bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained dechlorination of vinyl chloride to ethene inDehalococcoides-enriched cultures grown without addition of exogenous vitamins and at low pH
Authors: Puentes Jácome Luz A. , Wang Po-Hsiang , Molenda Olivia , Li Yi Xuan (Jine-Jine) , Islam M. Ahsanul , Edwards Elizabeth A. 
Published: April 2019

ABSTRACTTrichloroethene (TCE) is a ubiquitous groundwater pollutant. Successful TCE bioremediation has been demonstrated at field sites using specialized microbial consortia harboring TCE-respiringDehaloccocoideswhose growth is cobalamin (vitamin B12)-dependent. Bioaugmentation cultures grown ex situ with ample exogenous vitamins in the medium and at neutral pH may become vitamin-limited or inhibited by acidic pH once injected into field sites, resulting in incomplete TCE dechlorination and accumulation of more toxic vinyl chloride (VC). Here, we report growth of theDehalococcoides-containing bioaugmentation culture KB-1 in a TCE-amended mineral medium devoid of vitamins and in a VC-amended mineral medium at low pH (6.0 and 5.5). In cultures grown without exogenous vitamins or cobalamin,Acetobacterium, which can synthesize 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, andSporomusaare the dominant acetogens. At neutral pH, a growingAcetobacteriumpopulation supports complete TCE dechlorination byDehalococcoidesat millimolar levels with a substantial increase in the amount of measured cobalamin (~20-fold). Sustained dechlorination of VC to ethene was achieved at a pH as low as 5.5, yet at low pHAcetobacteriumis less abundant, potentially affecting the production of DMB and/or cobalamin. However, dechlorination activity at very low pH (< 5.0) was not stimulated by DMB supplementation, but was restored by raising pH to neutral. Assays in cell extracts revealed that vinyl chloride reductase (VcrA) activity declines significantly below pH 6.0 and is undetectable below pH 5.0. This study highlights the roles of and interplay between vitamin-producing populations and pH in microbial dechlorinating communities, and their importance for successful chlorinated ethenes bioremediation at field sites.
Estradiol modulates gut microbiota in femaleob/obmice fed a high fat diet
Authors: Acharya Kalpana D , Gao Xing , Bless Elizabeth P , Chen Jun , Tetel Marc J 
Published: April 2019

AbstractEstrogens protect against diet-induced obesity in women and female rodents. In support of these anorectic effects, lack of estrogens in postmenopausal women is associated with weight gain, increasing their risk for cardiovascular diseases and cancer. Estrogens act with leptin, a satiety hormone encoded by theobgene, to regulate energy homeostasis in females. Leptin-deficient mice (ob/ob) exhibit morbid obesity and insulin resistance. In addition to estrogens and leptin, the gut microbiome (gut microbes and their metabolites), is critical in regulating energy metabolism. The present study investigates whether estrogens and leptin modulate gut microbiota in ovariectomizedob/ob(obese) or heterozygote (lean) control mice fed a high-fat diet (HFD) that received either 17β-Estradiol (E2) or vehicle implants. E2 attenuated weight gain in both genotypes compared to vehicle counterparts. Moreover, both obesity (ob/obmice) and E2 reduced gut microbial diversity.ob/obmice exhibited lower species richness than control mice, while E2-treated mice had reduced evenness compared to vehicle mice. Regarding taxa, E2 treatment was associated with higher abundances of the family S24-7. Leptin was associated with higher abundances of Coriobacteriaceae,ClostridiumandLactobacillus. E2 and leptin had overlapping effects on relative abundances of some taxa, suggesting that interaction of these hormones is important in gut microbial homeostasis. Taken together, these findings suggest that E2 and leptin profoundly alter the gut microbiota of HFD-fed female mice. Understanding the function of E2 and leptin in regulating gut microbiota will allow the development of therapies targeting the gut microbiome for hormone-dependent metabolic disorders in women.
Adverse childhood experiences: associations with educational attainment and adolescent health, and the role of family and socioeconomic factors. Analysis of a prospective cohort study
Authors: Houtepen Lotte C , Heron Jon , Suderman Matthew J , Fraser Abigail , Chittleborough Catherine R , Howe Laura D 
Published: April 2019

AbstractBackgroundExperiencing multiple adverse childhood experiences (ACE) is a risk factor for many adverse outcomes. However, the role of family and socioeconomic factors in these associations is often overlooked.Methods and findingsUsing data from the Avon Longitudinal Study of Parents and Children, we assess associations of ACE between birth and 16 years (sexual, physical or emotional abuse, emotional neglect, parental substance abuse, parental mental illness or suicide attempt, violence between parents, parental separation, bullying, and parental criminal conviction) with educational attainment at 16 years (n=9,959) and health at age 17 years (depression, obesity, harmful alcohol use, smoking and illicit drug use, n=4,917). We explore the extent to which associations are robust to adjustment for family and socioeconomic factors, whether associations differ according to socioeconomic factors, and estimate the proportion of adverse educational and health outcomes attributable to ACE, family or socioeconomic measures.There were strong associations of ACE with lower educational attainment and higher risk of depression, drug use and smoking. Associations with educational attainment attenuated after adjustment but remained strong. Associations with depression, drug use and smoking were not altered by adjustment. Associations of ACE with harmful alcohol use and obesity were weak. We found no evidence that associations differed by socioeconomic factors. Between 5-15% of the cases of adverse educational and health outcomes occur amongst people experiencing 4+ ACE, and between 1-19% occur in people whose mothers have a low level of education.ConclusionsThis study demonstrates strong associations between ACE and lower educational attainment and worse health that are independent of family and socioeconomic factors. Our findings imply that interventions that focus solely on ACE or solely on socioeconomic deprivation, whilst beneficial, would miss most cases of adverse educational and health outcomes. Intervention strategies should therefore target a wide range of relevant factors, including ACE, socioeconomic deprivation, parental substance use and mental health.
Spatiotemporal restriction ofFUSCA3expression by class I BPC promotes ovule development and coordinates embryo and endosperm growth
Authors: Wu Jian , Petrella Rosanna , Dowhanik Sebastian , Gregis Veronica , Gazzarrini Sonia 
Published: April 2019

ABSTRACTSpatiotemporal regulation of gene expression plays an important role in developmental timing in plants and animals. FUSCA3 regulates the transition between different phases of development by acting as a link between different hormonal pathways in Arabidopsis. However, the mechanisms governing its spatiotemporal expression patterns are poorly understood. Here, we show thatFUS3is expressed in the chalaza and funiculus of the mature ovule and seed, but is repressed in the embryo sac, integuments and endosperm.FUS3repression requires class I BASIC PENTACYSTEINE (BPC) proteins, which directly bind to theFUS3locus and restrict its expression pattern. During vegetative and reproductive development, derepression ofFUS3inbpc1/2orpML1:FUS3misexpression lines results in dwarf plants carrying defective flowers and aborted ovules. Post-fertilization, ectopicFUS3expression in the endosperm increases endosperm nuclei proliferation and seed size and delays or arrests embryo development. These phenotypes are rescued inbpc1/2 fus3-3. Lastly, class I BPCs interact with FIS-PRC2 (FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2), which repressesFUS3in the endosperm. We propose that BPC1/2 promotes the transition from reproductive to seed development by repressingFUS3in ovule integuments. After fertilization, BPC1/2 and FIS-PRC2 repress FUS3 in the endosperm to coordinate endosperm and embryo growth.
Structure and functional implications of WYL-domain-containing transcription factor PafBC involved in the mycobacterial DNA damage response
Authors: Müller Andreas U. , Leibundgut Marc , Ban Nenad , Weber-Ban Eilika 
Published: April 2019

AbstractIn mycobacteria, transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage. Understanding the mechanism of PafBC activation is impeded by a lack of structural information on this transcription factor that contains a widespread, but poorly understood WYL domain frequently encountered in bacterial transcription factors. Here, we determined the crystal structure ofArthrobacter aurescensPafBC. The protein consists of two modules, each harboring an N-terminal helix-turn-helix DNA binding domain followed by a central WYL and a C-terminal extension (WCX) domain. The WYL domains exhibit Sm-folds, while the WCX domains adopt ferredoxin-like folds, both characteristic for RNA binding proteins. Our results suggest a mechanism of regulation in which WYL domain-containing transcription factors may be activated by binding RNA molecules. Using anin vivomutational screen inMycobacterium smegmatis, we identify potential co-activator binding sites on PafBC.
Does diversity beget diversity in microbiomes?
Authors: Madi Naïma , Vos Michiel , Murall Carmen Lia , Legendre Pierre , Shapiro B. Jesse 
Published: April 2019

AbstractMicrobes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. ‘Ecological Controls’ (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, ‘Diversity Begets Diversity’ (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favoring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).Impact statementMicrobiome diversity favors further diversity in a positive feedback that is strongest in lower-diversity biomes (e.g. guts) but which plateaus as niches are increasingly filled in higher-diversity biomes (e.g. soils).
Maternal antibodies provide partial protection from postnatal Zika viremia in nonhuman primates
Authors: Maness Nicholas J , Schouest Blake , Singapuri Anil , Dennis Maria , Gilbert Margaret H. , Bohm Rudolf P. , Schiro Faith , Aye Pyone P. , Baker Kate , Van Rompay Koen K. A. , Lackner Andrew A. , Bonaldo Myrna C. , Blair Robert V. , Permar Sallie R. , Coffey Lark L. , Panganiban Antonito T. , Magnani Diogo 
Published: April 2019

AbstractZika virus (ZIKV) will remain a public health threat until effective vaccines and therapeutics are made available in the hardest hit areas of the world. Recent data in a nonhuman primate model showed that infants postnatally infected with ZIKV were acutely susceptible to high viremia and neurological damage, suggesting the window of vulnerability extends beyond gestation. We addressed the susceptibility of two infant rhesus macaques born healthy to dams infected with Zika virus during pregnancy. Passively acquired neutralizing antibody titers dropped below detection limits between 2 and 3 months of age, while binding, possibly non-neutralizing antibodies remained detectable until viral infection at 5 months of age. Post-infection acute serum viremia was substantially reduced relative to adults infected with the same dose of the same stock of a Brazilian isolate of ZIKV (n=11 pregnant females) and another stock of the same isolate (n=4 males and 4 non-pregnant females). Virus was never detected in cerebrospinal fluid nor in neural tissues at necropsy two weeks after infection, suggesting reduced viral burden relative to adults and published data from infants. However, viral RNA was detected in lymph nodes, confirming some tissue dissemination. Though protection was not absolute, our data suggest infants born healthy to infected mothers may harbor a modest but important level of protection from postnatally acquired ZIKV for several months after birth, an encouraging result given the potentially severe infection outcomes of this population.
Optimal Mass Transport Kinetic Modeling for Head and Neck DCE-MRI: Initial Analysis
Authors: Elkin Rena , Nadeem Saad , LoCastro Eve , Paudyal Ramesh , Hatzoglou Vaios , Lee Nancy Y. , Shukla-Dave Amita , Deasy Joseph O. , Tannenbaum Allen 
Published: April 2019

AbstractCurrent state-of-the-art models for estimating the pharmacokinetic parameters do not account for intervoxel movement of the contrast agent (CA). We introduce an optimal mass transport (OMT) formulation that naturally handles intervoxel CA movement and distinguishes between advective and diffusive flows. Ten patients with head and neck squamous cell carcinoma (HNSCC) were enrolled in the study between June 2014 and October 2015 and under-went DCE MRI imaging prior to beginning treatment. The CA tissue concentration information was taken as the input in the data-driven OMT model. The OMT approach was tested on HNSCC DCE data that provides quantitative information for forward flux (ΦF) and backward flux (ΦB). OMT-derived ΦF was compared with the volume transfer constant for CA, Ktrans, derived from the Extended Tofts Model (ETM). The OMT-derived flows showed a consistent jump in the CA diffusive behavior across the images in accordance with the known CA dynamics. The mean forward flux was 0.0082 ± 0.0091 (min-1) whereas the mean advective component was 0.0052±0.0086 (min-1) in the HNSCC patients. The diffusive percentages in forward and backward flux ranged from 8.67–18.76% and 12.76–30.36%, respectively. The OMT model accounts for intervoxel CA movement and results show that the forward flux (ΦF) is comparable with the ETM-derived Ktrans. This is a novel data-driven study based on optimal mass transport principles applied to patient DCE imaging to analyze CA flow in HNSCC.
Population differences in aggression are shaped by cyclone-induced selection
Authors: Little Alexander G. , Fisher David N. , Schoener Thomas W. , Pruitt Jonathan N. 
Published: April 2019

AbstractSurprisingly little is known about the evolutionary impacts of rare but extreme black swan events, like tropical cyclones. By intercepting three cyclones in fall 2018, we evaluated cyclone-induced selection on collective behavior in a group-living spider. We further examined whether historic frequencies of cyclone landfalls are correlated with geographic variation in group behavior. Cyclones consistently selected for more aggressive spider societies. Furthermore, sites where cyclones have historically been more common also harbor more aggressive groups. Thus, two corroborative lines of evidence convey that that cyclone-induced selection can drive the evolution of colony behavior, and suggest that extreme black swan events can shape within-species diversity and local adaptation.One Sentence SummaryTropical cyclones drive the evolution of more aggressive spider societies.
Scalable, FACS-Free Genome-Wide Phenotypic Screening
Authors: Mair Barbara , Aldridge Peter M. , Atwal Randy S. , Masud Sanna N. , Zhang Meng , Philpott David , Tong Amy H.Y. , Sargent Edward H. , Angers Stéphane , Moffat Jason , Kelley Shana O. 
Published: April 2019

ABSTRACTGenome-scale functional genetic screens can identify key regulators of a phenotype of interest, such as determinants of protein expression or modification. Here, we present a rapid, high-throughput approach to phenotypic CRISPR-Cas9 screening. To study factors that modulate the display of CD47 on the cell surface, we processed an entire genome-wide screen containing more than 108cells in under one hour and maintained high levels of cell viability using a highly scalable cell sorting technology. We robustly identified modulators of CD47 function including QPCTL, an enzyme required for formation of the pyroglutamyl modification at the N-terminus of this protein.
baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data
Authors: Ozuna A. , Liberto D. , Joyce R. M. , Arnvig K.B. , Nobeli I. 
Published: April 2019

AbstractSummaryStandard bioinformatics pipelines for the analysis of bacterial transcriptomic data commonly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untranslated regions (UTRs) of mRNA transcripts. The root of this problem is the use of incomplete genome annotation files. Here, we present baerhunter, a method implemented in R, that automates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome. The core algorithm is part of a pipeline that facilitates downstream analysis of both coding and non-coding features. The method is simple, easy to extend and customize and, in limited tests with simulated and real data, compares favourably against the currently most popular alternative.AvailabilityThe baerhunter R package is available from: https://github.com/irilenia/baerhunterContacti.nobeli@bbk.ac.uk
Dissecting mechanisms of human islet differentiation and maturation through epigenome profiling
Authors: Alvarez-Dominguez Juan R. , Donaghey Julie , Kenty Jennifer H. R. , Rasouli Niloofar , Helman Aharon , Charlton Jocelyn , Straubhaar Juerg R. , Meissner Alexander , Melton Douglas A. 
Published: April 2019

SUMMARYInvestigating pancreatic islet differentiation from human stem cells in vitro provides a unique opportunity to dissect mechanisms that operate during human development in utero. We developed methods to profile DNA methylation, chromatin accessibility, and histone modifications from pluripotent stem cells to mature pancreatic islet cells, uncovering widespread epigenome remodeling upon endocrine commitment. Key lineage-defining loci are epigenetically primed before activation, foreshadowing cell fate commitment, and we show that priming of α-cell-specific enhancers steers polyhormonal cells toward an α-cell fate. We further dissect pioneer factors and core regulatory circuits across islet cell differentiation and maturation stages, which identify LMX1B as a key regulator of in vitro-derived endocrine progenitors. Finally, by contrasting maturing stem cell-derived to natural β-cells, we discover that circadian metabolic cycles trigger rhythmic control of insulin synthesis and release and promote mature insulin responsiveness via an increased glucose threshold. These findings form a basis for understanding mechanisms orchestrating human islet cell specification and maturation.
ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions
Authors: Tian Simon Zhongyuan , Capurso Daniel , Kim Minji , Lee Byoungkoo , Zheng Meizhen , Ruan Yijun 
Published: April 2019

AbstractChIA-Drop is a new experimental method for mapping multiplex chromatin interactions with single-molecule precision by barcoding chromatin complexes inside microfluidics droplets, followed by pooled DNA sequencing. The chromatin DNA reads with the same droplet-specific barcodes are inferred to be derived from the same chromatin interaction complex. Here, we describe an integrated computational pipeline, named ChIA-DropBox, that is specifically designed for reconstructing chromatin reads in each droplet and refining multiplex chromatin complexes from raw ChIA-Drop sequencing reads, and then visualizing the results. First, ChIA-DropBox maps and filters sequencing reads, and then reconstructs the “chromatin droplets” by parsing the barcode sequences and grouping together chromatin reads with the same barcode. Based on the concept of chromosome territories that most chromatin interactions take place within the same chromosome, potential mixing up of chromatin complexes derived from different chromosomes could be readily identified and separated. Accordingly, ChIA-DropBox refines these “chromatin droplets” into purely intra-chromosomal chromatin complexes, ready for downstream analysis. For visualization, ChIA-DropBox converts the ChIA-Drop data to pairwise format and automatically generates input files for viewing 2D contact maps in Juicebox and viewing loops in BASIC Browser. Finally, ChIA-DropBox introduces a new browser, named ChIA-View, for interactive visualization of multiplex chromatin interactions.
Elav-mediated exon skipping and alternative polyadenylation of the Dscam1 gene is required for axon outgrowth
Authors: Zhang Z. , So K. , Peterson R. , Bauer M. , Ng H. , Zhang Y. , Kim J.H. , Kidd T. , Miura P. 
Published: April 2019

SummaryMany metazoan genes express alternative long 3′ UTR isoforms in the nervous system, but their functions remain largely unclear. In Drosophila melanogaster, the Dscam1 gene generates short and long (Dscam1-L) 3′ UTR isoforms due to alternative polyadenylation (APA). Here, we found that the RNA-binding protein Embryonic Lethal Abnormal Visual System (Elav) impacts Dscam1 biogenesis at two levels, including regulation of long 3′ UTR biogenesis and skipping of an upstream exon (exon 19). MinION long-read sequencing confirmed the connectivity of this alternative splicing event to the long 3′ UTR. Knockdown or CRISPR deletion of Dscam1-L impaired axon growth in Drosophila. The Dscam1 long 3′ UTR was found to be required for correct Elav-mediated skipping of exon 19. Elav thus co-regulates APA and alternative splicing to generate specific Dscam1 transcripts that are essential for neural development. This coupling of APA to alternative splicing might represent a new class of regulated RNA processing.
Graphical AbstractHighlightsElav regulates Dscam1 long 3′ UTR (Dscam1-L) biogenesisLong-read sequencing reveals connectivity of long 3′ UTR to skipping of upstream exon 19Loss of Dscam1-L impairs axon outgrowthDscam1 long 3′ UTR is required for correct splicing of exon 19
Early urine proteome changes in an implanted bone cancer rat model
Authors: Wang Ting , Li Lujun , Qin Weiwei , Huan Yuhang , Gao Youhe 
Published: April 2019

AbstractIn this study, Walker 256 cells were implanted into rat tibiae. Urine samples were then collected on days 3, 5, 7, and 13 and were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). With label-free quantification, 25 proteins were found to change significantly in the urine of the tumor group mice compared with the proteins in the urine of the control group mice; this was even the case when there were no significant lesions identified in the Computed Tomography(CT) examination. Among these differentially proteins, 7 were reported to be associated with tumor bone metastasis. GO analysis shows that the differential proteins on day 3 were involved in several responses, including the acute phase response, the adaptive immune response and the innate immune response. The differentially proteins on day 7 were involved in the mineral absorption pathway. The differentially proteins on day 13 were involved in vitamin D binding and calcium ion binding. These processes may be associated with bone metastasis. Our results demonstrate that urine could sensitively reflect the changes in the early stage of implanted bone cancer; this provides valuable clues for future studies of urine biomarkers for tumor bone metastasis.