Similar Datasets
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoA-carrying AOA within these sediments.
2013-08-24 | GSE50163 | GEO
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoAÂ-carrying AOA within these sediments. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-08-24 | E-GEOD-50163 | biostudies-arrayexpress
Project description:Land cover change has long been recognized that marked effect the amount of soil organic carbon. However, little is known about microbial-mediated effect processes and mechanism on soil organic carbon. In this study, the soil samples in a degenerated succession from alpine meadow to alpine steppe meadow in Qinghai-Tibetan Plateau degenerated, were analyzed by using GeoChip functional gene arrays.
2017-01-05 | GSE93158 | GEO
Project description:This project builds upon a DOE Subsurface Biogeochemical Research (SBR) project on the transport and metabolism of fresh, photosynthetically-derived (mainly periphyton) particulate organic matter (POM) in near-surface riverbed sediments at the PNNL SFA Hanford 300 Area study site. We propose to utilize a combination of Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and polar metabolomics, together with metagenomic/transcriptomic sequencing to track, in a substrate-explicit manner, the degradation of fresh POM in Hanford 300 Area riverbed sediments. The overarching hypothesis behind our proposed research is that there will be detectable chemical and (meta)genomic responses to the input of fresh POM. Many previous studies have demonstrated distinct metabolic and bulk geochemical responses to fresh POM input, and a few studies have directly examined the uptake and degradation of POM in permeable marine sediments. In addition, our recent studies at the Hanford 300 Area indicate that in situ input of fresh POM (likely dominated by periphyton detritus) to the near-surface riverbed is an important driver of both microbial community composition and activity in the vicinity of the Hanford 300 Area.
This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:https://doi.org/10.46936/fics.proj.2021.60033/60000394) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).
2025-04-24 | MSV000097722 | MassIVE
Project description:Using WGBS we investigated blood DNA methylation profiles of Cooinda the Alpine dingo and determined putative regulatory elements (unmethylated regions, UMRs, and lowly methylated regions, LMRs).
2023-02-24 | GSE212509 | GEO
Project description:Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximise fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4 °C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4 °C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developingin specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.
2024-04-01 | GSE176054 | GEO
Project description:Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip. The analysis used a polygenic model where the dropping criteria was the Call Rate ≥ 0.95. The initial dataset was composed of ~ 60,000 rows of SNPs, 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50KBeadchip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provide precision breeding methods will thereby increase breeding value. Specific aims: 1) Improve on contributions to the phenotype repository, the Council on Dairy Cattle Breeding (CDCB) for milk quality traits that are economically important for goat production while developing a corresponding DNA repository for each of the animals with significant genotype-phenotype associations. 2) Develop genomic prediction tools and provide data for a better database for tools to predict phenotypic traits by initially using the high density Goat50KSNP BeadChip for the selection of more specific SNPs associated with select signatures (genes) for phenotypic traits in American Alpine goats. 3) To establish whether a low number of goat subjects (< 300 goats) will provide statistically significant (p < 0.05) predictive capabilities for desired breeding traits in American Alpine dairy goats.
2020-02-19 | GSE145419 | GEO
Project description:The altitude gradient limits the growth and distribution of alpine plants.Alpine plants have developed strategies to survive the extremely cold conditions prevailing at high altitudes; however, the mechanism underlying the evolution of these strategies remains unknown. The alpine plant Potentilla saundersiana is widespread in the Northwestern Tibetan Plateau. In this study, we conducted a comparative proteomics analysis to investigate the dynamic patterns of protein expression of P. saundersiana located at five different altitudes. We detected and functionally characterized 118 differentially expressed proteins. Our study confirmed that increasing levels of antioxidant proteins, and their respective activities, and accumulation of primary metabolites, such as proline and sugar, confer tolerance to the alpine environment in P. saundersiana. Proteins species associated with the epigenetic regulation of DNA stability and post-translational protein degradation were also involved in this process. Furthermore, our results showed that P. saundersiana modulated the root architecture and leaf phenotype to enhance adaptation to alpine environmental stress through mechanisms that involved hormone synthesis and signal transduction, particularly the cross-talk between auxin and strictosidine. Based on these findings, we conclude that P. saundersiana uses multiple strategies to adapt to the high-altitude environment of the Northwestern Tibetan Plateau.
2022-02-22 | PXD001112 | Pride
Project description:We have completed the high quality reference genome for domestic sheep (Oar v3.1) and performed a detailed survey of gene expression across different tissues. RNA-seq data of 7 tissue types from the reference female Texel and skin tissue from a Gansu alpine fine wool sheep were sequenced. Here is the part of the RNA-seq data sequenced in BGI, including 7 tissue types from the reference female Texel and skin type from a Gansu alpine fine wool sheep.
2014-06-06 | E-GEOD-56643 | biostudies-arrayexpress
Project description:Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. Domestic–wild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection.
2012-04-23 | GSE30555 | GEO