bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial community dynamics of surface water in British Columbia, Canada
Authors: Uyaguari-Diaz Miguel I. , Croxen Matthew A. , Cronin Kirby , Luo Zhiyao , Isaac-Renton Judith , Prystajecky Natalie A. , Tang Patrick 
Published: August 2019

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such asEscherichia coli, often tested as a weekly grab sample. To understand the stability ofE.coliconcentrations over time, we evaluated three approaches to measuringE. colilevels in water: microbial culture using Colilert, quantitative PCR foruidAand next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period.Enterobacteriaceaecomprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities ofE. colicompared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such asPrevotellaandBacteroidesshowed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.
Reference intervals of spot urine copper excretion in preschool children and potential application in pre-symptomatic screening of Wilson’s disease
Authors: Tang Nelson Leung-sang , Hui Joannie , Huang Dan , Tang Man Fung , Wang Xingyan , Wu Junyi , Chan Iris HS , Leung Ting Fan 
Published: August 2019

ABSTRACTBackgroundWith spot urine collected from a large control sample of preschool children (aged 3-7 years), reference range of spot urine copper excretion indexes and their biological variation were defined.MethodsIn order to investigate their test performance in screening of Wilson disease in this age group, multiple spot urine samples from 6 WD patients diagnosed at presymptomatic stage were analysed. Cut-off values for spot urine copper concentration, copper to creatinine ratio and copper to osmolality ratio at 0.5 µmol/L, 0.1 µmol/mmol and 0.00085 µmol/mOsmol (32 µg/L, 56 µg/g creatinine and 0.054 µg/mOsmol, respectively, in conventional units) have potential application in differentiation of WD patients.ResultsThe data provides a new insight that the inter-individual variation of spot urine copper indexes (CVg) were moderate with figures around 60% which was similar to other clinically useful urine tests, such as urine albumin excretion ratio. Spot urine copper excretion strongly correlated with both urine creatinine and osmolality. And more than 95% of data points in health preschool children fell within prediction regions by linear regression suggesting a good utility of normalisation by these 2 analytes. Receiver operator curve (ROC) showed that copper to osmolality ratio was the best index with an area under curve (AUC) greater than 0.98.ConclusionsBased on the data, a new WD screening time window targeting preschool children is proposed. Application of a bivariate screening strategy using spot urine copper concentration and urine osmolality may be useful in a population screening program for preschool children.
Antagonism between regular and atypical Cxcr3 receptors regulates macrophage migration during infection and injury in zebrafish
Authors: Sommer Frida , Torraca Vincenzo , Kamel Sarah , Lombardi Amber , Meijer Annemarie H. 
Published: August 2019

AbstractThe CXCR3-CXCL11 chemokine-signaling axis plays an essential role in infection and inflammation by orchestrating leukocyte trafficking in human and animal models, including zebrafish. Atypical chemokine receptors (ACKRs) play a fundamental regulatory function in signaling networks by shaping chemokine gradients through their ligand scavenging function, while being unable to signal in the classic G-protein-dependent manner. Two copies of the CXCR3 gene in zebrafish, cxcr3.2 and cxcr3.3, are expressed on macrophages and share a highly conserved ligand-binding site. However, Cxcr3.3 has structural characteristics of ACKRs indicative of a ligand-scavenging role. In contrast, we previously showed that Cxcr3.2 is an active CXCR3 receptor since it is required for macrophage motility and recruitment to sites of mycobacterial infection. In this study, we generated a cxcr3.3 CRISPR-mutant to functionally dissect the antagonistic interplay between the cxcr3 paralogs in the immune response. We observed that cxcr3.3 mutants are more susceptible to mycobacterial infection, while cxcr3.2 mutants are more resistant. Furthermore, macrophages in the cxcr3.3 mutant are more motile, show higher activation status, and are recruited more efficiently to sites of infection or injury. Our results suggest that Cxcr3.3 is an ACKR that regulates the activity of Cxcr3.2 by scavenging common ligands and that silencing the scavenging function of Cxcr3.3 results in an exacerbated Cxcr3.2 signaling. In human, splice variants of CXCR3 have antagonistic functions and CXCR3 ligands also interact with ACKRs. Therefore, in zebrafish, an analogous regulatory mechanism appears to have evolved after the cxcr3 gene duplication event, through diversification of conventional and atypical receptor variants.Summary sentenceCXCR3 paralogue with structural characteristics of atypical chemokine receptors regulates the activity of a conventional receptor involved in macrophage motility by scavenging shared ligands.
The paternal and maternal genetic history of Vietnamese populations
Authors: Macholdt Enrico , Arias Leonardo , Duong Nguyen Thuy , Ton Nguyen Dang , Phong Nguyen Van , Schröder Roland , Pakendorf Brigitte , Hai Nong Van , Stoneking Mark 
Published: August 2019

AbstractVietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and 2.34 mB sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with some limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.
Causal relationship of cerebrospinal fluid biomarkers with the risk of Alzheimer’s disease: A two-sample Mendelian randomization study
Authors: Kim Soyeon , Kim Kiwon , Nho Kwangsik , Myung Woojae , Won Hong-Hee 
Published: August 2019

AbstractWhether the epidemiological association of amyloid beta (Aβ) and tau pathology with Alzheimer’s disease (AD) is causal remains unclear. The recent failures to demonstrate the efficacy of several amyloid beta-modifying drugs may indicate the possibility that the observed association is not causal. These failures also led to efforts to develop tau-directed treatments whose efficacy is still tentative. Herein, we conducted a two-sample Mendelian randomization analysis to determine whether the relationship between the cerebrospinal fluid (CSF) biomarkers for amyloid and tau pathology and the risk of AD is causal. We used the summary statistics of a genome-wide association study (GWAS) for CSF biomarkers (Aβ1-42, phosphorylated tau181[p-tau], and total tau [t-tau]) in 3,146 individuals and for late-onset AD (LOAD) in 21,982 LOAD cases and 41,944 cognitively normal controls. We tested the association between the change in the genetically predicted CSF biomarkers and LOAD risk. We found a modest decrease in the LOAD risk per one standard deviation (SD) increase in the genetically predicted CSF Aβ (odds ratio [OR], 0.63 for AD; 95% confidence interval [CI], 0.38-0.87;P= 0.02). In contrast, we observed a significant increase in the LOAD risk per one SD increase in the genetically predicted CSF p-tau (OR, 2.37; 95% CI, 1.46-3.28;P= 1.09×10−5). However, no causal association was observed of the CSF t-tau with the LOAD risk (OR, 1.15; 95% CI, 0.85-1.45;P= 0.29). Our findings need to be validated in future studies with more genetic variants identified in larger GWASs for CSF biomarkers.
Extraction of active RhoGTPases by RhoGDI regulates spatiotemporal patterning of RhoGTPases
Authors: Golding Adriana , Visco Ilaria , Bieling Peter , Bement William 
Published: August 2019

AbstractThe RhoGTPases are characterized as membrane-associated molecular switches cycling between active, GTP-bound and inactive, GDP-bound states. However, 90-95% of RhoGTPases are maintained in a soluble form by RhoGDI, which is generally viewed as a passive shuttle for inactive RhoGTPases. Our current understanding of RhoGTPase:RhoGDI dynamics has been limited by two experimental challenges: direct visualization of the RhoGTPasesin vivoand reconstitution of the cyclein vitro. We developed methods to directly image vertebrate RhoGTPasesin vivoor on lipid bilayersin vitro. Using these tools, we identified pools of active and inactive RhoGTPase associated with the membrane, showed that RhoGDI can actively extract both inactive and active RhoGTPases, and that the extraction of active RhoGTPase contributes to their spatial regulation around wounds. In contrast to the textbook model of the RhoGTPase cycle, these results indicate that RhoGDI actively contributes to spatiotemporal patterning by removing active RhoGTPases from the plasma membrane.
Age-related changes to macrophages are detrimental to fracture healing
Authors: Clark Daniel , Brazina Sloane , Yang Frank , Hu Diane , Niemi Erene , Miclau Ted , Nakamura Mary , Marcucio Ralph 
Published: August 2019

AbstractThe elderly population suffers from higher rates of complications during fracture healing that result in increased morbidity and mortality. Inflammatory dysregulation is associated with increased age and is a contributing factor to the myriad of age-related diseases. Therefore, we investigated age-related changes to an important cellular regulator of inflammation, the macrophage, and the impact on fracture healing outcomes. We demonstrated that old mice (24 months) have delayed fracture healing with significantly less bone and more cartilage compared to young mice (3 months). The quantity of infiltrating macrophages into the fracture callus was similar in old and young mice. However, RNA-seq analysis demonstrated distinct differences in the transcriptomes of macrophages derived from the fracture callus of old and young mice, with an upregulation of M1/pro-inflammatory genes in macrophages from old mice as well as dysregulation of other immune-related genes. Preventing infiltration of the fracture site by macrophages in old mice improved healing outcomes, with significantly more bone in the calluses of treated mice compared to age-matched controls. After preventing infiltration by macrophages, the macrophages within the fracture callus were collected and examined via RNA-seq analysis, and their transcriptome resembled macrophages from young calluses. Taken together, infiltrating macrophages from old mice demonstrate detrimental age-related changes, and depleting infiltrating macrophages can improve fracture healing in old mice.
A putative ER-PM contact site complex relocalizes in response to Rare Earth Elements –induced endocytosis
Authors: Lee EunKyoung , Vila Nova Santana Brenda , Samuels Elizabeth , Benitez-Fuente Francisco , Corsi Erica , Botella Miguel A. , Perez-Sancho Jessica , Vanneste Steffen , Friml Jiří , Macho Alberto , Azevedo Aristea Alves , Rosado Abel 
Published: August 2019

ABSTRACTIn plant cells, environmental stressors induce changes in the cytosolic concentration of calcium ([Ca2+]cyt) that are transduced by Ca2+-sensing proteins. To confer specificity to the stress signaling response, [Ca2+]cytsensing must be tightly regulated in space and time; the molecular mechanisms that restrict the localization and dynamics of Ca2+sensors in plants, however, are largely unknown. In this report, we identify a putative Ca2+-sensitive complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+-dependent lipid binding protein (CLB1), which is enriched at ER-PM contact sites (EPCS) and relocalizes in response to Rare Earth Elements (REEs)-induced endocytosis. Our results show that endocytosed REEs influence cytosolic Ca2+signaling, as indicated by the activation of the Ca2+/Calmodulin-based ratiometric sensor GCaMP3, and promote the cytoskeleton-dependent accumulation of ER-PM contact sites at the cell cortex. Based on these results, we propose that the EPCS-localized SYT1/SYT5/CLB1 complex is part of an evolutionarily conserved and spatially regulated Ca2+-responsive mechanism that control cER-PM communication during stress episodes.
The Habenular Receptor GPR151 Regulates Addiction Vulnerability Across Drug Classes
Authors: Antolin-Fontes Beatriz , Li Kun , Ables Jessica L. , Riad Michael H. , Görlich Andreas , Williams Maya , Wang Cuidong , Lipford Sylvia M. , Dao Maria , Molina Henrik , Liu Jianxi , Kenny Paul J. , Ibañez-Tallon Ines 
Published: August 2019

SUMMARYThe habenula controls the addictive properties of nicotine but also densely expresses opioid and cannabinoid receptors. As such, identification of strategies to manipulate habenular activity may yield new approaches to treat substance use disorders. Here we show that GPR151, an orphan G protein-coupled receptor (GPCR) highly enriched in the habenula of humans and rodents plays a critical role in regulating habenular function and behavioral responses to addictive drugs. We show that GPR151 is expressed on axonal and presynaptic membranes and synaptic vesicles, and regulates synaptic fidelity and plasticity. We find that GPR151 associates with synaptic components controlling vesicle release and ion transport and couples to the G-alpha inhibitory protein Gαo1to reduce cAMP levels. Stable cell lines expressing GPR151 confirm that it signals via Gi/o and are amenable to ligand screens.Gpr151null mice show diminished behavioral responses to nicotine, and self-administer greater quantities of the drug, phenotypes rescued by viral re-expression ofGpr151in the habenula.Gpr151null mice are also insensitive to the behavioral actions of morphine and cannabinoids. These data identify GPR151 as a critical modulator of habenular function that controls addiction vulnerability across different drug classes.HighlightsHabenula neurons are enriched in nicotinic, opioid, cannabinoid and GPR151 receptorsGPR151 modulates synaptic fidelity and release probability at habenular terminals.Habenular GPR151 plays a role in drug abuse and food intake/weight controlGPR151 couples to the G-alpha inhibitory protein Gαo1to reduce cAMP levels.eTOC BlurbAntolin-Fontes at al. identify a G protein-coupled receptor, GPR151, which is highly enriched in human habenular neurons. These neurons are primarily enriched with nicotinic, opioid and cannabinoid receptors. We find that GPR151 modulates habenular synaptic vesicle release probability and behavioral responses to these drugs of abuse.
The Acute Myeloid Leukemia variant DNMT3A Arg882His is a DNMT3B-like enzyme
Authors: Norvil Allison B. , AlAbdi Lama , Liu Bigang , Forstoffer Nicole E. , Michie Amie R. , Chen Taiping , Gowher Humaira 
Published: August 2019

AbstractMutations in DNMT3A, particularly the Arg882His substitution is highly prevalent in acute myeloid leukemia. Although the reduced activity of DNMT3A Arg882His variant alters DNA methylation, the underlying cause of its oncogenic effect is not fully understood. Our data show that DNMT3A Arg882His variant acquires CpG flanking sequence preference highly similar to that of DNMT3B. Interestingly, a similar substrate preference was observed in DNMT3A WT enzyme upon the loss of cooperative kinetic mechanism. We tested if DNMT3A Arg882His could preferably methylate DNMT3B-specific target sites. Rescue experiments in Dnmt3a/3b double knockout mouse embryonic stem cells show that the corresponding Arg878His mutation in mouse DNMT3A severely impairs its ability to methylate major satellite DNA, a DNMT3A-preferred target, but has no overt effect on the ability to methylate minor satellite DNA, a DNMT3B-preferred target. Our data suggest that methylation of DNMT3B target sites by DNMT3A Arg882His variant could contribute to its oncogenic potential.
Parallel Tempering with Lasso for Model Reduction in Systems Biology
Authors: Gupta Sanjana , Lee Robin E.C. , Faeder James R. 
Published: August 2019

AbstractSystems Biology models reveal relationships between signaling inputs and observable molecular or cellular behaviors. The complexity of these models, however, often obscures key elements that regulate emergent properties. We use a Bayesian model reduction approach that combines Parallel Tempering with Lasso regularization to identify minimal subsets of reactions in a signaling network that are sufficient to reproduce experimentally observed data. The Bayesian approach finds distinct reduced models that fit data equivalently. A variant of this approach based on Group Lasso is applied to the NF-κB signaling network to test the necessity of feedback loops for responses to pulsatile and continuous pathway stimulation. Taken together, our results demonstrate that Bayesian parameter estimation combined with regularization can isolate and reveal core motifs sufficient to explain data from complex signaling systems.
LRP5-deficiency in OsxCreERT2 mice models intervertebral disc degeneration by aging and compression
Authors: Silva Matthew J. , Holguin Nilsson 
Published: August 2019

ABSTRACTOsterix is a critical transcription factor of mesenchymal stem cell fate, where its loss or loss of WNT signaling diverts differentiation to a chondrocytic lineage. Intervertebral disc (IVD) degeneration activates differentiation of prehypertrophic chondrocyte-like cells and inactivates WNT signaling, but its interacting role with osterix is unclear. First, compared to young-adult (5mo), mechanical compression of old (18mo) IVD induced greater IVD degeneration. Aging (5 vs 12mo) and/or compression reduced the transcription of osterix and notochordal marker T by 40-75%. Compression elevated transcription of hypertrophic chondrocyte marker MMP13 and pre-osterix transcription factor RUNX2, but less so in 12mo IVD. Next, using an Ai9/td reporter and immunohistochemistry, annulus fibrosus and nucleus pulposus cells of 5mo IVD expressed osterix, but aging and compression reduced its expression. Lastly, in vivo LRP5-deficiency in osterix-expressing cells degenerated the IVD, inactivated WNT signaling, reduced the biomechanical properties by 45-70%, and reduced transcription of osterix, notochordal markers and chondrocytic markers by 60-80%. Overall, these data indicate that age-related inactivation of WNT signaling in osterix-expressing cells may limit regeneration by depleting progenitors and attenuating the expansion of chondrocyte-like cells.
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Authors: Low Wai Yee , Tearle Rick , Liu Ruijie , Koren Sergey , Rhie Arang , Bickhart Derek M. , Rosen Benjamin D. , Kronenberg Zev N. , Kingan Sarah B. , Tseng Elizabeth , Thibaud-Nissen Françoise , Martin Fergal J. , Billis Konstantinos , Ghurye Jay , Hastie Alex R. , Lee Joyce , Pang Andy W.C. , Heaton Michael P. , Phillippy Adam M. , Hiendleder Stefan , Smith Timothy P.L. , Williams John L. 
Published: August 2019

AbstractWe present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants
Authors: Xiang Jiale , Peng Jiguang , Peng Zhiyu 
Published: August 2019

AbstractNull variants are prevalent within human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion (PVS1) for pathogenicity in the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. The refinement may improve interpretation consistency, but it also brings hurdles to biocurators because of the complicated workflows and multiple bioinformatics sources required. To address these issues, we developed an automatic classification tool called AutoPVS1 to streamline PVS1 interpretation. We assessed the performance of AutoPVS1 using 56 variants manually curated by ClinGen’s SVI Working Group and achieved an interpretation concordance of 95% (53/56). A further analysis of 28,586 putative loss-of-function variants by AutoPVS1 demonstrated that at least 27.6% of them do not reach a very strong strength level, with 17.4% based on variant-specific issues and 10.2% on disease mechanism considerations. Moreover, 40.7% (1,918/4,717) of splicing variants were assigned a decreased PVS1 strength level, significantly higher than frameshift and nonsense variants. Our results reinforce the necessity of considering variant-specific issues and disease mechanisms in variant interpretation, and demonstrate that AutoPVS1 is an accurate, reproducible, and reliable tool which facilitates PVS1 interpretation and will thus be of great importance to curators.