Antarctic Clam Laternula elliptica bulk RNAseq developmental stages
Ontology highlight
ABSTRACT:
ORGANISM(S): Laternula elliptica
SUBMITTER:
PROVIDER: S-BSST926 | biostudies-other |
SECONDARY ACCESSION(S): PRJNA803976
REPOSITORIES: biostudies-other
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Project description:The filter feeder clam Laternula elliptica is a key species in the Antarctic ecosystem. As a stenothermal benthic species, it has a poor capacity for adaptation to small temperature variations. Despite their ecological importance and sensitivity to climate change, studies on their microbiomes are lacking. The goal of this study was to characterize the bacterial communities of L. elliptica and the tissues variability of this microbiome to provide an initial insight of host-microbiota interactions. We investigated the diversity and taxonomic composition of bacterial communities of L. elliptica from five regions of the body using high-throughput 16S rRNA gene sequencing. The results showed that the microbiome of L. elliptica tended to differ from that of the surrounding seawater samples. However, there were no significant differences in the microbial composition between the body sites, and only two OTUs were present in all samples, being considered core microbiome (genus Moritella and Polaribacter). No significant differences were detected in diversity indexes among tissues (mean 626.85 for observed OTUs, 628.89 Chao1, 5.42 Shannon, and 0.87 Simpson). Rarefaction analysis revealed that most tissues reached a plateau of OTU number according to sample increase, with the exception of Siphon samples. Psychromonas and Psychrilyobacter were particularly abundant in L. elliptica whereas Fluviicola dominated seawater and siphons. Typical polar bacteria were Polaribacter, Shewanella, Colwellia, and Moritella. We detected the prevalence of pathogenic bacterial sequences, particularly in the family Arcobacteraceae, Pseudomonadaceae, and Mycoplasmataceae. The prokaryotic diversity was similar among tissues, as well as their taxonomic composition, suggesting a homogeneity of the microbiome along L. elliptica body. The Antarctic clam population can be used to monitor the impact of human activity in areas near Antarctic stations that discharge wastewater.
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2018-06-15 | GSE115796 | GEO
Project description:Heat shock protein 70 (designated Laternula elliptica Hsp70 (LEHsp70)) expression was investigated in an Antarctic mud clam to see whether or not the inducible heat shock response has been conserved throughout over 25 million years of adaptation to constant low environmental temperatures. LEHsp70 cDNA was cloned and sequenced from the Antarctic clam Laternula elliptica. We used degenerated primers designed in the highly conserved regions of Hsp to amplify the corresponding mRNA, and full-length cDNA was obtained by rapid amplification of cDNA ends (RACE). The full length of LEHsp70 cDNA was 2470 bp, with a 5' untranslated region (UTR) of 92 bp, a 3' UTR of 416 bp, and an open reading frame (ORF) of 1962 bp encoding a polypeptide of 653 amino acids with an estimated molecular mass of 71.266 kDa and an estimated isoelectric point of 5.20. LEHsp70 contained highly conserved functional motifs of the cytosolic Hsp70 family. Expression of the LEHsp70 gene was quantified by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) of digestive gland and gill tissues. Heat shock (10 degrees C for different time periods) caused rapid induction of LEHsp70. A significant 4.6 +/- 0.14-fold increase in the LEHsp70/beta-Actin mRNA ratio occurred in the gill at 12 hours, which returned to baseline after 48 hours. In contrast, the maximum expression in the digestive gland (3.6 +/- 0.36) was reached at 24 hours and was still significant after 48 hours (1.89 +/- 0.21). This indicates that LEHsp70 may play an important role in mediating thermal stress and tolerance in this clam.
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Project description:A computationally predicted gene regulatory network (GRN), generated from mantle-specific gene expression profiles in the Antarctic clam Laternula elliptica, was interrogated to test the regulation and interaction of duplicated inducible hsp70 paralogues. hsp70A and hsp70B were identified in the GRN with each paralogue falling into unique submodules that were linked together by a single shared second neighbour. Annotations associated with the clusters in each submodule suggested that hsp70A primarily shares regulatory relationships with genes encoding ribosomal proteins, where it may have a role in protecting the ribosome under stress. hsp70B, on the other hand, interacted with a suite of genes involved in signalling pathways, including four transcription factors, cellular response to stress and the cytoskeleton. Given the contrasting submodules and associated annotations of the two hsp70 paralogues, the GRN analysis suggests that each gene is carrying out additional separate functions, as well as being involved in the traditional chaperone heat stress response, and therefore supports the hypothesis that subfunctionalization has occurred after gene duplication. The GRN was specifically produced from experiments investigating biomineralization; however, this study shows the utility of such data for investigating multiple questions concerning gene duplications, interactions and putative functions in a non-model species.
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2012-06-26 | E-MTAB-1164 | biostudies-arrayexpress
Project description:ObjectiveTo systematically review and meta-analyze bulk RNA sequencing studies comparing Alzheimer's disease (AD) patients with controls in human brain tissue, assessing study quality and identifying key genes and pathways.MethodsWe searched PubMed, Web of Science, and Scopus on September 23, 2023, for studies using bulk RNAseq on primary human brain tissue from AD patients and controls. Excluded were non-primary tissue, re-analyses without new data, limited RNA types and gene panels. Quality was assessed with a 10-category tool. Meta-analysis used high-quality datasets.ResultsFrom 3,266 records, 24 studies met criteria. Meta-analysis found 571 differentially expressed genes (DEGs) in temporal lobe and 189 in frontal lobe; overlapping pathways included "Tube morphogenesis" and "Neuroactive ligand-receptor interaction."LimitationsStudy heterogeneity and limited data tables constrained the review.ConclusionsRigorous methods are vital in AD transcriptomic studies. Findings enhance understanding of transcriptomic changes, aiding biomarker and therapeutic development.RegistrationPROSPERO (CRD42023466522).
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Project description:We systematically reviewed and meta-analyzed bulk RNA sequencing (RNAseq) studies comparing Alzheimer's disease (AD) patients to controls in human brain tissue. We searched PubMed, Web of Science, and Scopus for human brain bulk RNAseq studies, excluding re-analyses and studies limited to small RNAs or gene panels. We developed 10 criteria for quality assessment and performed a meta-analysis on three high-quality datasets. Of 3266 records, 24 qualified for the systematic review, and one study with three datasets qualified for the meta-analysis. The meta-analysis identified 571 differentially expressed genes (DEGs) in the temporal lobe and 189 in the frontal lobe, including CLU and GFAP. Pathway analysis suggested reactivation of developmental processes in the adult AD brain. Limited data availability constrained the meta-analysis. These findings underscore the need for rigorous methods in AD transcriptomic research to better identify transcriptomic changes and advance biomarker and therapeutic development. This review is registered in PROSPERO (CRD42023466522).HighlightsComprehensive review: Conducted the first systematic review and meta-analysis of bulk RNA sequencing (RNAseq) studies comparing Alzheimer's disease (AD) patients with non-demented controls using primary human brain tissue.Key findingsIdentified 571 differentially expressed genes (DEGs) in the temporal lobe and 189 in the frontal lobe of patients with AD, revealing potential therapeutic targets. Pathway discovery: Highlighted key overlapping pathways such as "tube morphogenesis" and "neuroactive ligand-receptor interaction" that may play critical roles in AD.Quality assessmentEmphasized the importance of methodological rigor in transcriptomic studies, including quality assessment tools to guide future research in AD.Study limitationAcknowledged limited access to complete data tables and lack of diversity in existing datasets, which constrained some of the analysis.
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