"LRRK2 kinase activity regulates lysosomal glucocerebrosidase in Parkinson's disease pathogenesis" Sequencing Data
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 these genes in non-mutant cell lines.
Contributors: Massimo Turina, Marina Ciuffo, Marco Forgia, Marta Vallino, Marco Chiapello, Walter Chitarra, luca nerva, Giovanna Varese
... Alignments of viral RdRP sequences in Fasta/Pearsons format
Contributors: Silvia Liu
... Deletion and mutation of PTEN are frequent in human cancers. These alterations disturb PI3K signaling and increase survival of cancer cells. Here, we report a pro-cancer growth Pten-NOLC1 gene fusion originated from a chr10 rearrangement. Expressed as a nuclear chimera protein, Pten-NOLC1 interacts with the promoter regions of genes like EGFR, c-MET and GAB1 and promotes cancer cell growth, invasion, and increases survivals; and increases metastasis and mortality in vivo. Pten-NOLC1 fusion is detected in primary human cancer samples and cancer cell lines from different organs. Genomic interruption of Pten-NOLC1 induces large number of cancer cell death. Genome integration of this fusion gene coupled with somatic Pten deletion produces liver cancer in mice. Our studies show that genome rearrangement of Pten-NOLC1 is functional. The nuclear interaction of Pten-NOLC1 drives cancer growth, and disruption of this fusion gene may be a potential target in the treatment of human cancers.
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: 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)”.