ORCID Profile
0000-0002-9950-465X
Current Organisations
Universita' degli Studi di Milano
,
Okinawa Institute of Science and Technology Graduate University
,
Okinawa Institute of Science and Technology School Corp and Graduate University
,
James Cook 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)
Climate change impacts and adaptation | Ecological impacts of climate change and ecological adaptation | Global change biology | Evolutionary impacts of climate change | Marine and estuarine ecology (incl. marine ichthyology) |
ANZSRC Socio-Economic Objective (SEO)
Related Links
Publications
Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea
Publisher: Figshare
Date: 2015
Transcriptional regulatory networks in macrophages
Publisher: Wiley
Date: 09-03-2007
DOI: 10.1002/9780470062128.CH2
Abstract: The functions of macrophages in the innate immune system require the constitutive expression of a wide range of myeloid-specific genes, including various pattern recognition receptors, as well as the inducible expression of a suite of genes required to initiate inflammation and eliminate pathogens. Our overall aim is to understand the transcriptional networks that underlie both macrophage-specific transcription and the response to pathogen components such as lipopolysaccharide (LPS). The approaches used include detailed functional analysis of specific promoters, such as that of the CSF1 receptor, global cDNA microarray expression profiling, high throughput real-time PCR analysis of all the transcription factors encoded by the mammalian genome, full length cDNA library construction and sequencing, CAGE analysis to identify specific promoters used in macrophages and motif analysis to detect candidate cis-acting elements in co-regulated genes in macrophages. This review discusses some of the progress in moving towards a transcriptional network model for mouse macrophage activation by LPS, as well as insight into the role of alternative promoter usage and polyadenylation in generating functional protein variants that impact on signalling in macrophages.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Publisher: Elsevier BV
Date: 03-2010
of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression
Publisher: Wiley
Date: 07-2006
Abstract: Bacterial LPS triggers dramatic changes in gene expression in macrophages. We show here that LPS regulated several members of the histone deacetylase (HDAC) family at the mRNA level in murine bone marrow-derived macrophages (BMM). LPS transiently repressed, then induced a number of HDACs (Hdac-4, 5, 7) in BMM, whereas Hdac-1 mRNA was induced more rapidly. Treatment of BMM with trichostatin A (TSA), an inhibitor of HDACs, enhanced LPS-induced expression of the Cox-2, Cxcl2, and Ifit2 genes. In the case of Cox-2, this effect was also apparent at the promoter level. Overexpression of Hdac-8 in RAW264 murine macrophages blocked the ability of LPS to induce Cox-2 mRNA. Another class of LPS-inducible genes, which included Ccl2, Ccl7, and Edn1, was suppressed by TSA, an effect most likely mediated by PU.1 degradation. Hence, HDACs act as potent and selective negative regulators of proinflammatory gene expression and act to prevent excessive inflammatory responses in macrophages.
Mesenchymal stem cells cultured on magnetic nanowire substrates
Publisher: IOP Publishing
Date: 28-12-2016
Abstract: Stem cells have been shown to respond to extracellular mechanical stimuli by regulating their fate through the activation of specific signaling pathways. In this work, an array of iron nanowires (NWs) aligned perpendicularly to the surface was fabricated by pulsed electrodepositon in porous alumina templates followed by a partial removal of the alumina to reveal 2-3 μm of the NWs. This resulted in alumina substrates with densely arranged NWs of 33 nm in diameter separated by 100 nm. The substrates were characterized by scanning electron microscopy (SEM) energy dispersive x-ray analysis and vibrating s le magnetometer. The NW array was then used as a platform for the culture of human mesenchymal stem cells (hMSCs). The cells were stained for the cell nucleus and actin filaments, as well as immuno-stained for the focal adhesion protein vinculin, and then observed by fluorescence microscopy in order to characterize their spreading behavior. Calcein AM/ethidium homodimer-1 staining allowed the determination of cell viability. The interface between the cells and the NWs was studied using SEM. Results showed that hMSCs underwent a re-organization of actin filaments that translated into a change from an elongated to a spherical cell shape. Actin filaments and vinculin accumulated in bundles, suggesting the attachment and formation of focal adhesion points of the cells on the NWs. Though the overall number of cells attached on the NWs was lower compared to the control, the attached cells maintained a high viability (>90%) for up to 6 d. Analysis of the interface between the NWs and the cells confirmed the re-organization of F-actin and revealed the adhesion points of the cells on the NWs. Additionally, a net of filopodia surrounded each cell, suggesting the probing of the array to find additional adhesion points. The cells maintained their round shape for up to 6 d of culture. Overall, the NW array is a promising nanostructured platform for studying and influencing hMSCs differentiation.
Proteomic Changes between Male and Female Worms of the Polychaetous Annelid Neanthes arenaceodentata before and after Spawning
Publisher: Public Library of Science (PLoS)
Date: 30-08-2013
Molecular signatures of transgenerational response to ocean acidification in a species of reef fish
Publisher: Springer Science and Business Media LLC
Date: 08-2016
DOI: 10.1038/NCLIMATE3087
Functionalized magnetic nanowires for chemical and magneto-mechanical induction of cancer cell death
Publisher: Springer Science and Business Media LLC
Date: 24-10-2016
DOI: 10.1038/SREP35786
Abstract: Exploiting and combining different properties of nanomaterials is considered a potential route for next generation cancer therapies. Magnetic nanowires (NWs) have shown good biocompatibility and a high level of cellular internalization. We induced cancer cell death by combining the chemotherapeutic effect of doxorubicin (DOX)-functionalized iron NWs with the mechanical disturbance under a low frequency alternating magnetic field. (3-aminopropyl)triethoxysilane (APTES) and bovine serum albumin (BSA) were separately used for coating NWs allowing further functionalization with DOX. Internalization was assessed for both formulations by confocal reflection microscopy and inductively coupled plasma-mass spectrometry. From confocal analysis, BSA formulations demonstrated higher internalization and less agglomeration. The functionalized NWs generated a comparable cytotoxic effect in breast cancer cells in a DOX concentration-dependent manner, (~60% at the highest concentration tested) that was significantly different from the effect produced by free DOX and non-functionalized NWs formulations. A synergistic cytotoxic effect is obtained when a magnetic field (1 mT, 10 Hz) is applied to cells treated with DOX-functionalized BSA or APTES-coated NWs, (~70% at the highest concentration). In summary, a bimodal method for cancer cell destruction was developed by the conjugation of the magneto-mechanical properties of iron NWs with the effect of DOX producing better results than the in idual effects.
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network
Publisher: Springer Science and Business Media LLC
Date: 28-04-2011
Abstract: Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Like in any other organism, the response of corals to stress is tightly controlled by the coordinated interplay of many transcription factors. Here, we develop and apply a new system-wide approach in order to infer combinatorial transcription factor networks of the reef-building coral Acropora millepora . By integrating sequencing-derived transcriptome measurements, a network of physically interacting transcription factors, and phylogenetic network footprinting we were able to infer such a network. Analysis of the network across a phylogenetically broad s le of five species, including human, reveals that despite the apparent simplicity of corals, their transcription factors repertoire and interaction networks seem to be largely conserved. In addition, we were able to identify interactions among transcription factors that appear to be species-specific lending strength to the novel concept of "Taxonomically Restricted Interactions". This study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved.
Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2016
MOESM4 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen
Publisher: Springer New York
Date: 2016
DOI: 10.1007/978-1-4939-3335-8_10
Abstract: Intramacrophage pathogens subvert antimicrobial defence pathways using various mechanisms, including the targeting of host TLR-mediated transcriptional responses. Conversely, TLR-inducible host defence mechanisms subject intramacrophage pathogens to stress, thus altering pathogen gene expression programs. Important biological insights can thus be gained through the analysis of gene expression changes in both the host and the pathogen during an infection. Traditionally, research methods have involved the use of qPCR, microarrays and/or RNA sequencing to identify transcriptional changes in either the host or the pathogen. Here we describe the application of RNA sequencing using s les obtained from in vitro infection assays to simultaneously quantify both host and bacterial pathogen gene expression changes, as well as general approaches that can be undertaken to interpret the RNA sequencing data that is generated. These methods can be used to provide insights into host TLR-regulated transcriptional responses to microbial challenge, as well as pathogen subversion mechanisms against such responses.
Quantitative Proteomics Identify Molecular Targets That Are Crucial in Larval Settlement and Metamorphosis ofBugula neritina
Publisher: American Chemical Society (ACS)
Date: 07-01-2011
DOI: 10.1021/PR100817V
Abstract: The marine invertebrate Bugula neritina has a biphasic life cycle that consists of a swimming larval stage and a sessile juvenile and adult stage. The attachment of larvae to the substratum and their subsequent metamorphosis have crucial ecological consequences. Despite many studies on this species, little is known about the molecular mechanism of these processes. Here, we report a comparative study of swimming larvae and metamorphosing in iduals at 4 and 24 h postattachment using label-free quantitative proteomics. We identified more than 1100 proteins at each stage, 61 of which were differentially expressed. Specifically, proteins involved in energy metabolism and structural molecules were generally down-regulated, whereas proteins involved in transcription and translation, the extracellular matrix, and calcification were strongly up-regulated during metamorphosis. Many tightly regulated novel proteins were also identified. Subsequent analysis of the temporal and spatial expressions of some of the proteins and an assay of their functions indicated that they may have key roles in metamorphosis of B. neritina. These findings not only provide molecular evidence with which to elucidate the substantial changes in morphology and physiology that occur during larval attachment and metamorphosis but also identify potential targets for antifouling treatment.
Dynamic Epigenetic Control of Highly Conserved Noncoding Elements
Publisher: Public Library of Science (PLoS)
Date: 07-10-2014
Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea
Publisher: Wiley
Date: 06-2015
DOI: 10.1002/ECE3.1511
of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Magnetic nanowires and hyperthermia: How geometry and material affect heat production efficiency
Publisher: IEEE
Date: 05-2015
Methamphetamine abuse affects gene expression in brain-derived microglia of SIV-infected macaques to enhance inflammation and promote virus targets
Publisher: Figshare
Date: 2016
AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells
Publisher: Cold Spring Harbor Laboratory
Date: 20-01-2019
DOI: 10.1101/525527
Abstract: Aside from their roles in the cytoplasm, RNA-interference components have been reported to localize also in the nucleus of human cells. In particular, AGO1 associates with active chromatin and appears to influence global gene expression. However, the mechanistic aspects remain elusive. Here, we identify AGO1 as a paraspeckle component that in combination with the NEAT1 lncRNA maintains 3D genome architecture. We demonstrate that AGO1 interacts with NEAT1 lncRNA and its depletion affects NEAT1 expression and the formation of paraspeckles. By Hi-C analysis in AGO1 knockdown cells, we observed global changes in chromatin organization, including TADs configuration, and A/B compartment mixing. Consistently, distinct groups of genes located within the differential interacting loci showed altered expression upon AGO1 depletion. NEAT1 knockout cells displayed similar changes in TADs and higher-order A/B compartmentalization. We propose that AGO1 in association with NEAT1 lncRNA can act as a scaffold that bridges chromatin and nuclear bodies to regulate genome organization and gene expression in human cells.
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
Publisher: Public Library of Science (PLoS)
Date: 28-04-2006
Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish
Publisher: Wiley
Date: 24-10-2018
DOI: 10.1111/MEC.14884
Abstract: Global warming will have far-reaching consequences for marine species over coming decades, yet the magnitude of these effects may depend on the rate of warming across generations. Recent experiments show coral reef fishes can compensate the metabolic challenges of elevated temperature when warm conditions are maintained across generations. However, the effects of a gradual temperature increase across generations remain unknown. In the present study, we analysed metabolic and molecular traits in the damselfish Acanthochromis polyacanthus that were exposed to +1.5°C in the first generation and +3.0°C in the second (Step +3.0°C). This treatment of stepwise warming was compared to fish reared at current-day temperatures (Control), second-generation fish of control parents reared at +3.0°C (Developmental +3.0°C) and fish exposed to elevated temperatures for two generations (Transgenerational +1.5°C and Transgenerational +3.0°C). Hepatosomatic index, oxygen consumption and liver gene expression were compared in second-generation fish of the multiple treatments. Hepatosomatic index increased in fish that developed at +3.0°C, regardless of the parental temperature. Routine oxygen consumption of Step +3.0°C fish was significantly higher than Control however, their aerobic scope recovered to the same level as Control fish. Step +3.0°C fish exhibited significant upregulation of genes related to mitochondrial activity and energy production, which could be associated with their increased metabolic rates. These results indicate that restoration of aerobic scope is possible when fish experience gradual thermal increase across multiple generations, but the metabolic and molecular responses are different from fish reared at the same elevated thermal conditions in successive generations.
Correction: miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria
Publisher: Public Library of Science (PLoS)
Date: 11-04-2016
Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina
Publisher: Springer Science and Business Media LLC
Date: 24-05-2010
Abstract: Metamorphosis in the bryozoan Bugula neritina (Linne) includes an initial phase of rapid morphological rearrangement followed by a gradual phase of morphogenesis. We hypothesized that the first phase may be independent of de novo synthesis of proteins and, instead, involves post-translational modifications of existing proteins, providing a simple mechanism to quickly initiate metamorphosis. To test our hypothesis, we challenged B. neritina larvae with transcription and translation inhibitors. Furthermore, we employed 2D gel electrophoresis to characterize changes in the phosphoproteome and proteome during early metamorphosis. Differentially expressed proteins were identified by liquid chromatography tandem mass spectrometry and their gene expression patterns were profiled using semi-quantitative real time PCR. When larvae were incubated with transcription and translation inhibitors, metamorphosis initiated through the first phase but did not complete. We found a significant down-regulation of 60 protein spots and the percentage of phosphoprotein spots decreased from 15% in the larval stage to12% during early metamorphosis. Two proteins--the mitochondrial processing peptidase beta subunit and severin--were abundantly expressed and phosphorylated in the larval stage, but down-regulated during metamorphosis. MPPbeta and severin were also down-regulated on the gene expression level. The initial morphogenetic changes that led to attachment of B. neritina did not depend on de novo protein synthesis, but the subsequent gradual morphogenesis did. This is the first time that the mitochondrial processing peptidase beta subunit or severin have been shown to be down-regulated on both gene and protein expression levels during the metamorphosis of B. neritina . Future studies employing immunohistochemistry to reveal the expression locality of these two proteins during metamorphosis should provide further evidence of the involvement of these two proteins in the morphogenetic rearrangement of B. neritina .
Inductively actuated micro needles for on-demand intracellular delivery
Publisher: Springer Science and Business Media LLC
Date: 02-07-2018
DOI: 10.1038/S41598-018-28194-3
Abstract: Methods that provide controlled influx of molecules into cells are of critical importance for uncovering cellular mechanisms, drug development and synthetic biology. However, reliable intracellular delivery without adversely affecting the cells is a major challenge. We developed a platform for on-demand intracellular delivery applications, with which cell membrane penetration is achieved by inductive heating of micro needles. The micro needles of around 1 μm in diameter and 5 μm in length are made of gold using a silicon-based micro fabrication process that provides flexibility with respect to the needles’ dimensions, pitch, shell thickness and the covered area. Experiments with HCT 116 colon cancer cells showed a high biocompatibility of the gold needle platform. Transmission electron microscopy of the cell-needle interface revealed folding of the cell membrane around the needle without penetration, preventing any delivery, which was confirmed using the EthD-1 fluorescent dye. The application of an alternating magnetic field, however, resulted in the delivery of EthD-1 by localized heating of the micro needles. Fluorescence quantification showed that intracellular delivery, with as high as 75% efficiency, is achieved for specific treatment times between 1 and 5 minutes. Overexposure of the cells to the heated micro needles, i.e. longer magnetic field application, leads to an increase in cell death, which can be exploited for cleaning the platform. This method allows to perform intracellular deliver by remotely activating the micro needles via a magnetic field, and it is controlled by the application time, making it a versatile and easy to use method. The wireless actuation could also be an attractive feature for in-vivo delivery and implantable devices.
Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49
Publisher: American Society for Microbiology
Date: 05-2014
Abstract: The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.
Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula
Publisher: Cold Spring Harbor Laboratory
Date: 07-03-2018
DOI: 10.1101/278267
Abstract: The iconic orange clownfish, Amphiprion percula , is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula . We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
MOESM8 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Morphological characterization of virus-like particles in coral reef sponges
Publisher: PeerJ
Date: 17-10-2018
DOI: 10.7717/PEERJ.5625
Abstract: Marine sponges host complex microbial consortia that vary in their abundance, ersity and stability amongst host species. While our understanding of sponge-microbe interactions has dramatically increased over the past decade, little is known about how sponges and their microbial symbionts interact with viruses, the most abundant entities in the ocean. In this study, we employed three transmission electron microscopy (TEM) preparation methods to provide the first comprehensive morphological assessment of sponge-associated viruses. The combined approaches revealed 50 different morphologies of viral-like particles (VLPs) represented across the different sponge species. VLPs were visualized within sponge cells, within the sponge extracellular mesohyl matrix, on the sponge ectoderm and within sponge-associated microbes. Non-enveloped, non-tailed icosahedral VLPs were the most commonly observed morphotypes, although tailed bacteriophage, brick-shaped, geminate and filamentous VLPs were also detected. Visualization of sponge-associated viruses using TEM has confirmed that sponges harbor not only erse communities of microorganisms but also erse communities of viruses.
Coevolution within a transcriptional network by compensatory trans and cis mutations
Publisher: Cold Spring Harbor Laboratory
Date: 26-10-2010
Abstract: Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis -acting DNA sequences near genes as the main cause of ergence. What is less clear is how these changes interact with trans -acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata , in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis -regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an ex le of “coevolution” between a DNA-binding transcription factor and its cis -regulatory site, reminiscent of the coevolution of protein binding partners.
Magnetic core–shell nanowires as MRI contrast agents for cell tracking
Publisher: figshare
Date: 2020
Molecular Response to Extreme Summer Temperatures Differs Between Two Genetically Differentiated Populations of a Coral Reef Fish
Publisher: Frontiers Media SA
Date: 28-09-2018
Inflammation suppressor genes: Please switch out all the lights
Publisher: Oxford University Press (OUP)
Date: 17-03-2005
DOI: 10.1189/JLB.1204710
Abstract: An effective immune system requires rapid and appropriate activation of inflammatory mechanisms but equally rapid and effective resolution of the inflammatory state. A review of the canonical host response to gram-negative bacteria, the lipopolysaccharide-Toll-like receptor 4 signaling cascade, highlights the induction of repressors that act at each step of the activation process. These inflammation suppressor genes are characterized by their induction in response to pathogen, typically late in the macrophage activation program, and include an expanding class of dominant-negative proteins derived from alternate splicing of common signaling components. Despite the expanse of anti-inflammatory mechanisms available to an activated macrophage, the frailty of this system is apparent in the large numbers of genes implicated in chronic inflammatory diseases. This apparent lack of redundancy between inflammation suppressor genes is discussed with regard to evolutionary benefits in generating a heterogeneous population of immune cells and consequential robustness in defense against new and evolving pathogens.
MOESM9 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Iron-Based Core–Shell Nanowires for Combinatorial Drug Delivery and Photothermal and Magnetic Therapy
Publisher: American Chemical Society (ACS)
Date: 04-11-2019
Abstract: Combining different therapies into a single nanomaterial platform is a promising approach for achieving more efficient, less invasive, and personalized treatments. Here, we report on the development of such a platform by utilizing nanowires with an iron core and iron oxide shell as drug carriers and exploiting their optical and magnetic properties. The iron core has a large magnetization, which provides the foundation for low-power magnetic manipulation and magnetomechanical treatment. The iron oxide shell enables functionalization with doxorubicin through a pH-sensitive linker, providing selective intracellular drug delivery. Combined, the core-shell nanostructure features an enhanced light-matter interaction in the near-infrared region, resulting in a high photothermal conversion efficiency of >80% for effective photothermal treatment. Applied to cancer cells, the collective effect of the three modalities results in an extremely efficient treatment with nearly complete cell death (∼90%). In combination with the possibility of guidance and detection, this platform provides powerful tools for the development of advanced treatments.
Computational tools for genome-wide miRNA prediction and study
Publisher: Bentham Science Publishers Ltd.
Date: 02-11-2012
DOI: 10.2174/1874196701205010023
Abstract: MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3'-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages.
miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria
Publisher: Public Library of Science (PLoS)
Date: 12-02-2016
Systems biology of innate immunity
Publisher: Elsevier BV
Date: 12-2006
Review of In Vitro Toxicity of Nanoparticles and Nanorods—Part 2
Publisher: InTech
Date: 25-07-2018
Resilience and Adaptation to Local and Global Environmental Change
Publisher: CRC Press
Date: 03-11-2022
Semi-automated quantification of living cells with internalized nanostructures
Publisher: Springer Science and Business Media LLC
Date: 15-01-2016
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering
Publisher: Springer Science and Business Media LLC
Date: 2010
Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies
Publisher: Springer Science and Business Media LLC
Date: 14-02-2013
Involvement of Wnt Signaling Pathways in the Metamorphosis of the Bryozoan Bugula neritina
Publisher: Public Library of Science (PLoS)
Date: 20-03-2012
Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro
Publisher: Figshare
Date: 2017
Viral ecogenomics across the Porifera
Publisher: Springer Science and Business Media LLC
Date: 02-10-2020
DOI: 10.1186/S40168-020-00919-5
Abstract: Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide ersity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the ersity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae , Marseilleviridae , Phycodnaviridae , Ascoviridae , Iridoviridae , Asfarviridae and Poxviridae . Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. Our results highlight the erse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the erse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts.
The co‐transcriptome of uropathogenicE scherichia coli‐infected mouse macrophages reveals new insights into host–pathogen interactions
Publisher: Hindawi Limited
Date: 24-01-2015
DOI: 10.1111/CMI.12397
Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
Publisher: American Association for Cancer Research (AACR)
Date: 15-12-2007
DOI: 10.1158/0008-5472.CAN-07-1284
Abstract: Human mammary epithelial cells (HMEC) grown under standard cell culture conditions enter a growth phase referred to as selection, but a subpopulation is able to escape from arrest and continue to proliferate. These cells, called post-selection or variant HMECs, may be derived from progenitor cells found in normal mammary epithelium that subsequently acquire premalignant lesions, including p16INK4A promoter hypermethylation. Epigenetic silencing of tumor suppressor genes through DNA methylation and histone modification is an early event in tumorigenesis. A major challenge is to find genes or gene pathways that are commonly silenced to provide early epigenetic diagnostic and therapeutic cancer targets. To identify very early epigenetic events that occur in breast cancer, we used microarrays to screen for gene pathways that were suppressed in post-selection HMECs but reactivated after treatment with the demethylation agent 5-aza-2′-deoxycytidine. We found that several members of the transforming growth factor β (TGF-β) signaling pathway were consistently down-regulated in the post-selection HMEC populations, and this was associated with a marked decrease in Smad4 nuclear staining. Gene suppression was not associated with DNA methylation but with chromatin remodeling, involving a decrease in histone H3 lysine 27 trimethylation and an increase in histone H3 lysine 9 dimethylation and deacetylation. These results show for the first time that TGF-β2, its receptors TGF-βR1 and TGF-βR2, and activator thrombospondin-1 are concordantly suppressed early in breast carcinogenesis by histone modifications and indicate that the TGF-β signaling pathway is a novel target for gene activation by epigenetic therapy. [Cancer Res 2007 (24):11517–27]
Revealing microbial functional activities in the R ed S ea sponge S tylissa carteri by metatranscriptomics
Publisher: Wiley
Date: 09-07-2014
Abstract: Sponges are important components of marine benthic environments and are associated with microbial symbionts that carry out ecologically relevant functions. Stylissa carteri is an abundant, low-microbial abundance species in the Red Sea. We aimed to achieve the functional and taxonomic characterization of the most actively expressed prokaryotic genes in S. carteri. Prokaryotic mRNA was enriched from sponge total RNA, sequenced using Illumina HiSeq technology and annotated using the metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline. We detected high expression of archaeal ammonia oxidation and photosynthetic carbon fixation by members of the genus Synechococcus. Functions related to stress response and membrane transporters were among the most highly expressed by S. carteri symbionts. Unexpectedly, gene functions related to methylotrophy were highly expressed by gammaproteobacterial symbionts. The presence of seawater-derived microbes is indicated by the phylogenetic proximity of organic carbon transporters to orthologues of members from the SAR11 clade. In summary, we revealed the most expressed functions of the S. carteri-associated microbial community and linked them to the dominant taxonomic members of the microbiome. This work demonstrates the applicability of metatranscriptomics to explore poorly characterized symbiotic consortia and expands our knowledge of the ecologically relevant functions carried out by coral reef sponge symbionts.
SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification
Publisher: Public Library of Science (PLoS)
Date: 28-06-2012
Study of monocyte membrane proteome perturbation during lipopolysaccharide‐induced tolerance using iTRAQ‐based quantitative proteomic approach
Publisher: Wiley
Date: 27-07-2010
Abstract: Human monocytes' exposure to low-level lipopolysaccharide (LPS) induces temporary monocytic insensitivity to subsequent LPS challenge. The underlying mechanism of this phenomenon could have important clinical utilities in preventing and/or treating severe infections. In this study, we used an iTRAQ-based quantitative proteomic approach to comprehensively characterize the membrane proteomes of monocytes before and after LPS exposure. We identified a total of 1651 proteins, of which 53.6% were membrane proteins. Ninety-four percent of the proteins were quantified and 255 proteins were shown to be tightly regulated by LPS. Subcellular location analysis revealed organelle-specific response to LPS exposure: more than 90% of identified mitochondrial membrane proteins were significant downregulated, whereas the majority of proteins from other organelles such as ER, Golgi and ribosome were upregulated. Moreover, we found that the expression of most receptors potentially involved in LPS signal pathway (CD14, toll-like receptor 4, CD11/CD18 complex) were substantially decreased, while the expression of molecules involved in LPS neutralization were enhanced after LPS challenge. Together, these findings could be of significance in understanding the mechanism of LPS tolerance and provide values for designing new approaches for regulating monocytic responses in sepsis patients.
Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
Publisher: Oxford University Press (OUP)
Date: 19-06-2013
DOI: 10.1093/BIOINFORMATICS/BTT208
Abstract: Motivation: Most functions within the cell emerge thanks to protein–protein interactions (PPIs), yet experimental determination of PPIs is both expensive and time-consuming. PPI networks present significant levels of noise and incompleteness. Predicting interactions using only PPI-network topology (topological prediction) is difficult but essential when prior biological knowledge is absent or unreliable. Methods: Network embedding emphasizes the relations between network proteins embedded in a low-dimensional space, in which protein pairs that are closer to each other represent good candidate interactions. To achieve network denoising, which boosts prediction performance, we first applied minimum curvilinear embedding (MCE), and then adopted shortest path (SP) in the reduced space to assign likelihood scores to candidate interactions. Furthermore, we introduce (i) a new valid variation of MCE, named non-centred MCE (ncMCE) (ii) two automatic strategies for selecting the appropriate embedding dimension and (iii) two new randomized procedures for evaluating predictions. Results: We compared our method against several unsupervised and supervisedly tuned embedding approaches and node neighbourhood techniques. Despite its computational simplicity, ncMCE-SP was the overall leader, outperforming the current methods in topological link prediction. Conclusion: Minimum curvilinearity is a valuable non-linear framework that we successfully applied to the embedding of protein networks for the unsupervised prediction of novel PPIs. The rationale for our approach is that biological and evolutionary information is imprinted in the non-linear patterns hidden behind the protein network topology, and can be exploited for predicting new protein links. The predicted PPIs represent good candidates for testing in high-throughput experiments or for exploitation in systems biology tools such as those used for network-based inference and prediction of disease-related functional modules. Availability: ite/carlovittoriocannistraci/home Contact: kalokagathos.agon@gmail.com or timothy.ravasi@kaust.edu.sa Supplementary information: Supplementary data are available at Bioinformatics online.
Defining the protein interaction network of human malaria parasite Plasmodium falciparum
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.YGENO.2011.11.006
Abstract: Malaria, caused by the protozoan parasite Plasmodium falciparum, affects around 225 million people yearly and a huge international effort is directed towards combating this grave threat to world health and economic development. Considerable advances have been made in malaria research triggered by the sequencing of its genome in 2002, followed by several high-throughput studies defining the malaria transcriptome and proteome. A protein-protein interaction (PPI) network seeks to trace the dynamic interactions between proteins, thereby elucidating their local and global functional relationships. Experimentally derived PPI network from high-throughput methods such as yeast two hybrid (Y2H) screens are inherently noisy, but combining these independent datasets by computational methods tends to give a greater accuracy and coverage. This review aims to discuss the computational approaches used till date to construct a malaria protein interaction network and to catalog the functional predictions and biological inferences made from analysis of the PPI network.
Anti-cancer agents in Saudi Arabian herbals revealed by automated high-content imaging
Publisher: Public Library of Science (PLoS)
Date: 13-06-2017
High abundances of zooxanthellate zoantharians (Palythoa and Zoanthus) at multiple natural analogues: potential model anthozoans?
Publisher: Springer Science and Business Media LLC
Date: 15-04-2023
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2006
DOI: 10.1101/GR.4200206
Abstract: Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific “transcriptional noise.” Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.
Symbiodiniaceae diversity of Palythoa tuberculosa in the central and southern Red Sea influenced by environmental factors
Publisher: Springer Science and Business Media LLC
Date: 03-08-2020
PU.1 and ICSBP control constitutive and IFN-γ-regulated Tlr9 gene expression in mouse macrophages
Publisher: Oxford University Press (OUP)
Date: 14-03-2007
DOI: 10.1189/JLB.0107036
Abstract: Macrophages are activated by unmethylated CpG-containing DNA (CpG DNA) via TLR9. IFN-γ and LPS can synergize with CpG DNA to enhance proinflammatory responses in murine macrophages. Here, we show that LPS and IFN-γ up-regulated Tlr9 mRNA in murine bone marrow-derived macrophages (BMM). The ability of LPS and IFN-γ to induce Tlr9 mRNA expression in BMM was dependent on the presence of the growth factor, CSF-1, which is constitutively present in vivo. However, there were clear differences in mechanisms of Tlr9 mRNA induction. LPS stimulation rapidly removed the CSF-1 receptor (CSF-1R) from the cell surface, thereby blocking CSF-1-mediated transcriptional repression and indirectly inducing Tlr9 mRNA expression. By contrast, IFN-γ activated the Tlr9 promoter directly and only marginally affected cell surface CSF-1R expression. An ∼100-bp proximal promoter of the murine Tlr9 gene was sufficient to confer basal and IFN-γ-inducible expression in RAW264.7 cells. A composite IFN regulatory factor (IRF)/PU.1 site upon the major transcription start site was identified. Mutation of the binding sites for PU.1 or IRF impaired basal promoter activity, but only the IRF-binding site was required for IFN-γ induction. The mRNA expression of the IRF family member IFN consensus-binding protein [(ICSBP)/IRF8] was coregulated with Tlr9 in macrophages, and constitutive and IFN-γ-inducible Tlr9 mRNA expression was reduced in ICSBP-deficient BMM. This study therefore characterizes the regulation of mouse Tlr9 expression and defines a molecular mechanism by which IFN-γ lifies mouse macrophage responses to CpG DNA.
Proteomic and metabolomic profiles of marineVibriosp. 010 in response to an antifoulant challenge
Publisher: Informa UK Limited
Date: 08-2013
DOI: 10.1080/08927014.2013.805209
Abstract: Vibrio spp. have the ability to form biofilms, which may contribute to the subsequent successful colonization by microfouling and macrofouling organisms. The effects of an antifouling compound, poly-ether B, on Vibrio sp. 010 were investigated using flow cytometry, proteomics, and metabolomics. A 2-D gel-based proteomic analysis was used to identify proteins responsive to poly-ether B treatment. The profiles of biofilm metabolites were analyzed by ultra-performance liquid chromatography-mass spectrometry. Poly-ether B caused a significant reduction in viability. The proteins affected by the treatment were related to nucleotide metabolism, the glyoxylate cycle, and stress responses. Metabolites such as tripeptides, fatty acids, and quorum-sensing molecules were regulated differentially. Down-regulation of proteins and metabolites potentially led to a loss in colonisation ability, thereby affecting the structure of the biofilm. These results suggest that the proteins and metabolites identified may serve as target molecules for potent antifouling compounds.
Hologenome analysis of two marine sponges with different microbiomes
Publisher: Figshare
Date: 2016
Corrigendum to: Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/IS16059_CO
Abstract: The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of erse scientists, marked its second anniversary with a workshop in Munich, Germany in 2015, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training of talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritise taxonomic ersity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialised organism databases to globally advance invertebrate genomics. This article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research.
Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse
Publisher: Cold Spring Harbor Laboratory
Date: 06-2003
DOI: 10.1101/GR.954803
Abstract: With the completion of the human and mouse genome sequences, the task now turns to identifying their encoded transcripts and assigning gene function. In this study, we have undertaken a computational approach to identify and classify all of the protein kinases and phosphatases present in the mouse gene complement. A nonredundant set of these sequences was produced by mining Ensembl gene predictions and publicly available cDNA sequences with a panel of InterPro domains. This approach identified 561 candidate protein kinases and 162 candidate protein phosphatases. This cohort was then analyzed using TribeMCL protein sequence similarity clustering followed by CLUSTALV alignment and hierarchical tree generation. This approach allowed us to (1) distinguish between true members of the protein kinase and phosphatase families and enzymes of related biochemistry, (2) determine the structure of the families, and (3) suggest functions for previously uncharacterized members. The classifications obtained by this approach were in good agreement with previous schemes and allowed us to demonstrate domain associations with a number of clusters. Finally, we comment on the complementary nature of cDNA and genome-based gene detection and the impact of the FANTOM2 transcriptome project.
MOESM3 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Erratum: Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution
Publisher: Springer Science and Business Media LLC
Date: 09-2007
DOI: 10.1038/NG0907-1174B
Transcription Factor Tfec Contributes to the IL-4-Inducible Expression of a Small Group of Genes in Mouse Macrophages Including the Granulocyte Colony-Stimulating Factor Receptor
Publisher: The American Association of Immunologists
Date: 06-2005
DOI: 10.4049/JIMMUNOL.174.11.7111
Abstract: Expression of the mouse transcription factor EC (Tfec) is restricted to the myeloid compartment, suggesting a function for Tfec in the development or function of these cells. However, mice lacking Tfec develop normally, indicating a redundant role for Tfec in myeloid cell development. We now report that Tfec is specifically induced in bone marrow-derived macrophages upon stimulation with the Th2 cytokines, IL-4 and IL-13, or LPS. LPS induced a rapid and transient up-regulation of Tfec mRNA expression and promoter activity, which was dependent on a functional NF-κB site. IL-4, however, induced a rapid, but long-lasting, increase in Tfec mRNA, which, in contrast to LPS stimulation, also resulted in detectable levels of Tfec protein. IL-4-induced transcription of Tfec was absent in macrophages lacking Stat6, and its promoter depended on two functional Stat6-binding sites. A global comparison of IL-4-induced genes in both wild-type and Tfec mutant macrophages revealed a surprisingly mild phenotype with only a few genes affected by Tfec deficiency. These included the G-CSFR (Csf3r) gene that was strongly up-regulated by IL-4 in wild-type macrophages and, to a lesser extent, in Tfec mutant macrophages. Our study also provides a general definition of the transcriptome in alternatively activated mouse macrophages and identifies a large number of novel genes characterizing this cell type.
Integrated approaches to uncovering transcription regulatory networks in mammalian cells
Publisher: Elsevier BV
Date: 03-2008
DOI: 10.1016/J.YGENO.2007.11.005
Abstract: Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect high-throughput measurements of a cellular state as well as the most successful methods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals.
Targeted cancer cell death induced by biofunctionalized magnetic nanowires
Publisher: IEEE
Date: 02-2014
Identification and Predictive Value of Interleukin-6 + Interleukin-10 + and Interleukin-6 − Int
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 26-10-2012
DOI: 10.1161/CIRCRESAHA.111.262477
Abstract: At the onset of ST-elevation acute myocardial infarction (STEMI), patients can present with very high circulating interleukin-6 (IL-6 + ) levels or very low-IL-6 – levels. We compared these 2 groups of patients to understand whether it is possible to define specific STEMI phenotypes associated with outcome based on the cytokine response. We compared 109 patients with STEMI in the top IL-6 level (median, 15.6 pg/mL IL-6 + STEMI) with 96 in the bottom IL-6 level (median, 1.7 pg/mL IL-6 − STEMI) and 103 matched controls extracted from the multiethnic First Acute Myocardial Infarction study. We found minimal clinical differences between IL-6 + STEMI and IL-6 − STEMI. We assessed the inflammatory profiles of the 2 STEMI groups and the controls by measuring 18 cytokines in blood s les. We exploited clustering analysis algorithms to infer the functional modules of interacting cytokines. IL-6 + STEMI patients were characterized by the activation of 2 modules of interacting signals comprising IL-10, IL-8, macrophage inflammatory protein-1α, and C-reactive protein, and monocyte chemoattractant protein-1, macrophage inflammatory protein-1β, and monokine induced by interferon-γ. IL-10 was increased both in IL-6 + STEMI and IL-6 − STEMI patients compared with controls. IL-6 + IL-10 + STEMI patients had an increased risk of systolic dysfunction at discharge and an increased risk of death at 6 months in comparison with IL-6 − IL-10 + STEMI patients. We combined IL-10 and monokine induced by interferon-γ (derived from the 2 identified cytokine modules) with IL-6 in a formula yielding a risk index that outperformed any single cytokine in the prediction of systolic dysfunction and death. We have identified a characteristic circulating inflammatory cytokine pattern in STEMI patients, which is not related to the extent of myocardial damage. The simultaneous elevation of IL-6 and IL-10 levels distinguishes STEMI patients with worse clinical outcomes from other STEMI patients. These observations could have potential implications for risk-oriented patient stratification and immune-modulating therapies.
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage
Publisher: Cold Spring Harbor Laboratory
Date: 06-2003
DOI: 10.1101/GR.1056103
Abstract: The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the present study we have assessed the complexity of the transcriptome expressed in mouse macrophages before and after treatment with lipopolysaccharide, a global regulator of macrophage gene expression, using existing RIKEN 19K arrays. By comparison to array profiles of other cells and tissues, we identify a large set of macrophage-enriched genes, many of which have obvious functions in endocytosis and phagocytosis. In addition, a significant number of LPS-inducible genes were identified. The data suggest that macrophages are a complex source of mRNA for transcriptome studies. To assess complexity and identify additional macrophage expressed genes, cDNA libraries were created from purified populations of macrophage and dendritic cells, a functionally related cell type. Sequence analysis revealed a high incidence of novel mRNAs within these cDNA libraries. These studies provide insights into the depths of transcriptional complexity still untapped amongst products of inducible genes, and identify macrophage and dendritic cell populations as a starting point for s ling the inducible mammalian transcriptome.
Diel pCO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions
Publisher: Wiley
Date: 28-08-2021
DOI: 10.1111/MEC.16124
Abstract: Environmental partial pressure of CO 2 ( p CO 2 ) variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental p CO 2 fluctuates on a regular day–night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of p CO 2 . To evaluate the effects on the brain molecular response, we exposed two common reef fishes ( Acanthochromis polyacanthus and Amphiprion percula ) to two projected future p CO 2 levels (750 and 1,000 µatm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated p CO 2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional programme was more strongly affected by higher average p CO 2 in a stable treatment than for fluctuating treatments, but the largest difference in molecular response was between stable and fluctuating p CO 2 treatments. This indicates that a response to a change in environmental p CO 2 conditions is different for organisms living in a fluctuating than in stable environments. This differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among p CO 2 treatments, possibly accommodating a more flexible adaptive approach in the response to environmental changes. Our results suggest that environmental p CO 2 fluctuations might enable reef fishes to phase‐shift their clocks and anticipate p CO 2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.
Hologenome analysis of two marine sponges with different microbiomes
Publisher: Springer Science and Business Media LLC
Date: 29-02-2016
Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/IS16059
Abstract: The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of erse scientists, marked its second anniversary with a workshop in Munich, Germany in 2015, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training of talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritise taxonomic ersity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialised organism databases to globally advance invertebrate genomics. This article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research.
Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome
Publisher: Cold Spring Harbor Laboratory
Date: 06-2003
DOI: 10.1101/GR.1015703
Abstract: The chromodomain is 40–50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseudogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.
Probing the S100 protein family through genomic and functional analysis
Publisher: Elsevier BV
Date: 07-2004
Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages
Publisher: Elsevier BV
Date: 11-2011
DOI: 10.1016/J.IMBIO.2011.05.011
Abstract: Uropathogenic E. coli (UPEC) are the primary cause of urinary tract infections. Recent studies have demonstrated that UPEC can invade and replicate within epithelial cells, suggesting that this bacterial pathogen may occupy an intracellular niche within the host. Given that many intracellular pathogens target macrophages, we assessed the interactions between UPEC and macrophages. Colonization of the mouse bladder by UPEC strain CFT073 resulted in increased expression of myeloid-restricted genes, consistent with the recruitment of inflammatory macrophages to the site of infection. In in vitro assays, CFT073 was able to survive within primary mouse bone marrow-derived macrophages (BMM) up to 24h post-infection. Three additional well-characterized clinical UPEC isolates associated with distinct UTI symptomatologies displayed variable long-term survival within BMM. UPEC strains UTI89 and VR50, originally isolated from patients with cystitis and asymptomatic bacteriuria respectively, showed elevated bacterial loads in BMM at 24h post-infection as compared to CFT073 and the asymptomatic bacteriuria strain 83972. These differences did not correlate with differential effects on macrophage survival or initial uptake of bacteria. E. coli UTI89 localized to a L 1(+) vesicular compartment within BMM. In contrast to survival within mouse BMM, intracellular bacterial loads of VR50 were low in both human monocyte-derived macrophages (HMDM) and in human T24 bladder epithelial cells. Collectively, these data suggest that some UPEC isolates may subvert macrophage anti-microbial pathways, and that host species differences may impact on intracellular UPEC survival.
Novel systems biology insights using antifibrotic approaches for diabetic kidney disease
Publisher: Informa UK Limited
Date: 2010
DOI: 10.1586/EEM.09.72
Abstract: Although several interventions slow the progression of diabetic nephropathy, current therapies do not halt progression completely. Recent preclinical studies suggested that pirfenidone (PFD) prevents fibrosis in various diseases, but the mechanisms underlying its antifibrotic action are incompletely understood. To explore the therapeutic potential of PFD, we studied the PFD-treated db/db diabetic mouse kidney by liquid chromatography-tandem mass spectrometry proteomics. A total of 21 proteins unique to PFD-treated diabetic kidneys were identified. Analysis of gene ontology and protein-protein interactions of these proteins suggested that PFD may regulate RNA translation. Two key proteins involved in mRNA translation initiation and elongation were further evaluated and found to be regulated by PFD at the level of phosphorylation. In conclusion, insights from combining proteomics and bioinformatics improve the likelihood of rapid advancement of novel clinical therapies focused on reducing inflammation and fibrosis for diabetic complications.
Rapid transcriptome and proteome profiling of a non‐model marine invertebrate, Bugula neritina
Publisher: Wiley
Date: 08-2010
Abstract: Non-model organisms represent the majority of life forms in our planet. However, the lack of genetic information hinders us to understand the unique biological phenomena in non-model organisms at the molecular level. In this study, we applied a tandem transcriptome and proteome profiling on a non-model marine fouling organism, Bugula neritina. Using a 454 pyrosequencing platform with the updated titanium reagents, we generated a total of 48M bp transcriptome data consisting of 131 450 high-quality reads. Of these, 122 650 reads (93%) were assembled to produce 6392 contigs with an average length of 538 bases and the remaining 8800 reads were singletons. Of the total 15 192 unigenes, 13 863 ORFs were predicated, of which 6917 were functionally annotated based on gene ontology and eukaryotic orthologous groups. Subsequent proteome analysis identified and quantified 882 proteins from B. neritina. These results would provide fundamental and important information for the subsequent studies of molecular mechanism in larval biology, development, antifouling research. Furthermore, we demonstrated, for the first time, the combined use of two high-throughput technologies as a powerful approach for accelerating the studies of non-model but otherwise important species.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Publisher: Elsevier BV
Date: 04-2010
MOESM7 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris
Publisher: Oxford University Press (OUP)
Date: 30-03-2022
DOI: 10.1093/G3JOURNAL/JKAC074
Abstract: The false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris. The initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62% completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific ergence and behaviors of the clownfish branch. Overall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.
Cytotoxicity and intracellular dissolution of nickel nanowires
Publisher: Figshare
Date: 2016
Characterization of piRNAs across postnatal development in mouse brain
Publisher: Springer Science and Business Media LLC
Date: 26-04-2016
DOI: 10.1038/SREP25039
Abstract: PIWI-interacting RNAs (piRNAs) are responsible for maintaining the genome stability by silencing retrotransposons in germline tissues– where piRNAs were first discovered and thought to be restricted. Recently, novel functions were reported for piRNAs in germline and somatic cells. Using deep sequencing of small RNAs and CAGE of postnatal development of mouse brain, we identified piRNAs only in adult mouse brain. These piRNAs have similar sequence length as those of MILI-bound piRNAs. In addition, we predicted novel candidate regulators and putative targets of adult brain piRNAs.
Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro
Publisher: Springer Science and Business Media LLC
Date: 09-03-2017
The evolution of ultraconserved elements with different phylogenetic origins
Publisher: Springer Science and Business Media LLC
Date: 2012
Mouse neutrophilic granulocytes express mRNA encoding the macrophage colony-stimulating factor receptor (CSF-1R) as well as many other macrophage-specific transcripts and can transdifferentiate into macrophages in vitro in response to CSF-1
Publisher: Oxford University Press (OUP)
Date: 16-04-2007
DOI: 10.1189/JLB.1206713
Abstract: The differentiation of macrophages from their progenitors is controlled by macrophage colony-stimulating factor (CSF-1), which binds to a receptor (CSF-1R) encoded by the c-fms proto-oncogene. We have previously used the promoter region of the CSF-1R gene to direct expression of an enhanced green fluorescent protein (EGFP) reporter gene to resident macrophage populations in transgenic mice. In this paper, we show that the EGFP reporter is also expressed in all granulocytes detected with the Gr-1 antibody, which binds to Ly-6C and Ly-6G or with a Ly-6G-specific antibody. Transgene expression reflects the presence of CSF-1R mRNA but not CSF-1R protein. The same pattern is observed with the macrophage-specific F4/80 marker. Based on these findings, we performed a comparative array profiling of highly purified granulocytes and macrophages. The patterns of mRNA expression differed predominantly through granulocyte-specific expression of a small subset of transcription factors (Egr1, HoxB7, STAT3), known abundant granulocyte proteins (e.g., S100A8, S100A9, neutrophil elastase), and specific receptors (fMLP, G-CSF). These findings suggested that appropriate stimuli might mediate rapid interconversion of the major myeloid cell types, for ex le, in inflammation. In keeping with this hypothesis, we showed that purified Ly-6G-positive granulocytes express CSF-1R after overnight culture and can subsequently differentiate to form F4/80-positive macrophages in response to CSF-1.
Bacterial community profiles in low microbial abundance sponges
Publisher: Oxford University Press (OUP)
Date: 04-09-2012
DOI: 10.1111/J.1574-6941.2012.01467.X
Abstract: It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either 'low microbial abundance' (LMA) or 'high microbial abundance' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level ersity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community.
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development
Publisher: Springer Science and Business Media LLC
Date: 10-10-2014
DOI: 10.1038/SREP06534
Unusual bilateral color pattern in a regal angelfish from the Red Sea
Publisher: Bulletin of Marine Science
Date: 2019
MOESM2 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Genome-wide analysis of mammalian promoter architecture and evolution
Publisher: Springer Science and Business Media LLC
Date: 28-04-2006
DOI: 10.1038/NG1789
Abstract: Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.
Publisher: Springer Science and Business Media LLC
Date: 08-04-2013
DOI: 10.1038/SREP01613
Probing SWATH-MS as a tool for proteome level quantification in a non-model fish
Publisher: Cold Spring Harbor Laboratory
Date: 23-02-2020
DOI: 10.1101/2020.02.23.946913
Abstract: Quantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data-independent acquisition (SWATH/DIA-MS), an accurate, sensitive, and reproducible method for analyzing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species-specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for non-model organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins (DEPs) under fish exposure to environmental stressors we validated the application and usefulness of these different spectral libraries. Successful identification of significant DEPs from different environmental exposures occurred using the library with a combination of DIA+DDA data as well as both tissue types. Further analysis revealed expected patterns of significantly upregulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a coral reef fish and for a non-model organism. It represents a useful guide for the future building of accurate spectral library references in non-model organisms allowing the discovery of ecologically relevant changes in the proteome.
Viral ecogenomics across the Porifera
Publisher: figshare
Date: 2020
Parents exposed to warming produce offspring lower in weight and condition
Publisher: Wiley
Date: 07-2022
DOI: 10.1002/ECE3.9044
Abstract: The parental environment can alter offspring phenotypes via the transfer of non‐genetic information. Parental effects may be viewed as an extension of (within‐generation) phenotypic plasticity. Smaller size, poorer physical condition, and skewed sex ratios are common responses of organisms to global warming, yet whether parental effects alleviate, exacerbate, or have no impact on these responses has not been widely tested. Further, the relative non‐genetic influence of mothers and fathers and ontogenetic timing of parental exposure to warming on offspring phenotypes is poorly understood. Here, we tested how maternal, paternal, and biparental exposure of a coral reef fish ( Acanthochromis polyacanthus ) to elevated temperature (+1.5°C) at different ontogenetic stages (development vs reproduction) influences offspring length, weight, condition, and sex. Fish were reared across two generations in present‐day and projected ocean warming in a full factorial design. As expected, offspring of parents exposed to present‐day control temperature that were reared in warmer water were shorter than their siblings reared in control temperature however, within‐generation plasticity allowed maintenance of weight, resulting in a higher body condition. Parental exposure to warming, irrespective of ontogenetic timing and sex, resulted in decreased weight and condition in all offspring rearing temperatures. By contrast, offspring sex ratios were not strongly influenced by their rearing temperature or that of their parents. Together, our results reveal that phenotypic plasticity may help coral reef fishes maintain performance in a warm ocean within a generation, but could exacerbate the negative effects of warming between generations, regardless of when mothers and fathers are exposed to warming. Alternatively, the multigenerational impact on offspring weight and condition may be a necessary cost to adapt metabolism to increasing temperatures. This research highlights the importance of examining phenotypic plasticity within and between generations across a range of traits to accurately predict how organisms will respond to climate change.
Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change
Publisher: The Royal Society
Date: 28-01-2019
Abstract: How populations and species respond to modified environmental conditions is critical to their persistence both now and into the future, particularly given the increasing pace of environmental change. The process of adaptation to novel environmental conditions can occur via two mechanisms: (1) the expression of phenotypic plasticity (the ability of one genotype to express varying phenotypes when exposed to different environmental conditions), and (2) evolution via selection for particular phenotypes, resulting in the modification of genetic variation in the population. Plasticity, because it acts at the level of the in idual, is often hailed as a rapid-response mechanism that will enable organisms to adapt and survive in our rapidly changing world. But plasticity can also retard adaptation by shifting the distribution of phenotypes in the population, shielding it from natural selection. In addition to which, not all plastic responses are adaptive—now well-documented in cases of ecological traps. In this theme issue, we aim to present a considered view of plasticity and the role it could play in facilitating or hindering adaption to environmental change. This introduction provides a re-examination of our current understanding of the role of phenotypic plasticity in adaptation and sets the theme issue's contributions in their broader context. Four key themes emerge: the need to measure plasticity across both space and time the importance of the past in predicting the future the importance of the link between plasticity and sexual selection and the need to understand more about the nature of selection on plasticity itself. We conclude by advocating the need for cross-disciplinary collaborations to settle the question of whether plasticity will promote or retard species' rates of adaptation to ever-more stressful environmental conditions. This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
Neuro-molecular characterization of fish cleaning interactions
Publisher: Cold Spring Harbor Laboratory
Date: 23-06-2021
DOI: 10.1101/2021.06.22.449532
Abstract: Coral reef fish exhibit a large variety of behaviours crucial for fitness and survival. The cleaner wrasse Labroides dimidiatus displays cognitive abilities during interspecific interactions by providing services of ectoparasite cleaning, thus serving as a good ex le to understand the processes of complex social behaviour. However, little is known about the molecular underpinnings of cooperative behaviour between L. dimidiatus and a potential client fish (Acanthurus leucosternon). Therefore, we investigated the molecular mechanisms in three regions of the brain (fore-, mid-, and hindbrain) during the interaction of these fishes. Here we show, using transcriptomics, that most of the transcriptional response in both species was regulated in the hindbrain and forebrain regions and that the interacting behaviour responses of L. dimidiatus involved immediate early gene alteration, dopaminergic and glutamatergic pathways, the expression of neurohormones (such as isotocin) and steroids (e.g. progesterone and estrogen). In contrast, in the client, fewer molecular alterations were found, mostly involving pituitary hormone responses. The particular pathways found suggested learning and memory processes in the cleaner wrasse, while the client indicated stress relief.
Proteomic Changes Associated with Successive Reproductive Periods in Male Polychaetous Neanthes arenaceodentata
Publisher: Springer Science and Business Media LLC
Date: 04-09-2015
DOI: 10.1038/SREP13561
Abstract: The polychaetous annelid Neanthes acuminata complex has a widespread distribution, with the California population referred to as N. arenaceodentata . The reproductive pattern in this complex is unique, in that the female reproduces once and then dies, whereas the male can reproduce up to nine times. The male incubates the embryos until the larvae leave the male’s tube 21–28 days later and commences feeding. Reproductive success and protein expression patterns were measured over the nine reproductive periods. The percent success of the male in producing juveniles increased during the first three reproductive periods and then decreased, but the number of juveniles produced was similar through all nine periods. iTRAQ based quantitative proteomics were used to analyze the dynamics of protein expression patterns. The expression patterns of several proteins were found to be altered. The abundant expression of muscular and contractile proteins may have affected body weight and reproductive success. Sperm have never been observed fertilization occurs within the parent’s tube. Proteins associated with sperm maturation and fertilization were identified, including ATPase, clathrin, peroxiredoxins and enolase, which may provide clues to the molecular mechanisms enabling males to reproduce multiple times.
Transcriptomic responses in the nervous system and correlated behavioural changes of a cephalopod exposed to ocean acidification
Publisher: Authorea, Inc.
Date: 31-07-2023
DOI: 10.22541/AU.169052790.09398364/V2
Abstract: The nervous system is central to coordinating behavioural responses to environmental change, likely including ocean acidification (OA). However, a clear understanding of neurobiological responses to OA is lacking, especially for marine invertebrates. We evaluated the transcriptomic response of the central nervous system (CNS) and eyes of the two-toned pygmy squid ( Idiosepius pygmaeus ) to OA conditions, using a de novo transcriptome assembly created with long read PacBio ISO-sequencing data. We then correlated patterns of gene expression with CO treatment levels and OA-affected behaviours in the same in iduals. OA induced transcriptomic responses within the nervous system related to various different types of neurotransmission, neuroplasticity, immune function and oxidative stress. These molecular changes may contribute to OA-induced behavioural changes, as suggested by correlations between gene expression profiles, CO treatment and OA-affected behaviours. This study provides the first molecular insights into the neurobiological effects of OA on a cephalopod and correlates molecular changes with whole animal behavioural responses, helping to bridge the gap in our knowledge between environmental change and animal responses.
Quantitative Proteomics Study of Larval Settlement in the Barnacle Balanus amphitrite
Publisher: Public Library of Science (PLoS)
Date: 13-02-2014
Transcriptomic responses in the nervous system and correlated behavioural changes of a cephalopod exposed to ocean acidification
Publisher: Authorea, Inc.
Date: 28-07-2023
DOI: 10.22541/AU.169052790.09398364/V1
Abstract: The nervous system is central to coordinating behavioural responses to environmental change, likely including ocean acidification (OA). However, a clear understanding of neurobiological responses to OA is lacking, especially for marine invertebrates. We evaluated the transcriptomic response of the central nervous system (CNS) and eyes of the two-toned pygmy squid ( Idiosepius pygmaeus ) to OA conditions, using a de novo transcriptome assembly created with long read PacBio ISO-sequencing data. We then correlated patterns of gene expression with CO treatment levels and OA-affected behaviours in the same in iduals. OA induced transcriptomic responses within the nervous system related to various different types of neurotransmission, neuroplasticity, immune function and oxidative stress. These molecular changes may contribute to OA-induced behavioural changes, as suggested by correlations between gene expression profiles, CO treatment and OA-affected behaviours. This study provides the first molecular insights into the neurobiological effects of OA on a cephalopod and correlates molecular changes with whole animal behavioural responses, helping to bridge the gap in our knowledge between environmental change and animal responses.
Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling
Publisher: Springer Science and Business Media LLC
Date: 31-10-2016
DOI: 10.1038/SREP35860
Abstract: Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.
Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis
Publisher: Springer Science and Business Media LLC
Date: 17-10-2016
DOI: 10.1038/SREP35461
Abstract: Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.
Sex and time specific parental effects of warming on reproduction and offspring quality in a coral reef fish.
Publisher: Wiley
Date: 13-01-2021
DOI: 10.1111/EVA.13187
Abstract: Global warming can disrupt reproduction or lead to fewer and poorer quality offspring, owing to the thermally sensitive nature of reproductive physiology. However, phenotypic plasticity may enable some animals to adjust the thermal sensitivity of reproduction to maintain performance in warmer conditions. Whether elevated temperature affects reproduction may depend on the timing of exposure to warming and the sex of the parent exposed. We exposed male and female coral reef damselfish ( Acanthochromis polyacanthus ) during development, reproduction or both life stages to an elevated temperature (+1.5°C) consistent with projected ocean warming and measured reproductive output and newly hatched offspring performance relative to pairs reared in a present‐day control temperature. We found female development in elevated temperature increased the probability of breeding, but reproduction ceased if warming continued to the reproductive stage, irrespective of the male's developmental experience. Females that developed in warmer conditions, but reproduced in control conditions, also produced larger eggs and hatchlings with greater yolk reserves. By contrast, male development or pairs reproducing in higher temperature produced fewer and poorer quality offspring. Such changes may be due to alterations in sex hormones or an endocrine stress response. In nature, this could mean female fish developing during a marine heatwave may have enhanced reproduction and produce higher quality offspring compared with females developing in a year of usual thermal conditions. However, male development during a heatwave would likely result in reduced reproductive output. Furthermore, the lack of reproduction from an average increase in temperature could lead to population decline. Our results demonstrate how the timing of exposure differentially influences females and males and how this translates to effects on reproduction and population sustainability in a warming world.
A genomic view of the reef-building coral Porites lutea and its microbial symbionts
Publisher: Springer Science and Business Media LLC
Date: 23-09-2019
DOI: 10.1038/S41564-019-0532-4
Abstract: Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change
Transcriptional network dynamics in macrophage activation
Publisher: Elsevier BV
Date: 08-2006
DOI: 10.1016/J.YGENO.2006.03.022
Abstract: Transcriptional regulatory networks govern cell differentiation and the cellular response to external stimuli. However, mammalian model systems have not yet been accessible for network analysis. Here, we present a genome-wide network analysis of the transcriptional regulation underlying the mouse macrophage response to bacterial lipopolysaccharide (LPS). Key to uncovering the network structure is our combination of time-series cap analysis of gene expression with in silico prediction of transcription factor binding sites. By integrating microarray and qPCR time-series expression data with a promoter analysis, we find dynamic subnetworks that describe how signaling pathways change dynamically during the progress of the macrophage LPS response, thus defining regulatory modules characteristic of the inflammatory response. In particular, our integrative analysis enabled us to suggest novel roles for the transcription factors ATF-3 and NRF-2 during the inflammatory response. We believe that our system approach presented here is applicable to understanding cellular differentiation in higher eukaryotes.
Generation of diversity in the innate immune system: Macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes
Publisher: The American Association of Immunologists
Date: 2002
DOI: 10.4049/JIMMUNOL.168.1.44
Abstract: Microbial products such as LPS stimulate macrophages to produce a wide ersity of inducible gene products needed for immediate host defense and priming of an appropriate acquired immune response. In this study, we have examined LPS-inducible gene expression in subclones of a mouse macrophage cell line, RAW264, using cDNA microarrays. Even archetypal target genes such as TNF-α were not induced in all subclones, and there was no absolute correlation between expression of pairs of genes. Nevertheless, the array analysis revealed clusters of genes that were more likely to be coexpressed. RAW264 cells stably transfected with luciferase reporter genes driven by LPS-responsive promoters revealed the same kind of clonal heterogeneity. The results indicate that each LPS-inducible gene has its own inherent probability of activation in response to LPS.
MOESM1 of Semi-automated quantification of living cells with internalized nanostructures
Publisher: figshare
Date: 2019
Timing specific parental effects of ocean warming in a coral reef fish
Publisher: Cold Spring Harbor Laboratory
Date: 29-09-2023
The epigenetic landscape of transgenerational acclimation to ocean warming
Publisher: Springer Science and Business Media LLC
Date: 30-04-2018
The JNK are important for development and survival of macrophages
Publisher: The American Association of Immunologists
Date: 15-02-2006
DOI: 10.4049/JIMMUNOL.176.4.2219
Abstract: We report in this study that activation of the JNK by the growth factor, CSF-1 is critical for macrophage development, proliferation, and survival. Inhibition of JNK with two distinct classes of inhibitors, the pharmacological agent SP600125, or the peptide D-JNKI1 resulted in cell cycle inhibition with an arrest at the G2/M transition and subsequent apoptosis. JNK inhibition resulted in decreased expression of CSF-1R (c-fms) and Bcl-xL mRNA in mature macrophages and repressed CSF-1-dependent differentiation of bone marrow cells to macrophages. Macrophage sensitivity to JNK inhibitors may be linked to phosphorylation of the PU.1 transcription factor. Inhibition of JNK disrupted PU.1 binding to an element in the c-fms gene promoter and decreased promoter activity. Promoter activity could be restored by overexpression of PU.1. A comparison of expression profiles of macrophages with 22 other tissue types showed that genes that signal JNK activation downstream of tyrosine kinase receptors, such as focal adhesion kinase, Nck-interacting kinase, and Rac1 and scaffold proteins are highly expressed in macrophages relative to other tissues. This pattern of expression may underlie the novel role of JNK in macrophages.
Poster: Observing change in crowded data sets in 3D space - Visualizing gene expression in human tissues
Publisher: IEEE
Date: 03-2013
Highlighting nonlinear patterns in population genetics datasets
Publisher: Springer Science and Business Media LLC
Date: 30-01-2015
DOI: 10.1038/SREP08140
Abstract: Detecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate in iduals into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE's ability to better capture the phylogenetic signal in the s les, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.
Systems biology of transcription control in macrophages
Publisher: Wiley
Date: 15-11-2007
DOI: 10.1002/BIES.20683
Abstract: The study of the mammalian immune system offers many advantages to systems biologists. The cellular components of the mammalian immune system are experimentally tractable they can be isolated or differentiated from in vivo and ex vivo sources and have an essential role in health and disease. For these reasons, the major effectors cells of the innate immune system, macrophages, have been a particular focus in international genome and transcriptome consortia. Genome-scale analysis of the transcriptome, and transcription initiation has enabled the construction of predictive models of transcription control in macrophages that identify the points of control (the major nodes of networks) and the ways in which they interact.
Methods matter in repeating ocean acidification studies.
Publisher: Springer Science and Business Media LLC
Date: 21-10-2020
Questing for Circadian Dependence in ST-Segment–Elevation Acute Myocardial Infarction
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 10-05-2013
DOI: 10.1161/CIRCRESAHA.112.300778
Abstract: Four monocentric studies reported that circadian rhythms can affect left ventricular infarct size after ST-segment–elevation acute myocardial infarction (STEMI). To further validate the circadian dependence of infarct size after STEMI in a multicentric and multiethnic population. We analyzed a prospective cohort of subjects with first STEMI from the First Acute Myocardial Infarction study that enrolled 1099 patients (ischemic time hours) in Italy, Scotland, and China. We confirmed a circadian variation of STEMI incidence with an increased morning incidence (from 6:00 am till noon). We investigated the presence of circadian dependence of infarct size plotting the peak creatine kinase against time onset of ischemia. In addition, we studied the patients from the 3 countries separately, including 624 Italians all patients were treated with percutaneous coronary intervention. We adopted several levels of analysis with different inclusion criteria consistent with previous studies. In all the analyses, we did not find a clear-cut circadian dependence of infarct size after STEMI. Although the circadian dependence of infarct size supported by previous studies poses an intriguing hypothesis, we were unable to converge toward their conclusions in a multicentric and multiethnic setting. Parameters that vary as a function of latitude could potentially obscure the circadian variations observed in monocentric studies. We believe that, to assess whether circadian rhythms can affect the infarct size, future study design should not only include larger s les but also aim to untangle the molecular time–dynamic mechanisms underlying such a relation.
Molecular basis of parental contributions to the behavioural tolerance of elevated pCO 2 in a coral reef fish
Publisher: The Royal Society
Date: 08-12-2021
Abstract: Knowledge of adaptive potential is crucial to predicting the impacts of ocean acidification (OA) on marine organisms. In the spiny damselfish, Acanthochromis polyacanthus , in idual variation in behavioural tolerance to elevated pCO 2 has been observed and is associated with offspring gene expression patterns in the brain. However, the maternal and paternal contributions of this variation are unknown. To investigate parental influence of behavioural pCO 2 tolerance, we crossed pCO 2 -tolerant fathers with pCO 2 -sensitive mothers and vice versa, reared their offspring at control and elevated pCO 2 levels, and compared the juveniles' brain transcriptional programme. We identified a large influence of parental phenotype on expression patterns of offspring, irrespective of environmental conditions. Circadian rhythm genes, associated with a tolerant parental phenotype, were uniquely expressed in tolerant mother offspring, while tolerant fathers had a greater role in expression of genes associated with histone binding. Expression changes in genes associated with neural plasticity were identified in both offspring types: the maternal line had a greater effect on genes related to neuron growth while paternal influence impacted the expression of synaptic development genes. Our results confirm cellular mechanisms involved in responses to varying lengths of OA exposure, while highlighting the parental phenotype's influence on offspring molecular phenotype.
An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish
Publisher: Springer Science and Business Media LLC
Date: 18-12-2017
DOI: 10.1038/S41559-017-0428-8
Abstract: The impacts of ocean acidification will depend on the ability of marine organisms to tolerate, acclimate and eventually adapt to changes in ocean chemistry. Here, we use a unique transgenerational experiment to determine the molecular response of a coral reef fish to short-term, developmental and transgenerational exposure to elevated CO
Cytotoxic effects of nickel nanowires in human fibroblasts
Publisher: Elsevier BV
Date: 2016
A promoter-level mammalian expression atlas
Publisher: Springer Science and Business Media LLC
Date: 03-2014
DOI: 10.1038/NATURE13182
The sponge microbiome project
Publisher: Oxford University Press (OUP)
Date: 16-08-2017
Novel polymorphic microsatellite markers developed for a common reef sponge, Stylissa carteri
Publisher: Springer Science and Business Media LLC
Date: 04-04-2013
The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change
Publisher: Frontiers Media SA
Date: 2015
Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
Publisher: Cold Spring Harbor Laboratory
Date: 06-2003
DOI: 10.1101/GR.949803
Abstract: Zinc-finger-containing proteins can be classified into evolutionary and functionally ergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by cysteines and histidines. The zinc finger domain defines one of the largest protein superfamilies in mammalian genomes different conserved zinc finger domains are listed in InterPro (www.ebi.ac.uk/InterPro). Zinc finger proteins can bind to DNA, RNA, other proteins, or lipids as a modular domain in combination with other conserved structures. Owing to this combinatorial ersity, different members of zinc finger superfamilies contribute to many distinct cellular processes, including transcriptional regulation, mRNA stability and processing, and protein turnover. Accordingly, mutations of zinc finger genes lead to aberrations in a broad spectrum of biological processes such as development, differentiation, apoptosis, and immunological responses. This study provides the first comprehensive classification of zinc finger proteins in a mammalian transcriptome. Specific detailed analysis of the SP/Krüppel-like factors and the E3 ubiquitin-ligase RING-H2 families illustrates the importance of such an analysis for a more comprehensive functional classification of large protein families. We describe the characterization of a new family of C2H2 zinc-finger-containing proteins and a new conserved domain characteristic of this family, the identification and characterization of Sp8, a new member of the Sp family of transcriptional regulators, and the identification of five new RING-H2 proteins.
Species-specific molecular responses of wild coral reef fishes during a marine heatwave
Publisher: American Association for the Advancement of Science (AAAS)
Date: 20-03-2020
Abstract: Molecular responses of fishes to a heatwave are species specific and do not concur with measures of oxygen uptake in captivity.
First Proteome of the Egg Perivitelline Fluid of a Freshwater Gastropod with Aerial Oviposition
Publisher: American Chemical Society (ACS)
Date: 13-07-2012
DOI: 10.1021/PR3003613
Abstract: Pomacea canaliculata is a freshwater snail that deposits eggs on solid substrates above the water surface. Previous studies have emphasized the nutritional and protective functions of the three most abundant perivitelline fluid (PVF) protein complexes (ovorubin, PV2, and PV3) during its embryonic development, but little is known about the structure and function of other less abundant proteins. Using 2-DE, SDS-PAGE, MALDI TOF/TOF, and LC-MS/MS, we identified 59 proteins from the PVF of P. canaliculata, among which 19 are novel. KEGG analysis showed that the functions of the majority of these proteins are "unknown" (n=34), "environmental information processing" (10), 9 of which are related to innate immunity, and "metabolism" (7). Suppressive subtractive hybridization revealed 21 PVF genes to be specific to the albumen gland, indicating this organ is the origin of many of the PVF proteins. Further, the 3 ovorubin subunits were identified with 30.2-35.0% identity among them, indicating their common origin but ancient duplications. Characterization of the PVF proteome has opened the gate for further studies aiming to understand the evolution of the novel proteins and their contribution to the switch to aerial oviposition.
Interferon-γ: an overview of signals, mechanisms and functions
Publisher: Oxford University Press (OUP)
Date: 02-10-2003
DOI: 10.1189/JLB.0603252
Abstract: Interferon-γ (IFN-γ) coordinates a erse array of cellular programs through transcriptional regulation of immunologically relevant genes. This article reviews the current understanding of IFN-γ ligand, receptor, ignal transduction, and cellular effects with a focus on macrophage responses and to a lesser extent, responses from other cell types that influence macrophage function during infection. The current model for IFN-γ signal transduction is discussed, as well as signal regulation and factors conferring signal specificity. Cellular effects of IFN-γ are described, including up-regulation of pathogen recognition, antigen processing and presentation, the antiviral state, inhibition of cellular proliferation and effects on apoptosis, activation of microbicidal effector functions, immunomodulation, and leukocyte trafficking. In addition, integration of signaling and response with other cytokines and pathogen-associated molecular patterns, such as tumor necrosis factor-α, interleukin-4, type I IFNs, and lipopolysaccharide are discussed.
Actinomycetes from Red Sea Sponges: Sources for Chemical and Phylogenetic Diversity
Publisher: MDPI AG
Date: 12-05-2014
DOI: 10.3390/MD12052771
The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome
Publisher: Public Library of Science (PLoS)
Date: 18-12-2015
Genetic control of the innate immune response
Publisher: Springer Science and Business Media LLC
Date: 2003
Histone deacetylase inhibitors decrease Toll‐like receptor‐mediated activation of proinflammatory gene expression by impairing transcription factor recruitment
Publisher: Wiley
Date: 19-10-2007
The chromosome-scale genome assembly of the yellowtail clownfishAmphiprion clarkiiprovides insights into the melanic pigmentation of anemonefish
Publisher: Oxford University Press (OUP)
Date: 10-01-2023
DOI: 10.1093/G3JOURNAL/JKAD002
Abstract: Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.
Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system
Publisher: Springer Science and Business Media LLC
Date: 03-2005
DOI: 10.1007/S10969-005-0462-7
Abstract: We investigated the parallel production in medium throughput of mouse proteins, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. The methods were scaled up to allow the simultaneous processing of tens or hundreds of protein s les. Scale-up was achieved in two stages. In an initial study, 30 targets were processed manually but with common protocols for all targets. In the second study, these protocols were applied to 96 target proteins that were processed in an automated manner. The success rates at each stage of the study were similar for both the manual and automated approaches. Overall, 15 of the selected 126 target mouse genes (12%) yielded soluble protein products in a bacterial expression system. This success rate compares favourably with other protein screening projects, particularly for eukaryotic proteins, and could be further improved by modifications at the cloning step.
Cytotoxicity and intracellular dissolution of nickel nanowires
Publisher: Figshare
Date: 2015
Rapid evolution fuels transcriptional plasticity to ocean acidification
Publisher: Wiley
Date: 03-03-2022
DOI: 10.1111/GCB.16119
Abstract: Ocean acidification (OA) is postulated to affect the physiology, behavior, and life‐history of marine species, but potential for acclimation or adaptation to elevated p CO 2 in wild populations remains largely untested. We measured brain transcriptomes of six coral reef fish species at a natural volcanic CO 2 seep and an adjacent control reef in Papua New Guinea. We show that elevated p CO 2 induced common molecular responses related to circadian rhythm and immune system but different magnitudes of molecular response across the six species. Notably, elevated transcriptional plasticity was associated with core circadian genes affecting the regulation of intracellular pH and neural activity in Acanthochromis polyacanthus . Gene expression patterns were reversible in this species as evidenced upon reduction of CO 2 following a natural storm‐event. Compared with other species, Ac . polyacanthus has a more rapid evolutionary rate and more positively selected genes in key functions under the influence of elevated CO 2 , thus fueling increased transcriptional plasticity. Our study reveals the basis to variable gene expression changes across species, with some species possessing evolved molecular toolkits to cope with future OA.
Pirfenidone is renoprotective in diabetic kidney disease
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 08-2009
Research priorities for the sustainability of coral-rich western Pacific seascapes
Publisher: Springer Science and Business Media LLC
Date: 21-04-2023
DOI: 10.1007/S10113-023-02051-0
Abstract: Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 (‘Life below Water’) of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia–Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation elucidating drivers and mechanisms of change understanding how seascape functions and services are produced, and how people depend on them costs, benefits, and trade-offs to people in changing seascapes improving seascape technologies and practices learning to govern and manage seascapes for all sustainable use, justice, and human well-being bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.
An Inflammatory Role for the Mammalian Carboxypeptidase Inhibitor Latexin: Relationship to Cystatins and the Tumor Suppressor TIG1
Publisher: Elsevier BV
Date: 02-2005
DOI: 10.1016/J.STR.2004.12.013
Abstract: Latexin, the only known mammalian carboxypeptidase inhibitor, has no detectable sequence similarity with plant and parasite inhibitors, but it is related to a human putative tumor suppressor protein, TIG1. Latexin is expressed in the developing brain, and we find that it plays a role in inflammation, as it is expressed at high levels and is inducible in macrophages in concert with other protease inhibitors and potential protease targets. The crystal structure of mouse latexin, solved at 1.83 A resolution, shows no structural relationship with other carboxypeptidase inhibitors. Furthermore, despite a lack of detectable sequence duplication, the structure incorporates two topologically analogous domains related by pseudo two-fold symmetry. Surprisingly, these domains share a cystatin fold architecture found in proteins that inhibit cysteine proteases, suggesting an evolutionary and possibly functional relationship. The structure of the tumor suppressor protein TIG1 was modeled, revealing its putative membrane binding surface.
Brain transcriptome of gobies inhabiting natural CO2 seeps reveal acclimation strategies to long-term acidification
Publisher: Cold Spring Harbor Laboratory
Date: 19-09-2022
DOI: 10.1101/2022.09.18.508416
Abstract: Ocean acidification (OA) is known to affect the physiology, survival, behaviour, and fitness of various fish species with repercussions at the population, community, and ecosystem levels. Some fish species, however, seem to acclimate rapidly to OA conditions and even thrive in acidified environments. The molecular mechanisms that enable species to successfully inhabit high CO 2 environments has not been fully elucidated especially in wild fish populations. Here, we used the natural CO 2 seep in Vulcano Island, Italy to study the effects of elevated CO 2 exposure on the brain transcriptome of the anemone goby, a species with high population density in the CO 2 seep and investigate their potential for acclimation. When compared to fish from environments with ambient CO 2 , gobies living in the CO 2 seep showed differences in expression of transcripts involved in ion transport and pH homeostasis, cellular stress, immune response, circadian rhythm, and metabolism. We also found evidence of potential adaptive mechanisms to restore the functioning of GABAergic pathways, whose activity can be affected by exposure to elevated CO 2 levels. Our findings indicate that gobies living in the CO 2 seep may be capable of mitigating CO 2 induced oxidative stress and maintaining physiological pH while meeting the consequent increased energetic costs. The conspicuous difference in expression of core circadian rhythm transcripts could provide an adaptive advantage by increasing flexibility of physiological processes in elevated CO 2 conditions thereby facilitating acclimation. Our results show potential molecular processes of acclimation to elevated CO 2 in gobies enabling them to thrive in the acidified waters of Vulcano Island.
Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle
Publisher: Springer Science and Business Media LLC
Date: 22-12-2016
DOI: 10.1038/SREP39734
Abstract: Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium , possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium .
Exploring the genetics underlying autoimmune diseases with network analysis and link prediction
Publisher: IEEE
Date: 02-2014
Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors
Publisher: Wiley
Date: 17-03-2016
DOI: 10.1111/GCB.13249
Abstract: The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both in idual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.
Erratum: From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks
Publisher: Springer Science and Business Media LLC
Date: 21-07-2015
DOI: 10.1038/SREP09794
LPS regulates a set of genes in primary murine macrophages by antagonising CSF-1 action
Publisher: Elsevier BV
Date: 08-2005
DOI: 10.1016/J.IMBIO.2005.05.004
Abstract: We previously reported that bacterial products such as LPS and CpG DNA down-modulated cell surface levels of the Colony Stimulating Factor (CSF)-1 receptor (CSF-1R) on primary murine macrophages in an all-or-nothing manner. Here we show that the ability of bacterial products to down-modulate the CSF-1R rendered bone marrow-derived macrophages (BMM) unresponsive to CSF-1 as assessed by Akt and ERK1/2 phosphorylation. Using toll-like receptor (tlr)9 as a model CSF-1-repressed gene, we show that LPS induced tlr9 expression in BMM only when CSF-1 was present, suggesting that LPS relieves CSF-1-mediated inhibition to induce gene expression. Using cDNA microarrays, we identified a cluster of similarly CSF-1 repressed genes in BMM. By real time PCR we confirmed that the expression of a selection of these genes, including integral membrane protein 2B (itm2b), receptor activity-modifying protein 2 (r 2) and macrophage-specific gene 1 (mpg-1), were repressed by CSF-1 and were induced by LPS only in the presence of CSF-1. This pattern of gene regulation was also apparent in thioglycollate-elicited peritoneal macrophages (TEPM). LPS also counteracted CSF-1 action to induce mRNA expression of a number of transcription factors including interferon consensus sequence binding protein 1 (Icsbp1), suggesting that this mechanism leads to transcriptional reprogramming in macrophages. Since the majority of in vitro studies on macrophage biology do not include CSF-1, these genes represent a set of previously uncharacterised LPS-inducible genes. This study identifies a new mechanism of macrophage activation, in which LPS (and other toll-like receptor agonists) regulate gene expression by switching off the CSF-1R signal. This finding also provides a biological relevance to the well-documented ability of macrophage activators to down-modulate surface expression of the CSF-1R.
The effects of climate change on the ecology of fishes
Publisher: Public Library of Science (PLoS)
Date: 07-08-2023
DOI: 10.1371/JOURNAL.PCLM.0000258
Abstract: Ocean warming and acidification are set to reshuffle life on Earth and alter ecological processes that underpin the bio ersity, health, productivity, and resilience of ecosystems. Fishes contribute significantly to marine, estuarine, and freshwater species ersity and the functioning of marine ecosystems, and are not immune to climate change impacts. Whilst considerable effort has been placed on studying the effects of climate change on fishes, much emphasis has been placed on their (eco)physiology and at the organismal level. Fishes are affected by climate change through impacts at various levels of biological organisation and through a large variety of traits, making it difficult to make generalisations regarding fish responses to climate change. Here, we briefly review the current state of knowledge of climate change effects on fishes across a wide range of subfields of fish ecology and evaluate these effects at various scales of biological organisation (from genes to ecosystems). We argue that a more holistic synthesis of the various interconnected subfields of fish ecology and integration of responses at different levels of biological organisation are needed for a better understanding of how fishes and their populations and communities might respond or adapt to the multi-stressor effects of climate change. We postulate that studies using natural analogues of climate change, meta-analyses, advanced integrative modelling approaches, and lessons learned from past extreme climate events could help reveal some general patterns of climate change impacts on fishes that are valuable for management and conservation approaches. Whilst these might not reveal many of the underlying mechanisms responsible for observed bio ersity and community change, their insights are useful to help create better climate adaptation strategies for their preservation in a rapidly changing ocean.
Methamphetamine abuse affects gene expression in brain-derived microglia of SIV-infected macaques to enhance inflammation and promote virus targets
Publisher: Springer Science and Business Media LLC
Date: 23-04-2016
Functionalization of Magnetic Nanowires for Active Targeting and Enhanced Cell-Killing Efficacy
Publisher: American Chemical Society (ACS)
Date: 08-07-2020
Abstract: Conventional chemotherapy and radiation therapy are often insufficient in eliminating cancer and are accompanied by severe side effects, due to a lack in the specificity of their targeting. Magnetic iron nanowires have made a great contribution to the nanomedicine field because of their low toxicity and ease of manipulation with the magnetic field. Recently, they have been used in magnetic resonance imaging and wireless magnetomechanical and photothermal treatments. The addition of active targeting moieties to these nanowires thus creates a multifunctional tool that can boost therapeutic efficacies through the combination of different treatments toward a specific target. Colon cancer is the third most commonly occurring cancer, and 90 ± 2.5% of colon cancer cells express the glycoprotein CD44. Iron nanowires with an iron oxide surface are biocompatible, multifunctional materials that can be controlled by magnetic fields and heated by laser irradiation. Here, they were functionalized with anti-CD44 antibodies and used in a combination therapy that included magnetomechanical and photothermal treatments on colon cancer cells. The functionalization resulted in a 3-fold increase of nanowire internalization in colon cancer cells compared to control cells and did not affect the antigenicity and magnetic properties. It also increased the efficacy of killing from 35 ± 1% to more than 71 ± 2%, showing that the combination therapy was more effective than in idual therapies alone.
Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes
Publisher: Oxford University Press (OUP)
Date: 04-02-0001
DOI: 10.1093/BIOINFORMATICS/BTQ376
Abstract: Motivation: Nonlinear small datasets, which are characterized by low numbers of s les and very high numbers of measures, occur frequently in computational biology, and pose problems in their investigation. Unsupervised hybrid-two-phase (H2P) procedures—specifically dimension reduction (DR), coupled with clustering—provide valuable assistance, not only for unsupervised data classification, but also for visualization of the patterns hidden in high-dimensional feature space. Methods: ‘Minimum Curvilinearity’ (MC) is a principle that—for small datasets—suggests the approximation of curvilinear s le distances in the feature space by pair-wise distances over their minimum spanning tree (MST), and thus avoids the introduction of any tuning parameter. MC is used to design two novel forms of nonlinear machine learning (NML): Minimum Curvilinear embedding (MCE) for DR, and Minimum Curvilinear affinity propagation (MCAP) for clustering. Results: Compared with several other unsupervised and supervised algorithms, MCE and MCAP, whether in idually or combined in H2P, overcome the limits of classical approaches. High performance was attained in the visualization and classification of: (i) pain patients (proteomic measurements) in peripheral neuropathy (ii) human organ tissues (genomic transcription factor measurements) on the basis of their embryological origin. Conclusion: MC provides a valuable framework to estimate nonlinear distances in small datasets. Its extension to large datasets is prefigured for novel NMLs. Classification of neuropathic pain by proteomic profiles offers new insights for future molecular and systems biology characterization of pain. Improvements in tissue embryological classification refine results obtained in an earlier study, and suggest a possible reinterpretation of skin attribution as mesodermal. Availability: ite/carlovittoriocannistraci/home Contact: kalokagathos.agon@gmail.com massimo.alessio@hsr.it Supplementary information: Supplementary data are available at Bioinformatics online.
Selective phosphorylation during early macrophage differentiation
Publisher: Wiley
Date: 15-09-2015
Abstract: The differentiation of macrophages from monocytes is a tightly controlled and complex biological process. Although numerous studies have been conducted using biochemical approaches or global gene rotein profiling, the mechanisms of the early stages of differentiation remain unclear. Here we used SILAC-based quantitative proteomics approach to perform temporal phosphoproteome profiling of early macrophage differentiation. We identified a large set of phosphoproteins and grouped them as PMA-regulated and non-regulated phosphoproteins in the early stages of differentiation. Further analysis of the PMA-regulated phosphoproteins revealed that transcriptional suppression, cytoskeletal reorganization and cell adhesion were among the most significantly activated pathways. Some key involved regulators of these pathways are mTOR, MYB, STAT1 and CTNNB. Moreover, we were able to classify the roles and activities of several transcriptional factors during different differentiation stages and found that E2F is likely to be an important regulator during the relatively late stages of differentiation. This study provides the first comprehensive picture of the dynamic phosphoproteome during myeloid cells differentiation, and identifies potential molecular targets in leukemic cells.
Cytotoxicity and intracellular dissolution of nickel nanowires
Publisher: Informa UK Limited
Date: 05-02-2016
DOI: 10.3109/17435390.2015.1132343
Abstract: The assessment of cytotoxicity of nanostructures is a fundamental step for their development as biomedical tools. As widely used nanostructures, nickel nanowires (Ni NWs) seem promising candidates for such applications. In this work, Ni NWs were synthesized and then characterized using vibrating s le magnetometry, energy dispersive X-Ray analysis, and electron microscopy. After exposure to the NWs, cytotoxicity was evaluated in terms of cell viability, cell membrane damage, and induced apoptosis/necrosis on the model human cell line HCT 116. The influence of NW to cell ratio (10:1 to 1000:1) and exposure times up to 72 hours was analyzed for Ni NWs of 5.4 μm in length, as well as for Ni ions. The results show that cytotoxicity markedly increases past 24 hours of incubation. Cellular uptake of NWs takes place through the phagocytosis pathway, with a fraction of the dose of NWs dissolved inside the cells. Cell death results from a combination of apoptosis and necrosis, where the latter is the outcome of the secondary necrosis pathway. The cytotoxicity of Ni ions and Ni NWs dissolution studies suggest a synergistic toxicity between NW aspect ratio and dissolved Ni, with the cytotoxic effects markedly increasing after 24 hours of incubation.
Molecular processes of transgenerational acclimation to a warming ocean
Publisher: Springer Science and Business Media LLC
Date: 20-07-2015
DOI: 10.1038/NCLIMATE2724
Transcriptome and Quantitative Proteome Analysis Reveals Molecular Processes Associated with Larval Metamorphosis in the Polychaete Pseudopolydora vexillosa
Publisher: American Chemical Society (ACS)
Date: 29-01-2013
DOI: 10.1021/PR3010088
Abstract: Larval growth of the polychaete worm Pseudopolydora vexillosa involves the formation of segment-specific structures. When larvae attain competency to settle, they discard swimming chaetae and secrete mucus. The larvae build tubes around themselves and metamorphose into benthic juveniles. Understanding the molecular processes, which regulate this complex and unique transition, remains a major challenge because of the limited molecular information available. To improve this situation, we conducted high-throughput RNA sequencing and quantitative proteome analysis of the larval stages of P. vexillosa. Based on gene ontology (GO) analysis, transcripts related to cellular and metabolic processes, binding, and catalytic activities were highly represented during larval-adult transition. Mitogen-activated protein kinase (MAPK), calcium-signaling, Wnt/β-catenin, and notch signaling metabolic pathways were enriched in transcriptome data. Quantitative proteomics identified 107 differentially expressed proteins in three distinct larval stages. Fourteen and 53 proteins exhibited specific differential expression during competency and metamorphosis, respectively. Dramatic up-regulation of proteins involved in signaling, metabolism, and cytoskeleton functions were found during the larval-juvenile transition. Several proteins involved in cell signaling, cytoskeleton and metabolism were up-regulated, whereas proteins related to transcription and oxidative phosphorylation were down-regulated during competency. The integration of high-throughput RNA sequencing and quantitative proteomics allowed a global scale analysis of larval transcripts roteins associated molecular processes in the metamorphosis of polychaete worms. Further, transcriptomic and proteomic insights provide a new direction to understand the fundamental mechanisms that regulate larval metamorphosis in polychaetes.
Unexpected high abundance of aragonite-forming Nanipora (Octocorallia: Helioporacea) at an acidified volcanic reef in southern Japan
Publisher: Springer Science and Business Media LLC
Date: 02-2021
GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater
Publisher: Oxford University Press (OUP)
Date: 10-11-2014
Abstract: The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary licon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the s les. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of in idual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.
Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea
Publisher: Wiley
Date: 20-08-2013
DOI: 10.1111/MEC.12365
Abstract: Marine sponges are generally classified as high microbial abundance (HMA) and low microbial abundance (LMA) species. Here, 16S rRNA licon sequencing was applied to investigate the ersity, specificity and transcriptional activity of microbes associated with an LMA sponge ( Stylissa carteri ), an HMA sponge ( Xestospongia testudinaria ) and sea water collected from the central Saudi Arabia coast of the Red Sea. Altogether, 887 068 denoised sequences were obtained, of which 806 661 sequences remained after quality control. This resulted in 1477 operational taxonomic units ( OTUs ) that were assigned to 27 microbial phyla. The microbial composition of S. carteri was more similar to that of sea water than to that of X. testudinaria , which is consistent with the observation that the sequence data set of S. carteri contained many more possibly sea water sequences (~24%) than the X. testudinaria data set (~6%). The most abundant OTUs were shared between all three sources ( S. carteri , X. testudinaria , sea water), while rare OTUs were unique to any given source. Despite this high degree of overlap, each sponge species contained its own specific microbiota. The X. testudinaria ‐specific bacterial taxa were similar to those already described for this species. A set of S. carteri ‐specific bacterial taxa related to Proteobacteria and Nitrospira was identified, which are likely permanently associated with S. carteri . The transcriptional activity of sponge‐associated microorganisms correlated well with their abundance. Quantitative PCR revealed the presence of Poribacteria, representing typical sponge symbionts, in both sponge species and in sea water however, low transcriptional activity in sea water suggested that Poribacteria are not active outside the host context.
Rapid adaptive responses to climate change in corals
Publisher: Springer Science and Business Media LLC
Date: 09-2017
DOI: 10.1038/NCLIMATE3374
Exploitation of genetic interaction network topology for the prediction of epistatic behavior
Publisher: Elsevier BV
Date: 10-2013
DOI: 10.1016/J.YGENO.2013.07.010
Abstract: Genetic interaction (GI) detection impacts the understanding of human disease and the ability to design personalized treatment. The mapping of every GI in most organisms is far from complete due to the combinatorial amount of gene deletions and knockdowns required. Computational techniques to predict new interactions based only on network topology have been developed in network science but never applied to GI networks. We show that topological prediction of GIs is possible with high precision and propose a graph dissimilarity index that is able to provide robust prediction in both dense and sparse networks. Computational prediction of GIs is a strong tool to aid high-throughput GI determination. The dissimilarity index we propose in this article is able to attain precise predictions that reduce the universe of candidate GIs to test in the lab.
Biofunctionalizing Magnetic Nanowires Toward Targeting and Killing Leukemia Cancer Cells
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 02-2019
A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response
Publisher: Proceedings of the National Academy of Sciences
Date: 26-02-2008
Abstract: Duplication of genes encoding transcription factors plays an essential role in driving phenotypic variation. Because regulation can occur at multiple levels, it is often difficult to discern how each duplicated factor achieves its regulatory specificity. In these cases, a “systems approach” may distinguish the role of each factor by integrating complementary large-scale measurements of the regulatory network. To explore such an approach, we integrate growth phenotypes, promoter binding profiles, and gene expression patterns to model the DNA damage response network controlled by the Yeast-specific AP-1 (YAP) family of transcription factors. This analysis reveals that YAP regulatory specificity is achieved by at least three mechanisms: ( i ) ergence of DNA-binding sequences into two subfamilies ( ii ) condition-specific combinatorial regulation by multiple Yap factors and ( iii ) interactions of Yap 1, 4, and 6 with chromatin remodeling proteins. Additional microarray experiments establish that Yap 4 and 6 regulate gene expression through interactions with the histone deacetylase, Hda1. The data further highlight differences among Yap paralogs in terms of their regulatory mode of action (activation vs. repression). This study suggests how other large TF families might be disentangled in the future.
Magnetic core–shell nanowires as MRI contrast agents for cell tracking
Publisher: Springer Science and Business Media LLC
Date: 12-03-2020
DOI: 10.1186/S12951-020-00597-3
Abstract: Identifying the precise location of cells and their migration dynamics is of utmost importance for achieving the therapeutic potential of cells after implantation into a host. Magnetic resonance imaging is a suitable, non-invasive technique for cell monitoring when used in combination with contrast agents. This work shows that nanowires with an iron core and an iron oxide shell are excellent materials for this application, due to their customizable magnetic properties and biocompatibility. The longitudinal and transverse magnetic relaxivities of the core–shell nanowires were evaluated at 1.5 T, revealing a high performance as T 2 contrast agents. Different levels of oxidation and various surface coatings were tested at 7 T. Their effects on the T 2 contrast were reflected in the tailored transverse relaxivities. Finally, the detection of nanowire-labeled breast cancer cells was demonstrated in T 2 -weighted images of cells implanted in both, in vitro in tissue-mimicking phantoms and in vivo in mouse brain. Labeling the cells with a nanowire concentration of 0.8 μg of Fe/mL allowed the detection of 25 cells/µL in vitro, diminishing the possibility of side effects. This performance enabled an efficient labelling for high-resolution cell detection after in vivo implantation (~ 10 nanowire-labeled cells) over a minimum of 40 days. Iron-iron oxide core–shell nanowires enabled the efficient and longitudinal cellular detection through magnetic resonance imaging acting as T 2 contrast agents. Combined with the possibility of magnetic guidance as well as triggering of cellular responses, for instance by the recently discovered strong photothermal response, opens the door to new horizons in cell therapy and make iron-iron oxide core–shell nanowires a promising theranostic platform.
Proteomic Responses to Ocean Acidification in the Brain of Juvenile Coral Reef Fish
Publisher: Frontiers Media SA
Date: 30-07-2020
Proteomics insights: proteins related to larval attachment and metamorphosis of marine invertebrates
Publisher: Frontiers Media SA
Date: 31-10-2014
An Integrated Systems Analysis Implicates EGR1 Downregulation in Simian Immunodeficiency Virus Encephalitis-Induced Neural Dysfunction
Publisher: Society for Neuroscience
Date: 07-10-2009
DOI: 10.1523/JNEUROSCI.3180-09.2009
Abstract: Human immunodeficiency virus (HIV)-associated dementia (HAD) is a syndrome occurring in HIV-infected patients with advanced disease that likely develops as a result of macrophage and microglial activation as well as other immune events triggered by virus in the central nervous system. The most relevant experimental model of HAD, rhesus macaques exhibiting simian immunodeficiency virus (SIV) encephalitis (SIVE), closely reproduces the human disease and has been successfully used to advance our understanding of mechanisms underlying HAD. In this study we integrate gene expression data from uninfected and SIV-infected hippoc us with a human protein interaction network and discover modules of genes whose expression patterns distinguish these two states, to facilitate identification of neuronal genes that may contribute to SIVE/HIV cognitive deficits. Using this approach we identify several downregulated candidate genes and select one, EGR1, a key molecule in hippoc us-related learning and memory, for further study. We show that EGR1 is downregulated in SIV-infected hippoc us and that it can be downregulated in differentiated human neuroblastoma cells by treatment with CCL8, a product of activated microglia. Integration of expression data with protein interaction data to discover discriminatory modules of interacting proteins can be usefully used to prioritize differentially expressed genes for further study. Investigation of EGR1, selected in this manner, indicates that its downregulation in SIVE may occur as a consequence of the host response to infection, leading to deficits in cognition.
Matching maternal and paternal experiences underpin molecular thermal acclimation
Publisher: Cold Spring Harbor Laboratory
Date: 02-10-2023
Proteomic profiling during the pre-competent to competent transition of the biofouling polychaeteHydroides elegans
Publisher: Informa UK Limited
Date: 05-09-2014
DOI: 10.1080/08927014.2014.951341
Abstract: The polychaete, Hydroides elegans, is a tube-building worm that is widely distributed in tropical and subtropical seas. It is a dominant fouling species and thus a major target organism in antifouling research. Here, the first high-throughput proteomic profiling of pre-competent and competent larvae of H. elegans is reported with the identification of 1,519 and 1,322 proteins, respectively. These proteins were associated with a variety of biological processes. However, a large proportion was involved in energy metabolism, redox homeostasis, and microtubule-based processes. A comparative analysis revealed 21 proteins that were differentially regulated in larvae approaching competency.
Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula
Publisher: Wiley
Date: 10-09-2018
The alternative splicing landscape of a coral reef fish during a marine heatwave
Publisher: Wiley
Date: 03-2022
DOI: 10.1002/ECE3.8738
Abstract: Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post‐transcriptional modification of pre‐RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS n = 40) genes during the onset of the heatwave (i.e., 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding, and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto‐protection and post‐damage recovery ( n = 26). Two‐thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A . polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.
Probing SWATH‐MS as a tool for proteome level quantification in a nonmodel fish
Publisher: Wiley
Date: 04-08-2020
Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Related Organisations
University Of California, San Diego
Location: United States of America
Okinawa Institute Of Science And Technology Graduate University
Location: Japan
Okinawa Institute Of Science And Technology School Corp And Graduate University
Location: Japan
King Abdullah University Of Science And Technology
Location: Saudi Arabia
Related Funding Activities
Discovery Projects - Grant ID: DP230101932
Start Date: 2023
End Date: 12-2025
Amount: $510,893.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP230100078
Start Date: 2023
End Date: 12-2025
Amount: $348,364.00
Funder: Australian Research Council
View Funded Activity