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Fig. 4 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)

Fig. 4 Comparison of ML phylogenetic reconstructions based on ELAVI8 and concatentated ITS1 +2 sequence from 21 California, USA, Haplotrema specimens representing 9 described and 3 undescribed species. The ELAVI8 Haplotrema tree was rooted on a Discidae, a chondrinid, two Orthurethra and two Limacoidea species. This was not possible in

Fig. 5 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)

Fig. 5 Comparison of ML phylogenetic reconstructions based on ELAVI8 and 28S sequence from 50 specimens/37 genera representing all of the major panpulmonate land snail clades identified by

Fig. 3 Base pair coverage across the 1296 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)

Fig. 3 Base pair coverage across the 1296 aligned sites in the ELAVI8 MSA (see ELAVI8_panpul.fas in the Supporting Information). The y-axis represents the percentage of sites that are represented at that location across all specimens

Fig. 2 ELAVI8 PCR yield and stringency across using a 1.1 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)

Fig. 2 ELAVI8 PCR yield and stringency across using a 1.1% Agarose gel in 1 × TBE buffer with GoldView Dye and 3 µl of PCR product from each reaction. Panel A represents 50° C annealing temperature for 40 cycles while B represents the modified touchdown procedure of 54° C anneal for 10 cycles followed by 50° C for 30 cycles. The

opennotspecifiedNov 2021View details →

Fig. 3 in Mitochondrial marker-based analyses provide new insights into role of coral reef ecosystems in molluscan speciation

Fig. 3 Maximum likelihood phylogenetic tree based on partial mitochondrial 16S rRNA gene sequences. Images of rocky shore and coral reef ecophene of C. catus specimens and their habitats are provided

opennotspecifiedNov 2021View details →

Fig. 1 in Mitochondrial marker-based analyses provide new insights into role of coral reef ecosystems in molluscan speciation

Fig. 1 Map of localities of Lakshadweep and Andaman and Nicobar Islands; red dots indicate the sampling locations

opennotspecifiedNov 2016View details →

FIGURE 2 in Effectiveness of DNA barcoding markers in the description of a new and unusual calyptrate species of Myrcianthes (Myrtaceae)

FIGURE 2. Myrcianthes roncesvallensis. (A) Closed calyx detaching as a unit (C. Parra-O. & A. F. Bohórquez 853), (B) closed calyx tearing in two or three more or less regular lobes (C. Parra-O. & A. F. Bohórquez 849), (C) both types of calyx opening in flowers of the same inflorescence (C. Parra-O. & A. F. Bohórquez 857), (D) tissue remnants from the calyx opening that persist attached to the hypanthium (C. Parra-O. & A. F. Bohórquez 852), (E) remnants of the calyx in the fruit (C. Parra-O. & A. F. Bohórquez 852), (F) remnants of the calyx in the fruit (C. Parra-O. & A. F. Bohórquez 856). Photos: A. F. Bohórquez (A); C. Parra-O. (B, C, D, E, and F). Scale bar = 5 mm.

opennotspecifiedNov 2016View details →

FIGURE 1 in Effectiveness of DNA barcoding markers in the description of a new and unusual calyptrate species of Myrcianthes (Myrtaceae)

FIGURE 1. Myrcianthes roncesvallensis. (A) flowering branch, (B) inflorescence, (C) flower bud, (D) petal, (E) longitudinal section of hypanthium and ovary, (F) cross section of ovary, (G) fruit, (H) embryo. Illustration by Laura Giraldo Kalil; A, C, D, E, and F drawn from the holotype, B drawn from C. Parra-O. & A. F. Bohórquez 857, G and H drawn from C. Parra-O. & A. F. Bohórquez 852.

opennotspecifiedMay 2018View details →

FIGURE 1 in A new circumscription of the Mediterranean genus Anacyclus (Anthemideae, Asteraceae) based on plastid and nuclear DNA markers

FIGURE 1. Consensus tree (50% majority-rule) from Bayesian inference of the combined ITS + psbA-trnH dataset. Posterior probability values (PP) are indicated along branches (values below 0.50 are not shown). Colours of branches indicate tribal classification of the taxa. Phylogenetic placement of Anacyclus core species (Western Mediterranean species, WM) and Eastern Mediterranean (EM) species is highlighted in grey.

opencc-by-4.0Sep 2024View details →

FGF23 Expression Is a Promising Immunohistochemical Diagnostic Marker for Undifferentiated Pleomorphic Sarcoma of Bone (UPSb)

Raw data of the paper "FGF23 Expression Is a Promising Immunohistochemical Diagnostic Marker for Undifferentiated Pleomorphic Sarcoma of Bone (UPSb)" doi: 10.3390/genes15020242

opencc-by-4.0Sep 2024View details →

scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq

Single cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual cells from complex samples, facilitating the detection of cell type-specific marker genes. In scRNA-seq experiments with multiple donors, the population level variation brings an extra layer of complexity in cell type-specific gene detection, for example, they may not appear in all donors. Motivated by this observation, we develop a statistical model named scCTS to identify cell type-specific genes from population-level scRNA-seq data. Extensive data analyses demonstrate that the proposed method identifies more biologically meaningful cell type-specific genes compared to traditional methods.

opencc-by-4.0Oct 2024View details →

Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders, MetaPhlAn 3 profiles

Open the record for dataset details and reuse information.

opencc-by-4.0Sep 2024View details →

PROINFLAMMATORY AND ADIPOCYTE MARKERS AS INDICATORS OF MENSTRUAL CYCLE DISORDERS IN OVERWEIGHT ADOLESCENT GIRLS

Цель: определение сывороточного содержания ключевых адипокинов и провоспалительных цитокинов у девочек-подростков с избыточной массой тела для выявления их роли в развитии нарушений менструального цикла. Материал и методы. В исследовании участвовали 50 девочек подростков, из которых в основная группа вошли 25 девочек избыточной массой тела. В контрольную группу вошли 25 девочек с нормальной массой тела. Определение сывороточных уровней адипокинов и провоспалительных цитокинов проводили методом ИФА, в соответствии с рекомендациями производителя. Результаты. Установлено, что дисбаланс адипокинов и повышенные уровни провоспалительных цитокинов связаны с нарушениями менструальной функции у подростков с избыточной массой тела. Выводы. Изученные показатели являются значимыми предикторами менструальных нарушений. Ключевые слова: девочки, подростки менструальный цикл, сыворотка, цитокины, адипокины, дисбаланс.

opencc-zeroDec 2013View details →

Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.

opencc-zeroDec 2014View details →

Data from: "Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus tephrosceles), which is a highly threatened monkey due to habitat loss. We analyzed blood samples from 24 individuals from Kibale National Park (Uganda) using single-end RAD sequencing. We obtained 70,773,857 reads, of which 58,814,906 passed the filtering steps. Using the program STACKS v. 1.11 we identified 113,376 loci, of which 50,558 were polymorphic and had a mean observed heterozygosity of 0.25. These data will be used to study the effects of habitat fragmentation on genomic diversity, dispersal, and disease transmission in this species. Our approach provides a good example of the potential of RAD sequencing in studies of wild primate populations.

opencc-zeroDec 2014View details →

Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management.

opencc-zeroDec 2016View details →

Data from: Effects of gene action, marker density, and time since selection on the performance of landscape genomic scans of local adaptation

Genomic "scans" to identify loci that contribute to local adaptation are becoming increasingly common. Many methods used for such studies have assumed that local adaptation is created by loci experiencing antagonistic pleiotropy and that the selected locus itself is assayed, and few consider how signals of selection change through time. However, most empirical data sets have marker density too low to assume that a selected locus itself is assayed, researchers seldom know when selection was first imposed, and many locally adapted loci likely experience not antagonistic pleiotropy but conditional neutrality. We simulated data to evaluate how these factors affect the performance of tests for genotype-environment association. We found that three types of regression-based analyses (linear models, mixed linear models, and latent factor mixed models) and an implementation of BayEnv all performed well, with high rates of true positives and low rates of false positives, when the selected locus experienced antagonistic pleiotropy, and when the selected locus was assayed directly. However, all tests had reduced power to detect loci experiencing conditional neutrality, and the probability of detecting associations was sharply reduced when physically linked rather than causative loci were sampled. Antagonistic pleiotropy also maintained detectable genotype-environment associations much longer than conditional neutrality. Our analyses suggest that if local adaptation is often driven by loci experiencing conditional neutrality, genome-scan methods will have limited capacity to find loci responsible for local adaptation.

opencc-zeroDec 2011View details →

Data from: Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast

A surprisingly high frequency of interspecific sea turtle hybrids have been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as E. imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, since most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analyzed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years.

opencc-zeroDec 2013View details →

Data from: Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)

Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigación 'La Orden'. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (H O, H E) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.