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4,566 results for “marker”
Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
<p class="CuerpoAA">The genetic diversity of a population is the foundation of its adaptability to environmental challenges. The South American fur seal is a widely distributed pinniped in the south cone of South America. However, a large gap in the Pacific coast separates two distinct evolutionary units for the species: the Peruvian and the Southern Pacific/Atlantic populations. Throughout the Pacific, one of the main breeding colonies is located in Guafo Island, in the southern Chilean Patagonia. As the closest reproductive population to the isolated Peruvian group, Guafo's colony may potentially facilitate gene flow, contribute with new alleles and increase genetic variability to Peruvian populations', connecting the entire Pacific's distribution of the species. In this study, Guafo's Island South American fur seal population was characterized by the identification and genotyping of species-specific microsatellite markers. As a result, we confirm that Guafo's colony is a diverse group with mild evidence of genetic structure. Although a couple of family groups among seasons were observed, results indicate that half-siblings are rare and suggest that polygyny in this species is more relaxed than previously thought. Additionally, three full-sibling pairs were genetically identified within the 2017 season, which is the first genetic support that describes the presence of twins for the species. These attributes suggest that the colony at Guafo is a panmictic large group, and could serve as a potential genetic source for other isolated populations.</p>
SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
<p><i>Malus sylvestris</i> (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry and urbanization increasingly endanger <i>Malus sylvestris </i>natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple <i>Malus ×domestica</i> (Borkh.), threatens the genetic integrity of <i>M. sylvestris</i>.</p> <p>The present study investigated the number of hybrids, genetic diversity and genetic structure of 292 putative <i>M. sylvestris</i> that originate from five different natural <i>M. sylvestris</i> populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony.</p> <p>Eighty-seven percent of the wild apple accessions were identified as pure <i>M. sylvestris</i>. The cpDNA analysis showed six private haplotypes for <i>M. sylvestris,</i> whereas three haplotypes were present in <i>M. sylvestris </i>and<i> M. ×domestica.</i> The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure <i>M. sylvestris</i> and <i>M. ×domestica </i>individuals indicating a low gene flow between both species. The genetic diversity within the pure <i>M. sylvestris</i> populations was high with a weak genetic structure between the <i>M. sylvestris</i> populations indicating an unrestricted genetic exchange between these <i>M. sylvestris</i> populations.</p> <p>The clear distinguishing of <i>M. sylvestris</i> and <i>M. ×domestica</i> confirms our expectation of the existence of pure <i>M. sylvestris </i>accessions<i> </i>in this area and supports the argument for the implementation of preservation measures to protect the <i>M. sylvestris </i>populations in<i> </i>Saxony. </p>
On the Usages and Functions of the Case Marker -niu in Colloquial Liangmai
<p>This paper attempts to describe the morphosyntactic functions and the usages of -niu in Liangmai, a Tibeto-Burman language, primarily spoken in the Northeast Indian states namely, Manipur and Nagaland. Liangmai case marking system is quite complex and it has not been fully understood. A basic description on grammatical aspect of the case marker -niu have been presented in earlier studies. Charengna (2014: 399) describes -niu as a nominative marker while Mataina (2018: 18) analyzed it as an agentive marker. Daimai (2018) presented -niu as an ergative marker on his paper Ergativity in Liangmai at NEILS-10, Assam University, Silchar. The case marker -niu is typically used optionally with subjects of transitive clauses especially when the subject is acting in volition and usually is absent in intransitive clauses. Occasionally it can be omitted from highly agentive A arguments and can even be used with non-agentive A/S arguments (Mataina 2018: 19), and this makes it difficult to explain the difference between when -niu is omitted and when it is not. Analysis on the role of -niu becomes complicated due to its multi-functional nature. Incorporating earlier studies, this paper gives more detail on Liangmai case marker -niu and does generalization on the role of -niu.</p>
Nominal Anchoring Functions of Porohanon Common Noun Markers
<p>Porohanon, spoken in the Municipality of Poro, Camotes, Cebu, Philippines is a member of the Peripheral group of the Central Bisayan branch of the Bisayan complex. This study proposes a SPECIFIC vs. NONSPECIFIC contrast in the ABSOLUTIVE, ERGATIVE, and GENITIVE forms of the common noun markers, instead of a DEFINITE vs. INDEFINITE contrast stated in previous descriptions of the speech variety.</p>
TMEM97 is correlated with the clinical features and clinical prognosis, and acts as a potential marker of multiple myeloma
<p><strong>Abstract</strong></p> <p><strong>Background</strong>: TMEM97 has been proven to be involved in many biological processes of malignancies. This study was designed to investigate the role of TMEM97 in multiple myeloma progression and clinical features and prognosis. We also predicted the potential mechanism of TMEM97 in MM prognosis.</p> <p><strong>Methods:</strong> In the present study, five GEO datasets including GSE24080, GSE13591, GSE2113, GSE19784 and GSE2658 were obtained from the National Cancer for Biotechnology Information database for analysis of TMEM97 expression and clinical features and prognosis in MM.We performed GSEA analysis to investigate the potential mechanism of TMEM97 in MM.</p> <p><strong>Results: </strong>We collected multiple myeloma data based on GEO datasets, and demonstrated the expression level of TMEM97 increased with the progression of multiple myeloma. Also the expression level of TMEM97 was correlated significantly with ISS stage in MM patients.Additionally, TMEM97 was more likely to be associated with important factors of MM prognosis, such as cytogenetic, B2M, CRP, LDH, BMPC, MRI and HGB. The multivariate analysis showed that TMEM97 was an independent factor for OS and EFS. In addition, top positively correlated genes with TMEM97 covered PUS7, GGCT, PFAS, CTPS1, RFC4 and PRMT3.</p> <p><strong>Conclusion:</strong>The expression of TMEM97 was a factor affecting the survival and prognosis of MM patients. TMEM97 may be an important prognosis biomarker and promising therapeutic target in multiple myeloma.</p>
FIGURE 6 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 6. BI phylogenetic analysis for H. polii, H. sanctori, and different Mediterranean holothuroids is based on partial sequences of the 28S rDNA gene. Four Markov Chains Monte Carlo (MCMC) samples were analyzed for 10 million (ngen=10,000,000) generations. Bootstrap values are shown above the branches. Bold labels refer to sequences obtained in the current study for H. polii and H. sanctori.
FIGURE 3 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 3. Distribution of 28S rDNA-based genetic pairwise distances among different Mediterranean species obtained in the current study and available in the GenBank. (a): H. polii vs. Mediterranean holothuroids, (b) H. sanctori vs. the Mediterranean holothuroids.
FIGURE 5 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 5. BI phylogenetic analysis for H. polii, H. sanctori, and different Mediterranean holothuroids is based on partial sequences of the 16S rDNA gene. Four Markov Chains Monte Carlo (MCMC) samples were analyzed for 10 million (ngen=10,000,000) generations. Bootstrap values are shown above the branches. The abbreviation "Hap" denotes haplotype. Bold labels refer to sequences obtained in the current study for H. polii and H. sanctori.
FIGURE 2 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 2. Distribution of 16S rDNA-based genetic pairwise distances among different Mediterranean species obtained in the current study and available in the GenBank. (a): H. polii vs. Mediterranean holothuroids, (b) H. sanctori vs. the Mediterranean holothuroids. For the 28S rDNA, the genetic distance for H. polii was the lowest with H. forskali (0.01) but the highest with H. sanctori (1.08) (Fig. 2A). For H. sanctori, the lowest pairwise distance was with H. polii (1.08), while the highest was with P. longicauda (1.163) (Fig. 2B).
FIGURE 4 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 4. Distribution of H3-based genetic pairwise distances among different Mediterranean species obtained in the current study and available in the GenBank. (a): H. polii vs. Mediterranean holothuroids, (b) H. sanctori vs. the Mediterranean holothuroids.
FIGURE 7 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 7. BI phylogenetic analysis for H. polii, H. sanctori, and different Mediterranean holothuroids, based on partial sequences of H3 gene. Four Markov Chains Monte Carlo (MCMC) samples were analyzed for 10 million (ngen=10,000,000) generations. Bootstrap values are shown above the branches. Bold labels refer to sequences obtained in the current study for H. polii and H. sanctori.
Microsatellite marker data for Chernobyl Daphnia populations
<p>Populations experiencing varying levels of ionising radiation provide an excellent opportunity to study the fundamental drivers of evolution. Radiation can cause mutations, and thus supply genetic variation; it can also selectively remove individuals that are unable to cope with the physiological stresses associated with radiation exposure, or non-selectively cull swathes of the population, reducing genetic variation. Since the nuclear power plant explosion in 1986, the Chernobyl area has experienced a spatially heterogeneous exposure to varying levels of ionising radiation. We sampled <em>Daphnia pulex</em> (a freshwater crustacean) from lakes across the Chernobyl area, genotyped them at ten microsatellite loci, and also calculated the current radiation dose rates. We then investigated whether the pattern of genetic diversity was positively associated with radiation dose rates, consistent with radiation-mediated supply of de novo mutations, or negatively associated with radiation dose rates, as would be expected with strong radiation-mediated selection. We found that measures of genetic diversity, including expected heterozygosity and mean allelic richness (an unbiased indicator of diversity) were significantly higher in lakes that experienced the highest radiation dose rates. This suggests that mutation outweighs selection as the key evolutionary force in populations exposed to high radiation dose rates. We also found significant but weak population structure, indicative of low genetic drift, and clear evidence for isolation by distance between populations. This further suggests gene flow between nearby populations is eroding population structure, and that mutational input in high radiation lakes could, ultimately, supply genetic variation to lower radiation sites.</p>
Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation
<p><span><span><span><span><span><span><span><span><span><span><span>Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitation even more challenging, potentially resulting in taxonomic inconsistencies. Rockhopper penguins of the genus <i>Eudyptes</i> comprise three broadly recognized taxa: northern (<i>E. moseleyi</i>), southern (<i>E. chrysocome</i>), and eastern rockhopper (<i>E. filholi</i>). Their taxonomic status has been controversial for decades, with researchers disagreeing about whether <i>E. chrysocome</i> and <i>E. filholi</i>are distinct species or conspecific. Our goal is to evaluate genome-wide patterns of divergence to evaluate genetic differentiation and species delimitation in<i> </i>rockhopper penguins<i>, </i>and to assess which mechanisms may underlie previous discordance among nuclear versus mitochondrial analyses. We generated reduced-representation genomic libraries using Double Digest Restriction-site Associated DNA (ddRAD) sequencing to evaluate genetic differentiation, contemporary migration rates and admixture among colonies of rockhopper penguins. The extent of genetic differentiation among the three taxa was consistently higher than population-level genetic differentiation found within these and other penguin species. There was no evidence of admixture among the three taxa, suggesting the absence of ongoing gene flow among them. Species delimitation analyses based on molecular data, along with other lines of evidence, provide strong support for the taxonomic distinction of three species of rockhopper penguins. Our results provide strong support for the existence of three distinct species of rockhopper penguins. The recognition of this taxonomic diversity is crucial for the management and conservation of this widely distributed species group. This study illustrates that widespread dispersive seabird lineages lacking obvious morphological differences may nevertheless have complex evolutionary histories and comprise cryptic species diversity. </span></span></span></span></span></span></span></span></span></span></span></p>
Molecular and biochemical markers of oxidative stress in skeletal muscle
<p>Dataset of experimental animal study involved high-intensity interval training and molecular aspects of skeletal muscle.</p>
FIGURE 6 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 6. STRUCTURE analysis of L. rigidum populations (A: the relationship between k and Delta k; the grouping based on k=18 (top) and k=17 (below) (The population code is according to Table 1).
FIGURE 3 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 3. TCS Network of L. rigidum studied populations based on ISSR data (The population code is according to Table 1) (Numbers of branches reveal number of different loci among studied populations).
FIGURE 5 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 5. NeighborNet diagram of L. rigidum studied populations based on SCoT data (The population code is according to Table 1).
FIGURE 2 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 2. UPGMA dendrogram of L. rigidum specimens showing genetic differences of the studied populations based on ISSR data (The population code is according to Table 1).
FIGURE 4 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 4. STRUCTURE analysis of L. rigidum populations (A: the relationship between k and Delta k; the grouping based on k=18 (top) and k=3 (below) (The population code is according to Table 1).
Supplementary material 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S2. Class level identification of OTUs showing the number of OTUs produced with ITS2 and LSU and the proportion of the total OTU set on the rarefied data
ScienceDex guides
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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.