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6,383 results for “isolates”
UNAM Mexico City Shake Table Tests on an Isolated building_2018
<p>Video showing shake table tests of a 5-story miniature building isolated with double concave friction pendulums. Testing was conducted at the shaking table of the Instituto de Ingenieria, National University of Mexico, Mexico City.</p> <p>Ground acceleration record input: Llolleo, recorded March 3, 1985, Chile (Ms 7.8), record was not scaled</p> <p>Grant: CONACYT, Mexico, Grant No 167445</p> <p>The isolators were donated for this research by FIP Industriale (Italy)</p>
Automated Isolation for White-box Test Generation
<p>We present an approach for automated isolation in white-box test generation. This publication contains the data and the corresponding analysis script written in R.</p>
Specific monitoring results of ESBL-/AmpC-/carbapenemase-producing bacteria and specific monitoring of carbapenemase-producing bacteria, in the absence of isolates detected complementing the European Union Overview Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018
<p>This dataset derives from the specific monitoring of E. coli producers of ESBLs/AmpC/carbapenemases, as well as the specific monitoring of carbapenemase-producers (voluntary reporting), in the absence of any isolates detected. This dataset contains only data when Total units positive equals zero '0'.</p>
Phenotypic modulation of biofilm formation in a Staphylococcus epidermidis orthopedic clinical isolate grown under different mechanical stimuli: contribution from a combined proteomic study
<p>One of the major causes of prosthetic joint failure is infection. Recently, coagulase negative <em>Staphylococcus epidermidis</em> has been identified as an emergent, nosocomial pathogen involved in subclinical prosthetic join infections (PJIs). The diagnosis of PJIs mediated by <em>S. epidermidis</em> is usually complex and difficulties due to the absence of acute clinical signs derived from the host immune system response. Therefore, analysis of protein patterns in biofilm-producing <em>S. epidermidis</em> allows for the examination of the molecular basis of biofilm formation. Thus, in the present study, the proteome of a clinical isolate <em>S. epidermidis</em> was analyzed when cultured in its planktonic or sessile form to examine protein expression changes depending on culture conditions. After 24 hours of culture, sessile bacteria exhibited increased gene expression for ribosomal activity and for expression of proteins related to the initial attachment phase, involved in the capsular polysaccharide/adhesin, surface associated proteins and peptidoglycan biosynthesis. Likewise, planktonic <em>S. epidermidis</em> was able to aggregate after 24 hours, synthesizing the accumulation associate protein and cell-wall molecules through the activation of the YycFG and ArlRS, two component regulatory pathways. Prolonged culture under vigorous agitation generated a stressful growing environment triggering aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions.</p> <p>Further studies will be essential to support these findings in order to further delineate the complex mechanisms of biofilm formation of <em>S. epidermidis</em> and they could provide the groundwork for the development of new drugs against biofilm-related infections, as well as the identification of novel biomarkers of subclinical or chronic infections mediated by these emerging, low virulence pathogens.</p>
FIGURE 9 —Isolated chevron NMMNH P - 10 1 3. l in Tyrannosaurus rex from the McRae Formation (Lancian, Upper Cretaceous), Elephant Butte Resevoir, Sierra County, New Mexico
FIGURE 9 —Isolated chevron NMMNH P - 10 1 3. l Bar scale = 10 cm.
Data from: Antibacterial activity of graphene oxide nanosheet against multi drug resistant superbugs isolated from infected patients
Graphene oxide (GO) is a derivative of graphene nanosheet which is the most promising material of the decade in biomedical research. In particular, it has been known as an antimicrobial nanomaterial with good biocompatibility. In this study, we have synthesized and characterize GO and checked its antimicrobial property against different Gram-negative and Gram-positive multi drug resistant (MDR) hospital superbugs grown in solid agar-based nutrient plates with and without human serum through the utilization of agar well diffusion method, live/dead fluorescent staining and genotoxicity analysis. The main focus of the antimicrobial activity analysis is to distinguish the killing performance of GO in artificial and blood containing media because after injection into the bloodstream the activity of GO may be modified by adsorption of blood proteins or other biomolecules. No significant changes in antibacterial activity were found in these two different conditions. We also compare the bactericidal capability of GO with some commonly administrated antibiotics and in all cases the degree of inhibition is found to be higher. The data presented here are novel and show that GO is an effective bactericidal agents against different superbugs and can be used as a future antibacterial agent.
Adaptive zones shape the magnitude of premating reproductive isolation in Timema stick insects
<p>Simpson's fossil-record inspired model of 'adaptive zones' proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here we use ecological, phylogenetic, and behavioural data to test these predictions in <i>Timema </i>stick insects. We show that host use in <i>Timema</i> is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity</p>
Data from: Floral isolation and pollination in two hummingbird-pollinated heliconias data
Differences in feeding performance and aggressive abilities between species and sexes of hummingbirds are often associated with the partitioning of their food sources, but whether such partitioning results in floral isolation (reproductive isolation at the stage of pollination) has received little attention. We examined components of floral isolation and pollinator effectiveness of Heliconia caribaea and H. bihai on the island of Dominica, West Indies. The short flowers of H. caribaea match the short bills of male Anthracothorax jugularis, its primary pollinator, whereas the long flowers of H. bihai match the long bills of female A. jugularis, its primary pollinator. In pollination experiments, both sexes of A. jugularis were equally effective at pollinating the short flowers of H. caribaea, which they preferred to H. bihai, whereas females were more effective at pollinating the long flowers of H. bihai. Moreover, an average difference in length of 12 mm between H. caribaea and H. bihai flowers did not prevent heterospecific pollen transfer, and both sexes transported pollen between the two plant species. In field studies using powdered dyes as pollen analogs, however, heterospecific pollen transfer was minimal, with only 2 of 168 flowers receiving dye from the other species. The length of H. bihai flowers acted as an exploitation barrier to male A. jugularis, which were unable to completely remove nectar from 88% of the flowers they visited. In contrast, interference competition combined with high floral fidelity through traplining prevented female A. jugularis from transferring pollen between the two Heliconia species. A combination of exploitation barriers, interference and exploitative competition, and pollinator preferences maintains floral isolation between these heliconias, and may have contributed to the evolution of this hummingbird-plant system.
Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China
<p>The fruit fly <i>Drosophila</i> <i>melanogaster</i> is a model species in evolutionary studies. However, the population processes of this species in East Asia are poorly studied, even though this area was one of the first regions colonized outside of its native distribution range. Here we examined the population genetic structure of <i>D.</i> <i>melanogaster</i> across China. There were 14 mitochondrial haplotypes with ten unique ones out of 23 known from around the globe. Pairwise F<sub>ST</sub> values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full RDA analysis showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, three environmental variables of bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that a high level of gene flow, geographical isolation, and environmental factors have together shaped the population genetic structure of <i>D.</i> <i>melanogaster</i> after its introduction into China.</p>
Data from: K-13 Propeller gene polymorphisms isolated between 2014 and 2017 from Cameroonian Plasmodium falciparum malaria patients
The emergence of artemisinin-resistant parasites since the late 2000s at the border of Cambodia and Thailand poses serious threats to malaria control globally, particularly in Africa which bears the highest malaria transmission burden. This study aimed to obtain reliable data on the current state of the kelch13 molecular marker for artemisinin resistance in Plasmodium falciparum in Cameroon. DNA was extracted from the dried blood spots collected from epidemiologically distinct endemic areas in the Center, Littoral and North regions of Cameroon. Nested PCR products from the Kelch13-propeller gene were sequenced and analyzed on an ABI 3730XL automatic sequencer. Of 219 dried blood spots, 175 were sequenced successfully. We identified six K13 mutations in 2.9% (5/175) of samples, including 2 non-synonymous, the V589I allele had been reported in Africa already and one new allele E612K had not been reported yet. These two non-synonymous mutations were uniquely found in parasites from the Littoral region. One sample showed two synonymous mutations within the kelch13 gene. We also observed two infected samples with mixed K13 mutant and K13 wild-type infection. Taken together, our data suggested the circulation of the non-synonymous K13 mutations in Cameroon. Albeit no mutations known to be associated with parasite clearance delays in the study population, there is need for continuous surveillance for earlier detection of resistance as long as ACTs are used and scaled up in the community.
Data from: Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice (Onychomys)
Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities, and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long-distance acoustic signals to attract and localize mates; O. arenicola and O. torridus are acoustically similar and morphologically cryptic whereas O. leucogaster is larger and acoustically distinct. We used genotyping-by-sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, lab crosses between O. torridus
Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity
<p>Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (<i>Lucania goodei</i>) and rainwater killifish (<i>L. parva</i>) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioral, extrinsic, and intrinsic postzygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between <i>L. parva </i>and <i>L. goodei</i> to explore the genetic architecture of salinity tolerance, behavioral isolation, and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in <i>L. parva</i> (relative to <i>L. goodei</i>). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome, and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioral or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between <i>Lucania</i> species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioral and intrinsic isolation as a byproduct. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioral isolation instead, possibly facilitated by linkage between behavioral isolation and intrinsic isolation loci on the fused chromosome.</p>
Substituents isolated from analog series
<p>From ~24,000 analog series extracted from ChEMBL, more than 19,000 substituent fragments (SF) were identified. A subset of ~400 substituent fragments occurred most frequently in different compound classes (frequent SF, FSF). The entire SF/FSF collection is made available here as a part of a forthcoming publication in the Journal of Medicinal Chemistry. </p>
Competition for pollination and isolation from mates differentially impact four stages of pollination in a model grassland perennial
<p>1. Species that persist in small populations isolated by habitat destruction may experience reproductive failure. Self-incompatible plants face dual threats of mate-limitation and competition with co-flowering plants for pollination services. Such competition may lower pollinator visitation, increase heterospecific pollen transfer, and reduce the likelihood that a visit results in successful pollination.</p> <p>2. To understand how isolation from mates and competition with co-flowering species contribute to reproductive failure in fragmented habitat, we conducted an observational study of a tallgrass prairie perennial, <i>Echinacea angustifolia</i>. We quantified the isolation of focal individuals from mates, characterized species richness and counted inflorescences within 1m radius, observed pollinator visitation, collected pollinators, quantified pollen loads on pollinators and on <i>Echinacea</i> stigmas, and measured pollination success. Throughout the season, we sampled 223 focal plants.</p> <p>3. We present evidence that both co-flowering species and isolation from mates substantially limit reproduction in <i>Echinacea</i>. As the flowering season progressed, the probability of pollinator visitation to focal plants decreased and evidence for pollen-limited reproduction increased. Pollinators were most likely to visit <i>Echinacea</i> plants from low-richness floral neighbourhoods with close potential mates, or plants from high-richness neighbourhoods with distant potential mates. Frequent visitation only increased pollination success in the former case, likely because <i>Echinacea</i> in high-richness floral neighbourhoods received low-quality visits.</p> <p>4. Synthesis: In <i>Echinacea</i>, reproduction was limited by isolation from potential mates and the richness of co-flowering species. These aspects of the floral neighbourhood influenced pollinator visitation and pollination success, although conditions that predicted high visitation did not always lead to high pollination success. These results reveal how habitat modification and destruction, which influence floral neighbourhood and isolation from conspecific mates, can differentially affect various stages of reproductive biology in self-incompatible plants. Our results suggest that prairie conservation and restoration efforts that promote patches of greater floral diversity may improve reproductive outcomes in fragmented habitats.</p>
The rescue effect and inference from isolation-extinction relationships
<p>The rescue effect in metapopulations hypothesizes that less isolated patches are unlikely to go extinct because recolonization may occur between breeding seasons ("recolonization rescue"), or immigrants may sufficiently bolster population size to prevent extinction altogether ("demographic rescue"). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonization rescue for metapopulations of black rails (<i>Laterallus jamaicensis</i>) and Virginia rails (<i>Rallus limicola</i>) from occupancy surveys conducted during and between breeding seasons, and assessed the reliability of inferences about the occurrence of rescue drawn from isolation-extinction relationships, including autologistic isolation measures that corrected for unsurveyed patches and imperfect detection. Recolonization rescue occurred at expected rates, but was elevated during periods of disturbance that resulted in nonequilibrium metapopulation dynamics. Inferences from extinction-isolation relationships were unreliable, particularly for autologistic measures and for the more vagile Virginia rail.</p>
Interspecific introgression reveals a role of male genital morphology during the evolution of reproductive isolation in Drosophila
Rapid divergence in genital structures among nascent species has been posited to be an early-evolving cause of reproductive isolation, although evidence supporting this idea as a widespread phenomenon remains mixed. Using a collection of interspecific introgression lines between two Drosophila species that diverged ~240,000 years ago, we tested the hypothesis that even modest divergence in genital morphology can result in substantial fitness losses. We studied the reproductive consequences of variation in the male epandrial posterior lobes between Drosophila mauritiana and D. sechellia and found that divergence in posterior lobe morphology has significant fitness costs on several pre-fertilization and post-copulatory reproductive measures. Males with divergent posterior lobe morphology also significantly reduced the life span of their mates. Interestingly, one of the consequences of genital divergence was decreased oviposition and fertilization, which suggests that a sensory bias for posterior lobe morphology could exist in females, and thus posterior lobe morphology may be the target of cryptic female choice in these species. Our results provide evidence that divergence in genitalia can in fact give rise to substantial reproductive isolation early during species divergence, and they also reveal novel reproductive functions of the external male genitalia in Drosophila.
Staphylococcus aureus isolated from ruminants with mastitis in northern Greece dairy herds: genetic relatedness and phenotypic and genotypic characterization
<p>Figure S1: Dendrogram of SmaI PFGE pulsotypes (P) and characteristics of the 162 S. aureus isolates.</p>
Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho bleekeri) using genome wide SNP markers
<p>Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF-seq)-based genotyping was performed for Sichuan taimen with 43 yearling individuals from 3 locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (average F=2.6×10-3±0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < 0.001) and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic-relatedness-guided breeding and conservation strategy for wild fish species without pedigree information records.</p>
Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene-flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability", highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.
Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids
One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus <i>Pundamilia</i> and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum vs blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest vs blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant QTLs with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum x blue cross, whereas we find no significant QTLs in the non-sympatric red-chest x blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.
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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.