Contributors: Ilias Georgakopoulos Soares
... The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. We introduce a novel way to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our new analytical approach reveals new insights into the contribution of DNA repair towards indel mutagenesis in human cells.
Dataset: Acidic and thermal pretreatments for anaerobic digestion inoculum to improve hydrogen and volatile fatty acids production using xylose as the substrate
Contributors: Gustavo Mockaitis
... Raw data of biogas production and composition (relative pressures and concentrations of each of the biogas constituents) for batch experiments to evaluate the anaerobic digestion of xylose. Also, metagenomic sequencing data and analysis were reported. All data is available at Mendeley Data. 16S DNA sequencing data and metadata is available at MG-RAST (metagenomics.anl.gov/linkin.cgi?project=9961).
Contributors: Daniel Ysselstein
... Sequencing of GBA1 (all exons) and LRRK2 (Exon 31 and 41) for all lines included in the manuscript: LRRK2 kinase activity regulates lysosomal glucocerebrosidase in Parkinson's disease pathogenesis. We do not observed unexpected point mutations in theses genes in non-mutant cell lines.
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Contributors: Won Kim, Maria Rendon, Jeanine McLean, David Trees, Magdalene So
... Fasta (quiver) and gff.gz files generated from PacBio Single Molecule, Real-Time sequencing of Neisseria elongata chromosome. Overview Excel file contains base calling accuracy and quality of sequencing reads. These data were used to determine methylated sequence motifs in Neisseria elongata (Table S5).
Contributors: Juan_Gabriel Rueda-Bayona
... the folder contains input and setup files of the article An Alternative Method to Determine Extreme Hydrodynamic Forces with Data Limitations for Offshore Engineering
Tetrodotoxin-sensitive sodium channels mediate action potential firing and excitability in menthol-sensitive Vglut3-lineage sensory neurons
Contributors: Ellen Lumpkin
... Small-diameter vesicular glutamate transporter 3-lineage (Vglut3lineage) dorsal root ganglion (DRG) neurons play an important role in mechanosensation and thermal hypersensitivity; however, little is known about their intrinsic electrical properties. We therefore set out to investigate mechanisms of excitability within this population. Calcium microfluorimetry analysis demonstrated that the cooling compound menthol selectively activates a subset of Vglut3lineage neurons. Whole-cell electrophysiological recordings showed that these small-diameter Vglut3lineage DRG neurons fire menthol-evoked action potentials and exhibited robust, transient receptor potential melastatin 8 (TRPM8)-dependent discharges at room temperature. This heightened excitability was confirmed by current-clamp and action potential phase-plot analyses, which showed menthol-sensitive Vglut3lineage neurons to have more depolarized membrane potentials, lower firing thresholds, and higher evoked firing frequencies compared with menthol-insensitive Vglut3lineage neurons. A biophysical analysis revealed native voltage-gated sodium channel (NaV) currents in menthol-sensitive Vglut3lineage neurons were resistant to entry into slow inactivation compared with menthol-insensitive neurons, which could explain differences in excitability. Multiplex in situ hybridization showed similar distributions of tetrodotoxin (TTX)-sensitive NaVs transcripts between TRPM8-positive and -negative Vglut3lineage neurons; however, NaV1.8 transcripts, which encode TTX-resistant channels, were more prevalent in TRPM8-negative neurons. Conversely, pharmacological analyses identified distinct functional contributions of NaV subunits, with NaV1.1 driving firing in menthol-sensitive neurons, whereas other small-diameter Vglut3lineage neurons rely primarily on TTX-resistant NaV channels. Additionally, when NaV1.1 channels were blocked, the remaining NaV currents readily entered into slow inactivation in menthol-sensitive Vglut3lineage neurons. Thus, these data demonstrate that TTX-sensitive NaVs drive action potential firing in menthol-sensitive sensory neurons and contribute to their heightened excitability
Data for: Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data
Contributors: xiuguang mao, Georgia Tsagkogeorga, Stephen Rossiter, Vu Dinh Thong
... cytb_sanger_sinicus12.fas : Twelve cytb sequences generated by Sanger sequencing.
Contributors: Jeny Bastida, Alejandro Crampet, Melitta Meneghel, Victor Morais
... This dataset correspond to the proteomic analysis of the article entitle “Preliminary Biochemical and Venomic Characterization of the Venom of Phalotris lemniscatus (Serpentes, Colubridae)” sending to Current topics in medicinal chemistry. The data set include the raw files of each band of mass spectroscopy and the database used to identify the proteins. To observe the SDS page, please refer to the article. “Protein bands were excised and sent to the Spectroscopy and Biophysics Core, University of Nebraska, Lincoln (via Science Exchange) to in-gel trypsin digestion and peptide fragmentation by LC-MS/MS. The instrument was an LTQ Velos Pro (Thermo Scientific) equipped with dual pressure ion-trap. Raw data obtained by proteomic analysis was analyzed using MaxQuant software [30–32] with the default parameters (false discovery rate 0,01). As a sequence database to match for protein identification, a fasta file download from Uniprot was used. Database was constituted by all the reviewed sequenced proteins of snakes, around 2500 proteins from Swiss-Prot database (taxonomy:"Serpentes (snakes) " AND reviewed:yes)”.
An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae).
Contributors: Daniel Huston
... The following data relates to the manuscript "An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae)." which was accepted by the International Journal for Parasitology on 3 July 2019.
Contributors: Peter Seeber, Gayle McEwen, Ulrike Löber, Daniel Förster, Marion East, Jörg Melzheimer, Alex Greenwood
... Mitogenome sequence alignments from DNA isolated from water and sediment samples following hybridization capture enrichment. Abstract: Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystems where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for non-invasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment, and water filtered through glass fiber filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera produced fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of non-target mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.