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4,566 results for “marker”
Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of the major human malaria parasites, <i>Plasmodium falciparum</i> (Pf) and <i>Plasmodium vivax</i> (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium (mLD) post-LLIN was a positive indicator of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system
Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species, some of which are closely related to human life. A robust phylogeny and taxonomy of snakes is crucial for us to know, study, protect and make use of them. For a large group such as snakes, cross-study data utilization is important which can be facilitated by standardization of the loci used for systematic analyses. In this study, we combined 5 mitochondrial markers, 19 vertebrate-universal nuclear protein coding (NPC) markers and 72 snake-specific noncoding intron markers, and generated a unified multilocus marker system for studies of snake systematics. This marker system is an addition to the squamate conserved locus set compiled for large-scale sequence capture experiments. We applied this marker system to over 440 snake samples and constructed the currently most comprehensive systematics framework of the snakes in China. Robust snake phylogenetic relationships were recovered at both deep and shallow evolutionary depths, demonstrating the usefulness of this multilocus marker system. Discordance was revealed by a parallel comparison between the snake tree based on our multilocus marker system and that based on only the mitochondrial loci, highlighting the necessity of using multiple marker types to better understand the snake evolutionary histories. The divergence times of different snake groups were estimated with the multilocus data set. Our comprehensive snake tree not only confirms many important nodes inferred in previous studies but also contributes new insights into the phylogenetic relationships among snakes. Suggestions are made for the current snake taxonomy.
Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
<p>Pea (<em>Pisum</em> <em>sativum</em> L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (<em>Pisum</em> sp.) are remaining controversial. To characterize patterns of genetic and morphological variation and investigate the classification of <em>Pisum</em>, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea representing three species of <em>Pisum</em> utilizing 34 morphological traits and 87 polymorphic SSR markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of <em>Pisum fulvum</em>, <em>Pisum</em> <em>abyssinicum</em> and some wild <em>P. sativum</em> accessions, whereas groups II and III consisted of the two genetic groups under <em>P. sativum </em>representing different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of <em>Pisum</em>, <em>P. fulvum</em> and <em>P. abyssinicum</em> possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of <em>P. sativum</em> described by some authors were not supported in this study, with the exception of several genotypes of <em>P. sativum</em> subsp. <em>elatius</em> that were clustered with <em>P. fulvum</em> and <em>P. abyssinicum</em>. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.</p>
Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease
<p>End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We performed dense serial blood sampling in hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients) and used Olink immunoassays to measure 436 circulating proteins. Comparison to 51 non-infected ESKD patients revealed 221 proteins differentially expressed in COVID-19, of which 69.7% replicated in an independent cohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity scores, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g proteinase-3) and epithelial injury (e.g. KRT19). Random Forests machine learning identified predictors of current or future severity such as KRT19, PARP1, PADI2, CCL7, and IL1RL1 (ST2). Survival analysis with joint models revealed 69 predictors of death including IL22RA1, CCL28, and the neutrophil-derived chemotaxin AZU1 (Azurocidin). Finally, longitudinal modelling with linear mixed models uncovered 32 proteins that display different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. Our findings point to aberrant innate immune activation and leucocyte-endothelial interactions as central to the pathology of severe COVID-19. The data from this unique cohort of high-risk individuals provide a valuable resource for identifying drug targets in COVID-19.</p>
Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.
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>
Short-Tandem-Repeat (STR) marker set for Eurasian lynx for article: Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland
<p>Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (~23,000 km<sup>2</sup>) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult.</p>
Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
<p>Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread <i>Elymus</i> species. <i>Elymus excelsus</i> Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of <i>E. excelsus</i> germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of <i>E. excelsus</i> from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei's genetic diversity (H) and Shannon's diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of <i>E. excelsus</i> germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (<i>F</i><sub><i>st</i></sub> = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (<i>H</i><sub><i>e</i></sub> = 0.197) was greater than that of the GSC (<i>H</i><sub><i>e</i></sub> = 0.176) and XJC (<i>H</i><sub><i>e</i></sub> = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that <i>E. excelsus</i> accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable <i>E. excelsus</i> germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.</p>
Hunt honey bee markers
<p>Early honey bee QTL studies (e.g. Hunt et al 1995) relied on RAPD and STS markers. For the latter, the sequences were often not included in the final publication or were difficult to find in the literature. The author discovered the attached list of markers for honey bees on Greg Hunt's desktop computer in 2019. The list is composed of published and unpublished marker sequences corresponding to those in QTL papers from 1995 onwards. This is not a peer-reviewed data set. <br> <br> Hunt, Greg J., et al. "Major quantitative trait loci affecting honey bee foraging behavior." <i>Genetics</i> 141.4 (1995): 1537-1545.</p>
Data from: Is MHC diversity a better marker for conservation than neutral genetic diversity? a case study of two contrasting dolphin populations
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.
19th Century - CO, OK, NM Border Marker
Photogrammetric model of the 19th century border marker placed near the point where the modern states of Colorado, Oklahoma, and New Mexico meet. Visited this while doing field work in the area during the summer of 2017. Source: Objaverse 1.0 / Sketchfab
Grave Marker of James A. and Lillian Weatherwax
Grave marker of my great-granduncle and aunt (my paternal grandfather's aunt and uncle) James Archibald and Lillian (nee Poulton) Weatherwax. Son and daughter-in-law of [Myron E. and Annie Weatherwax](https://sketchfab.com/3d-models/grave-marker-of-myron-e-and-annie-weatherwax-e8233d21cb7841b7b61f62969b7620b1); brother and sister-in-law of [Myron W. Weatherwax](https://sketchfab.com/3d-models/grave-marker-of-myron-and-hazel-dunn-weatherwax-17cc6622bb1c4321813fe71dededf59d) and [Clifford T. Weatherwax](https://sketchfab.com/3d-models/grave-marker-of-clifford-t-weatherwax-family-2557e5f3df4e498ba0c28623108b27d5). Photogrammetric model created in Meshroom; camera: Canon EOS Rebel T100; postprocessing (topological repair, cropping, decimation and texure optimization) in Meshlab. Ashuelot Cemetery, Dalton, MA. Approximate geolocation: 42.47612° N, 73.18255° W. Source: Objaverse 1.0 / Sketchfab
Dermot MacMorrough's Grave Marker
Grave marker of the Irish kingdom Leinster's beloved king Dermot Mac Morrough in Ferns, Ireland. There is some debate as to whether or not Dermot is actually interred there or perhaps in St. Edan's Cathedral, but the marker is still stands in the Ferns Graveyard. Source: Objaverse 1.0 / Sketchfab
Lafayette Park - Washington 200th Marker
> **WASHINGTON** > FIRST TOOK COMMAND OF THE > AMERICAN ARMY UNDER THE > GRANDPARENT OF THIS ELM > AT CAMBRIDGE, MASS, > JULY 3, 1775 > ------- > RAISED AND PRESENTED BY MARYLAND > D.A.R., MARKED BY NEW YORK STATE > D.A.R., THIS TREE IS PLANTED > AS PART OF THE 200TH ANNI- > VERSARY OF THE BIRTH OF > GEORGE WASHINGTON, > 1732-1932 Ironically, the elm seems to be gone, but the marker remains. Photogrammetric model created from 75 LG V35 photos in Meshroom and postprocessed in Meshlab. Geolocation: 42.653138° N, 73.756128° W Source: Objaverse 1.0 / Sketchfab
Boundary Marker Spencer Park
A metal boundary marker on the east side of Spencer Park (road), Wandsworth, London. It reads: "BATTERSEA 1863". 60 photos taken in June 2021 with a Sony a6000 and processed in Reality Capture. Source: Objaverse 1.0 / Sketchfab
St Botolph's Without Aldersgate Boundary Marker
A small boundary marker plaque attached to the base of a pillar outside the rear of 1 St Martin's-le-Grand on King Edward Street, London. 70 photos taken in November 2020 with a Sony a6000 and processed in Reality Capture. Source: Objaverse 1.0 / Sketchfab
London Parish Boundary Marker
A rare London parish boundary marker that looks like a bollard. On the junction of King's Cross Road and Calthorpe Street. Dated 1886. Parishes: Clerkenwell, St James & St John. PBM412-2 Source: Objaverse 1.0 / Sketchfab
Kilburn Bros Stereoscopic view historical marker
Historical marker for the kilburn factory scan by austinbeaulier.com https://en.wikipedia.org/wiki/Benjamin_W._Kilburn Source: Objaverse 1.0 / Sketchfab
Oakland Marker Katie Malone Sullivan
Born in Dundalk Co. Louth, Ireland on June 17, 1840 and passed away in Atlanta, Georgia on August 17, 1091. She is buried in the older part of the cemetery. Her headstone is draped and there is a flower wreath on the back that has roses, daisies, and pansies. The front of the marble marker has daffodils, cross and crown, and ivy deeply relieved into the stone. It is a truly stunning marker, carved by Crouch M. Sc. G. Company. Source: Objaverse 1.0 / Sketchfab
Regents Park Boundary Marker 1
A parish boundary marker stone in Regents Park, London. It marked the boundary between St Marylebone and St Pancras. See map below for location (1). 81 photos taken in July 2020 with a Sony a6000 and processed in Reality Capture. Source: Objaverse 1.0 / Sketchfab
ScienceDex guides
Understand access before you commit
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.