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410 results for “eukaryotic”
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
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DNA-stimulated liquid-liquid phase separation by eukaryotic topoisomerase II modulates catalytic function
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Genetic survey of eukaryotic plankton communities of aquatic habitats in Green Lakes Valley, 2014 - 2017
Previous work has shown high-elevation ecosystems are especially susceptible to the effects of climate change, but little work has been done on microbial communities in high-elevation aquatic systems. Therefore, my research aimed to improve our understanding of the composition, stability, and factors controlling microbial communities in high-elevation lakes in the Front Range of the Colorado Rocky Mountains. I studied seasonal and inter-annual variations in bacterial (16S rDNA) and eukaryotic (18S rDNA) microbial communities at multiple locations (inlet, outlet, three depths in the water column) within alpine lakes over four years (2014-2017). Communities significantly differed between lake inlets and the lakes as a whole across sampling dates. The most significant variable controlling 16S and 18S community composition was lake discharge rate, indicating that water residence times play a strong role in structuring communities.
GenBank + BOLD CO1 Eukaryotic representative sequence set
<p>This is a representative sequence set for cytochrome oxidase subunit 1 (CO1 or COI) combining all available eukaryotic CO1 sequences from GenBank and BOLD, clustered at 99% similarity.</p> <p> </p> <p>TODO:</p> <p>generate and add 7-level taxonomies for each sequence in this rep set.</p>
Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
<p>Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focused on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic 'protists', with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro-eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro-eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods, and brings us closer to a full inventory of extant marine biodiversity.</p>
A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor
The insect chemosensory repertoires of Odorant Receptors (ORs) and Gustatory Receptors (GRs) together represent one of the largest families of ligand-gated ion channels. Previous analyses have identified homologous 'Gustatory Receptor-Like (GRL)' proteins across Animalia, but the evolutionary origin of this novel class of ion channels is unknown. We describe a survey of unicellular eukaryotic genomes for GRLs, identifying several candidates in fungi, protists and algae that contain many structural features characteristic of animal GRLs. The existence of these proteins in unicellular eukaryotes, together with ab initio protein structure predictions, provide evidence for homology between GRLs and a family of uncharacterized plant proteins containing the DUF3537 domain. Together, our analyses suggest an origin of this protein superfamily in the last common eukaryotic ancestor.
Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
<p>Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in <i>Drosophila </i>embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5′ vs. 3′ untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.</p>
Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing
<p>Analysis scripts and raw data for manuscript titled: "<em>Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing</em>" </p>
Figure 21. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 21. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., paratype, 3D model, volume rendering, created with CTVox, virtual rotation and dissection. Movie available at: YouTube.
Figure 22. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 22. - Movie of Eupolybothrus cavernicolus Komerički & Stoev sp. n., holotype, filmed ex-situ in a plastic container. Movie available at: YouTube.
Identification and analysis of functional associations among natural eukaryotic genome editing components
<p>The contents of the data files for the manuscript "Identification and analysis of functional associations among natural eukaryotic genome editing components" are described below.</p> <p>Dataset 1 - ies_retention.tab<br> = All IES retention scores used in the manuscript</p> <p>Dataset 2 - oes_retention.tab<br> = OES retention estimates.</p> <p>Supplementary Data S1 - ies_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for all IESs.</p> <p>Supplementary Data S2 - ies_retention_score_correlation_stats_len_le_35bp.txt<br> = Statistics for Spearman's correlations for IESs <= 35 bp.</p> <p>Supplementary Data S3 - ies_retention_score_correlation_stats_len_ge_500bp.txt<br> = Statistics for Spearman's correlations for IESs >= 500 bp.</p> <p>Supplementary Data S4 - oes_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for OESs (>= 300 bp and 3x-70x PGM-KD<br> coverage).</p> <p>Supplementary Data S5 - ies_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all IESs.</p> <p>Supplementary Data S6 - oes_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all OESs.</p> <p>Supplementary Data S7 - ies_vs_oes_retention_score_correlation.comparisons_stats.txt<br> = Statistics for comparisons of the differences in Spearman correlations<br> between IESs and OESs.</p> <p>Supplementary Data S8 - OES.v1.fa<br> = OES sequences.</p> <p> </p>
Metabarcoding dataset of surface microbial eukaryotes in the Western Arctic Ocean (Canada Basin/Beaufort Sea)
<p>Fasta file of amplicon sequence variant (ASV) sequences, ASV phylogeny in Newick format, ASV table of relative abundance in samples and table of taxonomic information associated with each ASV. Raw sequence data were processed using DADA2 v1.14 and taxonomic assignment of ASV sequences was done using the PR2 database v4.12.0. The table of standardised environmental metadata (z-scores) is also provided.</p><p>Additionally, the OTU (98%) table of relative abundances in samples and phylogeny in Newick format is available.</p>
Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes
<p>The spread of mobile genetic elements within and between the genomes of diverse organisms has greatly impacted biology across the tree of life. Inteins are an enigmatic type of mobile genetic element capable of self-splicing at the protein level. While inteins are generally rare in eukaryotes, we have discovered that three strains of the newly described eukaryotic microbe Anaeramoeba have many dozens of inteins encoded in their nuclear genomes. Genomic investigation shows that Anaeramoeba's inteins were acquired by lateral transfer from viruses and bacteria, and subsequently spread to many different genomic locations via allelic and, possibly, non-allelic homing. The promiscuous nature of inteins in Anaeramoeba makes them promising substrates for genetic engineering and biotechnological applications.</p>
Comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity using Oxford Nanopore sequencing
<p><span>Metagenomics has become a prominent technology for studying the functional potential of all organisms in a microbial and eukaryotic community. The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. To achieve this, we have developed a universal PCR assay that targets the most conservative nuclear regions of the ribosomal gene for all cellular organisms, including plants, algae, fungi, protists, insects</span>,<span> and animals. The amplification product contains polymorphic regions of both ribosomal genes and the intergenic spacer. The size of the PCR products varies by class, kingdom</span>,<span> or domain, ranging from 2 kb for fungi to 7 kb for birds. This assay is also adapted for use with the Oxford Nanopore Rapid Barcoding Library Kit, which enables metagenomic biodiversity analysis. Our approach provides a rapid, sensitive</span>,<span> and equally efficient way to study the composition of eDNA from mixed species in the environment. This protocol reduces the time and cost of metagenomic biodiversity analysis using Oxford Nanopore sequencing. We can efficiently analyze the biodiversity of mixed species present in environmental samples.</span></span></p>
Fig. 2 in Changing Views of Arctic Protists (Marine Microbial Eukaryotes) in a Changing Arctic
Fig. 2. Loboea, collected from Northern Baffin Bay. Scale bar: 8 µm.
Oxford Nanopore sequencing for comprehensive, targeted eukaryotic metagenomics analysis of environmental DNA biodiversity
<p><span>The study of symbiotic organisms from different classes or kingdoms, including those previously unknown, is possible with simultaneous and equally efficient metagenomic analysis of these species. A variety of targeted primer sets are used for eukaryotic metagenomic biodiversity, including those that are universal for specific families, classes</span><span>,<span> or kingdoms. The most universal for all existing cellular organisms is the presence of ribosomal RNA encoding gene sequences. For eukaryotic sequences, these are 16S and 23s rDNA, </span>and <span>for eukaryotic sequences of nuclear (18S and 28S) and mitochondrial (12S and 16S) ribosomal RNA. Here, we present the application of the eukaryotic metagenomics approach to the simultaneous, quantitative</span>,<span> and unbiased identification of most eukaryotic species. </span></span></p>
Intronization signatures in coding exons reveal the evolutionary fluidity of eukaryotic gene architecture
<p>This dataset accompanies the manuscript "Intronization signatures in coding exons reveal the evolutionary fluidity of eukaryotic gene architecture". It contains the relevant tables, scripts and figures used for and created during data analysis.</p>
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms
<p>G3PO (Gene and Protein Prediction PrOgrams) Benchmark was designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms (from human to protists). <br> </p>
Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between opisthokonts and all other lineages
<p>Advances in phylogenetic methods and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolutionary history of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most 'popular' (i.e. in textbooks and reviews) hypothesis for the root is between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion and a limited sampling of eukaryotic lineages. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within the Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses) nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. Our results estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative popular roots from the literature. Based on further analysis of genome size, we propose Opisthokonta + others as the most likely root. Finding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes.</p>
Supporting data and code for Nakov, Beaulieu, Alverson: Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)
<p>This archive includes:</p> <p>1. Character and species richness datasets</p> <p>2. Phylogenies and time-calibration files</p> <p>3. R scripts</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.