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116 results for “Bottlenecks”
Data from: Nonselective bottlenecks control the divergence and diversification of phase-variable bacterial populations
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Data from: Low bottleneck detection in long-lived species despite lost genetic diversity: a case study of tuatara and eastern massasauga rattlesnakes
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Direct probing of germinal center responses reveals immunological features and bottlenecks for nAb responses to an engineered HIV trimer
GEO Series GSE89148. Macaca mulatta. 24 samples. Type: Expression profiling by high throughput sequencing.
Relevance of the regulation of the brain-placental axis to the nocturnal bottleneck of mammals
GEO Series GSE261814. Sus scrofa. 2 samples. Type: Expression profiling by high throughput sequencing.
A human mitochondrial DNA genetic bottleneck prevents mutational meltdown by purifying the early maternal germ line
GEO Series GSE77882. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Data from: The impact of bottlenecks on microbial survival, adaptation and phenotypic switching in host-pathogen interactions
Microbial pathogens and viruses can often maintain sufficient population diversity to evade a wide range of host immune responses. However, when populations experience bottlenecks, as occurs frequently during initiation of new infections, pathogens require specialized mechanisms to regenerate diversity. We address the evolution of such mechanisms, known as stochastic phenotype switches, which are prevalent in pathogenic bacteria. We analyze a model of pathogen diversification in a changing host environment that accounts for selective bottlenecks, wherein different phenotypes have distinct transmission probabilities between hosts. We show that under stringent bottlenecks, such that only one phenotype can initiate new infections, there exists a threshold stochastic switching rate below which all pathogen lineages go extinct, and above which survival is a near certainty. We determine how quickly stochastic switching rates can evolve by computing a fitness landscape for the evolutionary dynamics of switching rates, and analyzing its dependence on both the stringency of bottlenecks and the duration of within-host growth periods. We show that increasing the stringency of bottlenecks or decreasing the period of growth results in faster adaptation of switching rates. Our model provides strong theoretical evidence that bottlenecks play a critical role in accelerating the evolutionary dynamics of pathogens.
Experimental habitat fragmentation disrupts host-parasite interaction over decades via life-cycle bottlenecks
Habitat loss and fragmentation are likely to seriously impact parasites, a less studied but critical component of ecosystems, yet we lack long-term experimental evidence. Parasites structure communities, increase connectivity in food webs, and account for a large proportion of an ecosystem's total biomass. Food web models predict that parasites with multiple obligate hosts are at greater risk of extinction because the local extinction, or reduction in abundance, of any host will result in a life-cycle bottleneck for the parasite. We examine the response of a parasite and its multiple hosts to forest fragmentation over 26 years in the Wog Wog Habitat Fragmentation Experiment in southeastern Australia. The parasite is the nematode Hedruris wogwogensis, its intermediate host is the amphipod, Arcitalitrus sylvaticus, and its definitive host is the skink, Lampropholis guichenoti. In the first decade after fragmentation, nematodes completely disappeared from the matrix (plantation forestry) and all but disappeared from their definitive host (skinks) in fragments, and by the third decade after fragmentation had not appreciably recovered anywhere in the fragmented landscape compared to continuous forest. The low prevalence of the nematode in the fragmented landscape was associated with the low abundance of one or the other host in different decades: low abundance of the intermediate host (amphipod) in the first decade and low abundance of the definitive host (skink) in the third decade. In turn, the low abundance of each host was associated with changes to the abiotic environment over time due largely to the dynamically changing matrix as the plantation trees grew. Our study provides rare long-term experimental evidence of how disturbance can cause local extinction in parasites with life cycles dependent on more than one host species through population bottlenecks at any life stage. Mismatches in the abundance of multiple hosts over time are likely to be common following disturbance, thus causing parasites with complex life cycles to be particularly susceptible to habitat fragmentation and other disturbances. The integrity of food webs, communities, and ecosystems in fragmented landscapes may be more compromised than presently appreciated due to the sensitivity of parasites to habitat fragmentation.
Understanding How Salmonella Typhi Infects Humans (Bottlenecks)
ClinicalTrials.gov study NCT03889067. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: The impact of bottlenecks on microbial survival, adaptation and phenotypic switching in host-pathogen interactions
Open the record for dataset details and reuse information.
Experimental habitat fragmentation disrupts host-parasite interaction over decades via life-cycle bottlenecks
Open the record for dataset details and reuse information.
Single-cell bottlenecks and dead-ends during glioma premalignancy
GEO Series GSE147360. Mus musculus. 240 samples. Type: Expression profiling by high throughput sequencing.
Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens
GEO Series GSE291368. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant
GEO Series GSE169427. Mus musculus. 768 samples. Type: Expression profiling by high throughput sequencing.
Key hub and bottleneck genes differentiate the macrophage response to virulent and attenuated Mycobacterium bovis
GEO Series GSE59774. Bos taurus. 41 samples. Type: Expression profiling by array.
Nucleoporin-93 overexpression overcomes trafficking bottlenecks in metastasis of breast cancer
GEO Series GSE156103. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Cell-generated forces contribute to bottleneck during somatic cell reprogramming
GEO Series GSE148580. Homo sapiens. 37 samples. Type: Expression profiling by high throughput sequencing.
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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.