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829
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Dataset results
829 results for “Evolvability”
H3K27me3 dynamics dictate evolving uterine states in pregnancy and parturition [RNA-seq]
GEO Series GSE105455. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Genetic properties underlying transcriptional plasticity and evolvability in E. coli
GEO Series GSE260863. Escherichia coli str. K-12 substr. MG1655; Escherichia coli. 16 samples. Type: Expression profiling by array.
L. lactis MG1363 transcriptome analysis of 4 evolved strains
GEO Series GSE67657. Lactococcus cremoris; Lactococcus cremoris subsp. cremoris MG1363. 4 samples. Type: Expression profiling by array.
Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case [CITE-seq]
GEO Series GSE165822. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of homoserine-evolved MG1655 strain (wild type) and of homoserine -treated wild type, mutant deleted for thrL and mutant bearing thrL* allele
GEO Series GSE206196. Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933. 24 samples. Type: Expression profiling by array.
Comparative transcriptome analysis between original and evolved recombinant lactose-consuming S. cerevisiae strains
GEO Series GSE12433. Saccharomyces cerevisiae. 4 samples. Type: Expression profiling by array.
Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies VII
GEO Series GSE100310. Gossypium hirsutum; Rhodotorula; Homo sapiens; Bos taurus; Mus musculus; Human immunodeficiency virus 1; Ovis aries; Oryctolagus cuniculus; Megathura crenulata; Frangula alnus; Quercus alba; Pandalus borealis; Oncorhynchus nerka; Sus scrofa domesticus; Ceratonia siliqua; Bothrops moojeni; Senegalia senegal; Dermestes lardarius; Trypanosoma cruzi; Gallus gallus; Pachymenia carnosa. 7 samples. Type: Protein profiling by protein array.
Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define growth physiology
GEO Series GSE152214. Escherichia coli str. K-12 substr. MG1655. 24 samples. Type: Expression profiling by high throughput sequencing.
Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies VI
GEO Series GSE100309. Gossypium hirsutum; Rhodotorula; Homo sapiens; Bos taurus; Mus musculus; Human immunodeficiency virus 1; Trypanosoma cruzi; Gallus gallus; Bothrops moojeni; Pachymenia carnosa; Pandalus borealis; Oncorhynchus nerka; Sus scrofa domesticus; Ovis aries; Ceratonia siliqua; Frangula alnus; Senegalia senegal; Dermestes lardarius; Quercus alba; Oryctolagus cuniculus; Megathura crenulata. 7 samples. Type: Protein profiling by protein array.
Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (scRNA-seq dataset)
GEO Series GSE149635. Mus musculus. 50 samples. Type: Expression profiling by high throughput sequencing.
Dynamic Control of Argonautes by a Rapidly Evolving Immunological Switch
GEO Series GSE283649. Caenorhabditis elegans. 44 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Industry Practices and Challenges for the Evolvability Assurance of Microservices: A Systematic Grey Literature Review
<p>This repository contains all publicly available artifacts related to a systematic grey literature review (GLR) about the evolvability assurance of microservices in industry. We selected and analyzed 295 practitioner online resources obtained via Google, Bing, and selected StackExchange communities. The study took place in 2020 from January to April.</p>
Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
<p><strong>Understanding the genetic regulatory code that governs gene expression is a primary challenge in molecular biology that opens up possibilities to cure human diseases and solve biotechnology problems. However, the fundamental question of how each of the individual coding and non-coding regions of the gene regulatory structure interact and contribute to the mRNA expression levels remains unanswered. Considering that all the information for gene expression regulation is already present in living cells, here we applied deep learning on over 20,000 mRNA datasets to discover the genetic regulatory code controlling mRNA expression in 7 model organisms ranging from bacteria to Human. We show that in all organisms, mRNA abundance can be predicted directly from the DNA sequence with high accuracy, demonstrating that up to 82% of the variation of gene expression levels is encoded in the gene regulatory structure. Coding and non-coding regions carry both overlapping and orthogonal information and jointly contribute to gene expression levels. By searching for DNA regulatory motifs present across the whole gene regulatory structure, we discover that motif interactions can regulate gene expression levels in a range of over three orders of magnitude. The uncovered co-evolution of coding and non-coding regions challenges the current paradigm that single motifs or regions are solely responsible for gene expression levels. Instead, we demonstrate how the holistic system that spans the entire gene regulatory structure, and which contains the right combination of all regulatory elements, is required to understand, control, and design any future gene expression systems.</strong></p>
Obtaining a Set of Recommendations for Evolving Executable Languages towards Systems-of-Systems Architecture Design
<p>Obtaining a Set of Recommendations for Evolving Executable Languages towards Systems-of-Systems Architecture Design</p>
Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection
High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.
Data from: Effective polyploidy causes phenotypic delay and influences bacterial evolvability
Whether mutations in bacteria exhibit a noticeable delay before expressing their corresponding mutant phenotype was discussed intensively in the 1940s to 1950s, but the discussion eventually waned for lack of supportive evidence and perceived incompatibility with observed mutant distributions in fluctuation tests. Phenotypic delay in bacteria is widely assumed to be negligible, despite the lack of direct evidence. Here, we revisited the question using recombineering to introduce antibiotic resistance mutations into E. coli at defined time points and then tracking expression of the corresponding mutant phenotype over time. Contrary to previous assumptions, we found a substantial median phenotypic delay of three to four generations. We provided evidence that the primary source of this delay is multifork replication causing cells to be effectively polyploid, whereby wild-type gene copies transiently mask the phenotype of recessive mutant gene copies in the same cell. Using modeling and simulation methods, we explored the consequences of effective polyploidy for mutation rate estimation by fluctuation tests and sequencing-based methods. For recessive mutations, despite the substantial phenotypic delay, the per-copy or per-genome mutation rate is accurately estimated. However, the per-cell rate cannot be estimated by existing methods. Finally, with a mathematical model, we showed that effective polyploidy increases the frequency of costly recessive mutations in the standing genetic variation (SGV), and thus their potential contribution to evolutionary adaptation, while drastically reducing the chance that de novo recessive mutations can rescue populations facing a harsh environmental change such as antibiotic treatment. Overall, we have identified phenotypic delay and effective polyploidy as previously overlooked but essential components in bacterial evolvability, including antibiotic resistance evolution.
West Nile Virus evolves at the pace of its avian hosts' life-history
<p>Disease resistant hosts are central in the spread, persistence, adaptation and diversification of infectious pathogens. In theory, resistant hosts must compromise on reproduction and invest more energy in self maintenance and immune defence. Here we investigated these hypotheses on the emergence of West Nile Virus (WNV) from 1999 to 2012 in the United States, when the virus caused mass mortality in some bird species. Our study comprehends two steps: First, we used regression tree meta-analysis on 233 reports of dead birds from 90 species, to test correlations between WNV-linked mortality and the birds' life history and ecological traits. Second, we tested links between diversification of WNV and the reproductive investment and self-maintenance of its avian hosts, by analysing the phylogeography of 520 genome sequences of WNV from 1999 to 2012. Statistical analyses revealed less WNV-linked mortality in both, species that incubate their eggs for few days (>17) and large species (>235g). The evolutionary trajectory of the virus suggests that there was no special viral strain infecting the most and the less vulnerable species. However, by 2012 the WNV strains found in large birds like American crows (<i>Corvus brachyrhynchos</i>) diversified and evolved separately from the rest. Together, our findings support that hosts' reproductive investment impairs disease resistance, and hosts investing in self-maintenance may lead WNV diversification.</p>
Data from: Can maternally inherited endosymbionts adapt to a novel host? Direct costs of Spiroplasma infection, but not vertical transmission efficiency, evolve rapidly after horizontal transfer into D. melanogaster
Maternally inherited symbionts are common in arthropods and many have important roles in host adaptation. The observation that specific symbiont lineages infect distantly related host species implies new interactions are commonly established by lateral transfer events. However, studies have shown that symbionts often perform poorly in novel hosts. We hypothesized selection on the symbiont may be sufficiently rapid that poor performance in a novel host environment is rapidly ameliorated, permitting symbiont maintenance. Here, we test this prediction for a Spiroplasma strain transinfected into the novel host Drosophila melanogaster. In the generations immediately following transinfection, the symbiont had low transmission efficiency to offspring and imposed severe fitness costs on its host. We observed that effects on host fitness evolved rapidly, being undetectable after 17 generations in the novel host, whereas vertical transmission efficiency was poorly responsive over this period. Our results suggest that long-term symbiosis may more readily be established in cases where symbionts perform poorly in just one aspect of symbiosis.
Data from: Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster
Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought.
Data from: Convergently evolved toxic secondary metabolites in plants drive the parallel molecular evolution of insect resistance
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae). These flies have colonized host plants in four botanical families that convergently evolved cardiac glycosides of two structural types: cardenolides and bufadienolides. We compared each of six fly species feeding on such plants to a phylogenetically related but nonadapted species. Irrespective of the type of cardiac glycoside in the host plant, five out of six exposed species displayed substitutions in the cardiac glycoside–binding site of the Na,K-ATPase that were previously described in other insect orders; in only one species was the gene duplicated. In vitro assays of nervous tissue extractions confirmed that the substitutions lead to increased resistance of the Na,K-ATPase. Our results demonstrate that target site insensitivity of Na,K-ATPase is a common response to dietary cardiac glycosides leading to highly predictable amino acid changes; nonetheless, convergent evolution of gene duplication for this multifunctional enzyme appears more constrained.
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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.