SNP dataset and Capture-Mark-Recapture dataset used in the analysis for the paper Rick et al.: Population genomics of Bettongia lesueur: admixing increases genetic diversity with no evidence of outbreeding depression
Contributors: Kate Rick
... Translocations can be used as an effective conservation tool to combat the loss of genetic diversity often experienced by small and isolated populations. Mixing animals from multiple genetically diverged sources in one method to optimize genetic diversity in translocated populations. However, admixture as a conservation tool is rarely utilized due to the risks of outbreeding depression. Using single nucleotide polymorphisms (SNPs) and life history data (capture-mark-recapture), this data was used to investigate the genetic and fitness consequences of admixing two genetically distinct subspeices of burrowing bettong (Bettongia lesueur) as described in the paper by Rick et al.: Population genomics of Bettongia lesueur: admixing increases genetic diversity with no evidence of outbreeding depression.
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.
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).
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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
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: Esteban Finol Berrueta
... raw DENV genomic data for Finol E. & Ooi EE. Iscience submision
Contributors: Gil Sharon
... Raw data (excluding raw sequencing and metabolomic data) used to construct figures for manuscript. Data is predominantly in csv or tsv format. qza and qzv files are QIIME2 outputs and can be viewed at https://view.qiime2.org/ . mat files are mat lab datasets. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice Gil Sharon1,*, Nikki Jamie Cruz1, Dae-Wook Kang2,3,21, Michael J. Gandal4,5,6,7, Bo Wang1, Young-Mo Kim8, Erika M. Zink8, Cameron P. Casey8, Bryn C. Taylor9, Christianne J. Lane10, Lisa M. Bramer11, Nancy G. Isern8, David W. Hoyt8, Cecilia Noecker12, Michael J. Sweredoski1, Annie Moradian1, Elhanan Borenstein12,13,14,15,16, Janet K. Jansson8, Rob Knight17,18,19, Thomas O. Metz8, Carlos Lois1, Daniel H. Geschwind4,5,6, Rosa Krajmalnik-Brown2,3, and Sarkis K. Mazmanian1,20,* Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically-developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD and TD controls into germ-free mice, and reveal that colonization with ASD microbiota was sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and affects neuronal excitability in the brain. We propose that the gut microbiome modulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.
Data for: Molecular evidence for the retention of the Thaumatopsyllidae in the order Cyclopoida (Copepoda) and establishment of four suborders and two families within the Cyclopoida
Contributors: Sahar Khodami, Nancy F. Mercado-Salas, Danny Tang, Pedro Martinez Arbizu
... The Supplementary information is the concatenated three gene fragments alignment analyzed in this study.