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291 results for “cycle gene”
Aqueous geochemical measurements and speciation calculations with concurrent copper resistance gene counts from sediment metagenomes over a seasonal cycle from 2015 to 2016 on Silver Bow Creek and Blacktail Creek near Butte, MT
<p>This dataset contains information from concurrently gathered geochemical and metagenomic samples collected from Silver Bow Creek and Blacktail Creek near Butte, MT (SBC/BC) during 2015 and 2016. SBC/BC is recovering from metal contamination related to extensive mining in the area. Full geochemical measurements, geochemical speciation calculations, and gene counts of sequences mapping to copper resistance genes using MG-RAST are included. </p>
Inter-generational nuclear crosstalk links the control of gene expression to programmed genome rearrangements during the Paramecium sexual cycle
<p>Multinucleate cells are found in many eukaryotes, but how multiple nuclei coordinate their functions is still poorly understood. In the cytoplasm of the ciliate <em>Paramecium tetraurelia</em>, two micronuclei (MIC) serving sexual reproduction coexist with a somatic macronucleus (MAC) dedicated to gene expression. During sexual processes, the MAC is progressively destroyed while still ensuring transcription and new MACs develop from copies of the zygotic MIC. Several gene clusters are successively induced and switched off before vegetative growth resumes. Concomitantly, programmed genome rearrangements (PGR) remove transposons and their relics from the new MACs. Development of the new MACs is controlled by the old MAC, since the latter expresses genes involved in PGR, including the <em>PGM</em> gene encoding the essential PiggyMac endonuclease that cleaves the ends of eliminated sequences. Using RNA deep sequencing and transcriptome analysis, we show that impairing PGR up-deregulates key PGR genes, together with ~600 other genes possibly also involved in PGR. Among these genes, 42% are no longer induced when no new MACs are formed, including 180 genes that are co-expressed with <em>PGM </em>under all tested conditions. We propose that bi-directional crosstalk between the two coexisting generations of MACs links gene expression to the progression of MAC development.</p>
data for publication "Dynamics of soil nitrogen and N-cycling-related genes following the application of biobased fertilizers"
<p>Dataset for the scientific publication titled "Dynamics of soil nitrogen and N-cycling-related genes following the application of biobased fertilizers" in the Journal <a href="https://www.sciencedirect.com/journal/applied-soil-ecology">Applied Soil Ecology</a>. </p><p><a href="https://doi.org/10.1016/j.apsoil.2023.105033">https://doi.org/10.1016/j.apsoil.2023.105033</a> </p>
Spatial and seasonal distribution of selected nitrogen cycle genes in deep waters of the Baltic Proper
<p>The dataset provides information on nitrogen cycle related bins and gene characteristics across selected depths within the IDEAL, P1, and BY15 sites in the Baltic Sea. The dataset includes details such as gene spans, gene lengths, gene names, and the processes to which each gene is assigned. Additionally, it contains raw read counts, RPKM (reads per kilobase of transcript, per million mapped reads), family, phylum, bin, site, common bin identifiers for sites, and seasonal variations. Bin parameters, along with lineage-specific markers, are included to estimate the completeness of the bins. We focused on nitrogen loss processes (denitrification, anammox), reduction processes (dissimilatory nitrate reduction (DNR), dissimilatory nitrate reduction to ammonium (DNRA)), and oxidation (nitrification). <span>The reported results were obtained within the framework of the statutory activities of the Institute of Oceanology of the Polish Academy of Sciences and the following research project: 2019/34/E/ST10/00217 funded by the Polish National Science Centre.</span></p>
Asymmetric responses of abundance and diversity of N-cycling genes to altered precipitation in arid grasslands
<p>Precipitation changes exert a fundamental effect on the nitrogen (N) cycle in water-limited grasslands. Soil microbes are essential drivers of N cycle, and the rates and their stabilities of interrelated N-cycling processes are reflected by the abundance and diversity of N-cycling genes. Yet, little is known about how altered precipitation affects the genes involved in the entire N-cycling pathways.</p> <p>By combining a 6-year precipitation manipulation experiment (-30%, ambient, +30%, +50%) with metagenomic sequencing, we investigated the responses of N-cycling gene abundance and diversity to altered precipitation at two soil depths (0-10 and 30-50 cm).</p> <p>We found that increased precipitation enhanced the abundance of numerous key genes, leading to an acceleration of N turnover, but decreased the diversity of ammonium assimilation genes. Decreased precipitation did not reduce abundance or diversity of N-cycling genes. Most N-cycling genes showed generally consistent responses to altered precipitation in the topsoil (0-10 cm) and subsoil (30-50 cm), albeit with clear distinctions in both abundance and diversity by soil depth. These precipitation-specific responses and depth-dependent variabilities of functional genes were attributed to the distinct taxonomic composition of each N-cycling gene. Further, we quantified gross N transformation rates and found that they were well predicted by the abundance of most N-cycling genes (e.g., genes involved in ammonium assimilation and nitrification).</p> <p>Our study sheds new light on the soil N cycle under precipitation alterations from the perspective of individual gene abundance and diversity, and shows that future increases in precipitation could accelerate soil N turnover in arid and semi-arid lands. </p>
Palbociclib in Treating Patients With Relapsed or Refractory Rb Positive Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Activating Alterations in Cell Cycle Genes (A Pediat
ClinicalTrials.gov study NCT03526250. IPD Sharing: Not stated. Countries: 2. Publications: 2.
Asymmetric responses of abundance and diversity of N-cycling genes to altered precipitation in arid grasslands
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Data from: NEK4 suppresses cell proliferation in BT20 triple-negative breast cancer cells by diminishing expression of cell cycle genes, while its depletion mitigates proliferation in other cell lines
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Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters
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Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages
Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.
Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.
Data from: Impacts of temperature and lunar day on gene expression profiles during a monthly reproductive cycle in the brooding coral Pocillopora damicornis
Reproductive timing in brooding corals has been correlated to temperature and lunar irradiance, but the mechanisms by which corals transduce these environmental variables into molecular signals are unknown. To gain insight into these processes, global gene expression profiles in the coral Pocillopora damicornis were examined (via RNA-Seq) across lunar phases and between temperature treatments, during a monthly planulation cycle. The interaction of temperature and lunar day together had the largest influence on gene expression. Mean timing of planulation, which occurred at lunar days 7.4 and 12.5 for 28- and 23°C-treated corals, respectively, was associated with an upregulation of transcripts in individual temperature treatments. Expression profiles of planulation-associated genes were compared between temperature treatments, revealing that elevated temperatures disrupted expression profiles associated with planulation. Gene functions inferred from homologous matches to online databases suggest complex neuropeptide signalling, with calcium as a central mediator, acting through tyrosine kinase and G protein-coupled receptor pathways. This work contributes to our understanding of coral reproductive physiology and the impacts of environmental variables on coral reproductive pathways.
Removing the effects of cell cycle genes data
<p>This data is used for the Galaxy Training Network tutorial 'Removing the effects of cell cycle genes'. It includes lists of cell cycle genes in mice and a dataset that is also used in the GTN tutorial 'Filter, Plot and Explore Single-cell RNA-seq Data'.</p> <p>The original dataset can be found here: Bacon, Wendi Anne. (2022). AnnData object for case study tutorials [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.7053673">https://doi.org/10.5281/zenodo.7053673</a> The version uploaded here has been processed according to the 'Filter, Plot and Explore Single-cell RNA-seq Data' tutorial up to the point of scaling the data. The data was published in Bacon, W. A., R. S. Hamilton, Z. Yu, J. Kieckbusch, D. Hawkes <em>et al.</em>, 2018 Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice. Frontiers in Immunology 9: <a href="https://doi.org/10.3389/fimmu.2018.02523">10.3389/fimmu.2018.02523</a></p> <p>The cell cycle gene lists were obtained from the Harvard Chan School: Bioinformatics Core tinyatlas (2017) cell_cycle/Mus_musculus via GitHub:<a href="https://github.com/hbc/tinyatlas/blob/master/cell_cycle/Mus_musculus.csv"> https://github.com/hbc/tinyatlas/blob/master/cell_cycle/Mus_musculus.csv</a> </p> <p> </p>
Hydrobates spp. – Circadian locomotor output cycles kaput (Clock) gene poly-glutamine repeats
<p>Annual cues in the environment result in physiological changes that allow organisms to time reproduction during periods of optimal resource availability. Understanding how circadian rhythm genes sense these environmental cues and stimulate the appropriate physiological changes in response is important for determining the adaptability of species, especially in the advent of changing climate. A first step involves characterizing the environmental correlates of natural variation in these genes. Band-rumped and Leach's storm-petrels (<em>Hydrobates</em> spp.) are pelagic seabirds that breed across a wide range of latitudes. Importantly, some populations have undergone allochronic divergence, in which sympatric populations use the same breeding sites at different times of year. We investigated the relationship between variation in key functional regions of four genes that play an integral role in the cellular clock mechanism – <em>Clock, Bmal1, Cry2 </em>and<em> Per2</em> – with both breeding season and absolute latitude in these two species complexes. We discovered that allele frequencies in two genes, <em>Clock</em> and <em>Bmal1</em>, differed between seasonal populations in one archipelago, and also correlated with absolute latitude of breeding colonies. These results indicate that variation in these circadian rhythm genes may be involved in allochronic speciation, as well as adaptation to photoperiod at breeding locations.</p>
Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages
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Hydrobates spp. – Circadian locomotor output cycles kaput (Clock) gene poly-glutamine repeats
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Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments
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Data from: Impacts of temperature and lunar day on gene expression profiles during a monthly reproductive cycle in the brooding coral Pocillopora damicornis
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Data from: Polyamines in the life of Arabidopsis: profiling the expression of S-adenosylmethionine decarboxylase (SAMDC) gene family during its life cycle
Arabidopsis has 5 paralogs of the S-adenosylmethionine decarboxylase (SAMDC) gene. Neither their specific role in development nor the role of positive/purifying selection in genetic divergence of this gene family is known. While some data are available on the organ-specific expression of AtSAMDC1, AtSAMDC2, AtSAMDC3 and AtSAMDC4 at transcript level, not much is known about their promoters including AtSAMDC5 (another paralog), which is believed to be non-functional.
Data from: A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells
Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ∼6000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.