MonMic
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB56101 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10230900_1.fastq.gz | Fastqsanger.gz | |||
| ERR10230900_2.fastq.gz | Fastqsanger.gz | |||
| ERR10231000_1.fastq.gz | Fastqsanger.gz | |||
| ERR10231000_2.fastq.gz | Fastqsanger.gz | |||
| ERR10230901_1.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.
2016-06-01 | GSE72417 | GEO
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.
2016-06-01 | GSE72416 | GEO
Project description:Black soldier fly larvae meal (BSFL) from Hermetia illucens is a promising alternative protein source in diets for farmed fish. The larvae can efficiently convert low-value organic material into high quality protein in a production cycle with low arable land and freshwater inputs. A few recent studies have shown that BSFL is a suitable protein source for Atlantic salmon (Salmo salar) in smaller controlled experiments. However, industry-relevant field trials conducted under large scale near-commercial conditions over a longer period are lacking. In this study, a feeding trial was performed to evaluate the impact of BSFL on growth performance and health of Atlantic salmon during the grow out phase in seawater, in a commercial site in Vestland county, Norway. A total of 320,000 post-smolt Atlantic salmon were distributed into six duplicate sea cages and fed one of three diets (commercial-like control diet and two test diets partially replacing the protein content of the control diet with 4 % and 8 % defatted BSFL meal) for 21 weeks, until a relevant commercial slaughter size of 4.5-5.0 kg was reached. Health parameters were assessed including histology of the distal intestine (DI), in addition to DI microbiota identification (by 16s rRNA-seq) and salmon RNA-seq of DI and head kidney (HK). The results showed that the inclusion of BSFL meal supported growth performance and had no adverse effect on gut health. The beta diversity of the distal intestine microbiota and the relative abundance of families Lactobacillaceae and the chitinolytic Bacillaceae increased in the fish fed the BSFL diets. Additionally, no histopathological changes were attributable to BSFL meal intake. Results from RNA-seq in DI revealed that BSFL inclusion modulates metabolic processes associated with lipids, the response to estrogens, the activity of immune receptors (to chemokines), phagocytosis and extracellular vesicles. Based on these results, black soldier fly larvae meal is a suitable alternative protein ingredient in inclusions of up to at least 8 % for Atlantic salmon under industrial fish farming conditions.
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Project description:The nasopharyngeal microbiota of healthy cattle vs. cattle diagnosed with BRD in a commercial feedlot setting was compared using a high-density 16S rRNA microarray (Phylochip). Nasopharyngeal samples were taken from both groups of animals (n=5) at feedlot entry (day 0) and >60 days later.
2015-06-21 | E-MTAB-3430 | biostudies-arrayexpress
Project description:Several aspects of a Western lifestyle such as increased obesity and decreased physical activity are associated with increased risk for gastrointestinal cancers1. Although high-fat diet (HFD) induced low-grade inflammation has been closely linked to tumorigenesis2, however, the microbial shift that occurs due to diet and consequent alterations in host immunity have merely been considered to play a critical role during carcinogenesis. Here we show that HFD promotes tumor progression in the small intestine of genetically susceptible mice, however, independently of obesity and diet-induced chronic inflammation. HFD consumption cooperates with mutant K-Ras to mediate a shift in the composition of microbiota, which is associated with a decrease in Paneth cell antimicrobial host defense that compromises dendritic cell (DC) recruitment and MHCII presentation in the gut-associated lymphoid tissues (GALTs). DC recruitment in GALTs can be normalized and tumor progression attenuated completely when K-Ras mutant mice are supplemented with the short chain fatty acid butyrate, a bacterial fermentation end product, or partially when provided with probiotics. Importantly, Myd88-deficiency completely blocks tumor progression in K-ras mutants, however, rather by substantial changes in the microbiota than host-mediated signaling mechanisms. Strikingly, transfer of fecal samples from diseased donors into healthy adult K-ras mutants is sufficient to enhance tumor progression in the absence of HFD suggesting a pivotal role for distinct microbiota shifts in aggravating disease in the small intestine. Collectively, these data underscore the reciprocal interaction between host and environmental factors for the composition of intestinal microbiota that favors carcinogenesis and suggest tumor progression could potentially be “transmitted” in genetically predisposed individuals. 13 samples; S103_396_GroupA_Arkan and S104_429_GroupA_Arkan represent the controls of the first group, S105_394_GroupB_Arkan and S106_429_GroupB_Arkan represent ViRas (mutated) mice of the first group. S982_groupA_ 1 and S983_groupA_2 represent the cotrols of the second group, S984_groupB_3, S985_groupB_4 and S986_groupB_5 represent ViRas (mutant) mice of the second group, S563_CO1979 represent the control of the third group, S564_KO1_1231, S565_KO2_1984 and S566_KO3_2013 represent the ViRas (mutant) mice of the third group. The first group are mice kept on HFD, second group kept on ND and third group kept on HFD plus treated with butyrate
2013-07-01 | E-GEOD-42840 | biostudies-arrayexpress
Project description:Several aspects of a Western lifestyle such as increased obesity and decreased physical activity are associated with increased risk for gastrointestinal cancers1. Although high-fat diet (HFD) induced low-grade inflammation has been closely linked to tumorigenesis2, however, the microbial shift that occurs due to diet and consequent alterations in host immunity have merely been considered to play a critical role during carcinogenesis. Here we show that HFD promotes tumor progression in the small intestine of genetically susceptible mice, however, independently of obesity and diet-induced chronic inflammation. HFD consumption cooperates with mutant K-Ras to mediate a shift in the composition of microbiota, which is associated with a decrease in Paneth cell antimicrobial host defense that compromises dendritic cell (DC) recruitment and MHCII presentation in the gut-associated lymphoid tissues (GALTs). DC recruitment in GALTs can be normalized and tumor progression attenuated completely when K-Ras mutant mice are supplemented with the short chain fatty acid butyrate, a bacterial fermentation end product, or partially when provided with probiotics. Importantly, Myd88-deficiency completely blocks tumor progression in K-ras mutants, however, rather by substantial changes in the microbiota than host-mediated signaling mechanisms. Strikingly, transfer of fecal samples from diseased donors into healthy adult K-ras mutants is sufficient to enhance tumor progression in the absence of HFD suggesting a pivotal role for distinct microbiota shifts in aggravating disease in the small intestine. Collectively, these data underscore the reciprocal interaction between host and environmental factors for the composition of intestinal microbiota that favors carcinogenesis and suggest tumor progression could potentially be “transmitted” in genetically predisposed individuals.
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Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.
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Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.
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Project description:This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages (34 dph (days post-hatching) alevin; 109 dph; fry and 162 dph parr;) and secondly, whether phenotypic differences at these stages were reflected in the protein samples collectedproteome from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n = 3) were first fed at 35 dph and then maintained by feeding to satiation on commercial feeds.
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