Ontology highlight
ABSTRACT:
PROVIDER: PRJNA616325 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11479300_1.fastq.gz | Fastqsanger.gz | |||
| SRR11479300_2.fastq.gz | Fastqsanger.gz | |||
| SRR11479400_1.fastq.gz | Fastqsanger.gz | |||
| SRR11479400_2.fastq.gz | Fastqsanger.gz | |||
| SRR11479500_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1062 |
Similar Datasets
Project description:Biologists have long been fascinated by the amazing diversity of animal colour patterns. Despite
much interest, the underlying evolutionary and developmental mechanisms contributing to
their rich variety remain largely unknown, especially the vivid and complex colour patterns seen
in vertebrates. The model [1] shows, that complex and camouflaged animal markings can be formed
by the ‘blending’ of simple colour patterns. A mathematical model predicts that crossing
between animals having inverted spot patterns (for example, ‘light spots on a dark background’
and ‘ dark spots on a light background’ ) will necessarily result in hybrid offspring that have
camouflaged labyrinthine patterns as ‘ blended ’ intermediate phenotypes. In [1] the authors
confirmed the broad applicability of the model prediction by empirical examination of natural and
artificial hybrids of salmonid fish. The results suggest an unexplored evolutionary process by means of
‘pattern blending’, as one of the possible mechanisms underlying colour pattern diversity and
hybrid speciation. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software
Morpheus (https://morpheus.gitlab.io) to simulate the time course (movie) of the spatio-temporal dynamics.
It resembles figure 3a from [1], where a 2D parameter space shows the transition from black to white spots
through intermediate labyrinthine patterns.
1. Miyazawa, Okamoto and Kondo, Blending of animal colour patterns by hybridization, Nature Communications, 2010
2023-09-07 | MODEL2304280001 | BioModels
Project description:Environmental monitoring for pharmaceuticals and endocrine disruptors in the aquatic environment traditionally employs a variety of methods including analytical chemistry, as well as a variety of histological and biochemical endpoints that correlate with the fish fitness. It is now clear that analytical chemistry alone is insufficient to identify aquatic environments that are compromised because these measurements do not identify the biologically available dose. The biological endpoints that are measured are important because they relate to known impairments, however, they are not specific to the contaminants and often focus on only a few known endpoints. These studies can be enhanced by looking more broadly at changes in gene expression, especially if the analysis focuses on biochemical pathways. The present study was designed to obtain additional information on well-characterized sites adjacent to sewage treatment plants in MN that are thought to be impacted by endocrine disruptors. Here we examine five sites that have been previously characterized and examine changes in gene expression in fathead minnows (Pimephales promelas) that have been caged for 48 h in each of the aquatic environments. We find that the gene expression changes are characteristic and unique at each of the five sites. Also, fish exposed to two of the sites, 7 and 12, display a more aggressive behavior compared to control fish. Our results show that short-term exposure to sewage treatment plant effluents was able to induce a site-specific gene expression pattern in the fathead minnow gonad and liver. The short-term exposure was also sufficient to affect fish sexual behavior. Our results also show that microarray analysis can be very useful for determining potential exposure to chemicals, and could be used routinely as a tool for environmental monitoring.
2009-06-19 | GSE16645 | GEO
Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin
2013-12-04 | GSE41016 | GEO
Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin Correlation between contaminant exposure and gene expression profiles of wild largescale suckers collected from three different sites in the Columbia River. At each site, liver samples of six to eight different fish were analyzed using microarrays.
2013-12-04 | E-GEOD-41016 | biostudies-arrayexpress
Project description:Infectious pancreatic necrosis virus (IPNV) is an aquatic virus that causes acute infection in freshwater and marine fish. The stage-specific expression of TNFα regulates Bad/Bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in IPNV-infected fish cells. Using microRNA microarray and real-time quantitative PCR assays, the expression patterns of microRNA were characterized in different replication stages of IPNV or stimulation of LPS.
2011-12-31 | GSE30262 | GEO
Project description:Feral organisms are affected by adverse environmental factors present in their habitat. It was hypothesized that transcript expression pattern in a suitable target organ of a sentinel feral organism compared to a reference transcript population may serve as a comprehensive biomarker of these adverse effects. This study was aimed at inquiring the applicability of such biomarker and establishing a procedure for its appropriate utilization. The examined system contains dual-labeled microarray-based evaluation of the hepatic transcript expression pattern in a sentinel fish sampled in two habitats, a polluted (Haifa Bay) and a clean (Dor) site, respectively, for two years. The hepatic expression patterns were compared to a reference RNA assumed to represent specimens that have no exposure history to pollution. The sentinel fish is Lithognathus mormyrus, which inhabits a marine coastal habitat along the Mediterranean coast of Israel. The hepatic transcript expression patterns were evaluated using a 1152-clone cDNA microarray, biased towards pollution-affected genes. The LIMMA software was used to calculate the log2 ratios of expressions (M) and to identify the differentially expressed genes in each sample (adjusted P<0.01). Keywords: Response of fish hepatic gene expression pattern to environmental conditions.
2009-12-01 | GSE14673 | GEO
Project description:Chemical signals are produced by aquatic organisms following predatory attacks or perturbations such as parasitic infection. Ectoparasites feeding on host fish are likely to cause release of similar alarm cues into the environment due to the stress, wounding and immune response stimulated upon infection. Alarm cues are often released in the form of proteins and peptides and provide important insights into bodily function and infection status. Here we outline a non-invasive method to identify potential chemical cues associated with infection in fish by extracting, purifying and characterizing proteins from water samples from cultured fish. Gel free proteomic methods were deemed the most suitable for protein detection in saline water samples. It was confirmed that proteins could be characterized from teleost water samples and that variation in protein profiles could be detected between infected and uninfected individuals and fish and parasite only water samples. Our novel assay provides a non-invasive method for assessing the health condition of both wild and farmed aquatic organisms. Similar to environmental DNA monitoring methods, these proteomic techniques could provide an important tool in applied biology and aquaculture biology
2019-01-02 | PXD010987 | Pride
Project description:Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for responding and elicit a coordinated response to stimuli. Mass spectrometry (MS)-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of cells but this is highly challenging involving laborious workflows that do not cover the phosphoproteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global (phospho)proteome dynamics across six distinct subcellular fractions. We benchmarked the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in-vitro in HeLa cells and in-vivo in mouse tissues. Finally, we investigated the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction.
2021-11-18 | PXD023690 | Pride