses of three grapevine cultivars differing in cold tolerance
Publisher: Springer Science and Business Media LLC
Date: 03-11-2017
Proteomic Analysis of Crop Plants Under Low Temperature: A Review of Cold Responsive Proteins
Publisher: Springer International Publishing
Date: 2016
Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients
Publisher: American Chemical Society (ACS)
Date: 29-07-2015
DOI: 10.1021/ACS.JPROTEOME.5B00520
Abstract: The human Y chromosome has an inevitable role in male fertility because it contains many genes critical for spermatogenesis and the development of the male gonads. Any genetic variation or epigenetic modification affecting the expression pattern of Y chromosome genes may thus lead to male infertility. In this study, we performed isoform-level gene expression profiling of Y chromosome genes within the azoospermia factor (AZF) regions, their X chromosome counterparts, and few autosomal paralogues in testicular biopsies of 12 men with preserved spermatogenesis and 68 men with nonobstructive azoospermia (NOA) (40 Sertoli-cell-only syndrome (SCOS) and 28 premiotic maturation arrest (MA)). This was undertaken using quantitative real-time PCR (qPCR) at the transcript level and Western blotting (WB) and immunohistochemistry (IHC) at the protein level. We profiled the expression of 41 alternative transcripts encoded by 14 AZFa, AZFb, and AZFc region genes (USP9Y, DDX3Y, XKRY, HSFY1, CYORF15A, CYORF15B, KDM5D, EIF1AY, RPS4Y2, RBMY1A1, PRY, BPY2, DAZ1, and CDY1) as well as their X chromosome homologue transcripts and a few autosomal homologues. Of the 41 transcripts, 18 were significantly down-regulated in men with NOA when compared with those of men with complete spermatogenesis. In contrast, the expression of five transcripts increased significantly in NOA patients. Furthermore, to confirm the qPCR results at the protein level, we performed immunoblotting and IHC experiments (based on 24 commercial and homemade antibodies) that detected 10 AZF-encoded proteins. In addition, their localization in testis cell types and organelles was determined. Interestingly, the two missing proteins, XKRY and CYORF15A, were detected for the first time. Finally, we focused on the expression patterns of the significantly altered genes in 12 MA patients with successful sperm retrieval compared to those of 12 MA patients with failed sperm retrieval to predict the success of sperm retrieval in azoospermic men. We showed that HSFY1-1, HSFY1-3, BPY2-1, KDM5C2, RBMX2, and DAZL1 transcripts could be used as potential molecular markers to predict the presence of spermatozoa in MA patients. In this study, we have identified isoform level signature that can be used to discriminate effectively between MA, SCOS, and normal testicular tissues and suggests the possibility of diagnosing the presence of mature sperm cell in azoospermic men to prevent additional testicular sperm extraction (TESE) surgery.
Proteomic analysis of the meristematic root zone in contrasting genotypes reveals new insights in drought tolerance in rice
Publisher: Wiley
Date: 21-08-2022
Abstract: Drought is responsible for major losses in rice production. Root tips contain meristematic and elongation zones that play major roles in determination of root traits and adaptive strategies to drought. In this study we analysed two contrasting genotypes of rice: IR64, a lowland, drought‐susceptible, and shallow‐rooting genotype and Azucena, an upland, drought‐tolerant, and deep‐rooting genotype. S les were collected of root tips of plants grown under control and water deficit stress conditions. Quantitative proteomics analysis resulted in the identification of 7294 proteins from the root tips of IR64 and 6307 proteins from Azucena. Data are available via ProteomeXchange with identifier PXD033343. Using a Partial Least Square Discriminant Analysis on 4170 differentially abundant proteins, 1138 statistically significant proteins across genotypes and conditions were detected. Twenty two enriched biological processes showing contrasting patterns between two genotypes in response to stress were detected through gene ontology enrichment analysis. This included identification of novel proteins involved in root elongation with specific expression patterns in Azucena, including four Expansins and seven Class III Peroxidases. We also detected an antioxidant network and a metallo‐sulfur cluster assembly machinery in Azucena, with roles in reactive oxygen species and iron homeostasis, and positive effects on root cell cycle, growth and elongation.
Direct conversion of human fibroblasts into dopaminergic neural progenitor-like cells using TAT-mediated protein transduction of recombinant factors
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.BBRC.2015.02.166
Abstract: Recent progress in the generation of induced neural progenitor cells (iNPCs) holds tremendous potential for regenerative medicine. However, a major limitation is the lack of a reliable source for cell replacement therapy in neurological diseases such as Parkinson's disease (PD). Here, we show that the combination of small molecules (SM) and TAT-mediated protein transduction of SOX2 and LMX1a in a 3D sphere culture directly convert human fibroblasts to induced dopaminergic neural progenitor-like cells (iDPCs). The generated iDPCs expressed various NPC markers (SOX2, PAX6, NESTIN, OLIG2) and midbrain progenitor markers (EN1, LMX1a, FOXA2, WNT1) as detected by immunostaining and real-time PCR. Following differentiation, the majority of cells expressed neuronal dopaminergic markers as indicated by co-expression of TH with NURR1, and/or PITX3. We found that SOX2 and LMX1a TAT-mediated protein transduction in the combination of SM could directly convert human fibroblasts to self-renewal iDPCs. In conclusion, to our best knowledge, this is the first report of generation of safe DPCs and may suggest an alternative strategy for cell therapy for the treatment of neurodegenerative disorders.
Psychosocial impact of testing human papillomavirus positive in Australia's human papillomavirus‐based cervical screening program: A cross‐sectional survey
Publisher: Wiley
Date: 12-02-2022
DOI: 10.1002/PON.5897
Abstract: To examine the impact of self‐reported human papillomavirus (HPV) test result (HPV negative, HPV positive, HPV result unknown) on a range of psychosocial outcomes. Women and other people with a cervix in Australia aged 25–74 years who reported having participated in cervical screening since December 2017 were recruited through Facebook and Instagram to complete an online survey. The primary outcome measures were anxiety, emotional distress, and general distress. Nine hundred fifteen participants completed the online survey 73.2% reported testing HPV negative (‘HPV−’), 15% reported testing HPV positive (‘HPV+’) and 11.8% reported that they did not know/remember their test result (‘HPV unknown’). Compared to participants testing HPV−, participants testing HPV+ had higher mean anxiety (41.67 vs. 37.08, p 0.001) and emotional distress scores (11.88 vs. 7.71, p 0.001). Concern about test result (34.3% vs. 1.3%, p 0.001), perceived risk compared to average women (55.4% vs. 14.1%, p 0.001), and cancer worry (27.8% vs. 5.9%, p 0.001) were also greater among HPV+ participants than participants testing HPV−. Participants testing HPV+ felt less reassured about their screening result than participants testing HPV− (16% vs. 75.1%, p 0.001). Participants testing HPV+ had greater knowledge of HPV (11.96 vs. 10.36 out of 16, p 0.001) and HPV testing (3.94 vs 3.28 out of 5, p 0.001) than participants who reported testing HPV−. Elevated levels of anxiety and emotional distress were found in those testing HPV+ compared with those testing HPV−. Future research should examine what strategies should be used to deliver test results and what additional information is provided, in order to alleviate anxiety among in iduals testing HPV+.
Erratum to: Nuclear Proteome Analysis of Monkey Embryonic Stem Cells During Differentiation
Publisher: Springer Science and Business Media LLC
Date: 27-02-2010
An education resource for human papillomavirus oropharyngeal cancer patients: think-aloud interviews
Publisher: Springer Science and Business Media LLC
Date: 11-02-2023
DOI: 10.1007/S00520-023-07592-Y
Abstract: The human papillomavirus (HPV) is well recognised as a factor in developing oropharyngeal cancer (OPC). A booklet for HPV-OPC patients aimed to deliver evidence-based messages in everyday language, in a way to minimise negative psychological impacts on patients. Our study explored the suitability of the booklet for use. Participants were recruited through social media and interviewed via Zoom. Participants were shown the booklet and a think-aloud method elicited real-time reactions to the content. Responses were analysed for each section and coded as either for or against for content, with other responses thematically analysed using NVivo. The s le comprised 24 participants: patients ( n = 19) who completed treatment for HPV-OPC and partners of survivors of HPV-OPC ( n = 5). All participants found the booklet useful, and most wished the resource had been available previously. Some indicated the information was new to them. The majority agreed the booklet would be best delivered by their specialist at point of diagnosis and would be a useful resource for friends and family. Most participants gave feedback on improvements to the booklet in terms of comprehension and design. Overall, participants found the content easy to understand. Most participants found that it helped to reduce shame and stigma associated with HPV as a sexually transmitted infection. An evidence-based booklet for HPV-OPC patients and their partners is acceptable. Implementation may be feasible in routine clinical practice, specifically at time of diagnosis. Adapting the content will help optimise the efficacy of the booklet in facilitating communication between all stakeholders.
Nuclear Proteome Analysis of Monkey Embryonic Stem Cells During Differentiation
Publisher: Springer Science and Business Media LLC
Date: 21-01-2010
DOI: 10.1007/S12015-009-9109-6
Abstract: The nuclear proteome enables, manages, and regulates the genome by the collective actions and interactions of proteins found in the nucleus. We applied a proteomic approach to analyze a nuclear proteome during embryonic stem cell (ESC) proliferation, and 3 and 9 days after initiation of differentiation. The nuclei were isolated from cells and their proteins were separated using 2-DE. Out of about 560 protein spots reproducible detected on any give gel, 49 differentially expressed proteins were identified by Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI TOF/TOF) mass spectrometry. Of them, several nuclear located proteins involved in chromatin remodeling, transcription regulation, apoptosis, cell proliferation, and differentiation were identified including CTBP1, MM-1, RUVBL1, HCC-1, SGTA, SUMO2, and Galectin-1. Functional interaction analysis of differentially expressed proteins revealed that most of nuclear proteins had a direct interaction with c-Myc and p53.
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
Publisher: Oxford University Press (OUP)
Date: 10-2016
DOI: 10.1093/NAR/GKW1030
Abstract: Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic s les. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (r/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from & ecologically erse metagenomic s les. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the s les, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
Differential adaptation strategies to different levels of soil water deficit in two upland and lowland genotypes of rice: a physiological and metabolic approach
Publisher: Wiley
Date: 18-12-2019
DOI: 10.1002/JSFA.10153
Abstract: Upland genotypes of rice are less sensitive to soil water deficit (SWD), making them suitable candidates for revealing the strategies underlying plant tolerance. The physiological factors, the biochemical traits needed to withstand oxidative stress, and the metabolite fluctuations of an upland genotype (Azucena) and an intolerant lowland genotype (IR64) genotype were measured under two levels of SWD (withholding water for 7- or 14 days) to identify SWD-responsive strategies associated with tolerance. After withholding water for 7 days, no significant changes in physiological and biochemical traits of Azucena were observed, whereas in IR64, significant decreases in physiological factors were recorded along with increases in oxidative-stress indicators. However, the root length of Azucena increased significantly, showing a clear stress avoidance strategy. Under a prolonged treatment (14 days), IR64 entered an oxidative-damage stage, whereas Azucena exhibited a highly efficient antioxidant system. Our metabolite analysis also revealed two different enriched pathways. After a 7-day SWD, the sugar levels were decreased in the leaves of Azucena but increased in IR64. The reduction in the sugar levels (up to 1.79-log2FC) in the Azucena leaves may be indicative of their transport to the roots, supplying the carbon source needed for root elongation. Under a 14-day treatment, proline and aspartate family members accumulated to the highest levels in Azucena, whereas an increase in the levels of aromatic amino acids with key roles in the biosynthesis of secondary metabolites was detected in IR64. The adaptation strategies identified in two types of rice genotypes in confronting SWD may assist researchers in finding the proper indicators for screening more tolerant genotypes. © 2019 Society of Chemical Industry.
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Publisher: CSIRO Publishing
Date: 16-05-2022
DOI: 10.1071/FP21315
Abstract: Seed dormancy ensures plant survival but many mechanisms remain unclear. A high-throughput RNA-seq analysis investigated the mechanisms involved in the establishment of dormancy in dimorphic seeds of Xanthium strumarium (L.) developing in one single burr. Results showed that DOG1, the main dormancy gene in Arabidopsis thaliana L., was over-represented in the dormant seed leading to the formation of two seeds with different cell wall properties. Less expression of DME/EMB1649, UBP26, EMF2, MOM, SNL2, and AGO4 in the non-dormant seed was observed, which function in the chromatin remodelling of dormancy-associated genes through DNA methylation. However, higher levels of ATXR7/SDG25, ELF6, and JMJ16/PKDM7D in the non-dormant seed that act at the level of histone demethylation and activate germination were found. Dramatically lower expression in the splicing factors SUA, PWI, and FY in non-dormant seed may indicate that variation in RNA splicing for ABA sensitivity and transcriptional elongation control of DOG1 is of importance for inducing seed dormancy. Seed size and germination may be influenced by respiratory factors, and alterations in ABA content and auxin distribution and responses. TOR (a serine/threonine-protein kinase) is likely at the centre of a regulatory hub controlling seed metabolism, maturation, and germination. Over-representation of the respiration-associated genes (ACO3, PEPC3, and D2HGDH) was detected in non-dormant seed, suggesting differential energy supplies in the two seeds. Degradation of ABA biosynthesis and/or proper auxin signalling in the large seed may control germinability, and suppression of endoreduplication in the small seed may be a mechanism for cell differentiation and cell size determination.
Proteomics study reveals the molecular mechanisms underlying water stress tolerance induced by Piriformospora indica in barley
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.JPROT.2013.09.017
Abstract: Piriformospora indica is a mutualistic root endophytic fungus, which transfers several benefits to hosts including enhance plant growth and increase yield under both normal and stress conditions. It has been shown that P. indica root-colonization enhances water stress tolerance based on general and non-specific plant-species mechanism. To better understand the molecular mechanism of P. indica-mediated drought stress tolerance, we designed a set of comparative experiments to study the impact of P. indica on barely plants cultivar "Golden Promise" grown under different drought levels [Filed capacity (F.C.) and 25% F.C.]. P. indica enhanced root and shoot biomass of colonized plants under both well-watered and water-deficit conditions. Proteome analysis of P. indica-colonized barley leaves under well-treated and water-deficit conditions resulted in detection of 726 reproducibly protein spots. Mass spectrometry analysis resulted in the identification of 45 differentially accumulated proteins involved in photosynthesis, reactive oxygen scavenging, metabolisms, signal transduction, and plant defense responses. Interestingly, P. indica increased the level of proteins involved in photosynthesis, antioxidative defense system and energy transport. We propose that P. indica-mediated drought stress tolerance in barely is through photosynthesis stimulation, energy releasing and enhanced antioxidative capacity in colonized plants. Plant mutualistic symbionts offer long-term abiotic stress tolerance through the host adaptation to environmental stress. There have been a few published proteomic studies of plant symbionts to drought, and this is thought to be the first proteomic analysis, demonstrating the impact of endophyte on barley plant under drought stress. For some of identified proteins like TCTP and PCNA, a connection to physiological function in plants is novel, and can be the best candidates for sources of drought tolerance in future studies.
Standard Guidelines for the Chromosome-Centric Human Proteome Project
Publisher: American Chemical Society (ACS)
Date: 26-03-2012
DOI: 10.1021/PR200824A
Abstract: The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of in idual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency of data, governance of the consortium, and collaborative benefits. A companion approach for the Biology and Disease-Driven HPP (B/D-HPP) component of the Human Proteome Project is currently being organized, building upon the Human Proteome Organization's organ-based and biofluid-based initiatives (esearch). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome.
Mining alfalfa (Medicago sativa L.) nodules for salinity tolerant non-rhizobial bacteria to improve growth of alfalfa under salinity stress
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.ECOENV.2018.06.092
Abstract: There are fewer reports on plant growth promoting (PGP) bacteria living in nodules as helper to tolerance to abiotic stress such as salinity and drought. The study was conducted to isolate rhizobial and non-rhizobial drought and salinity tolerant bacteria from the surface sterilized root nodules of alfalfa, grown in saline soils, and evaluate the effects of effective isolates on plant growth under salt stress. Based on drought and salinity tolerance of bacterial isolates and having multiple PGP traits, two non-rhizobial endophytic isolates and one rhizobial endophytic isolate were selected for further identification and characterization. Based on partial sequences of 16 S rRNA genes, non-rhizobial isolates and rhizobial isolate were closely related to Klebsiella sp., Kosakonia cowanii, and Sinorhizobium meliloti, respectively. None of the two non-rhizobial strains were able to form nodules on alfalfa roots under greenhouse and in vitro conditions. Co-inoculation of alfalfa plant with Klebsiella sp. A36, K. cowanii A37, and rhizobial strain S. meliloti ARh29 had a positive effect on plant growth indices under salinity stress. In addition, the single inoculation of non-rhizobial strains without rhizobial strain resulted in an increase in alfalfa growth indices compared to the plants non-inoculated and the ones inoculated with S. meliloti ARh29 alone under salinity stress, indicating that nodule non-rhizobial strains have PGP potentials and may be a promising way for improving effectiveness of Rhizobium bio-fertilizers in salt-affected soils.
A novel metagenome-derived thermostable and poultry feed compatible α-amylase with enhanced biodegradation properties.
Publisher: Elsevier BV
Date: 12-2020
Draft genome sequence of Ureibacillus thermosphaericus strain thermo-BF, isolated from Ramsar hot springs in Iran
Publisher: American Society for Microbiology
Date: 15-08-2012
DOI: 10.1128/JB.00634-12
Abstract: Ureibacillus thermosphaericus strain Thermo-BF is an aerobic, thermophilic bacillus which has been characterized to biosynthesize gold nanoparticles. Here we present the draft genome sequence of Ureibacillus thermosphaericus strain Thermo-BF which consists of a 2,864,162-bp chromosome. This is the first report of a shotgun sequenced draft genome of a species in the Ureibacillus genus.
A potential probiotic Enterococcus faecium isolated from camel rumen, fatty acids biotransformation, antilisteria activity and safety assessment
Publisher: Elsevier BV
Date: 10-2023
Y Chromosome Missing Protein, TBL1Y, May Play an Important Role in Cardiac Differentiation
Publisher: American Chemical Society (ACS)
Date: 13-09-2017
DOI: 10.1021/ACS.JPROTEOME.7B00391
Abstract: Despite evidence for sex-specific cardiovascular physiology and pathophysiology, the biological basis for this dimorphism remains to be explored. Apart from hormonal factors, gender-related characteristics may reside in the function of sex chromosomes during cardiac development. In this study, we investigated the differential expression of the male-specific region of the Y chromosome (MSY) genes and their X counterparts during cardiac differentiation of human embryonic stem cells (hESC). We observed alterations in mRNA and protein levels of TBL1Y, PCDH11Y, ZFY, KDM5D, USP9Y, RPS4Y1, DDX3Y, PRY, XKRY, BCORP1, RBMY, HSFY, and UTY, which accompanied changes in intracellular localization. Of them, the abundance of a Y chromosome missing protein, TBL1Y, showed a significant increase during differentiation while the expression level of its X counterpart decreased. Consistently, reducing TBL1Y cellular level using siRNA approach influenced cardiac differentiation by reducing its efficacy as well as increasing the probability of impaired contractions. TBL1Y knockdown may have negatively impacted cardiogenesis by CtBP stabilization. Furthermore, we presented compelling experimental evidence to distinguish TBL1Y from TBL1X, its highly similar X chromosome homologue, and proposed reclassification of TBL1Y as "found missing protein" (PE1). Our results demonstrated that MSY proteins may play an important role in cardiac development.
The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways
Publisher: Oxford University Press (OUP)
Date: 31-10-2020
DOI: 10.1093/GIGASCIENCE/GIAA116
Abstract: Generation of oligodendrocytes is a sophisticated multistep process, the mechanistic underpinnings of which are not fully understood and demand further investigation. To systematically profile proteome dynamics during human embryonic stem cell differentiation into oligodendrocytes, we applied in-depth quantitative proteomics at different developmental stages and monitored changes in protein abundance using a multiplexed tandem mass tag-based proteomics approach. Our proteome data provided a comprehensive protein expression profile that highlighted specific expression clusters based on the protein abundances over the course of human oligodendrocyte lineage differentiation. We identified the eminence of the planar cell polarity signalling and autophagy (particularly macroautophagy) in the progression of oligodendrocyte lineage differentiation—the cooperation of which is assisted by 106 and 77 proteins, respectively, that showed significant expression changes in this differentiation process. Furthermore, differentially expressed protein analysis of the proteome profile of oligodendrocyte lineage cells revealed 378 proteins that were specifically upregulated only in 1 differentiation stage. In addition, comparative pairwise analysis of differentiation stages demonstrated that abundances of 352 proteins differentially changed between consecutive differentiation time points. Our study provides a comprehensive systematic proteomics profile of oligodendrocyte lineage cells that can serve as a resource for identifying novel biomarkers from these cells and for indicating numerous proteins that may contribute to regulating the development of myelinating oligodendrocytes and other cells of oligodendrocyte lineage. We showed the importance of planar cell polarity signalling in oligodendrocyte lineage differentiation and revealed the autophagy-related proteins that participate in oligodendrocyte lineage differentiation.
Investigation of a Hot-Spring Extremophilic Ureibacillus thermosphaericus Strain Thermo-BF for Extracellular Biosynthesis of Functionalized Gold Nanoparticles
Publisher: Springer Science and Business Media LLC
Date: 23-04-2013
A Novel High Glucose-Tolerant β-Glucosidase: Targeted Computational Approach for Metagenomic Screening
Publisher: Frontiers Media SA
Date: 30-07-2020
Cellular and Molecular Characterization of Human Cardiac Stem Cells Reveals Key Features Essential for Their Function and Safety
Publisher: Mary Ann Liebert Inc
Date: 15-06-2015
MicroRNAs regulate the main events in rice drought stress response by manipulating the water supply to shoots
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7MB00298J
Abstract: MicroRNAs (miRNAs) are small endogenous regulatory RNAs that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses.
Efficient Differentiation of Human Embryonic Stem Cells Toward Dopaminergic Neurons Using Recombinant LMX1A Factor
Publisher: Springer Science and Business Media LLC
Date: 08-11-2014
DOI: 10.1007/S12033-014-9814-5
Abstract: Direct differentiation of dopaminergic (DA) neurons from human pluripotent stem cells (hPSCs) in the absence of gene manipulation is the most desired alternative to clinical treatment of Parkinson disease. Protein transduction-based methods could be efficient, safe approaches to enhance direct differentiation of human embryonic stem cells (hESCs) to DA neurons. In the present study, we compared the differentiation efficiency of DA neurons from hESCs with and without the application of LIM homeobox transcription factor 1 alpha (LMX1A), a master regulatory protein in the development of the midbrain neurons and SHH proteins. The results obtained revealed that the treatment of hESCs with recombinant LMX1A (rLMX1A) protein along with dual SMAD inhibition led to higher expression of LMX1B, LMX1A, FOXA2, PITX3, EN1, and WNT1 effector endogenous genes and two-fold expression of PITX3. Moreover, the highest expression level of PITX3 and TH was observed when rLMX1A was added to the induction medium supplemented with SHH. To our best knowledge, this is the first report demonstrating the application of TAT-LMX1A recombinant protein to enhance hESC differentiation to DA as shown by the expression of DA specific makers. These findings pave the way for enhancing the differentiation of hESCs to DA neurons safely and efficiently without genetic modification.
The Art of Validating Quantitative Proteomics Data
Publisher: Wiley
Date: 25-11-2018
Abstract: Western blotting as an orthogonal validation tool for quantitative proteomics data has rapidly become a de facto requirement for publication. In this viewpoint article, the pros and cons of western blotting as a validation approach are discussed, using ex les from our own published work, and how to best apply it to improve the quality of data published is outlined. Further, suggestions and guidelines for some other experimental approaches are provided, which can be used for validation of quantitative proteomics data in addition to, or in place of, western blotting.
Impact of environmental variables on yield related traits and bioactive compounds of the Persian fenugreek (Trigonella foenum-graecum L.) populations
Publisher: Springer Science and Business Media LLC
Date: 05-05-2022
DOI: 10.1038/S41598-022-10940-3
Abstract: Trigonella foenum-graecum is widely distributed worldwide and grown under a wide range of climatic conditions. The current research was conducted to study the effects of the environmental variables on yield related traits and metabolite contents of 50 different Persian fenugreeks at various geographical locations. Accordingly, multivariate statistical techniques including canonical correspondence analysis (CCA), hierarchical clustering on principal components, and partial least squares regression (PLSR) were applied to determine important proxy variables and establish a relevant model to predict bioactive compounds in fenugreeks. The interrelation of clustered groups emphasized the importance of functional groups of bioactive compounds and several yield related traits. The CCA indicated that two climatic variables of temperature and solar irradiation contributed prominently to 4-hydroxyisoleucine accumulation. The predicted model based on PLSR revealed climatic variables such as temperature, solar, and rain. The precursor of isoleucine was the predictive power for 4-hydroxyisoleucine accumulation while seed weight predicted trigonelline content. The current study's findings may provide helpful information for the breeding strategies of this multipurpose crop.
Plant–Microbe Symbiosis: What Has Proteomics Taught Us?
Publisher: Wiley
Date: 08-2019
Abstract: Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function
Publisher: American Chemical Society (ACS)
Date: 10-2018
Complete nucleotide sequence of Iranian tomato yellow leaf curl virus isolate
Publisher: Springer Science and Business Media LLC
Date: 25-03-2004
DOI: 10.1007/S00705-004-0308-9
Abstract: Complete nucleotide sequence of the Iranian strain of tomato yellow leaf curl virus (TYLCV-IR) was determined and compared with some begomoviruses. The complete sequence of TYLCV-IR clustered together with TYLCV and TYLCV-MId from Israel. A similar relationship holds when the deduced amino acid sequences of V1, V2, C2 and C3 and nucleotide sequences of IR, and RIR were compared. In contrast, phylogenetic analyses of amino acid sequences of C4, C1, and nucleotide sequences of LIR revealed that TYLCV-IR clustered with TLCIRV and two Indian species: ToLCBV- [Ban4], and ToLCKV. The phylogenetic analyses, Recombination Detection Program analyses, and sequence alignment survey provided evidence of the occurrence of recombination between an Israeli TYLCV-MId, as major parent, and TLCIRV, as minor parent. In this recombination event, a region (from nt 2149 to 2766) of TYLCV-MId genome were replaced with corresponding genome sequences of TLCIRV (RDP P-value = 5.976 x 10(-72)), which include LIR, C4, and N-terminal of C1. Infectivity of the cloned TYLCV-IR genome was demonstrated by successful agroinoculation of tomato ( Lycopersicon esculentum) and other plant species. The disease was transmitted by the natural vector Bemisia tabaci from agroinoculated plants to test plants, reproducing in this way the full biological cycle and proving that the genome of TYLCV-IR consists of only one circular single-stranded DNA molecule.
A proteomics view on the role of drought-induced senescence and oxidative stress defense in enhanced stem reserves remobilization in wheat
Publisher: Elsevier BV
Date: 09-2011
DOI: 10.1016/J.JPROT.2011.05.015
Abstract: Drought is one of the major factors limiting the yield of wheat (Triticum aestivum L.) particularly during grain filling. Under terminal drought condition, remobilization of pre-stored carbohydrates in wheat stem to grain has a major contribution in yield. To determine the molecular mechanism of stem reserve utilization under drought condition, we compared stem proteome patterns of two contrasting wheat landraces (N49 and N14) under a progressive post-anthesis drought stress, during which period N49 peduncle showed remarkably higher stem reserves remobilization efficiency compared to N14. Out of 830 protein spots reproducibly detected and analyzed on two-dimensional electrophoresis gels, 135 spots showed significant changes in at least one landrace. The highest number of differentially expressed proteins was observed in landrace N49 at 20days after anthesis when active remobilization of dry matter was observed, suggesting a possible involvement of these proteins in effective stem reserve remobilization of N49. The identification of 82 of differentially expressed proteins using mass spectrometry revealed a coordinated expression of proteins involved in leaf senescence, oxidative stress defense, signal transduction, metabolisms and photosynthesis which might enable N49 to efficiently remobilized its stem reserves compared to N14. The up-regulation of several senescence-associated proteins and breakdown of photosynthetic proteins in N49 might reflect the fact that N49 increased carbon remobilization from the stem to the grains by enhancing senescence. Furthermore, the up-regulation of several oxidative stress defense proteins in N49 might suggest a more effective protection against oxidative stress during senescence in order to protect stem cells from premature cell death. Our results suggest that wheat plant might response to soil drying by efficiently remobilize assimilates from stem to grain through coordinated gene expression.
Mouse model of Alzheimer's disease demonstrates differential effects of early disease pathology on various brain regions
Publisher: Wiley
Date: 09-03-2021
The Quest for Missing Proteins in Rice
Publisher: Elsevier BV
Date: 2019
Generation of human induced pluripotent stem cells from a Bombay individual: Moving towards “universal-donor” red blood cells
Publisher: Elsevier BV
Date: 2010
DOI: 10.1016/J.BBRC.2009.11.058
Abstract: Bombay phenotype is one of the rare phenotypes in the ABO blood group system that fails to express ABH antigens on red blood cells. Nonsense or missense mutations in fucosyltransfrase1 (FUT1) and fucosyltransfrase2 (FUT2) genes are known to create this phenotype. This blood group is compatible with all other blood groups as a donor, as it does not express the H antigen on the red blood cells. In this study, we describe the establishment of human induced pluripotent stem cells (iPSCs) from the dermal fibroblasts of a Bombay blood-type in idual by the ectopic expression of established transcription factors Klf4, Oct4, Sox2, and c-Myc. Sequence analyses of fibroblasts and iPSCs revealed a nonsense mutation 826C to T (276 Gln to Ter) in the FUT1 gene and a missense mutation 739G to A (247 Gly to Ser) in the FUT2 gene in the Bombay phenotype under study. The established iPSCs resemble human embryonic stem cells in morphology, passaging, surface and pluripotency markers, normal karyotype, gene expression, DNA methylation of critical pluripotency genes, and in-vitro differentiation. The directed differentiation of the iPSCs into hematopoietic lineage cells displayed increased expression of the hematopoietic lineage markers such as CD34, CD133, RUNX1, KDR, alpha-globulin, and gamma-globulin. Such specific stem cells provide an unprecedented opportunity to produce a universal blood group donor, in-vitro, thus enabling cellular replacement therapies, once the safety issue is resolved.
Zeolite-based nanocomposite as a smart pH-sensitive nanovehicle for release of xylanase as poultry feed supplement
Publisher: Springer Science and Business Media LLC
Date: 11-2021
DOI: 10.1038/S41598-021-00688-7
Abstract: Xylanase improves poultry nutrition by degrading xylan in the cell walls of feed grains and release the entrapped nutrients. However, the application of xylanase as a feed supplement is restricted to its low stability in the environment and gastrointestinal (GI) tract of poultry. To overcome these obstacles, Zeozyme NPs as a smart pH-responsive nanosystem was designed based on xylanase immobilization on zeolitic nanoporous as the major cornerstone that was modified with L-lysine. The immobilized xylanase was followed by encapsulating with a cross-linked CMC-based polymer. Zeozyme NPs was structurally characterized using TEM, SEM, AFM, DLS, TGA and nitrogen adsorption/desorption isotherms at liquid nitrogen temperature. The stability of Zeozyme NPs was evaluated at different temperatures, pH, and in the presence of proteases. Additionally, the release pattern of xylanase was investigated at a digestion model mimicking the GI tract. Xylanase was released selectively at the duodenum and ileum (pH 6–7.1) and remarkably preserved at pH ≤ 6 including proventriculus, gizzard, and crop (pH 1.6–5). The results confirmed that the zeolite equipped with the CMC matrix could enhance the xylanase thermal and pH stability and preserve its activity in the presence of proteases. Moreover, Zeozyme NPs exhibited a smart pH-dependent release of xylanase in an in vitro simulated GI tract.
Preconditioning of sperm with sublethal nitrosative stress: a novel approach to improve frozen–thawed sperm function
Publisher: Elsevier BV
Date: 03-2019
DOI: 10.1016/J.RBMO.2018.11.029
Abstract: Can sublethal stress induced by nitric oxide on fresh human spermatozoa protect the functional properties of post-thaw human spermatozoa? Semen s les were obtained from 46 donors. Twenty semen s les were used to determine toxicity level of nitric oxide by incubation of semen with different concentrations of nitric oxide (0.01 to 400 μM). Then, 26 semen s les were cryopreserved with optimized ranges of nitric oxide: control (NO-0.00), 0.01 μM nitric oxide (NO-0.01), 0.1 μM nitric oxide (NO-0.1), 1 μM nitric oxide (NO-1), 10 μM nitric oxide (NO-10), 100 μM nitric oxide (NO-100). Frozen-thawed spermatozoa were assessed for motion characteristics, viability, morphology, apoptosis-like changes, caspase 3 activity, DNA fragmentation and intracellular reactive oxygen species levels. Fertilization potential was investigated by heterologous piezo-intracytoplasmic sperm injection (piezo-ICSI) of human spermatozoa into mouse oocytes. In fresh spermatozoa, nitric oxide did not induce a negative effect, except a significant reduction in motility and viability at 200 µM and 400 µM (P < 0.05). Cryopreservation significantly reduced sperm motility and increased reactive oxygen species, apoptosis-like changes, caspase 3 activity, and DNA damage (P < 0.05). NO-0.01 significantly increased total and progressive motility versus the other groups (P < 0.05). The lowest percentage of caspase 3 activity was in the NO-0.01 and NO-0.1 compared with the other freezing groups. In the fertilization trial, the rate of two-cell embryo formation after heterologous piezo-ICSI was higher (P < 0.05) in NO-0.01 (69%) versus controls (42%). Sublethal oxidative stress induced by nitric oxide might improve human sperm function after cryopreservation.
Proteomic responses of rice young panicles to salinity
Publisher: Wiley
Date: 12-2006
Abstract: Rice (Oryza sativa) is most sensitive to salinity during the reproductive stage. We employed a proteomic approach to further understand the mechanism of plant responses to salinity at an early reproductive stage. Plants were grown in culture solution and salt stress imposed at panicle initiation. After 12 days of stress, young panicles were collected from control and salt stressed plants. The Na+ and K+ content of panicle and several yield components changed significantly in response to short-term salt stress. The collected panicles were sorted into three different sizes (7 +/- 1, 11 +/- 1, and 15 +/- 1 mm) and their proteome patterns were analyzed using 2-DE in triplicates. The expression pattern of 13 proteins significantly changed in all panicle sizes in response to stress. MS analysis of salt responsive proteins and 16 other highly abundant proteins of panicle led to the identification of proteins involved in several salt responsive mechanisms which may increase plant adaptation to salt stress including higher constitutive expression level and up-regulation of antioxidants, up-regulation of proteins involved in translation, transcription, signal transduction, and ATP generation. To the best of our knowledge, this is the first proteome analysis of plant young panicle which may enhance our understanding of plant molecular responses to salinity. Proteome reference map of rice young panicle is available at www.proteome.ir.
A comparative proteome approach to decipher the mechanism of rice adaptation to phosphorous deficiency
Publisher: Wiley
Date: 30-12-2008
Abstract: Mineral deficiency limits crop production in most soils and in Asia alone, about 50% of rice lands are phosphorous deficient. In an attempt to determine the mechanism of rice adaptation to phosphorous deficiency, changes in proteome patterns associated with phosphorous deficiency have been investigated. We analyzed the parental line Nipponbare in comparison to its near isogenic line (NIL6-4) carrying a major phosphorous uptake QTL (Pup1) on chromosome 12. Using 2-DE, the proteome pattern of roots grown under 1 and 100 microM phosphorous were compared. Out of 669 proteins reproducibly detected on root 2-DE gels, 32 proteins showed significant changes in the two genotypes. Of them, 17 proteins showed different responses in two genotypes under stress condition. MS resulted in identification of 26 proteins involved in major phosphorous deficiency adaptation pathways including reactive oxygen scavenging, citric acid cycle, signal transduction, and plant defense responses as well as proteins with unknown function. Our results highlighted a coordinated response in NIL in response to phosphorous deficiency which may confer higher adaptation to nutrient deficiency.
Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies
Publisher: Oxford University Press (OUP)
Date: 12-11-2020
DOI: 10.1093/GBE/EVAA231
Abstract: The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic ersity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per s le. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic ersity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and sw buffaloes indicated that these fixation signals persisted across river and sw buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.
Loss of Shp2 Rescues BDNF/TrkB Signaling and Contributes to Improved Retinal Ganglion Cell Neuroprotection
Publisher: Elsevier BV
Date: 02-2019
Complete Genome Sequence of Oceanimonas sp. GK1, a Halotolerant Bacterium from Gavkhouni Wetland in Iran
Publisher: American Society for Microbiology
Date: 15-04-2012
DOI: 10.1128/JB.00023-12
Abstract: Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium which was characterized as producing large amounts of poly-β-hydroxybutyrate. Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245 bp in length.
Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica
Publisher: Springer Science and Business Media LLC
Date: 22-03-2019
DOI: 10.1007/S10142-019-00671-6
Abstract: Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.
Mining of camel rumen metagenome to identify novel alkali-thermostable xylanase capable of enhancing the recalcitrant lignocellulosic biomass conversion
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.BIORTECH.2019.02.059
Abstract: The aim of this study was to isolate and characterize novel alkali-thermostable xylanase genes from the mixed genome DNA of camel rumen metagenome. In this study, a five-stage computational screening procedure was utilized to find the primary candidate enzyme with superior properties from the camel rumen metagenome. This enzyme was subjected to cloning, purification, and structural and functional characterization. It showed high thermal stability, high activity in a broad range of pH (6-11) and temperature (30-90 °C) and effectivity in recalcitrant lignocellulosic biomass degradation. Our results demonstrated the power of in silico analysis to discover novel alkali-thermostable xylanases, effective for the bioconversion of lignocellulosic biomass.
Transcriptomic and Metabolomic Analyses Reveal Inhibition of Hepatic Adipogenesis and Fat Catabolism in Yak for Adaptation to Forage Shortage During Cold Season
Publisher: Frontiers Media SA
Date: 17-01-2022
DOI: 10.3389/FCELL.2021.759521
Abstract: Animals have adapted behavioral and physiological strategies to conserve energy during periods of adverse conditions. Hepatic glucose is one such adaptation used by grazing animals. While large vertebrates have been shown to have feed utilization and deposition of nutrients—fluctuations in metabolic rate—little is known about the regulating mechanism that controls hepatic metabolism in yaks under grazing conditions in the cold season. Hence, the objective of this research was to integrate transcriptomic and metabolomic data to better understand how the hepatic responds to chronic nutrient stress. Our analyses indicated that the blood parameters related to energy metabolism (glucose, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, lipoprotein lipase, insulin, and insulin-like growth factor 1) were significantly ( p & 0.05) lower in the cold season. The RNA-Seq results showed that malnutrition inhibited lipid synthesis (particularly fatty acid, cholesterol, and steroid synthesis), fatty acid oxidation, and lipid catabolism and promoted gluconeogenesis by inhibiting the peroxisome proliferator-activated receptor (PPAR) and PI3K-Akt signaling pathways. For metabolite profiles, 359 metabolites were significantly altered in two groups. Interestingly, the cold season group remarkably decreased glutathione and phosphatidylcholine (18:2 (2E, 4E)/0:0). Moreover, integrative analysis of the transcriptome and metabolome demonstrated that glycolysis or gluconeogenesis, PPAR signaling pathway, fatty acid biosynthesis, steroid biosynthesis, and glutathione metabolism play an important role in the potential relationship between differential expression genes and metabolites. The reduced lipid synthesis, fatty acid oxidation, and fat catabolism facilitated gluconeogenesis by inhibiting the PPAR and PI3K-Akt signaling pathways to maintain the energy homeostasis of the whole body in the yak, thereby coping with the shortage of forages and adapting to the extreme environment of the Qinghai-Tibetan Plateau (QTP).
Growth and Water Use Response of Doubled-Haploid Rice Linesto Drought and Rewatering during the Vegetative Stage
Publisher: Informa UK Limited
Date: 2006
DOI: 10.1626/PPS.9.141
Induced pluripotent stem cells: A new era for hepatology
Publisher: Elsevier BV
Date: 10-2010
DOI: 10.1016/J.JHEP.2010.05.009
Abstract: Stem cell transplantation has been proposed as an attractive alternative approach to restore liver mass and function. Recent progress has been reported on the generation of induced pluripotent stem (iPS) cells from somatic cells. Human-iPS cells can be differentiated towards the hepatic lineage which presents possibilities for improving research on diseases, drug development, tissue engineering, the development of bio-artificial livers, and a foundation for producing autologous cell therapies that would avoid immune rejection and enable correction of gene defects prior to cell transplantation. This focused review will discuss how human iPS cell advances are likely to have an impact on hepatology.
Proteome Analysis of Ground State Pluripotency
Publisher: Springer Science and Business Media LLC
Date: 16-12-2015
DOI: 10.1038/SREP17985
Abstract: The differentiation potential of pluripotent embryonic stem cells (ESCs) can be manipulated via serum and medium conditions for direct cellular development or to maintain a naïve ground state. The self-renewal state of ESCs can thus be induced by adding inhibitors of mitogen activated protein kinase (MAPK) and glycogen synthase kinase-3 (Gsk3), known as 2 inhibitors (2i) treatment. We have used a shotgun proteomics approach to investigate differences in protein expressions between 2i- and serum-grown mESCs. The results indicated that 164 proteins were significantly upregulated and 107 proteins downregulated in 2i-grown cells compared to serum. Protein pathways in 2i-grown cells with the highest enrichment were associated with glycolysis and gluconeogenesis. Protein pathways related to organ development were downregulated in 2i-grown cells. In serum-grown ESCs, protein pathways involved in integrin and focal adhesion and signaling proteins involved in the actin cytoskeleton regulation were enriched. We observed a number of nuclear proteins which were mostly involved in self-renewal maintenance and were expressed at higher levels in 2i compared to serum - Dnmt1, Map2k1, Parp1, Xpo4, Eif3g, Smarca4/Brg1 and Smarcc1/Baf155. Collectively, the results provided an insight into the key protein pathways used by ESCs in the ground state or metastable conditions through 2i or serum culture medium, respectively.
Apolipoprotein ε in brain and retinal neurodegenerative diseases
Publisher: Aging and Disease
Date: 2023
Assessing Information Available for Health Professionals and Potential Participants on Lung Cancer Screening Program Websites: Cross-sectional Study
Publisher: JMIR Publications Inc.
Date: 30-08-2022
DOI: 10.2196/34264
Abstract: Lung cancer is the leading cause of cancer death worldwide. The US Preventive Services Task Force (USPSTF) updated recommendations for lung cancer screening in 2021, adjusting the age of screening to 50 years (from 55 years) and reducing the number of pack-years used to estimate total firsthand cigarette smoke exposure to 20 (from 30). With many in iduals using the internet to find health care information, it is important to understand what information is available for in iduals contemplating lung cancer screening. This study aimed to assess the eligibility criteria and information available on lung cancer screening program websites for both health professionals and potential screening participants. A descriptive cross-sectional analysis of 151 lung cancer screening program websites of academic (n=76) and community medical centers (n=75) in the United States with information for health professionals and potential screening participants was conducted in March 2021. Presentation of eligibility criteria for potential screening participants and presence of information available specific to health professionals about lung cancer screening were the primary outcomes. Secondary outcomes included presentation of information about cost and smoking cessation, inclusion of an online risk assessment tool, mention of any clinical guidelines, and use of multimedia to present information. Eligibility criteria for lung cancer screening was included in nearly all 151 websites (n=142, 94%), as well as age range (n=139, 92.1%) and smoking history (n=141, 93.4%). Age was only consistent with the latest recommendations in 14.5% (n=22) of websites, and no websites had updated smoking history. Half the websites (n=76, 50.3%) mentioned screening costs as related to the type of insurance held. A total of 23 (15.2%) websites featured an online assessment tool to determine eligibility. The same proportion (n=23, 15.2%) hosted information specifically for health professionals. In total, 44 (29.1%) websites referred to smoking cessation, and 46 (30.5%) websites used multimedia to present information, such as short videos or podcasts. Most websites of US lung cancer screening programs provide information about eligibility criteria, but this is not consistent and has not been updated across all websites following the latest USPSTF recommendations. Online resources require updating to present standardized information that is accessible for all.
Upregulation of Proteolytic Pathways and Altered Protein Biosynthesis Underlie Retinal Pathology in a Mouse Model of Alzheimer’s Disease
Publisher: Springer Science and Business Media LLC
Date: 02-2019
DOI: 10.1007/S12035-019-1479-4
Abstract: Increased amyloid β (Aβ) aggregation is a hallmark feature of Alzheimer's disease (AD) pathology. The APP/PS1 mouse model of AD exhibits accumulation of Aβ in the retina and demonstrates reduced retinal function and other degenerative changes. The overall molecular effects of AD pathology on the retina remain undetermined. Using a proteomics approach, this study assessed the molecular effects of Aβ accumulation and progression of AD pathology on the retina. Retinal tissues from younger (2.5 months) and older 8-month APP/PS1 mice were analysed for protein expression changes. A multiplexed proteomics approach using chemical isobaric tandem mass tags was applied followed by functional and protein-protein interaction analyses using Ingenuity pathway (IPA) and STRING computational tools. We identified approximately 2000 proteins each in the younger (upregulated 50 downregulated 36) and older set of APP/PS1 (upregulated 85 downregulated 79) mice retinas. Amyloid precursor protein (APP) was consistently upregulated two to threefold in both younger and older retinas (p < 0.0001). Mass spectrometry data further revealed that older APP/PS1 mice retinas had elevated levels of proteolytic enzymes cathepsin D, presenilin 2 and nicastrin that are associated with APP processing. Increased levels of proteasomal proteins Psma5, Psmd3 and Psmb2 were also observed in the older AD retinas. In contrast to the younger animals, significant downregulation of protein synthesis and elongation associated proteins such as Eef1a1, Rpl35a, Mrpl2 and Eef1e1 (p < 0.04) was identified in the older mice retinas. This study reports for the first time that not only old but also young APP/PS1 animals demonstrate increased amyloid protein levels in their retinas. Quantitative proteomics reveals new molecular insights which may represent a cellular response to clear amyloid build-up. Further, downregulation of ribosomal proteins involved in protein biosynthesis was observed which might be considered a toxicity effect.
Proteomic signature of human embryonic stem cells
Publisher: Wiley
Date: 06-2006
Abstract: Human embryonic stem cells (hESC) represent a population of undifferentiated pluripotent cells with both self-renewal and multilineage differentiation characteristics. Proteomics provides a powerful approach for studying the characteristics of hESC and discovering molecular markers. We have analyzed proteome profiles of three hESC lines using 2-DE and MALDI TOF-TOF. Out of 844 spots analyzed with MALDI TOF-TOF, 685 proteins were identified of which 60 proteins were classified as the most abundant proteins on 2-D gels. A large number of proteins particularly high abundant ones were identified as chaperones, heat shock proteins, ubiquitin roteasome, and oxidative stress responsive proteins underscoring the ability of these cells to resist oxidative stress and increase the life span. Several proteins involved in cell proliferation and differentiation were also among the highly expressed proteins. Although overall expression pattern of three hESC were similar, 54 spots changed quantitatively and 14 spots changed qualitatively among the hESC cell lines. Most of these proteins were identified as proteins involved in cell growth, metabolism and signal transduction, which may affect the self-renewal and pluripotency. To our knowledge, this study represents the first proteomic dataset for hESC and provides a better insight into the biology of hESC. Proteome maps of hESC are accessible at www.RoyanProteomics.ir.
Characterization of Three Key MicroRNAs in Rice Root Architecture under Drought Stress using In silico Analysis and Quantitative Real-time PCR
Publisher: Oriental Scientific Publishing Company
Date: 30-09-2014
DOI: 10.13005/BBRA/1306
Abstracts of the 34rd Annual Meeting of the European Society of Human Reproduction and Embryology
Publisher: Oxford University Press (OUP)
Date: 28-06-2017
The effect of Rho-associated kinase inhibition on the proteome pattern of dissociated human embryonic stem cells
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3MB70255C
Abstract: Rho-associated kinase (ROCK) is an immediate downstream target of the Rho GTPase signaling pathway which participates in transducing the Rho GTPase signal to the actin cytoskeleton, leading to the assembly of focal adhesions and stress fibers. Competitive inhibition of ROCK enhances post-thaw viability, improves cloning efficiency and decreases anoikis in human embryonic stem cells (hESCs). The molecular mechanisms by which ROCK inhibition mediates such responses are largely unknown. We have investigated the effect of Y-27632, a competitive ROCK inhibitor (ROCKi), on the proteome of hESCs. HESCs were exposed to ROCK inhibition directly by the addition of Y-27632 to the culture medium or to the Matrigel substratum. ROCK inhibition significantly increased cell survival and plating efficiency without any changes to the morphology, karyotype, or expression of pluripotency markers. We used a two-dimensional gel electrophoresis (2-DE) coupled with tandem mass spectrometry based protein identification and identified 29 ROCKi responsive proteins. As expected, cytoskeleton-related proteins comprised the major ROCKi responsive proteins. Differential proteomic analysis showed that ROCKi induced upregulation of some actin binding proteins such as tropomyosin, F-actin capping protein (CapZ) and transgelin and downregulation of tubulin. In addition, ROCK inhibition was accompanied by changes in expressions of some chromatin modifying proteins such as SMARCB1, ILF3, and Dpy-30-protein, further suggesting a link between ROCK inhibition and the epigenetic mechanism of gene regulation.
Amyloid β Induces Early Changes in the Ribosomal Machinery, Cytoskeletal Organization and Oxidative Phosphorylation in Retinal Photoreceptor Cells
Publisher: Frontiers Media SA
Date: 22-02-2019
Neuroserpin gene therapy inhibits retinal ganglion cell apoptosis and promotes functional preservation in glaucoma
Publisher: Elsevier BV
Date: 07-2023
Heritability and recursive influence of host genetics on the rumen microbiota drive body weight variance in male Hu sheep lambs
Publisher: Springer Science and Business Media LLC
Date: 29-08-2023
Discovery of Novel Cell Surface Markers for Purification of Embryonic Dopamine Progenitors for Transplantation in Parkinson's Disease Animal Models
Publisher: Elsevier BV
Date: 09-2018
Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach
Publisher: Springer Science and Business Media LLC
Date: 08-10-2022
DOI: 10.1007/S00122-021-03953-5
Abstract: Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.
Phytoplasma-Responsive microRNAs Modulate Hormonal, Nutritional, and Stress Signalling Pathways in Mexican Lime Trees
Publisher: Public Library of Science (PLoS)
Date: 18-06-2013
MicroRNA Profiling of Root Meristematic Zone in Contrasting Genotypes Reveals Novel Insight into in Rice Response to Water Deficiency
Publisher: Springer Science and Business Media LLC
Date: 23-12-2022
In-depth diversity analysis of the bacterial community resident in the camel rumen
Publisher: Elsevier BV
Date: 02-2015
DOI: 10.1016/J.SYAPM.2014.09.004
Abstract: The rumen compartment of the ruminant digestive tract is an enlarged fermentation chamber which houses a erse collection of symbiotic microorganisms that provide the host animal with a remarkable ability to digest plant lignocellulosic materials. Characterization of the ruminal microbial community provides opportunities to improve animal food digestion efficiency, mitigate methane emission, and develop efficient fermentation systems to convert plant biomasses into biofuels. In this study, 16S rRNA gene licon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen. Using 76,333 quality-checked, chimera- and singleton-filtered reads, 4954 operational taxonomic units (OTUs) were identified at a 97% species level sequence identity. At the phylum level, more than 96% of the reads were affiliated to OTUs belonging to Bacteroidetes (51%), Firmicutes (31%), Proteobacteria (4.8%), Spirochaetes (3.5%), Fibrobacteres (3.1%), Verrucomicrobia (2.7%), and Tenericutes (0.95%). A total of 15% of the OTUs (746) that contained representative sequences from all major taxa were shared by all animals and they were considered as candidate members of the core camel rumen microbiome. Analysis of microbial composition through the solid and liquid fractions of rumen digesta revealed differential enrichment of members of Fibrobacter, Clostridium, Ruminococcus, and Treponema in the solid fraction, as well as members of Prevotella, Verrucomicrobia, Cyanobacteria, and Succinivibrio in the liquid fraction. The results clearly showed that the camel rumen microbiome was structurally similar but compositionally distinct from that of other ruminants, such as the cow. The unique characteristic of the camel rumen microbiome that differentiated it from those of other ruminants was the significant enrichment for cellulolytic bacteria.
Assessing wheat (Triticum aestivum L.) genetic diversity using quality traits, amplified fragment length polymorphisms, simple sequence repeats and proteome analysis
Publisher: Wiley
Date: 14-11-2007
The effect of purmorphamine and sirolimus on osteogenic differentiation of human bone marrow-derived mesenchymal stem cells
Publisher: Elsevier BV
Date: 02-2013
DOI: 10.1016/J.BIOPHA.2012.10.004
Abstract: Small molecules have been introduced as less expensive biologically active compounds that can regulate different developmental phenomena. Purmorphamine and sirolimus are two small molecules that, according to some studies, possess certain osteomodulatory effects. This study was set out to highlight the appropriate dose and response time of these small molecules on enhancement of osteogenesis in human bone marrow-derived mesenchymal stem cells from early to mid and late stages of differentiation. Alkaline phosphatase activity, matrix mineralization and expression of osteoblast genes were quantitatively assessed in vitro. For the in vivo study, we transplanted stem cell-based constructs subcutaneously into rats, and treated them daily with the most promising doses of the small molecule. The constructs were analyzed by real-time PCR and histological staining. Our results showed that Sirolimus reduced osteogenic differentiation of mesenchymal stem cells by decreasing alkaline phosphatase activity at dose of 100nM after 14 days and mineralization of the matrix at 14 and 21 days post-induction. Purmorphamine induced up-regulation of alkaline phosphatase activity and expression of RUNX-2 at day 14. Up-regulation of osteocalcin was detected at the 3 and 5μM doses of purmorphamine on day 14 post-induction. Matrix mineralization remained unchanged in the presence or absence of purmorphamine. This dose of small molecule also accelerated expression of Alkaline phosphatase transcripts in vivo. In conclusion, sirolimus had an inhibitory effect on osteogenic differentiation of human bone marrow-derived mesenchymal stem cells while purmorphamine, particularly at a dose of 3μM, showed a promotive effect in vitro and in vivo.
Extracellular vesicles as reconfigurable therapeutics for eye diseases: Promises and hurdles
Publisher: Elsevier BV
Date: 06-2023
Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/FP14274
Abstract: Salinity is a limiting factor affecting crop growth. We evaluated the responses of a salt-tolerant recombinant inbred rice (Oryza sativa L.) line, FL478, and the salt-sensitive IR29. Seedlings were exposed to salt stress and the growth rate was monitored to decipher the effect of long-term stress. At Day 16, IR29 produced lower shoot biomass than FL478. Significant differences for Na+ and K+ concentrations and Na+ : K+ ratios in roots and shoots were observed between genotypes. Changes in the proteomes of control and salt-stressed plants were analysed, identifying 59 and 39 salt-responsive proteins in roots and leaves, respectively. Proteomic analysis showed greater downregulation of proteins in IR29. In IR29, proteins related to pathways involved in salt tolerance (e.g. oxidative stress response, amino acid biosynthesis, polyamine biosynthesis, the actin cytoskeleton and ion compartmentalisation) changed to combat salinity. We found significant downregulation of proteins related to photosynthetic electron transport in IR29, indicating that photosynthesis was influenced, probably increasing the risk of reactive oxygen species formation. The sensitivity of IR29 might be related to its inability to exclude salt from its transpiration stream, to compartmentalise excess ions and to maintain a healthy photosynthetic apparatus during salt stress, or might be because of the leakiness of its roots, allowing excess salt to enter apoplastically. In FL478, superoxide dismutase, ferredoxin thioredoxin reductase, fibre protein and inorganic pyrophosphatase, which may participate in salt tolerance, increased in abundance. Our analyses provide novel insights into the mechanisms behind salt tolerance and sensitivity in genotypes with close genetic backgrounds.
Applications of Quantitative Proteomics in Plant Research
Publisher: Springer International Publishing
Date: 2016
A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation
Publisher: Springer Science and Business Media LLC
Date: 02-08-2018
Guidelines for the use and interpretation of assays for monitoring autophagy
Publisher: Informa UK Limited
Date: 04-2012
DOI: 10.4161/AUTO.19496
The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate‐washed membrane standard
Publisher: Wiley
Date: 11-2010
Y Chromosome Genes May Play Roles in the Development of Neural Rosettes from Human Embryonic Stem Cells.
Publisher: Springer Science and Business Media LLC
Date: 03-06-2022
DOI: 10.1007/S12015-022-10392-2
Abstract: The human Y chromosome harbors genes that are mainly involved in the growth, development, sexual dimorphism, and spermatogenesis process. Despite many studies, the function of the male-specific region of the Y chromosome (MSY) awaits further clarification, and a cell-based approach can help in this regard. In this study, we have developed four stable transgenic male embryonic stem cell (ESCs) lines that can overexpress male-specific genes HSFY1, RBMY1A1, RPS4Y1, and SRY. As a proof of principle, we differentiated one of these cell lines (RPS4Y1 over-expressing ESCs) to the neural stem cell (rosette structure) and characterized them based on the expression level of lineage markers. RPS4Y1 expression in the Doxycycline-treated group was significantly higher than control groups at transcript and protein levels. Furthermore, we found Doxycycline-treated group had a higher differentiation efficiency than the untreated control groups. Our results suggest that the RPS4Y1 gene may play a critical role in neurogenesis. Also, the generated transgenic ESC lines can be widely employed in basic and preclinical studies, such as sexual dimorphism of neural and cardiac functions, the development of cancerous and non-cancerous disease models, and drug screening.
Linking transcriptomics and proteomics in Cryopreserved Human Sperm
Publisher: Elsevier BV
Date: 02-2018
Holistic sequencing
Publisher: Springer International Publishing
Date: 2016
Proteomics in Detection of Contaminations and Adulterations in Agricultural Foodstuffs
Publisher: Springer International Publishing
Date: 2016
Comprehensive transcriptional analysis unveils salt stress-regulated key pathways in Suaeda salsa leaves
Publisher: Elsevier BV
Date: 12-2023
Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.JPROT.2017.02.007
Abstract: Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS). The abundance of 520 proteins was significantly changed across three groups of s les. We were able to identify several functional biological pathways enriched in azoospermia s les and confirm selected differentially abundant proteins, using multiple histological methods. The results revealed that cell cycle and proteolysis, and RNA splicing were the most significant biological processes impaired by the substantial suppression of proteins related to the aforementioned categories in SCOS tissues. In the MA patient testes, generation of precursor metabolites and energy as well as oxidation-reduction were the most significantly altered processes. Novel candidate proteins identified in this study include key transcription factors, many of which have not previously been shown to be associated with azoospermia. Our findings can provide substantial insights into the molecular regulation of spermatogenesis and human reproduction. The obtained data showed a drastic suppression of proteins involved in spliceosome, cell cycle and proteasome proteins, as well as energy and metabolic production in Sertoli cell only syndrome testis tissue, and to a lesser extent in maturation arrest s les. Moreover, we identified new transcription factors that are highly down-regulated in SCOS and MA patients, thus helping to understand the molecular complexity of spermatogenesis in male infertility. Our findings provide novel candidate protein targets associated with SCOS or MA azoospermia.
Application of the immobilized enzyme on magnetic graphene oxide nano-carrier as a versatile bi-functional tool for efficient removal of dye from water
Publisher: Elsevier BV
Date: 2021
Proteome analysis of sugar beet leaves under drought stress
Publisher: Wiley
Date: 03-2005
Abstract: Drought is one of the major factors limiting the yield of sugar beet (Beta vulgaris L.). The identification of candidate genes for marker-assisted selection (MAS) could greatly improve the efficiency of breeding for increased drought tolerance. Drought-induced changes in the proteome could highlight important genes. Two genotypes of sugar beet (7112 and 7219-P.69) differing in genetic background were cultivated in the field. A line-source sprinkler irrigation system was used to apply irrigated and water deficit treatments beginning at the four-leaf stage. At 157 days after sowing, leaf s les were collected from well-watered and drought-stressed plants for protein extraction and to measure shoot biomass and leaf relative water content. Changes induced in leaf proteins were studied by two-dimensional gel electrophoresis and quantitatively analyzed using image analysis software. Out of more than 500 protein spots reproducibly detected and analyzed, 79 spots showed significant changes under drought. Some proteins showed genotype-specific patterns of up- or downregulation in response to drought. Twenty protein spots were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), leading to identification of Rubisco and 11 other proteins involved in redox regulation, oxidative stress, signal transduction, and chaperone activities. Some of these proteins could contribute a physiological advantage under drought, making them potential targets for MAS.
Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation
Publisher: Frontiers Media SA
Date: 21-02-2022
Abstract: Root system architecture (RSA) is an important agronomic trait with vital roles in plant productivity under water stress conditions. A deep and branched root system may help plants to avoid water stress by enabling them to acquire more water and nutrient resources. Nevertheless, our knowledge of the genetics and molecular control mechanisms of RSA is still relatively limited. In this study, we analyzed the transcriptome response of root tips to water stress in two well-known genotypes of rice: IR64, a high-yielding lowland genotype, which represents a drought-susceptible and shallow-rooting genotype and Azucena, a traditional, upland, drought-tolerant and deep-rooting genotype. We collected s les from three zones (Z) of root tip: two consecutive 5 mm sections (Z1 and Z2) and the following next 10 mm section (Z3), which mainly includes meristematic and maturation regions. Our results showed that Z1 of Azucena was enriched for genes involved in cell cycle and ision and root growth and development whereas in IR64 root, responses to oxidative stress were strongly enriched. While the expansion of the lateral root system was used as a strategy by both genotypes when facing water shortage, it was more pronounced in Azucena. Our results also suggested that by enhancing meristematic cell wall thickening for insulation purposes as a means of confronting stress, the sensitive IR64 genotype may have reduced its capacity for root elongation to extract water from deeper layers of the soil. Furthermore, several members of gene families such as NAC , AP2/ERF , AUX/IAA , EXPANSIN , WRKY , and MYB emerged as main players in RSA and drought adaptation. We also found that HSP and HSF gene families participated in oxidative stress inhibition in IR64 root tip. Meta-quantitative trait loci (QTL) analysis revealed that 288 differentially expressed genes were colocalized with RSA QTLs previously reported under drought and normal conditions. This finding warrants further research into their possible roles in drought adaptation. Overall, our analyses presented several major molecular differences between Azucena and IR64, which may partly explain their differential root growth responses to water stress. It appears that Azucena avoided water stress through enhancing growth and root exploration to access water, whereas IR64 might mainly rely on cell insulation to maintain water and antioxidant system to withstand stress. We identified a large number of novel RSA and drought associated candidate genes, which should encourage further exploration of their potential to enhance drought adaptation in rice.
A cold-adapted endoglucanase from camel rumen with high catalytic activity at moderate and low temperatures: an anomaly of truly cold-adapted evolution in a mesophilic environment
Publisher: Springer Science and Business Media LLC
Date: 12-01-2018
DOI: 10.1007/S00792-018-0999-6
Abstract: Endoglucanases are important enzymes in plant biomass degradation. They have current and potential applications in various industrial sectors including human and animal food processing, textile, paper, and renewable biofuel production. It is assumed that the cold-active endoglucanases, with high catalytic rates in moderate and cold temperatures, can improve the cost-effectiveness of industrial processes by lowering the need for heating and, thus, energy consumption. In this study, the endoglucanase CelCM3 was procured from a camel rumen metagenome via gene cloning and expression in Escherichia coli BL21 (DE3). The maximum activity of the enzyme on carboxymethyl cellulose (CMC) was obtained at pH 5 and 30 °C with a V
Proteome analysis of post-transplantation recovery mechanisms of an EAE model of multiple sclerosis treated with embryonic stem cell-derived neural precursors
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.JPROT.2013.06.008
Abstract: Multiple sclerosis (MS) is a chronic inflammatory and progressive disorder of the central nervous system (CNS), which ultimately causes demyelination and subsequent axonal injury. Experimental autoimmune encephalomyelitis (EAE) is a well-characterized animal model to study the etiology and pathogenesis of MS. This model can also be used to investigate various therapeutic approaches for MS. Herein we have treated a score 3 EAE mouse model with an embryonic stem cell-derived neural precursor. Clinical analysis showed recovery of the EAE model of MS following transplantation. We analyzed the proteome of spinal cords of healthy and EAE s les before and after transplantation. Proteome analysis revealed that expressions of 86 spinal cord protein spots changed in the EAE or transplanted mouse compared to controls. Mass spectrometry resulted in identification of 72 proteins. Of these, the amounts of 27 differentially expressed proteins in EAE s les returned to sham levels after transplantation, suggesting a possible correlation between changes at the proteome level and clinical signs of EAE in transplanted mice. The recovered proteins belonged to various functional groups that included disturbances in ionic and neurotransmitter release, apoptosis, iron hemostasis, and signal transduction. Our results provided a proteomic view of the molecular mechanisms of EAE recovery after stem cell transplantation. In this study, we applied proteomics to analyze the changes in proteome pattern of EAE mouse model after embryonic stem cell-derived neural precursor transplantation. Our proteome results clearly showed that the expression levels of several differentially expressed proteins in EAE s les returned to sham levels after transplantation, which suggested a possible correlation between changes at the proteome level and decreased clinical signs of EAE in transplanted mice. These results will serve as a basis to address new questions and design new experiments to elucidate the biology of EAE and recovery after transplantation. A thorough understanding of stem cell-mediated therapeutic mechanisms might result in the development of more efficacious therapies for MS than are currently available.
17th Chromosome-Centric Human Proteome Project Symposium in Tehran
Publisher: Wiley
Date: 29-03-2018
Abstract: This report describes the 17th Chromosome-Centric Human Proteome Project which was held in Tehran, Iran, April 27 and 28, 2017. A brief summary of the symposium's talks including new technical and computational approaches for the identification of novel proteins from non-coding genomic regions, physicochemical and biological causes of missing proteins, and the close interactions between Chromosome- and Biology/Disease-driven Human Proteome Project are presented. A synopsis of decisions made on the prospective programs to maintain collaborative works, share resources and information, and establishment of a newly organized working group, the task force for missing protein analysis are discussed.
A genomic catalog of Earth’s microbiomes
Publisher: Springer Science and Business Media LLC
Date: 09-11-2020
DOI: 10.1038/S41587-020-0718-6
Abstract: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to ,000 metagenomes collected from erse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic ersity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Prospective Isolation of ISL1+ Cardiac Progenitors from Human ESCs for Myocardial Infarction Therapy
Publisher: Elsevier BV
Date: 03-2018
Changes in root microbiome during wheat evolution
Publisher: Springer Science and Business Media LLC
Date: 26-02-2022
DOI: 10.1186/S12866-022-02467-4
Abstract: Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu , T. turgidum , T. durum , and T. aestivum along with their ancestral species Aegilops speltoides , and Ae. tauschii during vegetative and reproductive stages. In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii , suggesting potential breeding targets for plants surveyed. This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae . speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.
Proteome response of Elymus elongatum to severe water stress and recovery
Publisher: Oxford University Press (OUP)
Date: 06-11-2007
DOI: 10.1093/JXB/ERL226
Abstract: Tall wheatgrass (Elymus elongatum Host) is a drought-tolerant, cool-season forage grass native to Iran. A proteomic approach has been applied to identify mechanisms of drought responsiveness and tolerance in plants undergoing vegetative stage drought stress and then recovery after rewatering. Uniformed clones were reproduced from a parent plant collected from Brojen (central region of Iran). Clones were grown in pots and drought was initiated by withholding water for 16 d. The leaf s les were taken in triplicate from both stressed/rewatered plants and continuously watered controls at five times: (i) 75% FC, (ii) 50% FC, (iii) 25% FC, (iv) 3 d after rewatering, and (v) 14 d after rewatering. Changes in the proteome pattern of shoots were studied using two-dimensional gel electrophoresis. Following the 16 d water stress, both shoot dry weight and leaf width decreased up to 67% compared with the well-watered plants, whereas proline content increased up to 20-fold. Leaf relative water contents (RWC) also declined from 85% to 24%. Out of about 600 protein spots detected on any given two-dimensional gel, 58 protein spots were reproducibly and significantly changed during drought stress and recovery. Only one protein (abscisic acid- and stress-inducible protein) showed significant changes in expression and position in response to severe drought. The fifty-eight responsive proteins were categorized in six clusters including two groups of proteins specifically up- and down-regulated in response to severe drought stress. Eighteen proteins belonging to these two groups were analysed by liquid chromatography tandem mass spectrometry leading to the identification of 11 of them, including the oxygen-evolving enhancer protein 2, abscisic acid- and stress-inducible protein, several oxidative stress tolerance enzymes, two small heat shock proteins, and Rubisco breakdown. The results suggest that E. elongatum may tolerate severe drought stress by accumulating proline and several proteins related to drought-stress tolerance. Recovery after rewatering might be another mechanism by which plants tolerate erratic rainfall in semi-arid regions.
Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication
Publisher: Springer Science and Business Media LLC
Date: 05-06-2015
Comparative genome analysis of Oceanimonas sp. GK1, a halotolerant bacterium with considerable xenobiotics degradation potentials
Publisher: Springer Science and Business Media LLC
Date: 02-10-2015
Motivation is not enough: A qualitative study of lung cancer screening uptake in Australia to inform future implementation
Publisher: Public Library of Science (PLoS)
Date: 30-09-2022
DOI: 10.1371/JOURNAL.PONE.0275361
Abstract: Participation in lung cancer screening (LCS) trials and real-world programs is low, with many people at high-risk for lung cancer opting out of baseline screening after registering interest. We aimed to identify the potential drivers of participation in LCS in the Australian setting, to inform future implementation. Semi-structured telephone interviews were conducted with in iduals at high-risk of lung cancer who were eligible for screening and who had either participated (‘screeners’) or declined to participate (‘decliners’) in the International Lung Screening Trial from two Australian sites. Interview guide development was informed by the Precaution Adoption Process Model. Interviews were audio-recorded, transcribed and analysed using the COM-B model of behaviour to explore capability, opportunity and motivation related to screening behaviour. Thirty-nine participants were interviewed (25 screeners 14 decliners). Motivation to participate in screening was high in both groups driven by the lived experience of lung cancer and a belief that screening is valuable, however decliners unlike their screening counterparts reported low self-efficacy. Decliners in our study reported challenges in capability including ability to attend and in knowledge and understanding. Decliners also reported challenges related to physical and social opportunity, in particular location as a barrier and lack of family support to attend screening. Our findings suggest that motivation alone may not be sufficient to change behaviour related to screening participation, unless capability and opportunity are also considered. Focusing strategies on barriers related to capability and opportunity such as online/telephone support, mobile screening programs and financial assistance for screeners may better enhance screening participation. Providing funding for clinicians to support in iduals in decision-making and belief in self-efficacy may foster motivation. Targeting interventions that connect eligible in iduals with the LCS program will be crucial for successful implementation.
Comparative proteomic analysis of canola leaves under salinity stress
Publisher: Wiley
Date: 08-04-2011
Abstract: Although canola is a moderately salt-tolerant species, its growth, seed yield, and oil production are markedly reduced under salt stress, particularly during the early vegetative growth stage. To identify the mechanisms of salt responsiveness in canola, the proteins expressed in the second and third newly developed leaves of salt-tolerant, Hyola 308, and salt-sensitive, Sarigol, cultivars were analyzed. Plants were exposed to 0, 175, and 350 mM NaCl during the vegetative stage. An increase in the Na content and a reduction in growth were observed in the third leaves compared to the second leaves. The accumulation of Na was more pronounced in the salt-sensitive compared with the salt-tolerant genotype. Out of 900 protein spots detected on 2-DE gels, 44 and 31 proteins were differentially expressed in the tolerant and susceptible genotypes, respectively. Cluster analysis based on the expression level of total and responsive proteins indicated that the second leaves had a discriminator role between the two genotypes at both salinity levels. Using MS analysis, 46 proteins could be identified including proteins involved in responses to oxidative stress, energy production, electron transport, translation, and photosynthesis. Our results suggest that these proteins might play roles in canola adaptation to salt stress.
Extensive genetic diversity in Iranian pomegranate (Punica granatum L.) germplasm revealed by microsatellite markers
Publisher: Elsevier BV
Date: 10-2012
Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives
Publisher: American Chemical Society (ACS)
Date: 11-06-2015
DOI: 10.1021/ACS.JPROTEOME.5B00211
Abstract: In the rapidly growing economies of Asia and Oceania, food security has become a primary concern. With the rising population, growing more food at affordable prices is becoming even more important. In addition, the predicted climate change will lead to drastic changes in global surface temperature and changes in rainfall patterns that in turn will pose a serious threat to plant vegetation worldwide. As a result, understanding how plants will survive in a changing climate will be increasingly important. Such challenges require integrated approaches to increase agricultural production and cope with environmental threats. Proteomics can play a role in unraveling the underlying mechanisms for food production to address the growing demand for food. In this review, the current status of food crop proteomics is discussed, especially in regard to the Asia and Oceania regions. Furthermore, the future perspective in relation to proteomic techniques for the important food crops is highlighted.
Root endophytic fungus Piriformospora indica improves drought stress adaptation in barley by metabolic and proteomic reprogramming
Publisher: Elsevier BV
Date: 2019
A generalized machine‐learning aided method for targeted identification of industrial enzymes from metagenome: A xylanase temperature dependence case study
Publisher: Wiley
Date: 14-11-2020
DOI: 10.1002/BIT.27608
Impacts of drought stress on some physiological features of two important grapevine cultivars (Vitis vinefera cv; ‘Yaghuti’ and ‘Bidanesefid’)
Publisher: Springer Science and Business Media LLC
Date: 02-12-2022
MicroRNA-340 inhibits the proliferation and promotes the apoptosis of colon cancer cells by modulating REV3L
Publisher: Impact Journals, LLC
Date: 26-12-2018
Small RNA Sequencing Reveals Dlk1-Dio3 Locus-Embedded MicroRNAs as Major Drivers of Ground-State Pluripotency
Publisher: Elsevier BV
Date: 12-2017
Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145)
Publisher: American Chemical Society (ACS)
Date: 10-08-2015
DOI: 10.1021/ACS.JPROTEOME.5B00333
Abstract: One of the major objectives of the Human Y Chromosome Proteome Project is to characterize sets of proteins encoded from the human Y chromosome. Lysine (K)-specific demethylase 5D (KDM5D) is located on the AZFb region of the Y chromosome and encodes a JmjC-domain-containing protein. KDM5D, the least well-documented member of the KDM5 family, is capable of demethylating di- and trimethyl H3K4. In this study, we detected two novel splice variants of KDM5D with lengths of 2650bp and 2400bp that correspond to the 100 and 80 kDa proteins in the human prostate cancer cell line, DU-145. The knockdown of two variants using the short interfering RNA (siRNA) approach increased the growth rate of prostate cancer cells and reduced cell apoptosis. To explore the proteome pattern of the cells after KDM5D downregulation, we applied a shotgun label-free quantitative proteomics approach. Of 820 proteins present in all four replicates of two treatments, the abundance of 209 proteins changed significantly in response to KDM5D suppression. Of these, there were 102 proteins observed to be less abundant and 107 more abundant in KDM5D knockdown cells compared with control cells. The results revealed that KDM5D knockdown altered the abundance of proteins involved in RNA processing, protein synthesis, apoptosis, the cell cycle, and growth and proliferation. In conjunction, these results provided new insights into the function of KDM5D and its splice variants. The proteomics data are available at PRIDE with ProteomeXchange identifier PXD000416.
Agricultural proteomics volume 2
Publisher: Springer International Publishing
Date: 2016
Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase
Publisher: Springer Science and Business Media LLC
Date: 16-06-2017
DOI: 10.1038/S41598-017-03966-5
Abstract: The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes. Then, important structural features that exhibit considerable differences in dynamics of redox states are extracted by statistical machine learning methods. Mapping the structural variations to time series of residue interaction networks also provides a holistic representation of the dynamical redox differences. With emphasizing on persistent long-lasting interactions, an approach is proposed that compiled these time series networks to a single dynamic residue interaction network (DRIN). Differential comparison of DRIN in oxidized and reduced states reveals chains of residue interactions that represent potential allosteric paths between catalytic and ligand binding sites of hPDI.
Progress and Promise Towards Safe Induced Pluripotent Stem Cells for Therapy
Publisher: Springer Science and Business Media LLC
Date: 24-02-2010
DOI: 10.1007/S12015-010-9121-X
Abstract: The recent generation of induced pluripotent stem cells (iPSCs) from somatic cells provides an invaluable resource for drug or toxicology screening, medical research, and patient-specific cell therapy. However, there are currently a number of obstacles including virus integration and the genetic alteration of iPSCs that will need to be overcome before these cells may be considered safe for clinical applications. Here, we highlight the potential and challenges of iPSC research and review advances in reprogramming methods that have rapidly moved the field closer to realizing the goal of generating safe iPSCs for transplantation.
Retinal changes in Alzheimer's disease— integrated prospects of imaging, functional and molecular advances
Publisher: Elsevier BV
Date: 05-2021
DOI: 10.1016/J.PRETEYERES.2020.100899
Abstract: Alzheimer's Disease (AD) is a devastating neurodegenerative disorder of the brain, clinically characterised by cognitive deficits that gradually worsen over time. There is, at present, no established cure, or disease-modifying treatments for AD. As life expectancy increases globally, the number of in iduals suffering from the disease is projected to increase substantially. Cumulative evidence indicates that AD neuropathological process is initiated several years, if not decades, before clinical signs are evident in patients, and diagnosis made. While several imaging, cognitive, CSF and blood-based biomarkers have been proposed for the early detection of AD their sensitivity and specificity in the symptomatic stages is highly variable and it is difficult to justify their use in even earlier, pre-clinical stages of the disease. Research has identified potentially measurable functional, structural, metabolic and vascular changes in the retina during early stages of AD. Retina offers a distinctively accessible insight into brain pathology and current and developing ophthalmic technologies have provided us with the possibility of detecting and characterising subtle, disease-related changes. Recent human and animal model studies have further provided mechanistic insights into the biochemical pathways that are altered in the retina in disease, including amyloid and tau deposition. This information coupled with advances in molecular imaging has allowed attempts to monitor biochemical changes and protein aggregation pathology in the retina in AD. This review summarises the existing knowledge that informs our understanding of the impact of AD on the retina and highlights some of the gaps that need to be addressed. Future research will integrate molecular imaging innovation with functional and structural changes to enhance our knowledge of the AD pathophysiological mechanisms and establish the utility of monitoring retinal changes as a potential biomarker for AD.
Comparative proteomic analysis of tobacco expressing cyanobacterial flavodoxin and its wild type under drought stress
Publisher: Elsevier BV
Date: 03-2015
DOI: 10.1016/J.JPLPH.2014.11.001
Abstract: Tobacco plants expressing cyanobacterial flavodoxin (Fld) show enhanced tolerance to a wide range of abiotic stresses including drought, temperature and UV. The mechanisms of adaptation to stress conditions under Fld expression are largely unknown. Here, we applied comparative proteomic analysis to uncover the changes in the proteome profile of Fld-expressing plants in response to drought stress. Using high-resolution two-dimensional gel electrophoresis, we were able to detect 930 protein spots and compare their abundance. We found changes up to 1.5 fold for 52 spots under drought in transgenic and/or wild type plants. Using combined MALDI-TOF/TOF and ESI-Q/TOF analysis 39 (24 in wild type, 11 in transgenic, and 4 in both) drought-responsive proteins (DRPs) could be identified. The majority of DRPs are known to be involved in photosynthesis, carbohydrate and energy metabolism, amino acid and protein synthesis and processing, and oxidative stress responses. Among candidate DRPs, the abundance of remurin, ferredoxin-NADP reductase, chloroplast manganese stabilizing protein-II, phosphoglycerate mutase, and glutathione S-transferase decreased in drought stressed Fld-tobacco while S-formylglutathione hydrolase and pyridoxine biosynthesis protein abundance increased. In wild type plants, drought caused a reduction of proteins related to carbohydrate metabolism. These results suggest that the stress tolerance conferred by Fld expression is strongly related to control mechanisms regarding carbohydrate and energy metabolism as well as oxidative stress responses.
Embryonic Stem Cell Interactomics: The Beginning of a Long Road to Biological Function
Publisher: Springer Science and Business Media LLC
Date: 31-07-2012
DOI: 10.1007/S12015-012-9400-9
Abstract: Embryonic stem cells (ESCs) are capable of unlimited self-renewal while maintaining pluripotency. They are of great interest in regenerative medicine due to their ability to differentiate into all cell types of the three embryonic germ layers. Recently, induced pluripotent stem cells (iPSCs) have shown similarities to ESCs and thus promise great therapeutic potential in regenerative medicine. Despite progress in stem cell biology, our understanding of the exact mechanisms by which pluripotency and self-renewal are established and maintained is largely unknown. A better understanding of these processes may lead to discovery of alternative ways for reprogramming, differentiation and more reliable applications of stem cells in therapies. It has become evident that proteins generally function as members of large complexes that are part of a more complex network. Therefore, the identification of protein-protein interactions (PPI) is an efficient strategy for understanding protein function and regulation. Systematic genome-wide and pathway-specific PPI analysis of ESCs has generated a network of ESC proteins, including major transcription factors. These PPI networks of ESCs may contribute to a mechanistic understanding of self-renewal and pluripotency. In this review we describe different experimental approaches for the identification of PPIs along with various databases. We discuss biological findings and technical challenges encountered with interactome studies of pluripotent stem cells, and provide insight into how interactomics is likely to develop.
Effects of Synbiotic Supplementation on Breast Milk Levels of IgA, TGF-β1, and TGF-β2
Publisher: SAGE Publications
Date: 20-06-2013
Abstract: Effects of probiotics on the immunological composition of breast milk have been investigated in a few previous studies. The aims of this study were to determine the effects of synbiotic (probiotic plus prebiotic) supplementation on immunoglobulin A (IgA), transforming growth factor β1 (TGF-β1), and transforming growth factor β2 (TGF-β2) levels of breast milk and on diarrhea incidence in infants. In this randomized, double-blind, and placebo-controlled trial, we recruited 80 lactating mothers who were exclusively breastfeeding their 3-month-old infants. We randomly ided the mothers into 2 groups to receive a daily synbiotic supplement (n = 40) or a placebo (n = 40) for 30 days. Demographic and clinical data (ie, health status) were obtained through an interview. The IgA levels of breast milk were detected by nephelometry, and the levels of TGF-β1 and TGF-β2 were measured using a commercial Platinum ELISA kit. The breast milk IgA increased significantly from 0.41 ± 0.09 to 0.48 ± 0.15 g/L in the supplemented group ( P = .018), while in the placebo group, no significant changes were observed. Although the breast milk TGF-β1 levels did not change significantly, the TGF-β2 levels of breast milk increased significantly from 270 ± 37.8 to 382 ± 43.7 pg/mL in the supplemented group ( P = .043). Also, the incidence of diarrhea in infants decreased significantly in the supplemented group while no significant changes were observed in the placebo group after the experimental period. Synbiotic supplementation may have positive effects on the immune composition of breast milk and the reduction of diarrhea incidence in infants.
Proteomics Analysis of Trastuzumab Toxicity in the H9c2 Cardiomyoblast Cell Line and its Inhibition by Carvedilol
Publisher: Bentham Science Publishers Ltd.
Date: 28-11-2020
DOI: 10.2174/1389201021666200515135548
Abstract: Heart dysfunctions are the major complications of trastuzumab in patients with Human Epidermal growth factor Receptor-2 (HER2)-positive breast cancers. In this study, the cytotoxicity of trastuzumab on H9c2 cardiomyoblasts was demonstrated, and the proteome changes of cells were investigated by a tandem mass tagging quantitative approach. The Differentially Abundant Proteins (DAPs) were identified and functionally enriched. We determined that carvedilol, a non-selective beta-blocker, could effectively inhibit trastuzumab toxicity when administrated in a proper dose and at the same time. The proteomics analysis of carvedilol co-treated cardiomyoblasts showed complete or partial reversion in expressional levels of trastuzumab-induced DAPs. Downregulation of proteins involved in the translation biological process is one of the most important changes induced by trastuzumab and reversed by carvedilol. These findings provide novel insights to develop new strategies for the cardiotoxicity of trastuzumab.
Comparative SRY incorporation on the regulatory regions of pluripotency/differentiation genes in human embryonic carcinoma cells after retinoic acid induction
Publisher: Springer Science and Business Media LLC
Date: 30-01-2013
DOI: 10.1007/S11010-013-1562-5
Abstract: Members of the SOX (SRY box) family proteins play critical roles in multiple aspects of development. SRY, as a founder member of SOX family, has been long believed to be involved in the development of sexual gonads by triggering signaling cascades which lead to the formation of testis or ovary from bipotential gonads. However, less is known about other potential regulatory roles of SRY in the development and differentiation. In order to gain further insight into the possible roles of SRY during development, we looked into possible SRY-regulated genes and their levels of expression in a human embryonic carcinoma cell line, named NTera2, before and after induction of differentiation. For this respect, SRY incorporation on the regulatory regions of two groups of genes including OCT4, NANOG, and SOX2 as pluripotency marker genes, and NESTIN and PAX6 as differentiation marker genes were evaluated quantitatively. Chromatin immunoprecipitation using SRY antibody was performed on chromatin extract of a human embryonic carcinoma cell line, NT2/NTERA-2, before and after onset of differentiation. The results showed that incorporation of SRY in both groups of genes was increased after induction of differentiation. Besides, lower expression of OCT4, SOX2, and NANOG and higher expression of PAX6 and NESTIN genes in differentiated cells suggest that SRY may act as a transcription repressor for pluripotency-associated genes and as a transcription activator for differentiation-related genes.
Assessing information available for health professionals and potential participants on lung cancer screening program websites: a cross-sectional study (Preprint)
Publisher: JMIR Publications Inc.
Date: 14-10-2021
Abstract: ung cancer is the number one cause of cancer death worldwide. The US Preventive Services Task Force (USPSTF) updated recommendations for lung cancer screening in 2021, adjusting the age of screening to 50 years (from 55 years), and reducing the number of pack-years total firsthand cigarette smoke exposure to 20 (down from 30). With many in iduals using the internet for healthcare information, it is important to understand what information is available for in iduals contemplating lung cancer screening. o assess the eligibility criteria and information available on lung cancer screening program websites for both health professionals and potential screeners. descriptive cross-sectional analysis in March 2021 of 151 lung cancer screening program websites of academic (n=76) and community medical centers (n=75) in the United States for data related to information for health professionals and potential screeners was conducted. Presentation of eligibility criteria for potential participants and presence of information available specific to the health professionals about lung cancer screening, were the primary outcomes. Secondary outcomes included presentation of information about cost, smoking cessation, and inclusion of an online risk assessment tool, any clinical guidelines and multimedia used to present information. ligibility criteria is included in nearly all websites, with age range (92.1%) and smoking history (93.4%) included. Age was only consistent with the latest recommendations in 14.5% of the websites and no websites had updated smoking history. Half the websites mention screening costs as related to the type of insurance held. About one in six (15%) featured an online assessment tool to determine eligibility. A similar proportion (15%) hosted information specifically for health professionals. About a third (29%) of websites referred to smoking cessation. Almost a third of websites (30.5%) used multimedia to present information, such as short videos or podcasts. ost US websites of lung cancer screening programs provide information about eligibility criteria, but this is not consistent and has not been updated across all websites following the latest USPSTF recommendations. Online resources require updating to present standardized information that is accessible for all.
RETRACTED ARTICLE: Transient Activation of Reprogramming Transcription Factors Using Protein Transduction Facilitates Conversion of Human Fibroblasts Toward Cardiomyocyte-Like Cells
Publisher: Springer Science and Business Media LLC
Date: 16-05-2017
DOI: 10.1007/S12033-017-0007-X
Abstract: Derivation of cardiomyocytes directly from patients' own fibroblasts could offer a new therapeutic approach for those with ischemic heart disease. An essential step toward clinical application is to establish safe conversion of human fibroblasts into a cardiac fate. Here we aimed to efficiently and safely generate cardiomyocytes from human fibroblasts by direct delivery of reprogramming recombinant cell permeant form of reprogramming proteins followed by cardio-inductive signals. Human fetal and adult fibroblasts were transiently exposed to transactivator of transcription-fused recombinant OCT4, SOX2, KLF4 and c-MYC for 2 weeks and then were directly differentiated toward protein-induced cardiomyocyte-like cells (p-iCLCs) in a cardiac fate niche, carried out by treatment with a set of cardiogenic small molecules (sequential treatment of Chir, and IWP-2, SB431542 and purmorphamine). The cells showed cardiac phenotype over a period of 3 weeks without first undergoing reprogramming into or through a pluripotent intermediate, shown by lack of expression of key pluripotency markers. p-iCLCs exhibited cardiac features at both the gene and protein levels. Our study provides an alternative method for the generation of p-iCLCs which shortcut reprogramming toward allogeneic cardiomyocytes in a safe and efficient manner and could facilitate generation of genetic material-free cardiomyocytes.
Organellar Proteomics of Embryonic Stem Cells
Publisher: Elsevier
Date: 2014
Identification of cytoplasmic and membrane-associated complexes in human embryonic stem cells using blue native PAGE
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1MB05135K
Abstract: Human embryonic stem cells (hESCs) have great potential for use in developmental biology studies, functional genomics applications, drug screening, and regenerative medicine. A detailed understanding of the molecular mechanisms that are responsible for maintaining the undifferentiated and pluripotent nature of hESCs is essential for their effective therapeutic application. It has become evident that many complex cellular processes are carried out by assemblies of protein molecules (protein complexes). Blue native polyacrylamide gel electrophoresis (BN-PAGE) has been used to separate protein complexes from whole cell lysates. Using BN-PAGE, we resolved cytoplasmic and membrane-associated complexes from hESCs and characterised their composition, stoichiometry, and dynamics by denaturing SDS-PAGE. The reliability of the fractionation was examined by western blot analysis of membrane and cytosolic markers. MALDI TOF/TOF mass spectrometry identified 119 cytosolic and 69 membrane proteins from the BN-PAGE proteome maps. Potential protein complexes were validated by computational prediction of possible protein-protein interactions using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Based on BN-PAGE gels and validation by databases, 82 heteromultimeric and 47 homomultimeric protein complexes have been found in hESCs. Resolving some of the protein complexes provided insight into the function of previously uncharacterised complexes in hESCs.
Begomoviruses associated with yellow leaf curl disease of tomato in Iran
Publisher: Wiley
Date: 19-02-2009
Proteomic analysis of the Mexican lime tree response to “Candidatus Phytoplasma aurantifolia” infection
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1MB05268C
Abstract: "Candidatus Phytoplasma aurantifolia" is the causative agent of witches' broom disease in the Mexican lime tree (Citrus aurantifolia L.), and is responsible for major tree losses in Southern Iran and Oman. The pathogen is strictly biotrophic, and, therefore, completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. We applied a proteomics approach to analyse gene expression in Mexican limes infected with "Ca. Phytoplasma aurantifolia". Leaf s les were collected from healthy and infected plants and were analysed using 2-DE coupled with MS. Among 800 leaf proteins that were detected reproducibly in eight biological replicates of healthy and eight biological replicates of infected plants, 55 showed a significant response to the disease. MS resulted in identification of 39 regulated proteins, which included proteins that were involved in oxidative stress defence, photosynthesis, metabolism, and the stress response. Our results provide the first proteomic view of the molecular basis of the infection process and identify genes that could help inhibit the effects of the pathogen.
Data in support of comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance
Publisher: Elsevier BV
Date: 03-2015
MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence
Publisher: Frontiers Media SA
Date: 23-10-2020
200+ Protein Concentrations in Healthy Human Blood Plasma: Targeted Quantitative SRM SIS Screening of Chromosomes 18, 13, Y, and the Mitochondrial Chromosome Encoded Proteome
Publisher: American Chemical Society (ACS)
Date: 11-12-2018
DOI: 10.1021/ACS.JPROTEOME.8B00391
Abstract: This work continues the series of the quantitative measurements of the proteins encoded by different chromosomes in the blood plasma of a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and a gene-centric approach, which is the basis for the implementation of the international Chromosome-centric Human Proteome Project (C-HPP), were applied for the quantitative measurement of proteins in human blood plasma. Analyses were carried out in the frame of C-HPP for each protein-coding gene of the four human chromosomes: 18, 13, Y, and mitochondrial. Concentrations of proteins encoded by 667 genes were measured in 54 blood plasma s les of the volunteers, whose health conditions were consistent with requirements for astronauts. The gene list included 276, 329, 47, and 15 genes of chromosomes 18, 13, Y, and the mitochondrial chromosome, respectively. This paper does not make claims about the detection of missing proteins. Only 205 proteins (30.7%) were detected in the s les. Of them, 84, 106, 10, and 5 belonged to chromosomes 18, 13, and Y and the mitochondrial chromosome, respectively. Each detected protein was found in at least one of the s les analyzed. The SRM SIS raw data are available in the ProteomeXchange repository (PXD004374, PASS01192).
Generation of Liver Disease-Specific Induced Pluripotent Stem Cells Along with Efficient Differentiation to Functional Hepatocyte-Like Cells
Publisher: Springer Science and Business Media LLC
Date: 07-09-2010
DOI: 10.1007/S12015-010-9189-3
Abstract: The availability of disease-specific induced pluripotent stem cells (iPSCs) offers a unique opportunity for studying and modeling the effects of specific gene defects on human liver development in vitro and for testing small molecules or other potential therapies for relevant liver disorders. Here we report, for the first time, the derivation of iPSCs by the retroviral transduction of Yamanaka's factors in serum and feeder-free culture conditions from liver-specific patients with tyrosinemia, glycogen storage disease, progressive familial hereditary cholestasis, and two siblings with Crigler-Najjar syndrome. Furthermore, they were differentiated into functional hepatocyte-like cells efficiently. These iPSCs possessed properties of human embryonic stem cells (hESCs) and were successfully differentiated into three lineages that resembled hESC morphology, passaging, surface and pluripotency markers, normal karyotype, DNA methylation, and differentiation. The hepatic lineage-directed differentiation showed that the iPSC-derived hepatic cells expressed hepatocyte-specific markers. Their functionality was confirmed by glycogen and lipid storage activity, secretion of albumin, alpha-fetoprotein, and urea, CYP450 metabolic activity, as well as LDL and indocyanin green uptake. Our results provide proof of principal that human liver-disease specific iPSCs present an exciting potential venue toward cell-based therapeutics, drug metabolism, human liver development and disease models for liver failure disorders.
Induced Neural Lineage Cells as Repair Kits: So Close, Yet So Far Away
Publisher: Wiley
Date: 21-02-2014
DOI: 10.1002/JCP.24509
Abstract: Transdifferentiation or direct reprogramming of somatic cells into neural lineage cells has provided an invaluable new tool to advance the regenerative neural medicine. Here, we provide an overview of the various strategies currently available for producing of induced neural lineage cells in vitro as well as the direct reprogramming of neural cells in vivo. We also discussing some of the challenges faced in harnessing the potential of induced neural lineage cells for biomedical applications.
Distribution and development of molecularly distinct perineuronal nets in visual thalamus
Publisher: Wiley
Date: 26-11-2018
DOI: 10.1111/JNC.14614
Detection and characterization of phytoplasmas infecting ornamental and weed plants in Iran
Publisher: Wiley
Date: 24-04-2007
A computational learning paradigm to targeted discovery of biocatalysts from metagenomic data: A case study of lipase identification
Publisher: Wiley
Date: 03-02-2022
DOI: 10.1002/BIT.28037
Abstract: The growing adoption of enzymes as biocatalysts in various industries has accentuated the demand for acquiring access to the great natural ersity and, in the meantime, the advent and advancements of metagenomics and high‐throughput sequencing technologies have offered an unprecedented opportunity to explore this extensive resource. Lipases, enzymes responsible for the biological turnover of lipids, are among the most commercialized biocatalysts with numerous applications in different domains and therefore are of high industrial value. The relatively costly and time‐consuming wet‐lab experimental pipelines commonly used for novel enzyme discovery, highlight the necessity of agile in silico approaches to keep pace with the exponential growth of available sequencing data. In the present study, an in‐depth analysis of a tannery wastewater metagenome, including taxonomic and enzymatic profiling, was performed. Using sequence homology‐based screening methods and supervised machine learning‐based regression models aimed at prediction of lipases' pH and temperature optima, the metagenomic data set was screened for lipolytic enzymes, which led to the isolation of alkaline and highly thermophilic novel lipase. Moreover, MeTarEnz (metagenomic targeted enzyme miner) software was developed and made freely accessible (at cbb.ut.ac.ir/MeTarEnz ) as a part of this study. MeTarEnz offers several functions to automate the process of targeted enzyme mining from high‐throughput sequencing data. This study highlights the competence of computational approaches in exploring vast bio ersity within environmental niches, while providing a set of practical in silico tools as well as a generalized methodology to facilitate the sequence‐based mining of biocatalysts.
A proteomics approach to study the molecular basis of enhanced salt tolerance in barley (Hordeum vulgare L.) conferred by the root mutualistic fungus Piriformospora indica
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3MB70069K
Abstract: Piriformospora indica is a root-interacting mutualistic fungus capable of enhancing plant growth, increasing plant resistance to a wide variety of pathogens, and improving plant stress tolerance under extreme environmental conditions. Understanding the molecular mechanisms by which P. indica can improve plant tolerance to stresses will pave the way to identifying the major mechanisms underlying plant adaptability to environmental stresses. We conducted greenhouse experiments at three different salt levels (0, 100 and 300 mM NaCl) on barley (Hordeum vulgare L.) cultivar "Pallas" inoculated with P. indica. Based on the analysis of variance, P. indica had a significant impact on the barley growth and shoot biomass under normal and salt stress conditions. P. indica modulated ion accumulation in colonized plants by increasing the foliar potassium (K(+))/sodium (Na(+)) ratio, as it is considered a reliable indicator of salt stress tolerance. P. indica induced calcium (Ca(2+)) accumulation and likely influenced the stress signal transduction. Subsequently, proteomic analysis of the barley leaf sheath using two-dimensional electrophoresis resulted in detection of 968 protein spots. Of these detected spots, the abundance of 72 protein spots changed significantly in response to salt treatment and P. indica-root colonization. Mass spectrometry analysis of responsive proteins led to the identification of 51 proteins. These proteins belonged to different functional categories including photosynthesis, cell antioxidant defense, protein translation and degradation, energy production, signal transduction and cell wall arrangement. Our results showed that P. indica induced a systemic response to salt stress by altering the physiological and proteome responses of the plant host.
Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen
Publisher: PeerJ
Date: 11-01-2021
DOI: 10.7717/PEERJ.10463
Abstract: The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the ersity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen. We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage’s chemical characteristics and community structure of biofilm-embedded microbiota. Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial ersity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen. Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.
Lignocellulose degradation by rumen bacterial communities
Publisher: Elsevier BV
Date: 07-2023
Proteomic Analysis of Monkey Embryonic Stem Cell during Differentiation
Publisher: American Chemical Society (ACS)
Date: 18-02-2009
DOI: 10.1021/PR800880V
Abstract: Proteome analyses of embryonic stem cells (ESCs) will help to uncover mechanisms underlying cellular differentiation, expansion, and self-renewal. We applied a 2-DE based proteomic approach coupled with mass spectrometry to identify genes controlling monkey ESCs proliferation and differentiation. We analyzed proteome of ESCs during proliferation and different stages of spontaneous differentiation (day 3, 6, 12, and 30) by embryoid body formation. Out of about 663 +/- 15 protein spots reproducible detected on gels, 127 proteins showed significant changes during differentiation. Mass spectrometry analysis of differentially expressed proteins resulted in identification of 95 proteins involved in cell cycle progression and proliferation, cell growth, transcription and chromatin remodeling, translation, metabolism, energy production and Ras signaling. In addition, we created protein interaction maps and distinctly different topology was observed in the protein interaction maps of the monkey ESC proteome clusters compared with maps created using randomly generated sets of proteins. Taken together, the results presented here revealed novel key proteins and pathways that are active during ESC differentiation.
Concise Review: Trends in Stem Cell Proteomics
Publisher: Oxford University Press (OUP)
Date: 10-05-2007
DOI: 10.1634/STEMCELLS.2007-0107
Abstract: Gene expression analyses of stem cells (SCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal, pluripotency, and/or multipotency. In recent years, proteomic approaches have produced a wealth of data identifying proteins and mechanisms involved in SC proliferation and differentiation. Although many proteomics techniques have been developed and improved in peptide and protein separation, as well as mass spectrometry, several important issues, including s le heterogeneity, post-translational modifications, protein-protein interaction, and high-throughput quantification of hydrophobic and low-abundance proteins, still remain to be addressed and require further technical optimization. This review summarizes the methodologies used and the information gathered with proteome analyses of SCs, and it discusses biological and technical challenges for proteomic study of SCs. Disclosure of potential conflicts of interest is found at the end of this article.
In vitro bioprocessing of corn as poultry feed additive by the influence of carbohydrate hydrolyzing metagenome derived enzyme cocktail
Publisher: Springer Science and Business Media LLC
Date: 10-01-2022
DOI: 10.1038/S41598-021-04103-Z
Abstract: The carbohydrate-hydrolyzing enzymes play a crucial role in increasing the phenolic content and nutritional properties of polysaccharides substrate, essential for cost-effective industrial applications. Also, improving the feed efficiency of poultry is essential to achieve significant economic benefits. The current study introduced a novel thermostable metagenome-derived xylanase named PersiXyn8 and investigated its synergistic effect with previously reported α-amylase (PersiAmy3) to enhance poultry feed utilization. The potential of the enzyme cocktail in the degradation of poultry feed was analyzed and showed 346.73 mg/g poultry feed reducing sugar after 72 h of hydrolysis. Next, the impact of solid-state fermentation on corn quality was investigated in the presence and absence of enzymes. The phenolic content increased from 36.60 mg/g GAE in control s le to 68.23 mg/g in the presence of enzymes. In addition, the enzyme-treated s le showed the highest reducing power OD 700 of 0.217 and the most potent radical scavenging activity against ABTS (40.36%) and DPPH (45.21%) radicals. Moreover, the protein and ash contents of the fermented corn increased by 4.88% and 6.46%, respectively. These results confirmed the potential of the carbohydrate-hydrolyzing enzymes cocktail as a low-cost treatment for improving the phenolic content, antioxidant activity, and nutritional values of corn for supplementation of corn-based poultry feed.
Identification of squamous cell carcinoma associated proteins by proteomics and loss of beta tropomyosin expression in esophageal cancer
Publisher: Baishideng Publishing Group Inc.
Date: 2006
Abstract: To assess the proteome of normal versus tumor tissue in squamous cell carcinoma of the esophagus (SCCE) in Iranian patients and compare our results with former reports by using proteomics. Protein was extracted from normal and tumor tissues. Two dimensional electrophoresis was carried out and spots with differential expression were identified with mass spectrometry. RNA extraction and RT-PCR along with immunodetection were performed. Fourteen proteins were found whose expression levels differed in tumor compared to normal tissues. Mass spectrometric analysis resulted in the identification of beta-tropomyosin (TMbeta), myosin light chain 2 (and its isoform), myosin regulatory light chain 2, peroxyredoxin 2, annexin I and an unknown polypeptide as the down regulated polypeptides in tumor tissue. Heat shock protein 70 (HSP70), TPM4-ALK fusion oncoprotein 2, myosin light polypeptide 6, keratin I, GH16431p and calreticulin were the up-regulated polypeptides found in tumor tissue. Several of these proteins, such as TMbeta, HSP70, annexin I, calreticulin, TPM4-ALK and isoforms of myosins, have been well recognized in tumorigenesis of esophageal or other types of cancers. Our study not only supports the involvement of some of the formerly reported proteins in SCCE but also introduces additional proteins found to be lost in SCCE, including TMbeta.
Concise Review: Alchemy of Biology: Generating Desired Cell Types from Abundant and Accessible Cells
Publisher: Oxford University Press (OUP)
Date: 16-11-2011
DOI: 10.1002/STEM.760
Abstract: A major goal of regenerative medicine is to produce cells to participate in the generation, maintenance, and repair of tissues that are damaged by disease, aging, or trauma, such that function is restored. The establishment of induced pluripotent stem cells, followed by directed differentiation, offers a powerful strategy for producing patient-specific therapies. Given how laborious and lengthy this process can be, the conversion of somatic cells into lineage-specific stem rogenitor cells in one step, without going back to, or through, a pluripotent stage, has opened up tremendous opportunities for regenerative medicine. However, there are a number of obstacles to overcome before these cells can be widely considered for clinical applications. Here, we focus on induced transdifferentiation strategies to convert mature somatic cells to other mature cell types or progenitors, and we summarize the challenges that need to be met if the potential applications of transdifferentiation technology are to be achieved.
Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reports
Publisher: Informa UK Limited
Date: 29-10-2018
DOI: 10.1080/14789450.2018.1539669
Abstract: Human embryonic stem cells (hESCs) have unique biological features and attributes that make them attractive in various areas of biomedical research. With heightened applications, there is an ever increasing need for advancement of proteome analysis. Membrane proteins are one of the most important subset of hESC proteins as they can be used as surface markers. Areas covered: This review discusses commonly used surface markers of hESCs, and provides in-depth analysis of available hESC membrane proteome reports and the existence of these markers in many other cell types, especially cancer cells. Appreciating, existing ambiguity in the definition of a membrane protein, we have attempted a meta analysis of the published membrane protein reports of hESCs by using a combination of protein databases and prediction tools to find the most confident plasma membrane proteins in hESCs. Furthermore, responsiveness of plasma membrane proteins to differentiation has been discussed based on available transcriptome profiling data bank. Expert commentary: Combined transcriptome and membrane proteome analysis highlighted additional proteins that may eventually find utility as new cell surface markers.
Down-Regulation of a Male-Specific H3K4 Demethylase, KDM5D, Impairs Cardiomyocyte Differentiation
Publisher: American Chemical Society (ACS)
Date: 27-09-2019
DOI: 10.1021/ACS.JPROTEOME.9B00395
Abstract: Despite the small number of Y chromosome genes, their adequate expression is required for regulation of transcription, translation, and protein stability in males, not just for sex determination. In addition to the role in male fertility, the Y chromosome has a significant role in the development and sexual dimorphism of healthy and disease phenotypes. We observed that
Inhibition of Human Y Chromosome Gene, SRY, Promotes Naïve State of Human Pluripotent Stem Cells
Publisher: American Chemical Society (ACS)
Date: 03-10-2019
DOI: 10.1021/ACS.JPROTEOME.9B00396
Abstract: Although males and females have a variety of sexually dimorphic features related to hormonal effects, the genetic basis of dimorphism relies on early embryo development. Two pluripotent states, naïve and primed, emerge during early mammalian development. Identification of signaling pathways that induce differences between these two states can help to modulate conversion of primed cells to naïve cells. Naïve cells have a shorter doubling time and longer survival than their primed counterparts when passaged as single cells. In this study, we sought to explore the role of Y chromosome genes on human pluripotent stem cells (hPSCs) by investigating differential expressions of the male-specific region of the Y chromosome (MSY) genes in primed and naïve cells. Interestingly, we found that several MSY genes, including
An integrated proteomic approach to decipher the effect of methyl jasmonate elicitation on the proteome of Silybum marianum L. hairy roots
Publisher: Elsevier BV
Date: 09-2013
DOI: 10.1016/J.PLAPHY.2013.05.031
Abstract: Jasmonate and its methyl derivative, methyl jasmonate (MeJA), are naturally occurring compounds that mediate several plant physiological processes in response to pathogen attack, wounding, and ozone. Exogenous application of jasmonates triggers defense responses that resemble those initiated by pathogen infection and also modulates the production of certain secondary metabolites in a variety of plant species. In this study, we treated the hairy root cultures of Silybum marianum L. with 100 μM MeJA and then measured the content of Silymarin (SLM). We observed that the SLM content increased significantly after 48 h of MeJA treatment and remained constant for 120 h. However, MeJA treatment caused a significant growth reduction after 96 h incubation. The activity of lipoxygenase as a key enzyme in the jasmonate biosynthesis pathway and anti-oxidative enzymes peroxidase and ascorbate peroxidase was also significantly increased after MeJA treatment. To elucidate the global effect of jasmonate on gene expression of S. marianum, we employed high resolution two-dimensional gel electrophoresis coupled with tandem mass spectrometry. Out of 670 reproducibly detected protein spots which were analyzed on each given gel, 32 spots were up- or down regulated upon MeJA treatment. Of them, ten proteins such as ER binding protein, glutamine synthetase, pathogenesis-related protein, caffeoyl CoA O-methyltransferase, and profilin-1 could be identified by mass spectrometry analysis. The possible implications of the identified proteins on physiological outcome of MeJA application in S. marianum hairy root culture will be discussed.
A novel high performance in-silico screened metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions
Publisher: Springer Science and Business Media LLC
Date: 19-10-2020
DOI: 10.1186/S12896-020-00647-6
Abstract: Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant. The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. At first, the multi-step in-silico screening approach was utilized to find primary candidate enzymes with superior properties. Among the computationally selected candidates, PersiCel4 was found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes’ kinetic parameters, including V max , K m , and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85 °C and was able to retain more than 70% of its activity after 150 h of storage at 85 °C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl and several metal ions contains Mg 2+ , Mn 2+ , Cu 2+ , Fe 2+ and Ca 2+ . Our results showed that treatment with MnCl 2 could enhance the enzyme’s activity by 78%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 h in the harsh condition (T = 85 °C, pH = 8.5). Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.
Comparison of Dynamics of Udder Skin Microbiota From Grazing Yak and Cattle During the Perinatal Period on the Qinghai–Tibetan Plateau
Publisher: Frontiers Media SA
Date: 27-05-2022
DOI: 10.3389/FVETS.2022.864057
Abstract: The perinatal period has an important impact on the health of ruminants, and the imbalance of udder skin microbiota might be an important inducement of bovine mastitis. However, it is not clear how the perinatal period affects the microbial structure and stability of the udder skin of yak and cattle. Here, we used 16S rRNA gene high-throughput sequencing to analyze the udder skin microbiota of yak and cattle during the perinatal period. We found that the ersity and richness of microbiota of bovine udder skin during 1–2 weeks postpartum were significantly lower than those in the 1–2 weeks prenatal and 1-month postpartum period (Wilcoxon, p & 0.05). Besides, we found sharing of 2,533 OTUs in the udder skin microbiota of yak and cattle during the perinatal period, among which the core microbiota at the genera level was mainly composed of Staphylococcus, Moraxella , and Acinetobacter . However, the genus Acinetobacter was significantly abundant in the udder skin of cattle during 1–2 weeks postpartum. The NMDS and LEfSe results showed that the perinatal period had more effects on the composition and stability of microbial community in the udder skin of cattle compared to yak, particularly during 1–2 weeks postpartum. In addition, the average content of total whey proteins and immunoglobulin G of whey protein were significantly higher in the yak colostrum when compared to those found in the cattle ( p & 0.05). In conclusion, the structure of udder skin microbiota of yak during the perinatal period is more stable than that of cattle in the same habitat, and 1–2 weeks postpartum may be a potential window period to prevent cattle mastitis.
Plant isomiRs: origins, biogenesis, and biological functions
Publisher: Elsevier BV
Date: 09-2020
Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates
Publisher: Springer Science and Business Media LLC
Date: 08-06-2022
DOI: 10.1038/S41522-022-00309-9
Abstract: Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic ersity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the ersity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a erse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.
The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.JPLPH.2017.05.012
Abstract: Drought stress represents one of the most common stresses affecting the productivity of crop plants. A rather recently discovered component of the plant response to drought is the cellular population of microRNAs. Here, the microRNA content was revealed of two bread wheat cultivars contrasting strongly with respect to the ability to withstand drought stress. A total of 1813 miRNAs was identified, grouped into 106 families. Some 104 of these miRNAs were predicted to match 212 novel miRNA precursors. In the drought tolerant cultivar (SM), 105 (33 known and 72 novel) miRNAs were altered in abundance by the imposition of drought stress, while the equivalent number in the more sensitive cultivar (SW) was 51 (20 and 31). An in silico analysis predicted that these miRNAs target at least 1959 genes in SM and 1111 in SW, suggesting their broad contribution to the drought stress response. Among the target genes were several known stress-related genes, encoding, for ex le, superoxide dismutase, various MYB transcription factors, various ABA signaling proteins and various MADS-box transcription factors. In many cases, the more susceptible cultivar SW behaved in a contrasting manner. The suggestion is that miRNAs represent an important aspect of the drought stress response, post-transcriptionally regulating a range of stress-related genes.
Proteomic analysis of rice anthers under salt stress
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.PLAPHY.2012.07.013
Abstract: Salinity is a major factor that limits rice production worldwide. Rice is considered generally to be sensitive to salt stress during the reproductive stage. To determine the molecular mechanisms of salt tolerance at the reproductive stage, anther proteomic patterns for two contrasting rice genotypes IR64 (salt sensitive) and Cheriviruppu (salt tolerant) under salt stress were compared. Plants were grown in a greenhouse and salt stress (100 mM NaCl) was imposed at the booting stage. Anther s les were collected from control and salt-treated plants at the anthesis stage. The Na(+)/K(+) ratio in IR64 anthers under salt stress was >1.7 times greater than that under control conditions, whereas no significant change was observed in Cheriviruppu. We also observed an 83% reduction in IR64 pollen viability, whereas this reduction was only 23% in Cheriviruppu. Of 454 protein spots detected reproducibly on two-dimensional electrophoresis gels, 38 showed significant changes in at least one genotype in response to stress. Using Mass spectrometry (MALDI TOF/TOF) analysis, we identified 18 protein spots that were involved in several processes that might increase plant adaptation to salt stress, such as carbohydrate/energy metabolism, anther wall remodelling and metabolism, and protein synthesis and assembly. Three isoforms of fructokinase-2 were upregulated only in Cheriviruppu under salt stress. This upregulation might result in increased starch content in pollen, which would support pollen growth and development under salt stress. The results also suggested that anther and pollen wall remodelling/metabolism proteins contribute to the tolerance of rice to salt stress.
The Human Proteome Project: Current State and Future Direction
Publisher: Elsevier BV
Date: 07-2011
Promoting agriculture proteome research activities in the asia and oceania region
Publisher: American Chemical Society (ACS)
Date: 09-02-2012
DOI: 10.1021/PR300063Z
Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project
Publisher: American Chemical Society (ACS)
Date: 23-07-2015
DOI: 10.1021/PR5013009
Abstract: This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological s les that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wiki (c-hpp.webhosting.rug.nl/) and in the Supporting Information.
Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome
Publisher: Springer Science and Business Media LLC
Date: 19-03-2020
DOI: 10.1038/S41598-020-61942-Y
Abstract: Rumen microbial environment hosts a variety of microorganisms that interact with each other to carry out the feed digestion and generation of several by-products especially methane, which plays an essential role in global warming as a greenhouse gas. However, due to its multi-factorial nature, the exact cause of methane production in the rumen has not yet been fully determined. The current study is an attempt to use system modeling to analyze the relationship between interacting components of rumen microbiome and its role in methane production. Metagenomic data of sheep rumen, with equal numbers of high methane yield (HMY) and low methane yield (LMY) s les, were used. As a well-known approach for the systematic comparative study of complex traits, the co-abundance networks were constructed in both operational taxonomic unit (OTU) and gene levels. A gene-catalog of 1,444 different rumen microbial strains was developed as a reference to measure gene abundances. The results from both types of co-abundance networks showed that methanogens, which are the main ruminal source for methanogenesis, need other microbial species to accomplish the task of methane production through producing the main precursor molecules like H 2 and acetate for methanogenesis pathway as their byproducts. KEGG Orthology(KO) analysis of the current study shows that the metabolism and growth rate of methanogens will be increased due to the higher rate of the metabolism and carbohydrate/fiber digestion pathways in the hidden elements. This finding proposes that any ruminant methane yield alteration strategy should consider complex interactions of rumen microbiome components as one tightly integrated unit rather than several separate parts.
Retinal proteomics of experimental glaucoma model reveal intraocular pressure‐induced mediators of neurodegenerative changes
Publisher: Wiley
Date: 21-07-2020
DOI: 10.1002/JCB.29822
A proteomic view of cellular and molecular effects of cannabis
Publisher: MDPI AG
Date: 27-09-2021
DOI: 10.3390/BIOM11101411
Abstract: Cannabis (Cannabis sativa), popularly known as marijuana, is the most commonly used psychoactive substance and is considered illicit in most countries worldwide. However, a growing body of research has provided evidence of the therapeutic properties of chemical components of cannabis known as cannabinoids against several diseases including Alzheimer’s disease (AD), multiple sclerosis (MS), Parkinson’s disease, schizophrenia and glaucoma these have prompted changes in medicinal cannabis legislation. The relaxation of legal restrictions and increased socio-cultural acceptance has led to its increase in both medicinal and recreational usage. Several biochemically active components of cannabis have a range of effects on the biological system. There is an urgent need for more research to better understand the molecular and biochemical effects of cannabis at a cellular level, to understand fully its implications as a pharmaceutical drug. Proteomics technology is an efficient tool to rigorously elucidate the mechanistic effects of cannabis on the human body in a cell and tissue-specific manner, drawing conclusions associated with its toxicity as well as therapeutic benefits, safety and efficacy profiles. This review provides a comprehensive overview of both in vitro and in vivo proteomic studies involving the cellular and molecular effects of cannabis and cannabis-derived compounds.
Inner retinal injury in experimental glaucoma is prevented upon AAV mediated Shp2 silencing in a caveolin dependent manner
Publisher: Ivyspring International Publisher
Date: 2021
DOI: 10.7150/THNO.55472
Influence of ascites syndrome on growth pattern of chickens reared at normal or cold ambient temperature
Publisher: Walter de Gruyter GmbH
Date: 04-2015
Abstract: Ascites syndrome (AS) is a metabolic disorder usually seen in highly improved meat-type broiler strains. This syndrome causes major financial losses to the poultry industry. Previously it was believed that AS incidence was a side effect of intense selection for rapid growth rate (GR) or higher market weight. If this belief is the case, selection for further increase in GR will not be rational. However, it was later understood that there were significant genetic variations for both GR and susceptibility/resistance to AS thus selective breeding could be helpful in diminishing the incidence of AS while improving GR. Furthermore, it was hypothesized that genes controlling the GR were not genetically dependent on those genes controlling susceptibility to AS. In the current research, we aimed to study the association of GR traits with AS% in a pure sire line. A total of 1458 1-day-old chicks from 67 sire families were used. The results revealed that ascitic chicks were not significantly superior in early GR traits (i.e. before day 28) than the healthy ones. At later ages, probably due to the commencement of the syndrome, the ascitic chicks were significantly lighter in body weight (BW) than their healthy counterparts. The lack of significant genetic correlations between the GR traits and AS% indicated that there was considerable scope for simultaneous selection of birds for increased BW and GR while controlling susceptibility to AS.
Data for whole and mitochondrial proteome of human embryonic stem cells
Publisher: Elsevier BV
Date: 08-2017
Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body‐based differentiation
Publisher: Wiley
Date: 27-10-2009
Abstract: Gene expression analyses of embryonic stem cells (ESCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal and pluripotency. We employed a 2-DE-based proteomics approach to analyze human ESC line, Royan H5, in undifferentiated cells and different stages of spontaneous differentiation (days 3, 6, 12, and 20) by embryoid body formation. Out of 945 proteins reproducibly detected on gels, the expression of 96 spots changed during differentiation. Using MS, 87 ESC-associated proteins were identified including several proteins involved in cell proliferation, cell apoptosis, transcription, translation, mRNA processing, and protein folding. Transcriptional changes accompanying differentiation of Royan H5 were also analyzed using microarrays. We developed a comprehensive data set that shows the use of human ESC lines in vitro to mimic gastrulation and organogenesis. Our results showed that proteomics and transcriptomics data are complementary rather than duplicative. Although regulation of many genes during differentiation were observed only at transcript level, modulation of several proteins was revealed only by proteome analysis.
Human-Induced Pluripotent Stem Cells: Derivation, Propagation, and Freezing in Serum- and Feeder Layer-Free Culture Conditions
Publisher: Humana Press
Date: 2009
DOI: 10.1007/978-1-60761-369-5_23
Abstract: The recent discovery of genomic reprogramming of human somatic cells to an embryonic stem (ES) cell-like pluripotent state provides a unique opportunity for stem cell research. The reprogrammed cells, named as induced pluripotent stem (iPS) cells, possess many of the properties of ES cells and represent one of the most promising sources of patient-specific cells for use in disease model, development of pharmacology and toxicology, screening teratogens, and regenerative medicine. Here we describe the detailed methods for the generation of undifferentiated human iPS (hiPS) cells in feeder layer- and serum-free conditions. This system eliminates direct contact of stem cells with MEFs and reduces use of unknown serum factors that may have undesired activities and enables consistency in large-scale and long-term expansion of undifferentiated hiPS cells. Our findings greatly simplify the method for induction of pluripotency and bring it one step closer to clinical applications. Moreover, the established hiPS cells showed chromosomal stability during long-term culture.
Comprehensive Gene Expression Analysis of Human Embryonic Stem Cells during Differentiation into Neural Cells
Publisher: Public Library of Science (PLoS)
Date: 28-07-2011
Y chromosome is moving out of sex determination shadow
Publisher: Springer Science and Business Media LLC
Date: 04-01-2022
DOI: 10.1186/S13578-021-00741-Y
Abstract: Although sex hormones play a key role in sex differences in susceptibility, severity, outcomes, and response to therapy of different diseases, sex chromosomes are also increasingly recognized as an important factor. Studies demonstrated that the Y chromosome is not a ‘genetic wasteland’ and can be a useful genetic marker for interpreting various male-specific physiological and pathophysiological characteristics. Y chromosome harbors male‑specific genes, which either solely or in cooperation with their X-counterpart, and independent or in conjunction with sex hormones have a considerable impact on basic physiology and disease mechanisms in most or all tissues development. Furthermore, loss of Y chromosome and/or aberrant expression of Y chromosome genes cause sex differences in disease mechanisms. With the launch of the human proteome project (HPP), the association of Y chromosome proteins with pathological conditions has been increasingly explored. In this review, the involvement of Y chromosome genes in male-specific diseases such as prostate cancer and the cases that are more prevalent in men, such as cardiovascular disease, neurological disease, and cancers, has been highlighted. Understanding the molecular mechanisms underlying Y chromosome-related diseases can have a significant impact on the prevention, diagnosis, and treatment of diseases.
Upgrading the enzymatic hydrolysis of lignocellulosic biomass by immobilization of metagenome-derived novel halotolerant cellulase on the carboxymethyl cellulose-based hydrogel
Publisher: Springer Science and Business Media LLC
Date: 21-02-2021
Feeder- and serum-free establishment and expansion of human induced pluripotent stem cells
Publisher: UPV/EHU Press
Date: 2010
Abstract: Although human induced pluripotent stem cells (hiPSCs) hold great promise as a source of differentiated cells for vast therapeutic implications, many obstacles still need to be surmounted before this can become a reality. One obstacle, a robust feeder- and serum-free system to generate and expand hiPSCs in culture is still unavailable. Here, for the first time, we describe a novel establishment and maintenance culture technique that uses human dermal fibroblasts to generate hiPSCs by introducing four factors, Klf4, Oct4, Sox2, and c-Myc under serum- and feeder-independent conditions. We have used a serum replacement product, conditioned medium (CM), or feeder-free medium (FFM) supplemented with high elevated basic-fibroblast growth factor in the absence or presence of Matrigel. Our FFM system in the presence of Matrigel enhanced the efficiency of alkaline phosphatase-positive colonies at a frequency at least 10-fold greater than the conventional method on feeder cells. The established hiPSCs are similar to human embryonic stem cells in many aspects including morphology, passaging, surface and pluripotency markers, normal karyotype, gene expression, ultrastructure, and in vitro differentiation. Such hiPSCs could be useful particularly in the context of in vitro disease modeling, pharmaceutical screening and in cellular replacement therapies once the safety issues have been overcome.
Immobilization of enzyme cocktails on dopamine functionalized magnetic cellulose nanocrystals to enhance sugar bioconversion: A biomass reusing loop.
Publisher: Elsevier BV
Date: 03-2020
Drought tolerance in four-day-old seedlings of a drought-sensitive cultivar of wheat
Publisher: Informa UK Limited
Date: 14-12-2016
Red/ox states of human protein disulfide isomerase regulate binding affinity of 17 beta-estradiol
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.ABB.2017.02.010
Abstract: Human protein disulfide isomerase (hPDI) is a key redox-regulated thiol-containing protein operating as both oxidoreductase and molecular chaperone in the endoplasmic reticulum of cells. hPDI thiol-disulfide interchange reactions lead to the adoption of two distinct red/ox conformations with different substrate preferences. hPDI also displays high binding capacity for some endogenous steroid hormones including 17 beta-estradiol (E2) and thus contributes to the regulation of their intracellular concentration, storage and actions. The primary focus of this study was to investigate the impact of E2 binding on functional activity of recombinant hPDI. Then, we examined the effect of E2 binding on structural alteration of hPDI red/ox conformations and its influence on affinity and position of interaction using experimental and computational analysis. Our results revealed that interaction of one E2 per each hPDI molecule led to the inhibition of hPDI reductase activity and conformational changes in both oxidation states. Mutually, E2-binding position were also redox-regulated with higher affinity in oxidized hPDI compare to the reduced form. The importance of histidine-256 protonation states in distinct binding preferences of E2 were also demonstrated in hPDI red/ox conformations. These findings might pave the way for better understanding of the mechanisms behind the redox-dependent hormone-binding activity of hPDI.
Ethology of Sunn-pest oviposition in interaction with deltamethrin loaded on mesoporous silica nanoparticles as a nanopesticide
Publisher: Springer Science and Business Media LLC
Date: 26-04-2022
DOI: 10.1186/S40538-022-00296-1
Abstract: Wheat is one of the main food for around 2 billion people worldwide. Among the biological stressors, Eurygaster integriceps Puton is a damaging insect in wheat and barley fields, which harms them both quantitatively (by overwintered adults) and qualitatively (by instar nymphs). The ovipositional and the new generation’s production control are pivotal approaches to control the severe damages of Sunn-pest. In this study, to enhance the deltamethrin effectiveness while reducing its required dosage and also reducing the adverse health and environmental impacts, a novel MSN-based deltamethrin formulation was prepared and evaluated based on the laying-eggs number and oviposition behavior. To this, deltamethrin was loaded on KIT-6 mesoporous silica nanoparticles and characterized using SEM, TEM, and TGA analysis, and the insect potential of deltametrin@KIT6 was then evaluated. The results showed that there might be differences between the treatments (KIT-6, deltamethrin@KIT-6, deltamethrin commercial formulation, and water as a control) in terms of the insect control via the laying-egg and next-generation prevention. The results showed that KIT-6 and deltamethrin@KIT-6 could reduce the oviposition rate compared to water as the control. Deltamethrin@KIT-6 not only caused the less oviposition done but the eggs were scattered and the batch of eggs did not have a uniform-shape similar to the control mode. The deltamethrin@KIT-6 nanopesticide could increase the pesticide effectiveness by reducing the Sunn-pest’s oviposition and nymphal population and subsequently decreasing the damage caused by them. So that the concentrations of 10, 25, and 125 mg L −1 of deltamethrin@KIT-6 reduced oviposition by 63.24%, 66.11%, and 67.62%, respectively, compared to the control group. On the other hand, descriptive observations showed that another possible tension is created through insect eggs deposition on the boundary layer of leaves. The MSN-based nanoformulation could be effectively considered to control the next-generation population density of Sunn-pest.
Proteome analysis of endometrial tissue from patients with PCOS reveals proteins predicted to impact the disease
Publisher: Springer Science and Business Media LLC
Date: 24-10-2020
Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in cattle rumen
Publisher: Oxford University Press (OUP)
Date: 18-04-2020
Abstract: The attachment of rumen microbes to feed particles is critical to feed fermentation, degradation and digestion. However, the extent to which the physicochemical properties of feeds influence the colonization by rumen microbes is still unclear. We hypothesized that rumen microbial communities may have differential preferences for attachments to feeds with varying lignocellulose properties. To this end, the structure and composition of microbial communities attached to six common forages with different lignocellulosic compositions were analyzed following in situ rumen incubation in male Taleshi cattle. The results showed that differences in lignocellulosic compositions significantly affected the inter-s le ersity of forage-attached microbial communities in the first 24 h of rumen incubation, during which the highest dry matter degradation was achieved. However, extension of the incubation to 96 h resulted in the development of more uniform microbial communities across the forages. Fibrobacteres were significantly overrepresented in the bacterial communities attached to the forages with the highest neutral detergent fiber contents. Ruminococcus tended to attach to the forages with low acid detergent lignin contents. The extent of dry matter fermentation was significantly correlated with the populations of Fibrobacteraceae, unclassified Bacteroidales, Ruminococcaceae and Spirochaetacea. Our findings suggested that lignocellulosic compositions, and more specifically the cellulose components, significantly affected the microbial attachment to and thus the final digestion of the forages.
Recent Advances of Functional Proteomics in Gastrointestinal Cancers- a Path towards the Identification of Candidate Diagnostic, Prognostic, and Therapeutic Molecular Biomarkers
Publisher: MDPI AG
Date: 12-11-2020
DOI: 10.3390/IJMS21228532
Abstract: Gastrointestinal (GI) cancer remains one of the common causes of morbidity and mortality. A high number of cases are diagnosed at an advanced stage, leading to a poor survival rate. This is primarily attributed to the lack of reliable diagnostic biomarkers and limited treatment options. Therefore, more sensitive, specific biomarkers and curative treatments are desirable. Functional proteomics as a research area in the proteomic field aims to elucidate the biological function of unknown proteins and unravel the cellular mechanisms at the molecular level. Phosphoproteomic and glycoproteomic studies have emerged as two efficient functional proteomics approaches used to identify diagnostic biomarkers, therapeutic targets, the molecular basis of disease and mechanisms underlying drug resistance in GI cancers. In this review, we present an overview on how functional proteomics may contribute to the understanding of GI cancers, namely colorectal, gastric, hepatocellular carcinoma and pancreatic cancers. Moreover, we have summarized recent methodological developments in phosphoproteomics and glycoproteomics for GI cancer studies.
PlantPReS: A database for plant proteome response to stress
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.JPROT.2016.03.009
Abstract: About 75% of plant yield potential has been estimated to be lost to environmental stresses, even in developed agricultures. To facilitate the biotechnological improvement of crop productivity, genes and proteins that control crop adaptation to a wide range of environments will need to be identified. Due to the challenges faced in text/data mining, there is a large gap between the data available to researchers and the hundreds of published plant stress proteomics articles. Plant stress proteome database (PlantPReS www.proteome.ir) is an open online proteomic database, which currently (as of October 2015) comprises >20,413 entries from 456 manually curated articles, and contains >10,600 unique stress responsive proteins. Since every aspect of the experiments, including protein name, accession number, plant type, tissue, stress types, organelles, and developmental stage has been digitized, experimental data can be rapidly accessed and integrated. Furthermore, PlantPReS enables researchers to perform multiple analyses on the database using the filtration mode, and the results of each query indicate a series of proteins for which a set of selected criteria is met. The query results can be displayed in either text or graphical format. The promise of text and data mining to facilitate and enhance research fundamentally has not yet been achieved, mainly because great numbers of stress-associated proteins are not deposited in databases. PlantPReS is a valuable database for the vast majority of researchers working in proteomics and plant stress areas. It has a user-friendly interface with a number of useful features, including a search engine, analysis tools, gene ontology, a function for cross-referencing useful external databases, and the expression pattern of stress associated proteins.
Stress Preconditioning of Sperm for Cryopreservation: New Approach Based on Proteomics Characteristics
Publisher: Elsevier BV
Date: 02-2018
Identification and validation of Asteraceae miRNAs by the expressed sequence tag analysis
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.GENE.2011.11.024
Abstract: MicroRNAs (miRNAs) are small non-coding RNA molecules that play a vital role in the regulation of gene expression. Despite their identification in hundreds of plant species, few miRNAs have been identified in the Asteraceae, a large family that comprises approximately one tenth of all flowering plants. In this study, we used the expressed sequence tag (EST) analysis to identify potential conserved miRNAs and their putative target genes in the Asteraceae. We applied quantitative Real-Time PCR (qRT-PCR) to confirm the expression of eight potential miRNAs in Carthamus tinctorius and Helianthus annuus. We also performed qRT-PCR analysis to investigate the differential expression pattern of five newly identified miRNAs during five different cotyledon growth stages in safflower. Using these methods, we successfully identified and characterized 151 potentially conserved miRNAs, belonging to 26 miRNA families, in 11 genus of Asteraceae. EST analysis predicted that the newly identified conserved Asteraceae miRNAs target 130 total protein-coding ESTs in sunflower and safflower, as well as 433 additional target genes in other plant species. We experimentally confirmed the existence of seven predicted miRNAs, (miR156, miR159, miR160, miR162, miR166, miR396, and miR398) in safflower and sunflower seedlings. We also observed that five out of eight miRNAs are differentially expressed during cotyledon development. Our results indicate that miRNAs may be involved in the regulation of gene expression during seed germination and the formation of the cotyledons in the Asteraceae. The findings of this study might ultimately help in the understanding of miRNA-mediated gene regulation in important crop species.
Efficiency of an alkaline, thermostable, detergent compatible, and organic solvent tolerant lipase with hydrolytic potential in biotreatment of wastewater
Publisher: Elsevier BV
Date: 03-2023
Education messages and strategies to inform the public, potential screening candidates and healthcare providers about lung cancer screening: A systematic review
Publisher: Elsevier BV
Date: 04-2023
Chromosome-Centric Human Proteome Project Allies with Developmental Biology: A Case Study of the Role of Y Chromosome Genes in Organ Development
Publisher: American Chemical Society (ACS)
Date: 11-10-2017
DOI: 10.1021/ACS.JPROTEOME.7B00446
Abstract: One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination. From an evolutionary perspective, Y chromosome has preserved 3% of ancestral genes compared to 98% preservation of the X chromosome based on Ohno's law. Male specific region of Y chromosome (MSY) contains genes that contribute to central dogma and govern the expression of various targets throughout the genome. One of the most well-known functions of MSY genes is to decide the male-specific characteristics including sex, testis formation, and spermatogenesis, which are majorly formed by liconic gene families. Beyond its role in sex-specific gonad development, MSY genes in coexpression with their X counterparts, as single copy and broadly expressed genes, inhibit haplolethality and play a key role in embryogenesis. The role of X-Y related gene mutations in the development of hereditary syndromes suggests an essential contribution of sex chromosome genes to development. MSY genes, solely and independent of their X counterparts and/or in association with sex hormones, have a considerable impact on organ development. In this Review, we present major recent findings on the contribution of MSY genes to gonad formation, spermatogenesis, and the brain, heart, and kidney development and discuss how Y chromosome proteome project may exploit developmental biology to find missing proteins.
Defining pluripotent stem cells through quantitative proteomic analysis
Publisher: Informa UK Limited
Date: 02-2011
DOI: 10.1586/EPR.10.100
Abstract: Embryonic stem cells (ESCs) are at the center stage of intense research, inspired by their potential to give rise to all cell types of the adult in idual. This property makes ESCs suitable candidates for generating specialized cells to replace damaged tissue lost after injury or disease. However, such clinical applications require a detailed insight of the molecular mechanisms underlying the self-renewal, expansion and differentiation of stem cells. This has gained further relevance since the introduction of induced pluripotent stem cells (iPSCs), which are functionally very similar to ESCs. The key property that iPSCs can be derived from somatic cells lifts some of the major ethical issues related to the need for embryos to generate ESCs. Yet, this has only increased the need to define the similarity of iPSCs and ESCs at the molecular level, both before and after they are induced to differentiate. In this article, we describe the proteomic approaches that have been used to characterize ESCs with regard to self-renewal and differentiation, with an emphasis on signaling cascades and histone modifications. We take this as a lead to discuss how quantitative proteomics can be deployed to study reprogramming and iPSC identity. In addition, we discuss how emerging proteomic technologies can become a useful tool to monitor the (de)differentiation status of ESCs and iPSCs.
Biocatalytic decolorization of azo dye-containing wastewater by immobilizing metagenome-derived laccase on green synthesized Co-doped NiO NPs
Publisher: Elsevier BV
Date: 11-2023
Quantitative Proteomic Analysis of Human Embryonic Stem Cell Differentiation by 8-Plex iTRAQ Labelling
Publisher: Public Library of Science (PLoS)
Date: 18-06-2012
Low Focal Adhesion Signaling Promotes Ground State Pluripotency of Mouse Embryonic Stem Cells
Publisher: American Chemical Society (ACS)
Date: 13-09-2017
DOI: 10.1021/ACS.JPROTEOME.7B00322
Abstract: Mouse embryonic stem cells (mESCs) can be maintained in a pluripotent state when cultured with 2 inhibitors (2i) of extracellular signal-regulated kinase (MEK) and glycogen synthase kinase-3 (GSK3), and Royan 2 inhibitors (R2i) of FGF4 and TGFβ. The molecular mechanisms that control ESC self-renewal and pluripotency are more important for translating stem cell technologies to clinical applications. In this study, we used the shotgun proteomics technique to compare the proteome of the ground state condition (R2i- and 2i-grown cells) to that of serum. Out of 1749 proteins identified, 171 proteins were differentially expressed (p < 0.05) in the 2i, R2i, and serum s les. Gene ontology (GO) analysis of differentially abundant proteins showed that the focal adhesion signaling pathway significantly down-regulated under ground state conditions. mESCs had highly adhesive attachment under the serum condition, whereas in the 2i and R2i culture conditions, a loss of adhesion was observed and the cells were rounded and grew in compact colonies on gelatin. Quantitative RT-PCR showed reduced expression of the integrins family in the 2i and R2i conditions. The serum culture had more prominent phosphorylation of focal adhesion kinase (FAK) compared to 2i and R2i cultures. Activity of the extracellular signal-regulated kinase (ERK)1/2 decreased in the 2i and R2i cultures compared to serum. Activation of integrins by Mn
Metabolic and transcriptional response of central metabolism affected by root endophytic fungus Piriformospora indica under salinity in barley
Publisher: Springer Science and Business Media LLC
Date: 07-03-2016
DOI: 10.1007/S11103-016-0461-Z
Abstract: The root endophytic fungus Piriformospora indica enhances plant adaptation to environmental stress based on general and non-specific plant species mechanisms. In the present study, we integrated the ionomics, metabolomics, and transcriptomics data to identify the genes and metabolic regulatory networks conferring salt tolerance in P. indica-colonized barley plants. To this end, leaf s les were harvested at control (0 mM NaCl) and severe salt stress (300 mM NaCl) in P. indica-colonized and non-inoculated barley plants 4 weeks after fungal inoculation. The metabolome analysis resulted in an identification of a signature containing 14 metabolites and ions conferring tolerance to salt stress. Gene expression analysis has led to the identification of 254 differentially expressed genes at 0 mM NaCl and 391 genes at 300 mM NaCl in P. indica-colonized compared to non-inoculated s les. The integration of metabolome and transcriptome analysis indicated that the major and minor carbohydrate metabolism, nitrogen metabolism, and ethylene biosynthesis pathway might play a role in systemic salt-tolerance in leaf tissue induced by the root-colonized fungus.
Mitochondrial dysfunction in Alzheimer’s disease
Publisher: Informa UK Limited
Date: 03-04-2021
DOI: 10.1080/14789450.2021.1918550
Abstract: Mitochondrial dysfunction is involved in Alzheimer's disease (AD) pathogenesis. Mitochondria have their own genetic material however, most of their proteins (∼99%) are synthesized as precursors on cytosolic ribosomes, and then imported into the mitochondria. Therefore, exploring proteome changes in these organelles can yield valuable information and shed light on the molecular mechanisms underlying mitochondrial dysfunction in AD. Here, we review AD-associated mitochondrial changes including the effects of amyloid beta and tau protein accumulation on the mitochondrial proteome. We also discuss the relationship of ApoE genetic polymorphism with mitochondrial changes, and present a meta-analysis of various differentially expressed proteins in the mitochondria in AD.
Study of Sperm Protein Profile in Men With and Without Varicocele Using Two-Dimensional Gel Electrophoresis
Publisher: Elsevier BV
Date: 02-2013
DOI: 10.1016/J.UROLOGY.2012.06.027
Abstract: To compare the sperm protein profile between men with and without varicocele. The present study was designed as a case-control study. The research patients were recruited from the Infertility Unit of the Royan Institute in 2009. We included 20 sperm s les from normozoospermic men without varicocele (control group) and 20 sperm s les from oligozoospermic patients with varicocele, grade 3 (varicocele group) in the present study. The sperm protein profile in the 2 groups was characterized using 2-dimensional gel electrophoresis. Differences in protein expression were established using gel analysis software, and protein identification was performed using mass spectroscopy analysis. In the varicocele group, we noted 15 consistent differences in protein expression (1, spots missing 12, less abundant and 2, more abundant) compared with the control group (P < .01). The findings revealed that heat shock proteins, mitochondrial proteins, and cytoskeleton proteins are the proteins mainly affected by varicocele disease. To our knowledge, the present study is a novel study, with few studies describing the correlation between sperm protein in men with and without varicocele obtained using a 2-dimensional proteomic approach. It could be an important prerequisite to the development of diagnostic tests to predict varicocelectomy outcomes in patients with varicocele and abnormal findings on a spermogram in the clinical environment.
Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves
Publisher: Frontiers Media SA
Date: 06-06-2022
DOI: 10.3389/FMICB.2022.916735
Abstract: The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks ( Bos grunniens ). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle ( Bos taurus ) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves’ intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae , Bacteroidaceae , and Lachnospiraceae . The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P & 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.
Proteomics uncovers a role for redox in drought tolerance in wheat
Publisher: American Chemical Society (ACS)
Date: 08-03-2007
DOI: 10.1021/PR060570J
Abstract: Proteomic analysis offers a new approach to identify a broad spectrum of genes that are expressed in living systems. We applied a proteomic approach to study changes in wheat grain in response to drought, a major environmental parameter adversely affecting development and crop yield. Three wheat genotypes differing in genetic background were cultivated in field under well-watered and drought conditions by following a randomized complete block design with four replications. The overall effect of drought was highly significant as determined by grain yield and total dry matter. About 650 spots were reproducibly detected and analyzed on 2-DE gels. Of these, 121 proteins showed significant change under drought condition in at least one of the genotypes. Mass spectrometry analysis using MALDI-TOF/TOF led to the identification of 57 proteins. Two-thirds of identified proteins were thioredoxin (Trx) targets, in accordance with the link between drought and oxidative stress. Further, because of contrasting changes in the tolerant and susceptible genotypes studied, several proteins emerge as key participants in the drought response. In addition to providing new information on the response to water deprivation, the present study offers opportunities to pursue the breeding of wheat with enhanced drought tolerance using identified candidate genetic markers. The 2-DE database of wheat seed proteins is available for public access at www.proteome.ir.
Synergistic Effect of Metagenome‐Derived Starch‐Degrading Enzymes on Quality of Functional Bread with Antioxidant Activity
Publisher: Wiley
Date: 29-07-2021
Abstract: Starch‐degrading enzymes have gained particular importance in recent decades due to their crucial role in numerous industrial applications especially, in the bakery industry. In this study, a novel thermostable pullulanase (PersiPul1) is screened from the metagenomic data for improving the quality of functional bread. The novel PersiPul1 is active over a wide range of temperature (30–80 °C) and pH (4–9) and exhibits high thermal stability, retaining 58.70% of activity at 80 °C. A cocktail of thermostable pullulanase and α‐amylase (PersiPul1and PersiAmy2) is developed to be used in bread fortified with quinoa protein ( Chenopodium quinoa Willd). The bread fortified with 7% quinoa protein isolate possess the highest reducing power and ABTS (73.64%) and DPPH (72.27%) radical scavenging activities. The addition of the enzyme mixture decreases the hardness and chewiness of the bread. The porosity, specific volume, and browning index of bread with pullulanase and α‐amylase are higher than control. Also, sensory analysis of the functional bread reveals higher scores in the presence of enzymes. Based on the results, the novel starch‐degrading enzyme cocktail is a promising alternative for improving the physical and sensory characteristics of the antioxidant bread enriched with quinoa protein isolate to be used in the bakery industry as a potential bio‐additive.
Crop proteomics
Publisher: Wiley
Date: 08-2007
Abstract: The advent of proteomics has made it possible to identify a broad spectrum of proteins in living systems. This capability is especially useful for crops as it may give clues not only about nutritional value, but also about yield and how these factors are affected by adverse conditions. In this review, we describe the recent progress in crop proteomics and highlight the achievements made in understanding the proteomes of major crops. The major emphasis will be on crop responses to abiotic stresses. Rigorous genetic testing of the role of possibly important proteins can be conducted. The increasing ease with the DNA, mRNA and protein levels can be conducted and connected suggests that proteomics data will not be difficult to apply to practical crop breeding.
An efficient nano-biocatalyst for lignocellulosic biomass hydrolysis: Xylanase immobilization on organically modified biogenic mesoporous silica nanoparticles
Publisher: Elsevier BV
Date: 12-2020
Abiotic stress responsive microRNome and proteome: How correlated are they?
Publisher: Elsevier BV
Date: 09-2019
BMP4 signaling plays critical roles in self-renewal of R2i mouse embryonic stem cells
Publisher: Elsevier BV
Date: 08-2022
DOI: 10.1016/J.BBRC.2022.05.036
Abstract: Mouse embryonic stem cells (mESCs) can be maintained in a pluripotent state under R2i culture conditions that inhibit the TGF-β and ERK signaling pathways. BMP4 is another member of the TGF-β family that plays a crucial role in maintaining the pluripotency state of mESCs. It has been reported that inhibition of BMP4 caused the death of R2i-grown cells. In this study, we used the loss-of-function approach to investigate the role of BMP4 signaling in mESC self-renewal. Inhibition of this pathway with Noggin and dorsomorphin, two bone morphogenetic protein (BMP) antagonists, elicited a quick death of the R2i-grown cells. We showed that the canonical pathway of BMP4 (BMP/SMAD) was dispensable for self-renewal and maintaining pluripotency of these cells. Transcriptome analysis of the BMPi-treated cells revealed that the p53 signaling and two adhesion (AD) and apoptotic mitochondrial change (MT) pathways could be involved in the cell death of the BMPi-treated cells. According to our results, inhibition of BMP4 signaling caused a decrease in cell adhesion and ECM detachment, which triggered anoikis in the R2i-grown cells. Altogether, these findings demonstrate that endogenous BMP signaling is required for the survival of mESCs under the R2i condition.
Transcriptomic analysis of Aegilops tauschii during long-term salinity stress
Publisher: Springer Science and Business Media LLC
Date: 21-06-2018
DOI: 10.1007/S10142-018-0623-Y
Abstract: Aegilops tauschii is the diploid progenitor of the bread wheat D-genome. It originated from Iran and is a source of abiotic stress tolerance genes. However, little is known about the molecular events of salinity tolerance in Ae. tauschii. This study investigates the leaf transcriptional changes associated with long-term salt stress. Total RNA extracted from leaf tissues of control and salt-treated s les was sequenced using the Illumina technology, and more than 98 million high-quality reads were assembled into 255,446 unigenes with an average length of 1398 bp and an N50 of 2269 bp. Functional annotation of the unigenes showed that 93,742 (36.69%) had at least a significant BLAST hit in the SwissProt database, while 174,079 (68.14%) showed significant similarity to proteins in the NCBI nr database. Differential expression analysis identified 4506 salt stress-responsive unigenes. Bioinformatic analysis of the differentially expressed unigenes (DEUs) revealed a number of biological processes and pathways involved in the establishment of ion homeostasis, signaling processes, carbohydrate metabolism, and post-translational modifications. Fine regulation of starch and sucrose content may be important features involved in salt tolerance in Ae. tauschii. Moreover, 82% of DEUs mapped to the D-subgenome, including known QTL for salt tolerance, and these DEUs showed similar salt stress responses in other accessions of Ae. tauschii. These results could provide fundamental insight into the regulatory process underlying salt tolerance in Ae. tauschii and wheat and facilitate identification of genes involved in their salt tolerance mechanisms.
Induction of Neural Progenitor-Like Cells from Human Fibroblasts via a Genetic Material-Free Approach
Publisher: Public Library of Science (PLoS)
Date: 12-08-2015
Effects of selenite and tellurite on growth, physiology, and proteome of a moderately halophilic bacterium
Publisher: American Chemical Society (ACS)
Date: 04-05-2009
DOI: 10.1021/PR900005H
Abstract: We isolated a moderately halophilic bacterium with high level of tolerance to two toxic oxyanions, selenite and tellurite, from hypersaline soil in Garmsar, Iran. 16s rRNA sequence analysis revealed that the isolate, strain MAM, had 98% similarity with Halomonas elongate, and is closely related to other species of the genus Halomonas. We observed that the tolerance to tellurite and its removal increased significantly when both selenite and tellurite were added to the culture media, suggesting a positive synergism of selenite on tellurite tolerance and removal. We applied a proteomic approach to study the proteome response of Halomonas sp. strain MAM to selenite, tellurite, and selenite + tellurite. Out of approximately 800 protein spots detected on 2-DE gels, 208 spots were differentially expressed in response to at least one of treatments. Of them, 70 CBB stained spots were analyzed by MALDI TOF/TOF mass spectrometry, leading to identification of 36 proteins. Our results revealed that several mechanisms including fatty acid synthesis, energy production, cell transport, oxidative stress detoxification, DNA replication, transcription and translation contributed in bacterial response and/or adaptation. These results provided new insights into the general mechanisms on the tolerance of halophilic bacteria to these two toxic oxyanions and the use of them for bioremediation of contaminated saline soils and wastes discharge sites.
Defining microRNA signatures of hair follicular stem and progenitor cells in healthy and androgenic alopecia patients
Publisher: Elsevier BV
Date: 2021
SOX2 protein transduction directly converts human fibroblasts into oligodendrocyte-like cells
Publisher: Elsevier BV
Date: 04-2020
Identification of novel cold stress responsive microRNAs and their putative targets in ‘Sultana’ grapevine (Vitis vinifera) using RNA deep sequencing
Publisher: Springer Science and Business Media LLC
Date: 14-11-2023
MicroRNA Signatures of Drought Signaling in Rice Root
Publisher: Public Library of Science (PLoS)
Date: 08-06-2016
Two-dimensional blue native/SDS-PAGE analysis of whole cell lysate protein complexes of rice in response to salt stress
Publisher: Elsevier BV
Date: 08-2016
DOI: 10.1016/J.JPLPH.2016.05.023
Abstract: To understand the biology of a plant in response to stress, insight into protein-protein interactions, which almost define cell behavior, is thought to be crucial. Here, we provide a comparative complexomics analysis of leaf whole cell lysate of two rice genotypes with contrasting responses to salt using two-dimensional blue native/SDS-PAGE (2D-BN/SDS-PAGE). We aimed to identify changes in subunit composition and stoichiometry of protein complexes elicited by salt. Using mild detergent for protein complex solubilization, we were able to identify 9 protein assemblies as hetero-oligomeric and 30 as homo-oligomeric complexes. A total of 20 proteins were identified as monomers in the 2D-BN/SDS-PAGE gels. In addition to identifying known protein complexes that confirm the technical validity of our analysis, we were also able to discover novel protein-protein interactions. Interestingly, an interaction was detected for glycolytic enzymes enolase (ENO1) and triosephosphate isomerase (TPI) and also for a chlorophyll a-b binding protein and RuBisCo small subunit. To show changes in subunit composition and stoichiometry of protein assemblies during salt stress, the differential abundance of interacting proteins was compared between salt-treated and control plants. A detailed exploration of some of the protein complexes provided novel insight into the function, composition, stoichiometry and dynamics of known and previously uncharacterized protein complexes in response to salt stress.
Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics-Current achievements and perspectives
Publisher: Wiley
Date: 06-2013
Abstract: Salinity is a major threat limiting the productivity of crop plants. A clear demand for improving the salinity tolerance of the major crop plants is imposed by the rapidly growing world population. This review summarizes the achievements of proteomic studies to elucidate the response mechanisms of selected model and crop plants to cope with salinity stress. We also aim at identifying research areas, which deserve increased attention in future proteome studies, as a prerequisite to identify novel targets for breeding strategies. Such areas include the impact of plant-microbial communities on the salinity tolerance of crops under field conditions, the importance of hormone signaling in abiotic stress tolerance, and the significance of control mechanisms underlying the observed changes in the proteome patterns. We briefly highlight the impact of novel tools for future proteome studies and argue for the use of integrated approaches. The evaluation of genetic resources by means of novel automated phenotyping facilities will have a large impact on the application of proteomics especially in combination with metabolomics or transcriptomics.
Distinct changes in the proteome profile of endometrial tissues in polycystic ovary syndrome compared with healthy fertile women
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.RBMO.2018.04.043
Abstract: What is the molecular basis of infertility related to uterine dysfunction in women with polycystic ovary syndrome (PCOS)? In this study, differences in protein expression between PCOS and normal endometrium were identified using a proteomic approach based on two-dimensional electrophoresis (2-DE) coupled with mass spectrometry (MS). The proteome of endometrium were analysed during the proliferative (on day 2 or 3 before ovulation, n = 6) and luteal phases (on day 3-5 after ovulation, n = 6) from healthy women and PCOS patients (12-14 days after spontaneous bleeding, n = 12). The differentially expressed proteins were categorized based on the biological process using the DAVID bioinformatics resources. Over 803 reproducible protein spots were detected on gels, and 150 protein spots showed different intensities between PCOS and normal women during the proliferative and luteal phases. MS analysis detected 70 proteins out of 150 spots. For four of the 70 proteins, 14-3-3 protein, annexin A5, SERPINA1 and cathepsin D, 2-DE results were validated and localized by Western blot and immunohistochemistry, respectively, and their gene expression profiles were confirmed by real-time quantitative PCR. The obtained results corresponded to the proteomic analysis. The differentially expressed proteins identified are known to be involved in apoptosis, oxidative stress, inflammation and the cytoskeleton. The processes related to the differentially expressed proteins play important roles in fecundity and fecundability. The present study may reveal the cause of various endometrial aberrations as a limiting factor for achieving pregnancy in PCOS women.
Effects of salinity levels on proteome ofSuaeda aegyptiaca leaves
Publisher: Wiley
Date: 04-2006
Abstract: Saline soils are the major problem of cultivated lands of Iran. Suaeda aegyptiaca is a salt-tolerant plant (halophytes) that grow naturally in salt-affected areas of Iran. We have employed proteomics to identify the mechanisms of salt responsiveness in leaves of S. aegyptiaca grown under different salt concentrations. Ten-day-old plants were treated with 0, 150, 300, 450, and 600 mM NaCl. After 30 days of treatment, leaf s les were collected and analyzed using 2-D-PAGE. Out of 700 protein spots reproducible detected within replications, 102 spots showed significant response to salt treatment compared to 0 mM NaCl. We analyzed expression pattern of salt-responsive proteins using a hierarchical and two nonhierarchical (Fuzzy ART and SOM) statistical methods and concluded that Fuzzy ART is the superior method. Forty proteins of 12 different expression groups were analyzed using LC/MS/MS. Of these, 27 protein spots were identified including proteins involved in oxidative stress tolerance, glycinebetain synthesis, cytoskeleton remodeling, photosynthesis, ATP production, protein degradation, cyanide detoxification, and chaperone activities. The expression pattern of these proteins and their possible roles in the adaptation of S. aegyptiaca to salinity is discussed.
Stem Cell Research and Therapy in the Islamic Republic of Iran: Pioneering in the Islamic World
Publisher: Mary Ann Liebert Inc
Date: 2013
Abstract: In the early 2000s, the Iranian stem cell research and technology had a relatively strong start that benefited from religious blessings, political and public support, as well as scientific endeavors on the part of non-governmental and public research organizations and universities. Later on, it developed a dynamic niche market of public, private start-up, and spin-off companies and organizations that pioneered in the Islamic world in terms of ISI papers, clinical trials, and cell therapy. However, at present, it faces new challenges stemming from the insufficient finance and a comprehensive law and regulation structure to keep its momentum. To remedy this situation, the scientific community and other stakeholders need to have a series of shared long-time goals and try to build consensus on how to achieve them through nationally approved policy documents.
Application of free and immobilized novel bifunctional biocatalyst in biotransformation of recalcitrant lignocellulosic biomass
Publisher: Elsevier BV
Date: 12-2021
Comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.JPROT.2014.10.018
Abstract: Comparative physiology and proteomic analyses were conducted to monitor the stress response of two wheat genotypes (SERI M 82 (SE) and SW89.5193/kAu2 (SW)) with contrasting responses to drought stress. Under stress condition, the tolerant genotype (SE) produced higher shoot and root biomasses, longer roots and accumulated higher level of ABA in leaves. Physiological measurements suggested that the SE genotype was more efficient in water absorption and could preserve more water presumably by controlling stomata closure. Proteomic analysis showed an increased abundance of proteins related to defense and oxidative stress responses such as GLPs, GST, and SOD, and those related to protein processing such as small HSPs in roots of both genotypes in response to drought stress. Interestingly, the abundance of proteins such as endo-1,3-beta-glucosidase, peroxidase, SAMS, and MDH significantly increased in roots or leaves of the SE genotype and decreased in that of the SW one. In addition, an increased abundance of APX was detected in leaves and roots of the SE genotype and a decreased abundance of 14-3-3 and ribosomal proteins were noted in the SW one in response to drought stress. Our findings led to a better understanding about the integrated physiology and proteome responses of wheat genotypes with nearly contrasting responses to drought stress. We applied a comparative physiology and proteomic analysis to decipher the differential responses of two contrasting wheat genotypes to drought stress. Based on physiological measurements the tolerant genotype (SE) showed better drought response by developing deep root system, higher root and shoot biomasses, and higher level of ABA in leaves. Proteomic analysis showed an increased abundance of proteins related to defense and oxidative stress responses such as GLPs, GST, and SOD, and those related to protein processing such as small HSPs in roots of both genotypes in response to drought stress. In addition, the abundance of proteins such as glucan endo-1,3-beta-glucosidase, peroxidases, SAMS, and MDH increased in roots or leaves of the tolerant genotype (SE) and decreased in that of the sensitive genotype (SW). Overall, proteins related to oxidative stress, protein processing and photosynthesis showed decreased abundance to a greater extent in the sensitive genotype (SW).
Amyloid-beta and tau protein beyond Alzheimer's disease
Publisher: Medknow
Date: 02-10-2024
Efficient removal of various textile dyes from wastewater by novel thermo-halotolerant laccase
Publisher: Elsevier BV
Date: 10-2021
Identification of genes differentially expressed during interaction of Mexican lime tree infected with candidatus Phytoplasma aurantifolia
Publisher: Springer Science and Business Media LLC
Date: 2011
Abstract: "Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees ( Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- lified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by " Ca . Phytoplasma aurantifolia". We carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective lifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection. The present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with " Candidatus Phytoplasma aurantifolia". These results should help to elucidate the molecular basis of the infection process and to identify genes that could be targeted to increase plant resistance and inhibit the growth and reproduction of the pathogen.
Highly efficient removal of dyes from wastewater using nanocellulose from quinoa husk as a carrier for immobilization of laccase
Publisher: Elsevier BV
Date: 04-2022
DOI: 10.1016/J.BIORTECH.2022.126833
Abstract: In this study, the synthesis of nanocellulose (NC) from an agro-waste of quinoa husks (QS) was reported for the first time. The NC nano-carrier was utilized for immobilization of a model laccase enzyme (PersiLac1) providing an innovative, green, and practical nano-biocatalyst for efficient removal of two different model dyes (malachite green (MG) and congo red (CR)) from water. This nano-biocatalyst developed a synergistic adsorption-degradation approach leading the dye molecules easily gathered near the nano-carrier by adsorption and then degraded effectively by the enzyme. Upon enzyme immobilization, the dye removals (%) were remarkably improved for both 150 mg/L of dyes (from 54% and 12%, for MG and CR, respectively, in case of the pristine NCs, to 98% and 60% for the immobilized enzyme). The immobilized PersiLac1 could decolorize the concentrated dye solutions and showed superior reusability (up to 83% dye removal after 18th runs for MG) and remarkable performance from complex real textile effluents.
Enhancing the ethanol production by exploiting a novel metagenomic-derived bifunctional xylanase/β-glucosidase enzyme with improved β-glucosidase activity by a nanocellulose carrier
Publisher: Frontiers Media SA
Date: 04-01-2023
DOI: 10.3389/FMICB.2022.1056364
Abstract: Some enzymes can catalyze more than one chemical conversion for which they are physiologically specialized. This secondary function, which is called underground, promiscuous, metabolism, or cross activity, is recognized as a valuable feature and has received much attention for developing new catalytic functions in industrial applications. In this study, a novel bifunctional xylanase/β-glucosidase metagenomic-derived enzyme, PersiBGLXyn1, with underground β-glucosidase activity was mined by in-silico screening. Then, the corresponding gene was cloned, expressed and purified. The PersiBGLXyn1 improved the degradation efficiency of organic solvent pretreated coffee residue waste (CRW), and subsequently the production of bioethanol during a separate enzymatic hydrolysis and fermentation (SHF) process. After characterization, the enzyme was immobilized on a nanocellulose (NC) carrier generated from sugar beet pulp (SBP), which remarkably improved the underground activity of the enzyme up to four-fold at 80°C and up to two-fold at pH 4.0 compared to the free one. The immobilized PersiBGLXyn1 demonstrated 12 to 13-fold rise in half-life at 70 and 80°C for its underground activity. The amount of reducing sugar produced from enzymatic saccharification of the CRW was also enhanced from 12.97 g/l to 19.69 g/l by immobilization of the enzyme. Bioethanol production was 29.31 g/l for free enzyme after 72 h fermentation, while the immobilized PersiBGLXyn1 showed 51.47 g/l production titre. Overall, this study presented a cost-effective in-silico metagenomic approach to identify novel bifunctional xylanase/β-glucosidase enzyme with underground β-glucosidase activity. It also demonstrated the improved efficacy of the underground activities of the bifunctional enzyme as a promising alternative for fermentable sugars production and subsequent value-added products.
Preface
Publisher: Springer International Publishing
Date: 2016
A novel thermostable cellulase cocktail enhances lignocellulosic bioconversion and biorefining in a broad range of pH
Publisher: Elsevier BV
Date: 07-2020
Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins
Publisher: American Chemical Society (ACS)
Date: 11-09-2018
DOI: 10.1021/ACS.JPROTEOME.8B00407
Abstract: Human embryonic stem cells (hESCs) have the capacity for self-renewal and multilineage differentiation, which are of clinical importance for regeneration medicine. Despite the significant progress of hESC study, the complete hESC proteome atlas, especially the surface protein composition, awaits delineation. According to the latest release of neXtProt database (January 17, 2018 19 658 PE1, 2, 3, and 4 human proteins), membrane proteins present the major category (1047 48%) among all 2186 missing proteins (MPs). We conducted a deep subcellular proteomics analysis of hESCs to identify the nuclear, cytoplasmic, and membrane proteins in hESCs and to mine missing membrane proteins in the very early cell status. To our knowledge, our study achieved the largest data set with confident identification of 11 970 unique proteins (1% false discovery rate at peptide, protein, and PSM levels), including the most-comprehensive description of 6 138 annotated membrane proteins in hESCs. Following the HPP guideline, we identified 26 gold (neXtProt PE2, 3, and 4 MPs) and 87 silver (potential MP candidates with a single unique peptide detected) MPs, of which 69 were membrane proteins, and the expression of 21 gold MPs was further verified either by multiple reaction monitoring mass spectrometry or by matching synthetic peptides in the Peptide Atlas database. Functional analysis of the MPs revealed their potential roles in the pluripotency-related pathways and the lineage- and tissue-specific differentiation processes. Our proteome map of hESCs may provide a rich resource not only for the identification of MPs in the human proteome but also for the investigation on self-renewal and differentiation of hESC. All mass spectrometry data were deposited in ProteomeXchange via jPOST with identifier PXD009840.
Conceptual framework for drought phenotyping during molecular breeding
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.TPLANTS.2009.07.007
Abstract: Drought is a major threat to agricultural production and drought tolerance is a prime target for molecular approaches to crop improvement. To achieve meaningful results, these approaches must be linked with suitable phenotyping protocols at all stages, such as the screening of germplasm collections, mutant libraries, mapping populations, transgenic lines and breeding materials and the design of OMICS and quantitative trait loci (QTLs) experiments. Here we present a conceptual framework for molecular breeding for drought tolerance based on the Passioura equation of expressing yield as the product of water use (WU), water use efficiency (WUE) and harvest index (HI). We identify phenotyping protocols that address each of these factors, describe their key features and illustrate their integration with different molecular approaches.
Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice
Publisher: Springer Science and Business Media LLC
Date: 27-03-2023
DOI: 10.1186/S12864-023-09246-Z
Abstract: The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown. This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways. Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.
Related Organisations
Related Funding Activities
Discovery Projects - Grant ID: DP190103140
Start Date: 06-2019
End Date: 12-2023
Amount: $400,000.00
Funder: Australian Research Council
View Funded Activity