cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1623222.v2
title: Biogeochemical Importance of the Bacterial Community in Uranium Waste Deposited at Key Lake, Northern Saskatchewan

description: The long-term stability of immobilized elements of concern in uranium tailings deposited in the Deilmann Tailings Management Facility (DTMF), northern Saskatchewan, is dependent upon maintenance of highly oxic conditions within the tailings mass. The main objective of this study was to investigate the effect of stimulating microbial activity on the redox potential and state of ferrihydrite, which are considered to be the primary controlling condition and mineral phase, respectively, within the tailings. To determine the potential for biologically mediated decreases in redox potential and ferrihydrite reduction, a series of microcosm assays were performed. Non-sterile material from the tailings–water interface of the DTMF site was inoculated with indigenous flora previously isolated from the tailings material and enriched with a carbon source (50 ppm trypticase soy broth) and incubated under continuous-flow or intermittent-flow conditions, and compared with an uninoculated, no-carbon control that received continuous flow. Highly reducing conditions with redox potentials of less than −300 mV were detected after 2 days of incubation within the carbon-enriched tailings of microcosms receiving continuous flow, and less than −280 mV after 11 days of incubation within carbon-enriched tailings in microcosms receiving intermittent flow. The lowest recorded Eh value (−545 mV) was recorded after 14 days in a carbon-enriched microcosm receiving intermittent flow. In contrast, the redox conditions in the control microcosm never dropped below −93 mV; thus, it was clear that microbial activity and available carbon drove the Eh conditions to become highly reducing. The occurrence of low redox conditions was concomitant with the bulk chemical detection of Fe (II) in the effluent of treated microcosms. Sites of microbial ferrihydrite reduction were also detected using scanning transmission X-ray microscopy where Fe (II) species were observed in close proximity with bacterial cells. Analysis of the microbial diversity present within the microcosms confirmed that microbes indigenous to the DTMF system have the potential to generate conditions suitable for the proliferation of sulfate and iron reducing bacteria, such as <i>Desulfosporosinus</i>, which was detected by high-throughput 16S rRNA gene sequencing.
DOI: 10.6084/m9.figshare.1625303.v1
title: <i>In vitro</i> and <i>in vivo</i> genotoxic effects of straight <i>versus</i> tangled multi-walled carbon nanotubes

description: Some multi-walled carbon nanotubes (MWCNTs) induce mesothelioma in rodents, straight MWCNTs showing a more pronounced effect than tangled MWCNTs. As primary and secondary genotoxicity may play a role in MWCNT carcinogenesis, we used a battery of assays for DNA damage and micronuclei to compare the genotoxicity of straight (MWCNT-S) and tangled MWCNTs (MWCNT-T) <i>in vitro</i> (primary genotoxicity) and <i>in vivo</i> (primary or secondary genotoxicity). C57Bl/6 mice showed a dose-dependent increase in DNA strand breaks, as measured by the comet assay, in lung cells 24 h after a single pharyngeal aspiration of MWCNT-S (1-200 µg/mouse). An increase was also observed for DNA strand breaks in lung and bronchoalveolar lavage (BAL) cells and for micronucleated alveolar type II cells in mice exposed to aerosolized MWCNT-S (8.2-10.8 mg/m<sup>3</sup>) for 4 days, 4 h/day. No systemic genotoxic effects, assessed by the γ-H2AX assay in blood mononuclear leukocytes or by micronucleated polychromatic erythrocytes (MNPCEs) in bone marrow or blood, were observed for MWCNT-S by either exposure technique. MWCNT-T showed a dose-related <i>decrease</i> in DNA damage in BAL and lung cells of mice after a single pharyngeal aspiration (1-200 µg/mouse) and in MNPCEs after inhalation exposure (17.5 mg/m<sup>3</sup>). <i>In vitro</i> in human bronchial epithelial BEAS-2B cells, MWCNT-S induced DNA strand breaks at low doses (5 and 10 µg/cm<sup>2</sup>), while MWCNT-T increased strand breakage only at 200 µg/cm<sup>2</sup>. Neither of the MWCNTs was able to induce micronuclei <i>in vitro</i>. Our findings suggest that both primary and secondary mechanisms may be involved in the genotoxicity of straight MWCNTs.
DOI: 10.6084/m9.figshare.1623222.v1
title: Biogeochemical importance of the bacterial community in uranium waste deposited at Key Lake, Northern Saskatchewan

description: The long-term stability of immobilized elements of concern in uranium tailings deposited in the Deilmann Tailings Management Facility (DTMF), northern Saskatchewan, is dependent upon maintenance of highly-oxic conditions within the tailings mass. The main objective of this study was to investigate the effect of stimulating microbial activity on the redox potential and state of ferrihydrite, which are considered to be the primary controlling condition and mineral phase, respectively, within the tailings. To determine the potential for biologically-mediated decreases in redox potential and ferrihydrite reduction, a series of microcosm assays were performed. Non-sterile material from the tailings-water interface of the DTMF site was inoculated with indigenous flora previously isolated from the tailings material and enriched with a carbon source (50 ppm tryptic soy broth) and incubated under continuous-flow or intermittent-flow conditions, and compared with an uninoculated, no-carbon control that received continuous-flow. Highly reducing conditions with redox potentials of less than −300 mV were detected after 2 days of incubation within the carbon-enriched tailings of microcosms receiving continuous-flow, and less than −280 mV after 11 days of incubation within carbon-enriched tailings in microcosms receiving intermittent-flow. The lowest recorded Eh value (−545 mV) was recorded after 14 days in a carbon-enriched microcosm receiving intermittent flow. In contrast, the redox conditions in the control microcosm never dropped below −93 mV; thus, it was clear that microbial activity and available carbon drove the Eh conditions to become highly reducing. The occurrence of low redox conditions was concomitant with the bulk chemical detection of Fe (II) in the effluent of treated microcosms. Sites of microbial ferrihydrite reduction were also detected using scanning transmission X-ray microscope (STXM) image analyses where Fe (II) species were observed in close proximity with bacterial cells. Analysis of the microbial diversity present within the microcosms confirmed that microbes indigenous to the DTMF system have the potential to generate conditions suitable for the proliferation of sulphate and iron reducing bacteria, such as <i>Desulfosporosinus</i>, which was detected by high throughput 16S rRNA gene sequencing.
DOI: 10.6084/m9.figshare.1623221.v2
title: Amnion Epithelial Cells of Buffalo (<i>Bubalus bubalis</i>) Term Placenta Expressed Embryonic Stem Cells Markers and Differentiated into Cells of Neurogenic Lineage <i>In Vitro</i>

description: Aim of the present study was the isolation, culture, and characterization of amniotic membrane-derived epithelial cells (AE) from term placenta collected postpartum in buffalo. We found that cultured cells were of polygonal in shape, resistance to trypsin digestion and expressed cytokeratin-18 indicating that they were of epithelial origin. These cells have negative expression of mesenchymal stem cell markers (CD29, CD44, and CD105) and positive for pluripotency marker (OCT4) genes indicated that cultured cells were not contaminated with mesenchymal stem cells. Immunofluorescence staining with pluripotent stem cell surface markers, SSEA-1, SSEA-4, TRA-1-60, and TRA-1-81 indicated that these cells may retain pluripotent stem cell characteristics even after long period of differentiation. Differentiation potential of these cells was determined by their potential to differentiate into cells of neurogenic lineages using retinoic acid. In conclusion, we demonstrate that AE cells expressed pluripotent stem cell markers and have propensity to differentiate into cells of neurogenic lineage upon directed differentiation <i>in vitro</i>.
DOI: 10.6084/m9.figshare.1623217
title: The impact of concussion on cardiac autonomic function: A systematic review

description: <i>Primary objective</i>: To evaluate the evidence regarding the effect of concussion on cardiac autonomic function (CAF). <i>Inclusion criteria</i>: Original research; available in English; included participants with concussion or mild traumatic brain injury (mTBI) and a comparison group; included measures of heart rate (HR) and/or heart rate variability (HRV) as outcomes. Studies of humans (greater than 6 years old) and animals were included. <i>Critical appraisal tools</i>: The Downs and Black (DB) criteria and Structured Effectiveness Quality Evaluation Scale (SEQES). <i>Results</i>: Nine full-length articles and four abstracts were identified. There is conflicting evidence regarding CAF at rest following concussion. There is evidence of elevated HR and reduced HRV with low-intensity, steady-state exercise up to 10 days following concussion. There was no significant difference in HRV during isometric handgrip testing or HR while performing cognitive tasks following concussion. The validity of current literature is limited by small sample sizes, lack of female or paediatric participants, methodological heterogeneity and lack of follow-up. <i>Conclusions</i>: While there is some evidence to suggest CAF is altered during physical activity following concussion, methodological limitations highlight the need for further research. Understanding the effect of concussion on CAF will contribute to the development of more comprehensive concussion management strategies.
DOI: 10.6084/m9.figshare.1623221.v1
title: Amnion Epithelial Cells of Buffalo (<i>Bubalus Bubalis</i>) Term Placenta Expressed Embryonic Stem Cells Markers and Differentiated into Cells of Neurogenic Lineage <i>In Vitro</i>

description: ABSTRACTAim of the present study was the isolation, culture, and characterization of amniotic membrane-derived epithelial cells (AE) from term placenta collected postpartum in buffalo. We found that cultured cells were of polygonal in shape, resistance to trypsin digestion and expressed cytokeratin-18 indicating that they were of epithelial origin. These cells have negative expression of mesenchymal stem cell markers (CD29, CD44, and CD105) and positive for pluripotency marker (OCT4) genes indicated that cultured cells were not contaminated with mesenchymal stem cells. Immunofluorescence staining with pluripotent stem cell surface markers, SSEA-1, SSEA-4, TRA-1-60, and TRA-1-81 indicated that these cells may retain pluripotent stem cell characteristics even after long period of differentiation. Differentiation potential of these cells was determined by their potential to differentiate into cells of neurogenic lineages using retinoic acid. In conclusion, we demonstrate that AE cells expressed pluripotent stem cell markers and have propensity to differentiate into cells of neurogenic lineage upon directed differentiation <i>in vitro</i>.
DOI: 10.6084/m9.figshare.1623217.v1
title: The impact of concussion on cardiac autonomic function: A systematic review

description: <i>Primary objective</i>: To evaluate the evidence regarding the effect of concussion on cardiac autonomic function (CAF). <i>Inclusion criteria</i>: Original research; available in English; included participants with concussion or mild traumatic brain injury (mTBI) and a comparison group; included measures of heart rate (HR) and/or heart rate variability (HRV) as outcomes. Studies of humans (greater than 6 years old) and animals were included. <i>Critical appraisal tools</i>: The Downs and Black (DB) criteria and Structured Effectiveness Quality Evaluation Scale (SEQES). <i>Results</i>: Nine full-length articles and four abstracts were identified. There is conflicting evidence regarding CAF at rest following concussion. There is evidence of elevated HR and reduced HRV with low-intensity, steady-state exercise up to 10 days following concussion. There was no significant difference in HRV during isometric handgrip testing or HR while performing cognitive tasks following concussion. The validity of current literature is limited by small sample sizes, lack of female or paediatric participants, methodological heterogeneity and lack of follow-up. <i>Conclusions</i>: While there is some evidence to suggest CAF is altered during physical activity following concussion, methodological limitations highlight the need for further research. Understanding the effect of concussion on CAF will contribute to the development of more comprehensive concussion management strategies.
DOI: 10.6084/m9.figshare.1623213
title: A human haploid gene trap collection to study lncRNAs with unusual RNA biology

description: Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized <i>LOC100288798</i> lncRNA as a model to answer this question. Using public RNA-seq data we show that <i>LOC100288798</i> is ubiquitously expressed, but inefficiently spliced. The minor spliced <i>LOC100288798</i> isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that <i>LOC100288798</i> RNA biology differs markedly from typical mRNAs. <i>De novo</i> assembly from RNA-seq data suggests that <i>LOC100288798</i> extends 289kb beyond its annotated 3' end and overlaps the downstream <i>SLC38A4</i> gene. Three cell lines with independent gene trap insertions in <i>LOC100288798</i> were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon <i>LOC100288798</i> truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized <i>LOC100288798</i> as a potential gene regulator.
DOI: 10.6084/m9.figshare.1623213.v2
title: A human haploid gene trap collection to study lncRNAs with unusual RNA biology

description: Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized <i>LOC100288798</i> lncRNA as a model to answer this question. Using public RNA-seq data we show that <i>LOC100288798</i> is ubiquitously expressed, but inefficiently spliced. The minor spliced <i>LOC100288798</i> isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that <i>LOC100288798</i> RNA biology differs markedly from typical mRNAs. <i>De novo</i> assembly from RNA-seq data suggests that <i>LOC100288798</i> extends 289kb beyond its annotated 3' end and overlaps the downstream <i>SLC38A4</i> gene. Three cell lines with independent gene trap insertions in <i>LOC100288798</i> were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon <i>LOC100288798</i> truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized <i>LOC100288798</i> as a potential gene regulator.
DOI: 10.6084/m9.figshare.1623213.v1
title: A human haploid gene trap collection to study lncRNAs with unusual RNA biology

description: ABSTRACTMany thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized <i>LOC100288798</i> lncRNA as a model to answer this question. Using public RNA-seq data we show that <i>LOC100288798</i> is ubiquitously expressed, but inefficiently spliced. The minor spliced <i>LOC100288798</i> isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that <i>LOC100288798</i> RNA biology differs markedly from typical mRNAs. <i>De novo</i> assembly from RNA-seq data suggests that <i>LOC100288798</i> extends 289kb beyond its annotated 3′ end and overlaps the downstream <i>SLC38A4</i> gene. Three cell lines with independent gene trap insertions in <i>LOC100288798</i> were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon <i>LOC100288798</i> truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized <i>LOC100288798</i> as a potential gene regulator.
DOI: 10.6084/m9.figshare.1623207
title: Autophagy-mediated longevity is modulated by lipoprotein biogenesis

description: Autophagy-dependent longevity models in <i>C. elegans</i> display altered lipid storage profiles, but the contribution of lipid distribution to life-span extension is not fully understood. Here we report that lipoprotein production, autophagy and lysosomal lipolysis are linked to modulate life span in a conserved fashion. We find that overexpression of the yolk lipoprotein VIT/vitellogenin reduces the life span of long-lived animals by impairing the induction of autophagy-related and lysosomal genes necessary for longevity. Accordingly, reducing vitellogenesis increases life span via induction of autophagy and lysosomal lipolysis. Life-span extension due to reduced vitellogenesis or enhanced lysosomal lipolysis requires nuclear hormone receptors (NHRs) NHR-49 and NHR-80, highlighting novel roles for these NHRs in lysosomal lipid signaling. In dietary-restricted worms and mice, expression of VIT and hepatic APOB (apolipoprotein B), respectively, are significantly reduced, suggesting a conserved longevity mechanism. Altogether, our study demonstrates that lipoprotein biogenesis is an important mechanism that modulates aging by impairing autophagy and lysosomal lipolysis.
DOI: 10.6084/m9.figshare.1623210
title: CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs

description: Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.
DOI: 10.6084/m9.figshare.1623207.v1
title: Autophagy-mediated longevity is modulated by lipoprotein biogenesis

description: Autophagy-dependent longevity models in <i>C. elegans</i> display altered lipid storage profiles, but the contribution of lipid distribution to life-span extension is not fully understood. Here we report that lipoprotein production, autophagy and lysosomal lipolysis are linked to modulate life span in a conserved fashion. We find that overexpression of the yolk lipoprotein VIT/vitellogenin reduces the life span of long-lived animals by impairing the induction of autophagy-related and lysosomal genes necessary for longevity. Accordingly, reducing vitellogenesis increases life span via induction of autophagy and lysosomal lipolysis. Life-span extension due to reduced vitellogenesis or enhanced lysosomal lipolysis requires nuclear hormone receptors (NHRs) NHR-49 and NHR-80, highlighting novel roles for these NHRs in lysosomal lipid signaling. In dietary-restricted worms and mice, expression of VIT and hepatic APOB (apolipoprotein B), respectively, are significantly reduced, suggesting a conserved longevity mechanism. Altogether, our study demonstrates that lipoprotein biogenesis is an important mechanism that modulates aging by impairing autophagy and lysosomal lipolysis.
DOI: 10.6084/m9.figshare.1623209
title: ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing <i>in vivo</i>

description: Adenosine deaminases bind double stranded RNA and convert adenosine to inosine. Editing creates multiple isoforms of neurotransmitter receptors, such as with <i>Gria2</i>. <i>Adar2</i> KO mice die of seizures shortly after birth, but if the <i>Gria2</i> Q/R editing site is mutated to mimic the edited version then the animals are viable. We performed RNA-Seq on frontal cortices of <i>Adar2</i><sup>-/-</sup> <i>Gria2</i><sup>R/R</sup> mice and littermates. We found 56 editing sites with significantly diminished editing levels in <i>Adar2</i> deficient animals with the majority in coding regions. Only two genes and 3 exons showed statistically significant differences in expression levels. This work illustrates that ADAR2 is important in site-specific changes of protein coding sequences but has relatively modest effects on gene expression and splicing in the adult mouse frontal cortex.