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345 results for “DNA typing”
Proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitor therapy reduces the level of DNA damage in patients with heterozygous familial hypercholesterolemia
<p><span><span>Heterozygous Familial Hypercholesterolaemia (HeFH) is a common autosomal dominant genetic disease (1:300) characterized by elevated LDL-C leading to premature atherosclerosis. Treatment with a PCSK9 inhibitor (iPCSK9) is recommended in high cardiovascular risk FH patients if the treatment goal is not achieved on maximal tolerated statin plus ezetimibe. </span></span><span>The aim of this study was to </span><span><span>examine the changes in DNA damage in HeFH patients associated with iPCSK9 use. </span></span><span>Fifty-seven patients were included: a normolipidemic group (control; n=20) and patients with HeFH (study group; n=36). DNA damage was determined by alkaline comet assay. PCSK9 protein level was assessed by ELISA. </span><span>The levels of Lp(a) in human serum were quantitatively turbidimetrically assay.</span><span> </span><span>PCSK9i treatment was associated with lower DNA damage, Lp(a), PCSK9 and lipid profile than before treatment. However, 20 of 36 patients still had Lp(a) values above 125 nmol/L, and reduced Lp(a) did not correlate with reduced DNA damage. Reduced PCSK9 moderately (r=0.48) correlates with reduced DNA damage</span><span><span>. PCSK9i therapy reduces the level of DNA damage in HeFH patients, regardless of the type of inhibitor. The reduction in DNA damage is not related to the changes in lipid profile or Lp(a) induced by PCSK9i, but it is dependent on PCSK9 level.</span></span></p>
Data and Code for "Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements"
<p>This is a release of the gitlab repository "meta-methylome" (https://gitlab.com/okartal/meta-methylome.git) that, in addition to the code, also contains the resulting genomic data.</p> <p>Extract the directory on the command line using</p> <pre><code class="language-bash">$ tar -xhzvf meta-methylome.tar.gz</code></pre> <p>to preserve the symbolic links.</p>
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Multi-cell type deconvolution using a probabilistic model for single-molecule DNA methylation haplotypes
<p>Files required to run deconvolution with CelFIE-ISH and Epistate, in U250 regions from Loyfer et al. 2023, in both "pat" and "epiread" formats. </p>
Figure 1. DNA extraction with two different protocols from different noninvasive samples. Lines 1, 3, 5 in Evaluation of methods for molecular sex-typing of three heron species from different DNA sources
Figure 1. DNA extraction with two different protocols from different noninvasive samples. Lines 1, 3, 5, and 7: DNA extraction with commercial kit; Lines 2, 4, 6, and 8: DNA extracted with modified standard protocol. Lines 1–2: eggshells (Grey Heron); lines 3–4: eggshell swabs (Grey Heron); lines 5–6: pin feathers (Purple Heron); lines 7–8: contour feathers (Great Egret); 9: negative control; M: molecular marker.
Figure 2. Heron sex-typing with 2550F in Evaluation of methods for molecular sex-typing of three heron species from different DNA sources
Figure 2. Heron sex-typing with 2550F/2718R primers. Lines 1–7: Purple Heron nestlings, males (600 bp for Z chromosome); 8–10: Great Egret nestlings, females (600 bp for Z chromosome and 450 bp for W chromosome); 11: negative control; M: molecular marker.
Systematic review and meta-analysis: water type and temperature affect environmental DNA decay metadata
<p>Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to disentangle study-specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta-analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for < 200 bp sequences in the available literature means this relationship was not assessed with longer sequences (<em>e.g.</em> > 800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta-analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments. This dryad entry contains the metadata which formed the basis for the meta-analysis.</p>
New methods for the genotyping of Legionella pneumophila - Establishment, validation and implementation of a DNA-based microarray and a core genome multilocus sequence typing
<p>This data presented here are part a doctoral thesis with the focus on new genotyping methods for the human pathogen <em>Legionella pneumophila</em>. The data are partially published in articles. </p> <p>The thesis can be downloaded: update of the URL is coming soon</p>
A Phase II Trial of the DNA Methyl Transferase Inhibitor, Guadecitabine (SGI-110), in Children and Adults With Wild Type GIST,Pheochromocytoma and Paraganglioma Associated With Succinate Dehydrogenase
ClinicalTrials.gov study NCT03165721. IPD Sharing: NO. Countries: 1. Publications: 1.
DNA-PKcs RNASeq data: DNA-PKcs wilde-type or kinase-dead protein regulate basal and etoposide-induced gene expression changes
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Data from: Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types
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Systematic review and meta-analysis: water type and temperature affect environmental DNA decay metadata
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Data from: DNA methylation changes associated with type 2 diabetes and diabetic kidney disease in an East Asian population
<p><b>Objective:</b> There is growing body of evidence that epigenetic changes including DNA methylation influence the risk of type 2 diabetes and its microvascular complications. We conducted a methylome-wide association study (MWAS) to identify differentially methylated regions (DMRs) of type 2 diabetes and diabetic kidney disease (DKD) in Korean population.</p> <p><b>Methods:</b> We performed an initial MWAS in 232 participants in a case-control study design with type 2 diabetes and 197 non-diabetic controls with Illumina EPIC bead chip using peripheral blood leukocytes. Type 2 diabetes group was subdivided to 87 DKD cases and 80 non-DKD controls. Additional 819 individuals from two population-based cohorts were used to investigate the association of the identified DMRs with quantitative metabolic traits. We developed a DNA methylation score using identified DMRs to predict the occurrence of type 2 diabetes. To examine the causal relationship between the metabolic traits and differentially methylated status, we performed Mendelian randomization (MR) analyses.</p> <p><b>Results:</b> We identified eight DMRs (each at <i>BMP8A</i>, <i>NBPF20, STX18, ZNF365, CPT1A,</i> and <i>TRIM37</i>, and two at <i>TXNIP</i>) which were significantly associated with risk of type 2 diabetes (P < 9.0×10<sup>-8</sup>), including three that were previously known (DMRs in <i>TXNIP</i> and<i> CPT1A</i>), in 429 type 2 diabetes cases and controls. DNA methylation score consisted of these DMRs differentiated the risk of developing type 2 diabetes in an independent prospective cohort with a relative risk of 2.44 (95% confidence interval 1.39–4.28) between the lowest and highest deciles of DNA methylation score. DMRs in <i>CPT1A</i> and <i>TXNIP</i> were associated with quantitative metabolic traits, including fasting glucose, HbA1c, and body mass index. We also identified three DMRs (on <i>COMMD1</i>, <i>TMOD1</i>, and <i>FHOD1</i>) associated with DKD in 167 DKD cases and controls. The DMRs of DKD did not show meaningful overlap with those of type 2 diabetes. In MR analysis, the estimated glomerular filtration rate was causally associated with DNA methylation of these three DMRs.</p> <p><b>Conclusions</b>: In an East Asian population, we identified eight DMRs, including five novel ones, associated with type 2 diabetes and three DMRs associated with DKD at methylome-wide statistical significance. Our findings suggest that epigenetics of DKD may share little with those responsible for the development of type 2 diabetes.</p>
Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)
Recent research has shown that the helmeted terrapin (Pelomedusa subrufa), a species that occurs throughout sub-Saharan Africa, in Madagascar and the southwestern Arabian Peninsula, consists of several deeply divergent genetic lineages. Here we examine all nominal taxa currently synonymized with Pelomedusa subrufa (Bonnaterre, 1789) and provide mitochondrial DNA sequences of type specimens or topotypic material for most taxa. Lectotypes are designated for Testudo galeata Schoepff, 1792, Pentonyx capensis Duméril & Bibron, 1835, Pelomedusa nigra Gray, 1863, Pelomedusa galeata var. disjuncta Vaillant & Grandidier, 1910, and Pelomedusa galeata damarensis Hewitt, 1935. For Pelomedusa gasconi Rochebrune, 1884, a taxon without preserved type material, a neotype is designated. Type material of Pentonix americana Cornalia, 1849, a nominal species without credible type locality, is lost and its identity remains questionable. Also the holotype of Pelomedusa galeata orangensis Hewitt, 1935 is lost, but its allocation to the only genetic lineage occurring in South Africa is unambiguous. Phylogenetic analyses of type sequences or topotypic material reveal that the remaining nominal taxa represent three of the nine previously identified lineages of Pelomedusa. Among these three lineages is the South African one. Type specimens of Pentonyx gehafie Rüppell, 1835 correspond to an additional distinct lineage. The present study provides a sound basis for a subsequent integrative taxonomic revision of the Pelomedusa complex.
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment.
Figure 10 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 10. Mantidactylus (Mantidactylus) radaka sp. nov. being prepared for human consumption. (a) Frogs and crabs are collected from broad streams. Then (b) the frogs are gutted and skinned, and the head, hands and feet removed. The frog is then rinsed in the stream, leaving (c) cleaned animals for cooking in a stew. Note the ovaries full with hundreds of eggs.
Figure 9 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 9. Preserved type specimens of the four nomina in the Mantidactylus subgenus Mantidactylus and one of the paralectotypes of Rana guttulata.
Figure 7 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 7. Photographs of living specimens of Mantidactylus (Mantidactylus) guttulatus, M. (M.) grandidieri, and of three candidate species. (a, b) M. (M.) guttulatus, female ZSM 1013/2003 (FGMV 2002.438) from Ranomafana. (c) Unidentified specimen from Ranomafana, assigned tentatively to M. (M.) guttulatus (no genetic evidence). (d, e) M. (M.) guttulatus, specimen KU 340853 (CRH729) from Ranomafana. (f) M. (M.) grandidieri, specimen ZSM 5077/2005 (ZCMV 2159) from Nosy Mangabe. (g) M. (M.) grandidieri, specimen ZSM 276/2005 (FGZC 2682) from Vohidrazana. (h) M. (M.) grandidieri, unidentified specimen (probably subadult) from Andranofotsy. (i, j) M. (M.) grandidieri, specimen KU
Figure 5. Per-base coverage plots for the 16S in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 5. Per-base coverage plots for the 16S fragment in four Mantidactylus type specimens from the MNHN and BMNH collections. (a) BMNH 1947.2.25.48 (paralectotype of Rana guttulata); (b) BMNH 1947.2.25.51 (paralectotype of Rana guttulata); (c) MNHN 1895.255 (syntype of M. grandidieri); (d) MNHN 1883.520 (syntype of M. grandidieri).
Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.
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Allen Brain Atlas
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