Estuarine Archaea metabarcoding
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB65254 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11857922_1.fastq.gz | Fastqsanger.gz | |||
| ERR11857922_2.fastq.gz | Fastqsanger.gz | |||
| ERR11857923_1.fastq.gz | Fastqsanger.gz | |||
| ERR11857923_2.fastq.gz | Fastqsanger.gz | |||
| ERR11857924_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 90 |
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Project description:Across the tree of life, DNA in living cells is associated with proteins that coat chromosomes, constrain their structure and influence DNA-templated processes such as transcription and replication. In bacteria and eukaryotes, HU and histones, respectively, are the principal constituents of chromatin, with few exceptions. Archaea, in contrast, have more diverse repertoires of nucleoid-associated proteins (NAPs). The evolutionary and ecological drivers behind this diversity are poorly understood. Here, we combine a systematic phylogenomic survey of known and predicted NAPs with quantitative protein abundance data to shed light on the forces governing the evolution of archaeal chromatin. Our survey identifies the Diaforarchaea as a hotbed of NAP gain and loss and we validate novel candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis, using sucrose gradient-based nucleoid enrichment coupled to quantitative mass spectrometry. Comparative analysis across a panel of 19 archaea revealed that investment in NAP production varies over two orders of magnitude, from <0.03% to >5% of total protein. Integrating genomic and ecological data, we demonstrate that growth temperature is an excellent predictor of relative NAP investment across archaea. Our results suggest that high levels of chromatinization have evolved as a mechanism toprevent uncontrolled helix opening and runaway denaturation – rather than, for example, to globally orchestrate gene expression – with implications for the origin of chromatin in both archaea and eukaryotes.
2022-10-17 | PXD034568 | Pride
Project description:The diverse mixture of contaminants frequently present in estuarine wetlands complicates their assessment by routine chemical or biological analyses. We investigated the use of gene expression to assess contaminant exposure and the condition of southern California (USA) estuarine fish. Liver gene expression, plasma estradiol concentrations and gonad histopathology were used to investigate the biological condition of longjaw mudsuckers (Gillichthys mirabilis). A wide array of metals, legacy organochlorine pesticides, PCBs and contaminants of emerging concern were detected in sediments and whole fish. Overall gene expression patterns were characteristic to each of four sites investigated in this study. Differentially expressed genes belonged to several functional categories including xenobiotic metabolism, detoxification, disease and stress responses. In general, plasma estradiol concentrations were similar among fish from all areas. Some fish gonads had pathologic changes (e.g. infection, inflammation) that could indicate weakened immune systems and chronic stress. The differential expression of some genes involved in stress responses correlated with the prevalence of histologic gonad lesions. This study indicates that sentinel fish gene expression data is a promising tool for assessing the biological condition of fish exposed to environmental contaminants. Key Words: Gene expression, fish, contaminants, estuaries. This abstract belongs to a manuscript that has been submitted to Environmental Science and Technology. The manuscript has been invited as part of an especial Omics Issue which is expected to be published in 2012. In this study, we used hepatic gene expression in wild longjaw mudsuckers (Gillichthys mirabilis) to assess biological responses from anthropogenically influenced wetlands. We investigated the relationships among gene expression responses, chemical exposure and additional biological responses in this species. We studied estuarine wetlands that had diverse contaminant characteristics and received three main types of contaminant inputs in different proportions: agricultural runoff, urban runoff and municipal wastewater.
2011-04-19 | E-GEOD-28695 | biostudies-arrayexpress
Project description:The diverse mixture of contaminants frequently present in estuarine wetlands complicates their assessment by routine chemical or biological analyses. We investigated the use of gene expression to assess contaminant exposure and the condition of southern California (USA) estuarine fish. Liver gene expression, plasma estradiol concentrations and gonad histopathology were used to investigate the biological condition of longjaw mudsuckers (Gillichthys mirabilis). A wide array of metals, legacy organochlorine pesticides, PCBs and contaminants of emerging concern were detected in sediments and whole fish. Overall gene expression patterns were characteristic to each of four sites investigated in this study. Differentially expressed genes belonged to several functional categories including xenobiotic metabolism, detoxification, disease and stress responses. In general, plasma estradiol concentrations were similar among fish from all areas. Some fish gonads had pathologic changes (e.g. infection, inflammation) that could indicate weakened immune systems and chronic stress. The differential expression of some genes involved in stress responses correlated with the prevalence of histologic gonad lesions. This study indicates that sentinel fish gene expression data is a promising tool for assessing the biological condition of fish exposed to environmental contaminants. Key Words: Gene expression, fish, contaminants, estuaries. This abstract belongs to a manuscript that has been submitted to Environmental Science and Technology. The manuscript has been invited as part of an especial Omics Issue which is expected to be published in 2012.
2011-04-19 | GSE28695 | GEO