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75 results for “Dynamic conservation”
An information theory-based machine learning approach to detecting functionally conserved and coordinated protein dynamics
<p>The application of machine learning classification to the molecular dynamics of the functional states of protein allows for application of an information theoretic framework familiar to traditional bioinformatics. The functional states of proteins involving binding interactions with partners comprised of protein, DNA or small molecules can first be defined in a binary fashion (i.e. bound vs unbound), subsequently simulated in molecular dynamics software, and then employed as a comparative training set for a binary machine learning classifier capable of discerning the complex dynamical consequences of binding interaction. This learner can subsequently be deployed on new simulations of the functionally bound state to validate its ability to recognize the molecular motions that are supporting binding function. Regions of proteins with functionally conserved dynamics will induce significant local correlations in learning performance across independent validation runs. Through case studies of Rbp subunit 4/7 interaction in RNA Pol II and DNA-protein interactions of TATA binding protein, we demonstrate this method of detecting functionally conserved protein dynamics. We also demonstrate how Shannon information, relative entropy and mutual information can be applied to these binary classification states of dynamic simulations in order to compare dynamics and identify concerted motions involved in dynamic interactions across sites.</p>
dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'
<p>This data supports the Figures in the preprint titled</p> <p><strong>Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease</strong></p> <p><strong>working abstract</strong></p> <p>The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease, which is a critical dynamic region involved in non-specific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV). We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.</p>
Extinction dynamics under extreme conservation threat: The flora of St. Helena
<p><span><span><span><span><span><span><span><span><span><span><span>The flora of the island of St Helena provides an amplified system for the study of extinction by reason of the island's high endemism, small size, vulnerable biota, length of time of severe disturbance (since 1502) and severity of threats. Endemic plants have been eliminated from 96.5% of St Helena by habitat loss. There are eight recorded extinctions in the vascular flora since 1771 giving an extinction rate of 581 extinctions per million species per year (E/MSY). This is considerably higher than background extinction rates, variously estimated at 1 or 0.1 E/MSY. We have no information for plant extinctions prior to 1771 but applying the same extinction rate to the period 1502 to 1771 suggests that there may be around ten unrecorded historical extinctions. We use census data and population decline estimates to project likely extinction forward in time. The projected overall extinction rate for the next 200 years is somewhat higher at 625 E/MSY. However, our data predict an extinction crunch in the next 50 years with 4 species out of the remaining 48 likely to become extinct during this period. It is interesting that during a period when the native plant areas dropped to 3.5% of the original, the extinction rate appears to have remained shallowly linear with under 30% of the endemic flora becoming extinct.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research
The greatest extent of Afromontane environments in the world is found in Ethiopia. These areas support exceptional biodiversity, but forest cover and ecological integrity have declined sharply in recent decades. Conservation and management efforts are hampered in part by an inadequate understanding of the basic ecology of major tree species. We investigated population structure and inferred population dynamics from size frequency distributions of 22 forest tree species encountered in montane forests of Ethiopia. We collected new empirical data from four sites in the Bale Mountains, where some of the country's most extensive and least disturbed forests remain, and conducted a systematic review and analysis of all such studies that reported population structure for one or more of these species in Ethiopia. Thirteen widespread montane tree species showed a reverse-J size distribution, indicating a relatively stable population structure. Six other species had size-frequency distributions that indicate episodic recruitment and/or removal of certain size classes. Specific causes of these patterns are uncertain: they may involve timber harvesting, herbivory, fire, or natural disturbances, but patterns were inconsistent and locality dependent. For three other tree species, existing data are inadequate for any interpretation of population structure and dynamics. A species of particular conservation concern that emerged from this analysis was Hagenia abyssinica, which was found in all areas to consist only of larger individuals with no recent recruitment. For management and conservation purposes, the species in most urgent need of new research are those with inadequate or inconsistent data, and H. abyssinica..
Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus
<p>The oceanic whitetip shark, <em>Carcharhinus longimanus</em>, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet, little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide, mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with <em>F</em><sub>ST </sub>but not Φ<sub>ST</sub>) indicated differentiation between Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (Φ<sub>ST</sub> = 0.051; F<sub>ST</sub> = 0.092). Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark's status falls in the middle to upper ranges compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong conservation measures are effectively implemented.</p>
Integrating dynamic processes into waterfowl conservation prioritization tools
<p><b>Aim: </b> Traditional approaches for including species' distributions in conservation planning have presented them as long-term averages of variation. Like these approaches, the main waterfowl conservation targeting tool in the United States Prairie Pothole Region (US PPR) is based primarily on long-term averaged distributions of breeding pairs. While this tool has supported valuable conservation, it does not explicitly consider spatiotemporal changes in spring wetland availability and does not assess wetland availability during the brood rearing period. We sought to develop a modeling approach and targeting tool that incorporated these types of dynamics for breeding waterfowl pairs and broods. This goal also presented an opportunity for us to compare predictions from a traditional targeting tool based on long-term averages to predictions from spatiotemporal models. Such a comparison facilitated tests of the underlying assumption that this traditional targeting tool could provide an effective surrogate measure for conservation objectives such as brood abundance and climate refugia.</p> <p><b>Location: </b>US PPR</p> <p><b>Methods:</b> We developed spatiotemporal models of waterfowl pair and brood abundance within the PPR of the US. We compared the distributions predicted by these models and assessed similarity with the averaged pair data that is used to develop the current waterfowl targeting tool.</p> <p><b>Results:</b> Results demonstrated low similarity and correlation between the averaged pair data and spatiotemporal brood and pair models. The spatiotemporal pair model distributions served as better surrogates for brood abundance than the averaged pair data.</p> <p><b>Main conclusions:</b> Our study underscored the contributions that the current targeting tool has made to waterfowl conservation but also suggested that conservation plans in the region would benefit from the consideration of inter- and intra-annual dynamics. We suggested that using only the averaged pair data and derived products might result in the omission of 46-98% of important pair and brood habitat, respectively, from conservation plans.</p>
Landscape-scale dynamics of a threatened species respond to local-scale conservation management
<p><span>Landscape-scale approaches are increasingly advocated for species conservation but ensuring landscape level persistence by enlarging the size of patches or increasing their physical connectivity is often impractical. Here, we test how such barriers can be overcome by management of habitat at the local (site-based) level, using a rare butterfly as an exemplar. We used four surveys of the entire UK distribution of the Lulworth Skipper (<em>Thymelicus</em> <em>acteon</em>) over 40 years to test how local habitat influences population density and colonization / extinction dynamics, and parameterized, validated and applied a metapopulation model to simulate effects of varying local habitat quality on regional persistence. We found the total number of populations in four distribution snapshots between 1978 and 2017 varied between 59–84, and from 1997 to 2017, 34% of local populations showed turnover (colonization or extinction). Population density was closely linked to vegetation characteristics indicative of management, namely height and food plant frequency, both of which changed through time. Simulating effects of habitat quality on metapopulation dynamics 40 years into the future suggests coordinated changes to two key components of quality (vegetation height and food plant frequency) would increase patch occupancy above the range observed in the past 40 years (50–80%). In contrast, deterioration of either component below threshold levels leads to metapopulation retraction to core sub-networks of patches, or eventual extirpation. Our results indicate that changes to habitat quality can overcome constraints imposed by habitat patch area and spatial location on relative rates of colonization and local extinction, demonstrating the sensitivity of regional dynamics to targeted in situ management. Local habitat management therefore plays a key role in landscape-scale conservation. Monitoring of population density, and the monitoring and management of local (site-level) habitat quality, therefore represent effective and important components of conservation strategies in fragmented landscapes.</span></p>
Post-translocation dynamics of black-tailed prairie dogs (Cynomys ludovicianus): A successful conservation and human-wildlife conflict mitigation tool
<p>Prairie dogs have declined by 98% throughout their range in the grasslands of North America. Translocations have been used as a conservation tool to reestablish colonies of this keystone species and to mitigate human-wildlife conflict. Understanding the behavioral responses of prairie dogs to translocation is of utmost importance to enhance the persistence of the species and for species that depend on them, including the critically endangered black-footed ferret. In 2017 and 2018, we translocated 658 black-tailed prairie dogs on the Lower Brule Indian Reservation in central South Dakota, USA, a black-footed ferret recovery site. Here, we describe and evaluate the effectiveness of translocating prairie dogs into augered burrows and soft released within presumed coteries to reestablish colonies in previously occupied habitat. We released prairie dogs implanted with passive integrated transponders (PIT tags) and conducted recapture events approximately 1-month and 1-year post-release. We hypothesized that these methods would result in a successful translocation and that prairie dogs released as coteries would remain close to where they were released because of their highly social structure. In support of these methods leading to a successful translocation, 69% of marked individuals were captured 1-month post-release, and 39% were captured 1-year post-release. Furthermore, considerable recruitment was observed with 495 unmarked juveniles captured during the 1-year post-release trapping event, and the reestablished colony had more than doubled in area by 2021. Contrary to our hypothesis, yet to our knowledge a novel finding, there was greater initial movement within the colony 1-month post-release than expected based on recapture locations compared to published average territory size; however, 1-year after release most recaptured individuals were captured within the expected territory size when compared to capture locations 1-month post-release. This research demonstrates that while translocating prairie dogs may be socially disruptive initially, it is an important conservation tool.</p>
Niche dynamics of Memecylon in Sri Lanka: distribution patterns, climate change effects, and conservation priorities
<p><b>Aim</b>: Recent climate projections have shown that the distribution of organisms in island biotas is highly affected by climate change. Here, we present the results of the analysis of niche dynamics of a plant group, <i>Memecylon</i> on Sri Lanka, an island, using species occurrences and climate data. We aim to determine which climate variables explain current distribution, model how climate change impacts the availability of suitable habitat for <i>Memecylon,</i> and determine conservation priority areas for Sri Lankan <i>Memecylon</i>.</p> <p><b>Location</b>: Sri Lanka</p> <p><b>Methods</b>: We used georeferenced occurrence data of Sri Lankan <i>Memecylon</i> to develop ecological niche models and assess both current and future potential distributions under six climate change scenarios in 2041-2060 and 2061-2080. We also overlaid land-cover, and protected area maps and performed a gap analysis to understand the impacts of land-cover changes on <i>Memecylon</i> distributions and propose new areas for conservation.</p> <p><b>Results</b>: Differences among suitable habitats of <i>Memecylon</i> were found to be related to patterns of endemism. Under varying future climate scenarios, endemic groups were predicted to experience habitat shifts, gains, or losses. The narrow endemic <i>Memecylon </i>restricted to the montane zone were predicted to be the most impacted by climate change. Projections also indicated that changes in species' habitats can be expected as early as 2041-2060. Gap analysis showed that while narrow endemic categories are considerably protected as demonstrated by their overlap with protected areas, more conservation efforts in Sri Lankan forests containing wide endemic and non-endemic <i>Memecylon</i> are needed.</p> <p><b>Main conclusions</b>: This research helped clarify general patterns of responses of Sri Lankan <i>Memecylon </i>to global climate change. Data from this study are useful for designing measures aimed at filling the gaps in forest conservation on this island.</p>
Land use and ecosystem service value spatiotemporal dynamics, topographic gradient effect and their driving factors in typical alpine ecosystems of the east Qinghai-Tibet Plateau: Implications for conservation and development
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Integrating dynamic processes into waterfowl conservation prioritization tools
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A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics
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Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research
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Post-translocation dynamics of black-tailed prairie dogs (Cynomys ludovicianus): A successful conservation and human-wildlife conflict mitigation tool
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Landscape-scale dynamics of a threatened species respond to local-scale conservation management
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Demography and dynamics of Giant Kelp cohorts across four decades: Lessons for conservation and resilience planning
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Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus
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Local sub-population dynamics of a Central European Grey Partridge meta-population support a large-scale conservation approach to halt its ongoing decline
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Extinction dynamics under extreme conservation threat: The flora of St. Helena
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Niche dynamics of Memecylon in Sri Lanka: distribution patterns, climate change effects, and conservation priorities
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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.