ORCID Profile
0000-0003-0152-4394
Current Organisation
University of Tasmania
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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)
Separation Science | Proteomics and Intermolecular Interactions (excl. Medical Proteomics) | Plant Physiology | Other Chemical Sciences | Biochemistry and Cell Biology | Chemical Oceanography | Environmental Chemistry (incl. Atmospheric Chemistry)
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Environmental Sciences | Neurodegenerative Disorders Related to Ageing | Expanding Knowledge in the Biological Sciences |
Related Links
Publications
Identification of pH-specific protein expression responses by Campylobacter jejuni strain NCTC 11168
Publisher: Elsevier BV
Date: 06-2023
Optimisation of Sporosori Purification and Protein Extraction Techniques for the Biotrophic Protozoan Plant Pathogen Spongospora subterranea
Publisher: MDPI AG
Date: 08-07-2020
DOI: 10.3390/MOLECULES25143109
Abstract: Spongospora subterranea is a soil-borne plant pathogen responsible for the economically significant root and powdery scab diseases of potato. However, the obligate biotrophic nature of S. subterranea has made the detailed study of the pathogen problematic. Here, we first compared the benefits of sporosori partial purification utilizing Ludox® gradient centrifugation. We then undertook optimization efforts for protein isolation comparing the use of a urea buffer followed by single-pot solid-phase-enhanced s le preparation (SP3) and a sodium dodecyl sulphate (SDS) buffer followed by suspension-trapping (S-Trap). Label-free, quantitative proteomics was then used to evaluate the efficiency of the sporosori purification and the protein preparation methods. The purification protocol produced a highly purified suspension of S. subterranea sporosori without affecting the viability of the spores. The results indicated that the use of a combination of SDS and S-Trap for s le clean-up and digestion obtained a significantly higher number of identified proteins compared to using urea and SP3, with 218 and 652 proteins identified using the SP3 and S-Trap methods, respectively. The analysis of proteins by mass spectrometry showed that the number of identified proteins increased by approximately 40% after the purification of spores by Ludox®. These results suggested a potential use of the described spore purification and protein preparation methods for the proteomics study of obligate biotrophic pathogens such as S. subterranea.
Ablation of the miRNA Cluster 24 Has Profound Effects on Extracellular Matrix Protein Abundance in Cartilage
Publisher: MDPI AG
Date: 09-06-2020
DOI: 10.3390/IJMS21114112
Abstract: MicroRNAs (miRNAs) regulate cartilage differentiation and contribute to the onset and progression of joint degeneration. These small RNA molecules may affect extracellular matrix organization (ECM) in cartilage, but for only a few miRNAs has this role been defined in vivo. Previously, we showed that cartilage-specific genetic ablation of the Mirc24 cluster in mice leads to impaired cartilage development due to increased RAF/MEK/ERK pathway activation. Here, we studied the expression of the cluster in cartilage by LacZ reporter gene assays and determined its role for extracellular matrix homeostasis by proteome and immunoblot analysis. The cluster is expressed in prehypertrophic/hypertrophic chondrocytes of the growth plate and we now show that the cluster is also highly expressed in articular cartilage. Cartilage-specific loss of the cluster leads to increased proteoglycan 4 and matrix metallopeptidase 13 levels and decreased aggrecan and collagen X levels in epiphyseal cartilage. Interestingly, these changes are linked to a decrease in SRY-related HMG box-containing (SOX) transcription factors 6 and 9, which regulate ECM production in chondrocytes. Our data suggests that the Mirc24 cluster is important for ECM homoeostasis and the expression of transcriptional regulators of matrix production in cartilage.
Protein disulfide Isomerase Acts as a Molecular Chaperone during the Assembly of Procollagen
Publisher: Elsevier BV
Date: 04-1998
Proteomic analysis of mouse growth plate cartilage
Publisher: Wiley
Date: 12-2006
Abstract: Cartilage is a highly specialized load-bearing tissue with a small number of cells and a high proportion of extracellular matrix (ECM). The abundance of heavily sulfated proteoglycans and a poorly soluble collagenous ECM presents a major technical challenge to 2-DE. Here we report proteomic analysis of mouse growth plate cartilage using novel methodology for tissue dissection and s le prefractionation. We have successfully resolved cartilage tissue extracts by 2-DE for the first time and identified cartilage ECM proteins by Western blotting and MS/MS.
Serum metabolic profile predicts adverse central haemodynamics in patients with type 2 diabetes mellitus
Publisher: Springer Science and Business Media LLC
Date: 04-09-2015
DOI: 10.1007/S00592-015-0802-4
Abstract: People with type 2 diabetes mellitus (T2DM) have abnormal peripheral and central haemodynamics at rest and during exercise, probably due to metabolic perturbations, but mechanisms are unknown. We used untargeted metabolomics to determine the relationships between metabolic perturbations and haemodynamics (peripheral and central) measured at rest and during exercise. Serum s les from 39 participants with T2DM (62 ± 9 years 46 % male) and 39 controls (52 ± 10 years 51 % male) were analysed by liquid chromatography-mass spectrometry, nuclear magnetic resonance spectroscopy and principal component analysis. Scores on principal components (PC) were used to assess relationships with haemodynamics including peripheral and central BP, central augmentation index (AIx) and central augmentation pressure (AP). Participants with T2DM had higher resting and exercise haemodynamics (peripheral and central BP, central AIx and central AP) compared to controls (p < 0.05). PC that comprised of a signature metabolic pattern of T2DM was independently associated with resting and exercise central AIx and central AP (p < 0.05). Serum metabolic profile was associated with central, but not peripheral, haemodynamics in T2DM participants, suggesting that metabolic irregularities may explain abnormal central haemodynamics in T2DM patients.
Discovery of Biomarkers for Tasmanian Devil Cancer (DFTD) by Metabolic Profiling of Serum
Publisher: American Chemical Society (ACS)
Date: 23-09-2016
DOI: 10.1021/ACS.JPROTEOME.6B00629
Abstract: Devil facial tumor disease (DFTD) is a transmissible cancer threatening Tasmanian devils (Sarcophilus harrisii) with extinction. There is no preclinical test available for DFTD, and thus our aim was to find biomarkers for DFTD by metabolic fingerprinting. Seventy serum s les from wild Tasmanian devils (35 controls, 35 with tumors) were analyzed by liquid chromatography-high-resolution mass spectrometry. Features were selected by multivariate models (PLS/DA, random forests) comparing age-matched training set (n = 20 × 2) and further complying with fold-change threshold (≥1.4) and Mann-Whitney U-tests with correction for multiple hypotheses (false discovery rate (FDR) q 0.45, p < 0.01). Additional potential markers included amino acid and lipid metabolites, while cortisol and urea were the most significant health predictors (AUC ≥ 0.90). PLS/DA resulted in AUC = 0.997 for the training set and overall sensitivity of 91% and specificity of 97%. A support vector machine model utilizing only the major peptide marker and seven other metabolites led to overall 94% sensitivity and specificity. The novel findings in this first DFTD metabolomics study shed light on metabolic changes in Tasmanian devils affected by DFTD and provide a valuable step toward the development of prognostic biomarkers.
Comment on ?Structural characterization of dissolved organic matter: a review of current techniques for isolation and analysis? by E. C. Minor, M. M. Swenson, B. M. Mattson, and A. R. Oyler, Environ. Sci.: Processes Impacts, 2014, 16, 2064
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4EM00631C
Abstract: This letter discusses the origins of certain components of dissolved organic matter.
A cautionary note when using pepsin as a probe for the formation of a collagen triple helix
Publisher: Elsevier BV
Date: 07-1998
DOI: 10.1016/S0945-053X(98)90062-2
Abstract: The ability of the collagen triple helix to resist digestion with proteases has been used as a conformational probe to ascertain whether a collagenous molecule has formed a correctly aligned helix during biosynthesis or during refolding of the protein in vitro. During our studies into the synthesis and folding of a variety of engineered procollagen polypeptide chains, we noted that resistance to digestion with proteases, in particular pepsin, could be misleading and does not necessarily indicate the formation of a collagen triple helix. These results clearly show that resistance to pepsin digestion alone should not be used to indicate correct folding and that preferably an alternative assay should be used to unequivocally demonstrate the formation of a correctly aligned triple helix.
Multi-lumen capillary based trypsin micro-reactor for the rapid digestion of proteins
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8AN01330F
Abstract: In this work we evaluated a novel microreactor prepared using a surface modified, high surface-to-volume ratio multi-lumen fused silica capillary (MLC).
In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host–Pathogen Interaction
Publisher: MDPI AG
Date: 28-08-2021
Abstract: Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen during the invasion of roots of a susceptible and a resistant potato cultivar. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 42 proteins significantly changed in comparisons between resistant and susceptible cultivars. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivar suggests a probable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of differentially expressed proteins were related to the metabolic processes and transporter activity. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea infection and development in planta and illuminates the role of host immunity in affecting pathogen responses.
A robust method for proteomic characterization of mouse cartilage using solubility-based sequential fractionation and two-dimensional gel electrophoresis
Publisher: Elsevier BV
Date: 10-2008
DOI: 10.1016/J.MATBIO.2008.07.007
Abstract: Identification of protein expression differences using two-dimensional electrophoresis (2-DE) and multidimensional liquid chromatography (MDLC)-based proteomics depends critically on reproducibility throughout s le preparation and analysis. This applies particularly where s le fractionation is used to remove high abundance or interfering components to facilitate deeper mining of the proteome. Here we present a procedure for solubility-based cartilage fractionation using sequential extraction with 1 M sodium chloride followed by 4 M guanidinium hydrochloride. We characterized the extracts by 1-D electrophoresis and immunoblotting for in idual cellular and matrix components and more globally by 2-DE. In general, NaCl extracts were highly enriched for cellular proteins and GuHCl extracts were predominantly matrix components, with some interesting exceptions. Importantly, we observed high inter-s le reproducibility and strong correlation between targeted and global analysis, indicating that our method can be applied to differential proteomic analysis of normal and pathological cartilage sub-proteomes.
Mutations ofCOL10A1 in Schmid metaphyseal chondrodysplasia
Publisher: Hindawi Limited
Date: 2005
DOI: 10.1002/HUMU.20183
Abstract: Schmid metaphyseal chondrodysplasia (SMCD) is a dominantly inherited cartilage disorder caused by mutations in the gene for the hypertrophic cartilage extracellular matrix structural protein, collagen X (COL10A1). Thirty heterozygous mutations have been described, about equally ided into two mutation types, missense mutations, and mutations that introduce premature termination signals. The COL10A1 mutations are clustered (33/36) in the 3' region of exon 3, which codes for the C-terminal NC1 trimerization domain. The effect of COL10A1 missense mutations have been examined by in vitro expression and assembly assays and cell transfection studies, which suggest that a common consequence is the disruption of collagen X trimerization and secretion, with consequent intracellular degradation. The effect of COL10A1 nonsense mutations in cartilage tissue has been examined in two patients, demonstrating that the mutant mRNA is completely removed by nonsense mediated mRNA decay. Thus for both classes of mutations, functional haploinsufficiency is the most probable cause of the clinical phenotype in SMCD.
Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage
Publisher: Elsevier BV
Date: 10-2021
Investigation into dissolved neutral sugars and their microbial conversion in natural and artificially produced dissolved organic matter using ion chromatography with pulsed amperometric detection and reversed-phase liquid chromatography-high resolution mass spectrometry
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3AY41549J
Transcriptome and proteome profiling reveals stress-induced expression signatures of imiquimod-treated Tasmanian devil facial tumor disease (DFTD) cells
Publisher: Impact Journals, LLC
Date: 23-03-2018
Preliminary validation of a high docosahexaenoic acid (DHA) and -linolenic acid (ALA) dietary oil blend: tissue fatty acid composition and liver proteome response in Atlantic salmon (Salmo salar) smolts
Publisher: Public Library of Science (PLoS)
Date: 24-08-2016
Comparative Proteomic Analysis of Normal and Collagen IX Null Mouse Cartilage Reveals Altered Extracellular Matrix Composition and Novel Components of the Collagen IX Interactome
Publisher: Elsevier BV
Date: 05-2013
Simple, quantitative method for low molecular weight dissolved organic matter extracted from natural waters based upon high performance counter-current chromatography
Publisher: Elsevier BV
Date: 02-2016
DOI: 10.1016/J.ACA.2016.01.003
Abstract: A simple, high-performance counter-current chromatography method with sequential UV absorbance (254 nm) and evaporative light scattering detection (ELSD) was developed for the quantification of pre-extracted low molecular weight dissolved organic matter (DOM) extracted from natural waters. The method requires solid-phase extraction (SPE) extraction of only small volumes of water s les, here using poly(styrene inylbenzene)-based extraction cartridges (Varian PPL). The extracted and concentrated DOM was quantified using reversed-phase high-performance counter-current chromatography (HPCCC), with a water/methanol (5:5) mobile phase and hexane/ethyl acetate (3:7) stationary phase. The critical chromatographic parameters were optimised, applying a revolution speed of 1900 rpm and a flow-rate of 1 mL min(-1). Under these conditions, 50 μL of extracted DOM solution could be injected and quantified using calibration against a reference natural dissolved material (Suwannee River), based upon UV absorbance at 254 nm and ELSD detection. Both detection methods provided excellent linearity (R(2) > 0.995) for DOM across the concentration ranges of interest, with limits of detection of 4 μg ml(-1) and 7 μg ml(-1) for ELSD and UV absorbance, respectively. The method was validated for peak area precision ( 95% recovery). The developed method was applied to the determination of the concentration of DOM in seawater, based upon initial s le volumes as small as 20 mL.
S100A8 and S100A9 in experimental osteoarthritis.
Publisher: Springer Science and Business Media LLC
Date: 2010
DOI: 10.1186/AR2917
A simple apparatus for electrokinetic removal of sodium dodecyl sulfate from protein digests
Publisher: Elsevier BV
Date: 09-2020
Umbilical Cord Stromal Cell Differentiation: little correlation with known markers of the chondrocyte phenotype or cartilage extracellular matrix
Publisher: Elsevier BV
Date: 04-2012
Proteomics makes progress in cartilage and arthritis research
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.MATBIO.2009.01.004
Abstract: Understanding biology at the systems level is a powerful method for discovery of previously unrecognized molecular pathways and mechanisms in human disease. The application of proteomics to arthritis research has lagged behind many other clinical targets, partly due to the unique biochemical properties of cartilage and associated biological fluids such as synovial fluid. In recent years, however, proteomic-based studies in cartilage and arthritis research have risen sharply and have started to make a significant impact on our understanding of joint disease, including the discovery of new and promising biomarkers of cartilage degeneration, a hallmark of arthritis. In this review we will make the case for the ongoing proteomic analysis of cartilage and other tissues affected by joint disease, overview some of the core proteomic techniques and discuss how the challenge of cartilage proteomics has been met through technical innovation. The major outcomes and information obtained from recent proteomic analysis of synovial fluid, cartilage and chondrocytes will also be described. In addition, we present some novel insights into post-translational regulation of cartilage proteins, through proteomic identification of proteolytic fragments in mouse cartilage extracts and explant culture media. We conclude with our prediction of how emerging proteomic technologies that have yet to be applied in arthritis research are likely to contribute further important information.
Comprehensive Profiling of Cartilage Extracellular Matrix Formation and Maturation Using Sequential Extraction and Label-free Quantitative Proteomics
Publisher: Elsevier BV
Date: 06-2010
Salinity Effects on Guard Cell Proteome in Chenopodium quinoa
Publisher: MDPI AG
Date: 04-01-2021
DOI: 10.3390/IJMS22010428
Abstract: Epidermal fragments enriched in guard cells (GCs) were isolated from the halophyte quinoa (Chenopodium quinoa Wild.) species, and the response at the proteome level was studied after salinity treatment of 300 mM NaCl for 3 weeks. In total, 2147 proteins were identified, of which 36% were differentially expressed in response to salinity stress in GCs. Up and downregulated proteins included signaling molecules, enzyme modulators, transcription factors and oxidoreductases. The most abundant proteins induced by salt treatment were desiccation-responsive protein 29B (50-fold), osmotin-like protein OSML13 (13-fold), polycystin-1, lipoxygenase, alpha-toxin, and triacylglycerol lipase (PLAT) domain-containing protein 3-like (eight-fold), and dehydrin early responsive to dehydration (ERD14) (eight-fold). Ten proteins related to the gene ontology term “response to ABA” were upregulated in quinoa GC this included aspartic protease, phospholipase D and plastid-lipid-associated protein. Additionally, seven proteins in the sucrose–starch pathway were upregulated in the GC in response to salinity stress, and accumulation of tryptophan synthase and L-methionine synthase (enzymes involved in the amino acid biosynthesis) was observed. Exogenous application of sucrose and tryptophan, L-methionine resulted in reduction in stomatal aperture and conductance, which could be advantageous for plants under salt stress. Eight aspartic proteinase proteins were highly upregulated in GCs of quinoa, and exogenous application of pepstatin A (an inhibitor of aspartic proteinase) was accompanied by higher oxidative stress and extremely low stomatal aperture and conductance, suggesting a possible role of aspartic proteinase in mitigating oxidative stress induced by saline conditions.
Fractionation of Dissolved Organic Matter on Coupled Reversed-Phase Monolithic Columns and Characterisation Using Reversed-Phase Liquid Chromatography-High Resolution Mass Spectrometry
Publisher: Springer Science and Business Media LLC
Date: 25-05-2018
Differentially expressed proteins in gill and skin mucus of Atlantic salmon (Salmo salar) affected by amoebic gill disease
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.FSI.2014.06.025
Abstract: The external surfaces of fish, such as gill and skin, are covered by mucus, which forms a thin interface between the organism and water. Amoebic gill disease (AGD) is a parasitic condition caused by Neoparamoeba perurans that affects salmonids worldwide. This disease induces excessive mucus production in the gills. The host immune response to AGD is not fully understood, and research tools such as genomics and proteomics could be useful in providing further insight. Gill and skin mucus s les were obtained from Atlantic salmon (Salmo salar) which were infected with N. perurans on four successive occasions. NanoLC tandem mass spectrometry (MS/MS) was used to identify proteins in gill and skin mucus of Atlantic salmon affected by AGD. A total of 186 and 322 non-redundant proteins were identified in gill and skin mucus respectively, based on stringent filtration criteria, and statistics demonstrated that 52 gill and 42 skin mucus proteins were differentially expressed in mucus s les from AGD-affected fish. By generating protein-protein interaction networks, some of these proteins formed part of cell to cell signalling and inflammation pathways, such as C-reactive protein, apolipoprotein 1, granulin, cathepsin, angiogenin-1. In addition to proteins that were entirely novel in the context in the host response to N. perurans, our results have confirmed the presence of protein markers in mucus that have been previously predicted on the basis of modified mRNA expression, such as anterior gradient-2 protein, annexin A-1 and complement C3 factor. This first proteomic analysis of AGD-affected salmon provides new information on the effect of AGD on protein composition of gill and skin mucus. Future research should focus on better understanding of the role these components play in the response against infection with N. perurans.
Metabolomics reveals increased isoleukotoxin diol (12,13-DHOME) in human plasma after acute intralipid infusion
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1194/JLR.P027706
Triploid Atlantic salmon shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.CBD.2017.02.005
Abstract: There is currently renewed interest in farming triploid Atlantic salmon. Improving farming requires identifying triploid specific phenotypic and physiological traits that are uniquely derived from ploidy per se and developed under optimal growing conditions. This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages [34dph (days post-hatching) alevin, 109dph fry, and 162dph parr] and secondly, whether phenotypic differences at these stages were reflected in protein s les collected from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n=3) were first fed at 35dph and then maintained by feeding to satiation on commercial feeds. Triploids were significantly lower in weight at the late alevin and fry stages but matched diploid weight at the parr stage. The whole-body lipid content was significantly higher for triploids at the parr stage, while the whole-body lipid class profile was broadly similar and was largely not affected by ploidy. Comparative label-free shotgun proteomic analysis did not detect significant alterations in protein expression between diploids and triploids at any growth stage. The present results indicate that ploidy under optimal growing conditions and during early freshwater stages only result in small phenotypic differences in weight and whole body lipid content that were not reflected at the proteome level. These findings suggest that optimal husbandry conditions for freshwater Atlantic salmon are similar between ploidies, at least for all-female populations.
Proteomics makes progress in cartilage and arthritis research
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.MATBIO.2009.01.004
Abstract: Understanding biology at the systems level is a powerful method for discovery of previously unrecognized molecular pathways and mechanisms in human disease. The application of proteomics to arthritis research has lagged behind many other clinical targets, partly due to the unique biochemical properties of cartilage and associated biological fluids such as synovial fluid. In recent years, however, proteomic-based studies in cartilage and arthritis research have risen sharply and have started to make a significant impact on our understanding of joint disease, including the discovery of new and promising biomarkers of cartilage degeneration, a hallmark of arthritis. In this review we will make the case for the ongoing proteomic analysis of cartilage and other tissues affected by joint disease, overview some of the core proteomic techniques and discuss how the challenge of cartilage proteomics has been met through technical innovation. The major outcomes and information obtained from recent proteomic analysis of synovial fluid, cartilage and chondrocytes will also be described. In addition, we present some novel insights into post-translational regulation of cartilage proteins, through proteomic identification of proteolytic fragments in mouse cartilage extracts and explant culture media. We conclude with our prediction of how emerging proteomic technologies that have yet to be applied in arthritis research are likely to contribute further important information.
Cartilage-specific ablation of XBP1 signaling in mouse results in a chondrodysplasia characterized by reduced chondrocyte proliferation and delayed cartilage maturation and mineralization
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.JOCA.2015.01.001
Abstract: To investigate the in vivo role of the IRE1/XBP1 unfolded protein response (UPR) signaling pathway in cartilage. Xbp1(flox/flox).Col2a1-Cre mice (Xbp1(CartΔEx2)), in which XBP1 activity is ablated specifically from cartilage, were analyzed histomorphometrically by Alizarin red/Alcian blue skeletal preparations and X-rays to examine overall bone growth, histological stains to measure growth plate zone length, chondrocyte organization, and mineralization, and immunofluorescence for collagen II, collagen X, and IHH. Bromodeoxyuridine (BrdU) and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) analyses were used to measure chondrocyte proliferation and cell death, respectively. Chondrocyte cultures and microdissected growth plate zones were analyzed for expression profiling of chondrocyte proliferation or endoplasmic reticulum (ER) stress markers by Quantitative PCR (qPCR), and of Xbp1 mRNA splicing by RT-PCR to monitor IRE1 activation. Xbp1(CartΔEx2) displayed a chondrodysplasia involving dysregulated chondrocyte proliferation, growth plate hypertrophic zone shortening, and IRE1 hyperactivation in chondrocytes. Deposition of collagens II and X in the Xbp1(CartΔEx2) growth plate cartilage indicated that XBP1 is not required for matrix protein deposition or chondrocyte hypertrophy. Analyses of mid-gestation long bones revealed delayed ossification in Xbp1(CartΔEx2) embryos. The rate of chondrocyte cell death was not significantly altered, and only minimal alterations in the expression of key markers of chondrocyte proliferation were observed in the Xbp1(CartΔEx2) growth plate. IRE1 hyperactivation occurred in Xbp1(CartΔEx2) chondrocytes but was not sufficient to induce regulated IRE1-dependent decay (RIDD) or a classical UPR. Our work suggests roles for XBP1 in regulating chondrocyte proliferation and the timing of mineralization during endochondral ossification, findings which have implications for both skeletal development and disease.
Misfolding of Collagen X Chains Harboring Schmid Metaphyseal Chondrodysplasia Mutations Results in Aberrant Disulfide Bond Formation, Intracellular Retention, and Activation of the Unfolded Protein Re
Publisher: Elsevier BV
Date: 04-2005
Metabolomics Data Normalization with EigenMS
Publisher: Public Library of Science (PLoS)
Date: 30-12-2014
Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress
Publisher: Public Library of Science (PLoS)
Date: 25-10-2018
Changes in the Chondrocyte and Extracellular Matrix Proteome during Post-natal Mouse Cartilage Development
Publisher: Elsevier BV
Date: 2012
Cathelicidin-3 associated with serum extracellular vesicles enables early diagnosis of a transmissible cancer
Publisher: Cold Spring Harbor Laboratory
Date: 07-12-2021
DOI: 10.1101/2021.12.06.471373
Abstract: The identification of practical early diagnosis biomarkers is a cornerstone of improved prevention and treatment of cancers. Such a case is devil facial tumour disease (DFTD), a highly lethal transmissible cancer afflicting virtually an entire species, the Tasmanian devil ( Sarcophilus harrisii ). Despite a latent period that can exceed one year, to date DFTD diagnosis requires visual identification of tumour lesions. To enable earlier diagnosis, which is essential for the implementation of effective conservation strategies, we analysed the extracellular vesicle (EV) proteome of 87 Tasmanian devil serum s les. The antimicrobial peptide cathelicidin-3 (CATH3) was enriched in serum EVs of both devils with clinical DFTD (87.9% sensitivity and 94.1% specificity) and devils with latent infection (i.e., collected while overtly healthy, but 3-6 months before subsequent DFTD diagnosis 93.8% sensitivity and 94.1% specificity). As antimicrobial peptides can play a variety of roles in the cancer process, our results suggest that the specific elevation of serum EV-associated CATH3 may be mechanistically involved in DFTD pathogenesis. This EV-based approach to biomarker discovery is directly applicable to improving understanding and diagnosis of a broad range of diseases in other species, and these findings directly enhance the capacity of conservation strategies to ensure the viability of the imperilled Tasmanian devil population.
Chronic β2‐adrenoceptor agonist treatment alters muscle proteome and functional adaptations induced by high intensity training in young men
Publisher: Wiley
Date: 12-11-2017
DOI: 10.1113/JP274970
Heat shock proteins expressed in the marsupial Tasmanian devil are potential antigenic candidates in a vaccine against devil facial tumour disease
Publisher: Public Library of Science (PLoS)
Date: 27-04-2018
Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions
Publisher: MDPI AG
Date: 19-01-2022
DOI: 10.3390/PROTEOMES10010005
Abstract: The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant–pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant–pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the erse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant–pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant–pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
Targeted Induction of Endoplasmic Reticulum Stress Induces Cartilage Pathology
Publisher: Public Library of Science (PLoS)
Date: 16-10-2009
Extensive Gene Acquisition in the Extremely Psychrophilic Bacterial Species Psychroflexus torquis and the Link to Sea-Ice Ecosystem Specialism
Publisher: Oxford University Press (OUP)
Date: 2014
DOI: 10.1093/GBE/EVT209
The translocation, folding, assembly and redox-dependent degradation of secretory and membrane proteins in semi-permeabilized mammalian cells
Publisher: Portland Press Ltd.
Date: 05-1995
DOI: 10.1042/BJ3070679
Abstract: We describe here a semi-permeabilized cell-system which reconstitutes the efficient synthesis, translocation, folding, assembly and degradation of membrane and secretory proteins. Cells grown in culture were treated with the detergent digitonin which selectively permeabilized the plasma membrane leaving the cellular organelles, such as the endoplasmic reticulum (ER) and trans-Golgi network intact. These permeabilized cells were added to an in vitro translation system, either wheatgerm or reticulocyte lysate, supplemented with RNA coding for either membrane or secretory proteins. Efficient translocation and modification of proteins by these cells was demonstrated by protease protection, photocross-linking of nascent chains to components of the translocation apparatus and by post-translational modifications such as glycosylation or hydroxylation. A comparison was made between the ability of semi-permeabilized cells and microsomal vesicles to fold and assemble proteins. The results show that the intact ER within these cells can assemble proteins much more efficiently than vesicularized ER. Furthermore, the semi-permeabilized cells carried out the redox-dependent degradation of tissue-type plasminogen activator. This system has all the advantages of conventional cell-free systems, including speed and, importantly, the ability to manipulate the components of the assay, while retaining intracellular organelles and, therefore, allowing cellular processes to occur as they would in the intact cell.
Attached and planktonic listeria monocytogenes global proteomic responses and associated influence of strain genetics and temperature
Publisher: American Chemical Society (ACS)
Date: 09-01-2015
DOI: 10.1021/PR501114E
Abstract: Contamination of industrial and domestic food usage environments by the attachement of bacterial food-borne pathogen Listeria monocytogenes has public health and economic implications. Comprehensive proteomics experiments using label-free liquid chromatography/tandem mass spectrometry were used to compare the proteomes of two different L. monocytogenes strains (Siliken_1/2c and F2365_4b), which show very different capacities to attach to surfaces. Growth temperature and strain type were highly influential on the proteomes in both attached and planktonic cells. On the basis of the proteomic data, it is highly unlikely that specific surface proteins play a direct role in adherence to inanimate surfaces. Instead, strain-dependent responses related to cell envelope polymer biosynthesis and stress response regulation likely contribute to a different ability to attach and also to survive external stressors. Collectively, the ergent proteome-level responses observed define strain- and growth-temperature-dependent differences relevant to attachment efficacy, highlight relevant proteins involved in stress protection in attached cells, and suggest that strain differences and growth conditions are important in relation to environmental persistence.
Prolonged Heat Stress of Lactobacillus paracasei GCRL163 Improves Binding to Human Colorectal Adenocarcinoma HT-29 Cells and Modulates the Relative Abundance of Secreted and Cell Surface-Locate
Publisher: American Chemical Society (ACS)
Date: 28-02-2020
Chromatographic methods for the isolation, separation and characterisation of dissolved organic matter
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5EM00223K
Abstract: This review presents an overview of the separation techniques applied to the complex challenge of dissolved organic matter characterisation.
A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae.
Publisher: Wiley
Date: 02-12-2019
DOI: 10.1111/MMI.14426
Abstract: Commensal bacteria serve as an important line of defense against colonisation by opportunisitic pathogens, but the underlying molecular mechanisms remain poorly explored. Here, we show that strains of a commensal bacterium, Haemophilus haemolyticus, make hemophilin, a heme-binding protein that inhibits growth of the opportunistic pathogen, non-typeable Haemophilus influenzae (NTHi) in culture. We purified the NTHi-inhibitory protein from H. haemolyticus and identified the hemophilin gene using proteomics and a gene knockout. An x-ray crystal structure of recombinant hemophilin shows that the protein does not belong to any of the known heme-binding protein folds, suggesting that it evolved independently. Biochemical characterisation shows that heme can be captured in the ferrous or ferric state, and with a variety of small heme-ligands bound, suggesting that hemophilin could function under a range of physiological conditions. Hemophilin knockout bacteria show a limited capacity to utilise free heme for growth. Our data suggest that hemophilin is a hemophore and that inhibition of NTHi occurs by heme starvation, raising the possibility that competition from hemophilin-producing H. haemolyticus could antagonise NTHi colonisation in the respiratory tract.
The proteomic response is linked to regional lung volumes in ventilator-induced lung injury
Publisher: American Physiological Society
Date: 10-2020
DOI: 10.1152/JAPPLPHYSIOL.00097.2020
Abstract: This study provides novel insights into the regional response to mechanical ventilation in the setting of acid-induced lung injury and highlights the complex interaction between tidal stretch and low end-expiratory lung volumes both of which caused altered regulation of different injury pathways.
Spironolactone reduces aortic stiffness via blood pressure-dependent effects of canrenoate
Publisher: Springer Science and Business Media LLC
Date: 13-06-2013
Identification of key pro-survival proteins in isolated colonic goblet cells of Winnie, a murine model of spontaneous colitis
Publisher: Oxford University Press (OUP)
Date: 24-08-2019
DOI: 10.1093/IBD/IZZ179
Abstract: This proteomics study reveals novel proteins and pathways that potentially underpin the survival and proliferation of goblet cells in the colon of Winnie mice, an ulcerative colitis model caused by misfolding of mucin-2 that results in endoplasmic reticulum stress.
Towards complete identification of allergens in Jack Jumper (Myrmecia pilosula) ant venom and their clinical relevance: An immunoproteomic approach
Publisher: Wiley
Date: 03-08-2018
DOI: 10.1111/CEA.13224
Abstract: The venomous stings of Jack Jumper ant (JJA species of the Myrmecia pilosula taxonomic group) are a significant public health issue in parts of south-eastern and south-western Australia, causing anaphylaxis in approximately 3% of the population. Three allergenic peptides, Myr p 1, Myr p 2 and Myr p 3, and one histamine-releasing peptide, pilosulin 5, have been fully described, but there are at least 5 additional high molecular weight IgE-binding components that have not been identified. To identify IgE-binding components in JJA venom (JJAV) and to relate the IgE recognition of these components to relevant clinical parameters. Identification of IgE-binding components and determination of their sensitizing prevalence was performed using SDS-PAGE immunoblot assay and sera from 90 patients with confirmed allergy to JJAV. Tandem mass spectrometry was used for identification of novel JJAV components fractionated by size exclusion chromatography (SEC) and SDS-PAGE. Using SDS-PAGE immunoblot, 10 IgE-binding bands were identified in JJAV, two of which were recognized by 81% and 47% of the population studied. Mass spectrometry identified 17 novel JJAV proteins, including 2 glycoproteins, and confirmed the presence of 4 known Myr p and pilosulin peptides in JJAV. Most of the newly identified IgE-binding proteins were enzymes, including phospholipase A This study has for the first time revealed the identity of various proteins with IgE-binding capacity in the venom of JJA and demonstrated their clinical relevance in the diagnosis and treatment of JJAV allergy.
Sugar beet (Beta vulgaris) guard cells responses to salinity stress: A proteomic analysis
Publisher: MDPI AG
Date: 27-03-2020
DOI: 10.3390/IJMS21072331
Abstract: Soil salinity is a major environmental constraint affecting crop growth and threatening global food security. Plants adapt to salinity by optimizing the performance of stomata. Stomata are formed by two guard cells (GCs) that are morphologically and functionally distinct from the other leaf cells. These microscopic sphincters inserted into the wax-covered epidermis of the shoot balance CO2 intake for photosynthetic carbon gain and concomitant water loss. In order to better understand the molecular mechanisms underlying stomatal function under saline conditions, we used proteomics approach to study isolated GCs from the salt-tolerant sugar beet species. Of the 2088 proteins identified in sugar beet GCs, 82 were differentially regulated by salt treatment. According to bioinformatics analysis (GO enrichment analysis and protein classification), these proteins were involved in lipid metabolism, cell wall modification, ATP biosynthesis, and signaling. Among the significant differentially abundant proteins, several proteins classified as “stress proteins” were upregulated, including non-specific lipid transfer protein, chaperone proteins, heat shock proteins, inorganic pyrophosphatase 2, responsible for energized vacuole membrane for ion transportation. Moreover, several antioxidant enzymes (peroxide, superoxidase dismutase) were highly upregulated. Furthermore, cell wall proteins detected in GCs provided some evidence that GC walls were more flexible in response to salt stress. Proteins such as L-ascorbate oxidase that were constitutively high under both control and high salinity conditions may contribute to the ability of sugar beet GCs to adapt to salinity by mitigating salinity-induced oxidative stress.
WARP Is a Novel Multimeric Component of the Chondrocyte Pericellular Matrix That Interacts with Perlecan
Publisher: Elsevier BV
Date: 03-2006
Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent
Publisher: Springer Science and Business Media LLC
Date: 20-06-2013
Impact of lactose starvation on the physiology of Lactobacillus casei GCRL163 in the presence or absence of Tween 80
Publisher: American Chemical Society (ACS)
Date: 23-10-2013
DOI: 10.1021/PR400661G
Abstract: The global proteomic response of the nonstarter lactic acid bacteria Lactobacillus casei strain GCRL163 under carbohydrate depletion was investigated to understand aspects of its survival following cessation of fermentation. The proteome of L. casei GCRL163 was analyzed quantitatively after growth in modified MRS (with and without Tween 80) with different levels of lactose (0% lactose, starvation 0.2% lactose, growth limiting 1% lactose, non-growth-limited control) using gel-free proteomics. Results revealed that carbohydrate starvation lead to suppression of lactose and galactose catabolic pathways as well as pathways for nucleotide and protein synthesis. Enzymes of the glycolysis/gluconeogenesis pathway, amino acid synthesis, and pyruvate and citrate metabolism become more abundant as well as other carbohydrate catabolic pathways, suggesting increased optimization of intermediary metabolism and scavenging. Tween 80 did not affect growth yield however, proteins related to fatty acid biosynthesis were repressed in the presence of Tween 80. The data suggest that L. casei adeptly switches to a scavenging mode, using both citrate and Tween 80, and efficiently adjusts energetic requirements when carbohydrate starved and thus can sustain survival for weeks to months. Explaining the adaptation of L. casei during lactose starvation will assist efforts to maintain viability of L. casei and extend its utility as a beneficial dietary adjunct and fermentation processing aid.
Collagen X Chains Harboring Schmid Metaphyseal Chondrodysplasia NC1 Domain Mutations Are Selectively Retained and Degraded in Stably Transfected Cells
Publisher: Elsevier BV
Date: 04-2002
Dark metabolism: a molecular insight into how the Antarctic sea‐ice diatom Fragilariopsis cylindrus survives long‐term darkness
Publisher: Wiley
Date: 07-05-2019
DOI: 10.1111/NPH.15843
Misfolding of Collagen X Chains Harboring Schmid Metaphyseal Chondrodysplasia Mutations Results in Aberrant Disulfide Bond Formation, Intracellular Retention, and Activation of the Unfolded Protein Re
Publisher: Elsevier BV
Date: 04-2005
Mutations ofCOL10A1 in Schmid metaphyseal chondrodysplasia
Publisher: Hindawi Limited
Date: 2005
DOI: 10.1002/HUMU.20183
Abstract: Schmid metaphyseal chondrodysplasia (SMCD) is a dominantly inherited cartilage disorder caused by mutations in the gene for the hypertrophic cartilage extracellular matrix structural protein, collagen X (COL10A1). Thirty heterozygous mutations have been described, about equally ided into two mutation types, missense mutations, and mutations that introduce premature termination signals. The COL10A1 mutations are clustered (33/36) in the 3' region of exon 3, which codes for the C-terminal NC1 trimerization domain. The effect of COL10A1 missense mutations have been examined by in vitro expression and assembly assays and cell transfection studies, which suggest that a common consequence is the disruption of collagen X trimerization and secretion, with consequent intracellular degradation. The effect of COL10A1 nonsense mutations in cartilage tissue has been examined in two patients, demonstrating that the mutant mRNA is completely removed by nonsense mediated mRNA decay. Thus for both classes of mutations, functional haploinsufficiency is the most probable cause of the clinical phenotype in SMCD.
Proteome profiles of intramuscular connective tissue: influence of aging and physical training
Publisher: American Physiological Society
Date: 05-2023
DOI: 10.1152/JAPPLPHYSIOL.00675.2022
Abstract: We investigated the impact of aging and exercise on extracellular matrix components of intramuscular connective tissue using proteomics. Middle-aged and old mice were subjected to three different levels of regular physical activity for 10 wk (high-resistance wheel running, low-resistance wheel running, or sedentary controls). We prepared extracts of extracellular matrix proteins depleted of cellular proteins. Our findings indicate that intramuscular connective tissue alters its soluble protein content with age but is unaffected by training.
Identification of vitamin D sensitive pathways during lung development
Publisher: Springer Science and Business Media LLC
Date: 27-04-2016
Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates
Publisher: MDPI AG
Date: 15-08-2023
Abstract: Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 erse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.
Comprehensive Profiling of Cartilage Extracellular Matrix Formation and Maturation Using Sequential Extraction and Label-free Quantitative Proteomics
Publisher: Elsevier BV
Date: 06-2010
Cartilage proteomics: Challenges, solutions and recent advances
Publisher: Wiley
Date: 02-2008
Abstract: The mammalian skeleton is largely composed of cartilage and bone. The major functions of cartilage are first to provide a transient template for development of the axial and appendicular skeleton and secondly to provide permanent articulating joint surfaces. The unique cartilage extracellular matrix (ECM) is essential for the load-bearing and viscoelastic properties of cartilage tissues. Maintained by the chondrocytes, the ECM contains a myriad of proteins and proteoglycans organized into precise networks. Many cartilage disorders result from genetic disruption of cartilage ECM components, their interactions and/or degradation. Although technically challenging, the proteomic analysis of cartilage in development and disease is now emerging as a clinically important research area. In this article, we will review progress in the proteomic characterization of cartilage-related s les.
Temporal changes in the microglial proteome of male and female mice after a diffuse brain injury using label-free quantitative proteomics
Publisher: Cold Spring Harbor Laboratory
Date: 02-05-2022
DOI: 10.1101/2022.05.01.490239
Abstract: Traumatic brain injury (TBI) triggers neuroinflammatory cascades mediated by microglia, which promotes tissue repair in the short-term. These cascades may exacerbate TBI-induced tissue damage and symptoms in the months to years post-injury. However, the progression of the microglial function across time post-injury and whether this differs between biological sexes is not well understood. In this study, we examined the microglial proteome in the days (3- and 7-days) to 1 month (28 days) after a midline fluid percussion injury (mFPI) in male and female mice using label-free quantitative proteomics. We identified a reduction in microglial proteins involved with clearance of neuronal debris via phagocytosis at 3- and 7-days post-injury. At 28 days post-injury pro-inflammatory proteins were decreased and anti-inflammatory proteins were increased in microglia. These results indicate a reduction in microglial clearance of neuronal debris in the days post-injury with a shift to anti-inflammatory function by 1 month. The changes in the microglial proteome that occurred across time post-injury did not differ between biological sexes. However, we did identify an increase in microglial proteins related to pro-inflammation as well as insulin and estrogen signalling in males compared with female mice that occurred with or without a brain injury. Although microglial response was similar between males and females up to 1 month following TBI, biological sex differences in the basal microglial proteome has implications for the efficacy of treatment strategies targeting the microglial response post-injury.
Enzymatic Investigation of Spongospora subterranea Zoospore Attachment to Roots of Potato Cultivars Resistant or Susceptible to Powdery Scab Disease
Publisher: MDPI AG
Date: 09-02-2023
DOI: 10.3390/PROTEOMES11010007
Abstract: For potato crops, host resistance is currently the most effective and sustainable tool to manage diseases caused by the plasmodiophorid Spongospora subterranea. Arguably, zoospore root attachment is the most critical phase of infection however, the underlying mechanisms remain unknown. This study investigated the potential role of root-surface cell-wall polysaccharides and proteins in cultivars resistant/susceptible to zoospore attachment. We first compared the effects of enzymatic removal of root cell-wall proteins, N-linked glycans and polysaccharides on S. subterranea attachment. Subsequent analysis of peptides released by trypsin shaving (TS) of root segments identified 262 proteins that were differentially abundant between cultivars. These were enriched in root-surface-derived peptides but also included intracellular proteins, e.g., proteins associated with glutathione metabolism and lignin biosynthesis, which were more abundant in the resistant cultivar. Comparison with whole-root proteomic analysis of the same cultivars identified 226 proteins specific to the TS dataset, of which 188 were significantly different. Among these, the pathogen-defence-related cell-wall protein stem 28 kDa glycoprotein and two major latex proteins were significantly less abundant in the resistant cultivar. A further major latex protein was reduced in the resistant cultivar in both the TS and whole-root datasets. In contrast, three glutathione S-transferase proteins were more abundant in the resistant cultivar (TS-specific), while the protein glucan endo-1,3-beta-glucosidase was increased in both datasets. These results imply a particular role for major latex proteins and glucan endo-1,3-beta-glucosidase in regulating zoospore binding to potato roots and susceptibility to S. subterranea.
Proteomic analysis of cartilage proteins
Publisher: Elsevier BV
Date: 05-2008
DOI: 10.1016/J.YMETH.2008.01.008
Abstract: While the analysis of the cartilage proteome is important for our comprehensive understanding of the development and disease of this important tissue, several unique features of cartilage present some technical obstacles. Firstly, cartilage is difficult to obtain in adequate quantities for many protein analyses, especially from mice which are otherwise powerful experimental models. Furthermore, the cartilage extracellular matrix contains an insoluble network of collagen II-containing fibrils that are integrated within an abundant anionic network of aggrecan and hyaluronan aggregates. These interacting networks provide a structural scaffold for the covalent and non-covalent attachment of other proteins and glycoproteins. Consequently, proteomic analysis of cartilage requires extraction of proteins with chaotropic agents to achieve and significant protein solubilization. Finally, isolated chondrocytes are phenotypically unstable, which requires rapid isolation of cells or the use of specific culture conditions. Despite these problems, recent improvements in the sensitivity and reproducibility of two-dimensional electrophoresis (2-DE) and tandem mass spectrometry (MS/MS) techniques, combined with improved tissue preparation and s le pre-fractionation approaches, have made the proteomic characterization of cartilage tissues possible. Here we review the approaches that have been used and describe in detail protocols for the proteomic analysis of cartilage tissues and cells.
The metabolomics of alpha-synuclein (SNCA) gene deletion and mutation in mouse brain
Publisher: Springer Science and Business Media LLC
Date: 28-06-2013
The extracellular matrix: an underexplored but important proteome
Publisher: Informa UK Limited
Date: 12-2010
DOI: 10.1586/EPR.10.93
Changes in the Chondrocyte and Extracellular Matrix Proteome during Post-natal Mouse Cartilage Development
Publisher: Elsevier BV
Date: 2012
Ultra-Fast Continuous-Flow Photo Degradation of Organic Peroxide Explosives for Their Efficient Conversion into Hydrogen Peroxide and Possible Application
Publisher: Wiley
Date: 26-01-2016
Comparative Proteomic Analysis of Potato Roots from Resistant and Susceptible Cultivars to Spongospora subterranea Zoospore Root Attachment In Vitro
Publisher: MDPI AG
Date: 15-09-2022
DOI: 10.3390/MOLECULES27186024
Abstract: Potato (Solanum tuberosum L.) exhibits broad variations in cultivar resistance to tuber and root infections by the soilborne, obligate biotrophic pathogen Spongospora subterranea. Host resistance has been recognised as an important approach in potato disease management, whereas zoospore root attachment has been identified as an effective indicator for the host resistance to Spongospora root infection. However, the mechanism of host resistance to zoospore root attachment is currently not well understood. To identify the potential basis for host resistance to S. subterranea at the molecular level, twelve potato cultivars differing in host resistance to zoospore root attachment were used for comparative proteomic analysis. In total, 3723 proteins were quantified from root s les across the twelve cultivars using a data-independent acquisition mass spectrometry approach. Statistical analysis identified 454 proteins that were significantly more abundant in the resistant cultivars 626 proteins were more abundant in the susceptible cultivars. In resistant cultivars, functional annotation of the proteomic data indicated that Gene Ontology terms related to the oxidative stress and metabolic processes were significantly over-represented. KEGG pathway analysis identified that the phenylpropanoid biosynthesis pathway was associated with the resistant cultivars, suggesting the potential role of lignin biosynthesis in the host resistance to S. subterranea. Several enzymes involved in pectin biosynthesis and remodelling, such as pectinesterase and pectin acetylesterase, were more abundant in the resistant cultivars. Further investigation of the potential role of root cell wall pectin revealed that the pectinase treatment of roots resulted in a significant reduction in zoospore root attachment in both resistant and susceptible cultivars. This study provides a comprehensive proteome-level overview of resistance to S. subterranea zoospore root attachment across twelve potato cultivars and has identified a potential role for cell wall pectin in regulating zoospore root attachment.
Type-III procollagen assembly in semi-intact cells: chain association, nucleation and triple-helix folding do not require formation of inter-chain disulphide bonds but triple-helix nucleation does req
Publisher: Portland Press Ltd.
Date: 07-1996
DOI: 10.1042/BJ3170195
Abstract: Procollagen assembly is initiated within the endoplasmic reticulum by three α-chains associating via their C-propeptides (C-terminal propeptides). To study the requirements for the association of procollagen monomers at synthesis we have reconstituted the initial stages in the folding, assembly and modification of procollagen using semi-permeabilized cells. By translating a type-III procollagen ‘mini-gene’ which lacks part of the triple-helical domain, we demonstrate that these cells efficiently carry out the assembly of hydroxylated, triple-helical, procollagen trimers and allow the identification of specific disulphide-bonded intermediates in the folding pathway. Mutant chains, which lack the ability to form inter-chain disulphide bonds within the C-propeptide, were still able to assemble within this system. Furthermore, characterization of the trimeric molecules formed suggested that inter-chain disulphide bonds had formed within the C-telopeptide (C-terminal telopeptide). However, when hydroxylation of prolyl and lysyl residues was inhibited no inter-chain disulphide bonds were formed in the C-telopeptide, indicating that hydroxylation is required for the initial nucleation of the triple-helical domain. Mutant chains which lacked the ability to form inter-chain disulphide bonds within the C-propeptide or the C-telopeptide could still assemble to form trimeric triple-helical molecules linked by inter-chain disulphide bonds within the N-propeptide (N-terminal propeptide). These results indicate that inter-chain disulphide bond formation within the C-propeptide or the C-telopeptide is not required for chain association and triple-helix formation.
Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar)
Publisher: Wiley
Date: 23-06-2016
Abstract: Understanding diet- and environmentally induced physiological changes in fish larvae is a major goal for the aquaculture industry. Proteomic analysis of whole fish larvae comprising multiple tissues offers considerable potential but is challenging due to the very large dynamic range of protein abundance. To extend the coverage of the larval phase of the Atlantic salmon (Salmo salar) proteome, we applied a two-step sequential extraction (SE) method, based on differential protein solubility, using a nondenaturing buffer containing 150 mM NaCl followed by a denaturing buffer containing 7 M urea and 2 M thiourea. Extracts prepared using SE and one-step direct extraction were characterized via label-free shotgun proteomics using nanoLC-MS/MS (LTQ-Orbitrap). SE partitioned the proteins into two fractions of approximately equal amounts, but with very distinct protein composition, leading to identification of ∼40% more proteins than direct extraction. This fractionation strategy enabled the most detailed characterization of the salmon larval proteome to date and provides a platform for greater understanding of physiological changes in whole fish larvae. The MS data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366.
Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii)
Publisher: Springer Science and Business Media LLC
Date: 02-08-2019
DOI: 10.1007/S00018-019-03259-2
Abstract: Devil facial tumour disease (DFTD) comprises two genetically distinct transmissible cancers (DFT1 and DFT2) endangering the survival of the Tasmanian devil (Sarcophilus harrisii) in the wild. DFT1 first arose from a cell of the Schwann cell lineage however, the tissue-of-origin of the recently discovered DFT2 cancer is unknown. In this study, we compared the transcriptome and proteome of DFT2 tumours to DFT1 and normal Tasmanian devil tissues to determine the tissue-of-origin of the DFT2 cancer. Our findings demonstrate that DFT2 expresses a range of Schwann cell markers and exhibits expression patterns consistent with a similar origin to the DFT1 cancer. Furthermore, DFT2 cells express genes associated with the repair response to peripheral nerve damage. These findings suggest that devils may be predisposed to transmissible cancers of Schwann cell origin. The combined effect of factors such as frequent nerve damage from biting, Schwann cell plasticity and low genetic ersity may allow these cancers to develop on rare occasions. The emergence of two independent transmissible cancers from the same tissue in the Tasmanian devil presents an unprecedented opportunity to gain insight into cancer development, evolution and immune evasion in mammalian species.
Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature
Publisher: Springer Science and Business Media LLC
Date: 12-02-2018
Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels
Publisher: American Chemical Society (ACS)
Date: 30-07-2015
DOI: 10.1021/ACS.JPROTEOME.5B00241
Abstract: The extremely psychrophilic proteorhodopsin-containing bacterial species Psychroflexus torquis is considered to be a model sea-ice microorganism, which has adapted to an epiphytic lifestyle. So far, not much is known about proteorhodopsin-based phototrophy and associated life strategies of sea ice bacteria, although it has been previously shown that P. torquis can gain growth advantage from light using a proteorhodopsin proton pump, the activity of which is influenced by environmental salinity. The comprehensive quantitative proteomic study performed here indicated that P. torquis responds to changing salinity and illumination conditions. Proteins in the electron-transfer chain were down-regulated at a suboptimal salinity level, TonB-dependent transporters increased in abundance under supra-optimal salinity and decreased under suboptimal salinity. In addition, several anaplerotic CO2 fixation proteins and three putative light sensing proteins that contain PAS and GAF domains became more abundant under illumination. Furthermore, central metabolic pathways (TCA and glycolysis) were also induced by both salinity stress and illumination. The data suggest that P. torquis responded to changes in both light energy and salinity to modulate membrane and central metabolic proteins that are involved in energy production as well as nutrient uptake and gliding motility processes that would be especially advantageous during the polar summer ice algal bloom.
Challenges of an Emerging Disease: The Evolving Approach to Diagnosing Devil Facial Tumour Disease
Publisher: MDPI AG
Date: 28-12-2021
DOI: 10.3390/PATHOGENS11010027
Abstract: Devil Facial Tumour Disease (DFTD) is an emerging infectious disease that provides an excellent ex le of how diagnostic techniques improve as disease-specific knowledge is generated. DFTD manifests as tumour masses on the faces of Tasmanian devils, first noticed in 1996. As DFTD became more prevalent among devils, karyotyping of the lesions and their devil hosts demonstrated that DFTD was a transmissible cancer. The subsequent routine diagnosis relied on microscopy and histology to characterise the facial lesions as cancer cells. Combined with immunohistochemistry, these techniques characterised the devil facial tumours as sarcomas of neuroectodermal origin. More sophisticated molecular methods identified the origin of DFTD as a Schwann cell, leading to the Schwann cell-specific protein periaxin to discriminate DFTD from other facial lesions. After the discovery of a second facial cancer (DFT2), cytogenetics and the absence of periaxin expression confirmed the independence of the new cancer from DFT1 (the original DFTD). Molecular studies of the two DFTDs led to the development of a PCR assay to differentially diagnose the cancers. Proteomics and transcriptomic studies identified different cell phenotypes among the two DFTD cell lines. Phenotypic differences were also reflected in proteomics studies of extracellular vesicles (EVs), which yielded an early diagnostic marker that could detect DFTD in its latent stage from serum s les. A mesenchymal marker was also identified that could serve as a serum-based differential diagnostic. The emergence of two transmissible cancers in one species has provided an ideal opportunity to better understand transmissible cancers, demonstrating how fundamental research can be translated into applicable and routine diagnostic techniques.
Related Organisations
University Of Manchester
Location: United Kingdom of Great Britain and Northern Ireland
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Linkage Infrastructure, Equipment And Facilities - Grant ID: LE180100059
Start Date: 2018
End Date: 12-2018
Amount: $350,790.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP130101518
Start Date: 2013
End Date: 06-2016
Amount: $480,000.00
Funder: Australian Research Council
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