bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Structures of Secretory and Dimeric Immunoglobulin A
Authors: Bharathkar Sonya Kumar , Parker Benjamin W. , Malyutin Andrey G. , Haloi Nandan , Huey-Tubman Kathryn E. , Tajkhorshid Emad , Stadtmueller Beth M. 
Published: February 2020

AbstractSecretory (S) Immunoglobulin (I) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a β-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen binding fragments (Fabs) and preserves steric accessibility to receptor binding sites, likely influencing antigen binding and effector functions.
The tRNA pseudouridine synthase TruB1 regulates the maturation and function of let-7 miRNA
Authors: Kurimoto Ryota , Chiba Tomoki , Ito Yoshiaki , Matsushima Takahide , Yano Yuki , Miyata Kohei , Suzuki Tsutomu , Tomita Kozo , Asahara Hiroshi 
Published: February 2020

AbstractLet-7 is an evolutionary conserved microRNA that mediates post-transcriptional gene silencing to regulate a wide range of biological processes, including development, differentiation, and tumor suppression. Let-7 biogenesis is tightly regulated by several RNA-binding proteins, including Lin28A/B, which represses let-7 maturation. To identify new regulators of let-7, we devised a cell-based functional screen of RNA-binding proteins using a let-7 sensor luciferase reporter, and identified the tRNA pseudouridine synthase, TruB1. TruB1 enhanced maturation specifically of let-7 family members. Rather than inducing pseudouridylation of the miRNAs, HITS-CLIP (High throughput sequencing crosslinking immunoprecipitation) and biochemical analyses revealed direct binding between endogenous TruB1 and the stem-loop structure of pri-let-7, which also binds Lin28A/B. TruB1 selectively enhanced the interaction between pri-let-7 and the microprocessor DGCR-8, which mediates miRNA maturation. Finally, TruB1 suppressed cell proliferation, which was mediated in part by let-7. Altogether, we reveal an unexpected function for TruB1 in promoting let-7 maturation and function.
Semiautomated detection ofPseudomonas aeruginosafrom diverse water samples using highly selective Z-broth and a redox potential monitor
Authors: Szita Géza , Katalin Szakmár , Bernáth Sándor , Sövényi József , Fülöp Gábor , Janaki Hadjiev , Csikó György , Solymosi Norbert , Makrai László 
Published: February 2020

AbstractPseudomonas aeruginosais a facultative bacterial pathogen with increasing public health risk potential. Contaminated water in hospital environments is a growing cause of multidrug-resistentP. aeruginosanosocomial infections that are life-threatening and are costly to treat.P. aeruginosais common in natural water bodies, but it is not unusual in drinking water and has been detected in bottled water, also. Suppliers in Europe must eliminate live forms of the bacterium in drinking water to meet human consumption requirements. Laboratory testing for the presence of viableP. aeruginosais mostly done manually using culture media but conductance/impedimetry measurements for detection are also available. In order to improve expedience and cost efficiency as well as to automate the detection and the data registration, we applied the highly selective Z-broth culture media and redox potential monitoring to detectP. aeruginosafrom water. The Z-broth is based on only a few, stable chemicals that provide consistency of quality and long shelf life. It limits growth toP. aeruginosaand, thus, eliminates the need for subsequent microbiological identification steps of the European Standard procedure defined in ISO 16 266:2006 (2018). A redox potential monitor was used in this work, that simultaneously recorded 64 sample curves and automatically marked positive samples reliably within 24 hours after sample initialization. In comparison, the standard method requires additional tests that prolongs identification to some days. Practical applicability and reliability of the method in this paper was demonstrated by testing a total of 739 water samples of which 222 were tap water, 342 well water and 145 had been taken from swimming pools.It is considered this method is well suited to process large numbers of samples for purposes of detectingP. aeruginosacontamination with relative ease, little cost in shortened time. Using Z-broth in combination with redox potential monitoring can be recommended for central laboratories for routine testing of drinking water for liveP. aeruginosapresence. As well, using this method for testing of fluids and surfaces forP. aeruginosacontamination would be advantageous in such environments as the hospital industry, swimming pools and spas, where cleaning routines andP. aeruginosatransmission prevention protocols could be made much more resultful and cost-effective due to ease and speed of processing both spot check and water samples.HighlightsA method was applied for detection of viablePseudomonas aeruginosain 739 water samples.Redox potential monitoring of Z-broth cultures exclusively registered growth ofP. aeruginosa.The method is highly selective, reliable and partly automated, with lower labor costs.The method is suited for testing of water and hospital environments forP. aeruginosa.
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
Authors: Kamimoto Kenji , Hoffmann Christy M. , Morris Samantha A. 
Published: February 2020

SummaryHere, we present CellOracle, a computational tool that integrates single-cell transcriptome and epigenome profiles to infer gene regulatory networks (GRNs), critical regulators of cell identity. Leveraging inferred GRNs, we simulate gene expression changes in response to transcription factor (TF) perturbation, enabling network configurations to be interrogatedin silico, facilitating their interpretation. We validate the efficacy of CellOracle to recapitulate known regulatory changes across hematopoiesis, correctly predicting the outcomes of well-characterized TF perturbations. Integrating CellOracle analysis with lineage tracing of direct reprogramming reveals distinct network configurations underlying different reprogramming failure modes. Furthermore, analysis of GRN reconfiguration along successful reprogramming trajectories identifies new factors to enhance target cell yield, uncovering a role for the AP-1 subunit Fos, with the hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations, at high-resolution, promoting new mechanistic insights into the regulation and reprogramming of cell identity.
Induction Of Chronic Stress Reveals An Interplay Of Stress Granules And TDP-43 Pathological Aggregates In Human ALS Fibroblasts And iPSC-Neurons
Authors: Ratti Antonia , Gumina Valentina , Lenzi Paola , Bossolasco Patrizia , Fulceri Federica , Volpe Clara , Bardelli Donatella , Pregnolato Francesca , Maraschi AnnaMaria , Fornai Francesco , Silani Vincenzo , Colombrita Claudia 
Published: February 2020

AbstractAmyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative diseases characterized by the presence of neuropathological aggregates of phosphorylated TDP-43 (P-TDP-43). The RNA-binding protein TDP-43 is also a component of stress granules (SG), cytoplasmic foci forming to arrest translation under sub-lethal stress conditions. Although commonly considered as distinct structures, a link between SG and pathological TDP-43 inclusions may occur despite evidence that TDP-43 pathology directly arises from SG is still under debate. Primary fibroblasts and iPSC-derived neurons (iPSC-N) from ALS patients carrying mutations inTARDBP(n=3) andC9ORF72(n=3) genes and from healthy controls (n=3) were exposed to oxidative stress by sodium arsenite. SG formation and cell response to stress was evaluated and quantified by immunofluorescence and electron microscopy analyses. We found that, not only an acute, but also a chronic oxidative insult, better mimicking a persistent condition of stress as in neurodegeneration, is able to induce SG formation in primary fibroblasts and iPSC-N. Importantly, only upon chronic stress, we observed TDP-43 recruitment into SG and the formation of distinct P-TDP-43 aggregates, very similar to the abnormal inclusions observed in ALS/FTD autoptic brains. Moreover, in fibroblasts, cell response to stress was different in control compared with mutant ALS cells, probably due to their different vulnerability. A quantitative analysis revealed also differences in terms of number of SG-forming cells and SG size, suggesting a different composition of foci in acute and chronic stress. In condition of prolonged stress, SG and P-TDP-43 aggregate formation was concomitant with p62 increase and autophagy dysregulation in both ALS fibroblasts and iPSC-N, as confirmed by immunofluorescence and ultrastructural analyses. We found that exposure to a chronic oxidative insult promotes the formation of both SG and P-TDP-43 aggregates in patient-derived cells, reinforcing the idea that SG fail to properly disassemble, interfering with the protein quality control system. Moreover, we obtained a disease cell model recapitulating ALS/FTD P-TDP-43 aggregates, which represents an invaluable bioassay to study TDP-43 pathology and develop therapeutic strategies aimed at disaggregating or preventing the formation of pathological inclusions.
Whole genome assembly ofCulex tarsalis
Authors: Main Bradley J. , Marcantonio Matteo , Johnston J. Spencer , Rasgon Jason L. , Brown C. Titus , Barker Christopher M. 
Published: February 2020

AbstractThe mosquito,Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted onCx. tarsalisecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. Salivary gland-specific gene expression has also revealed genes involved in blood feeding. However, genetic studies of this mosquito have been hindered by the lack of a reference genome. To facilitate genomic studies inCx. tarsalis, we have assembled and annotated a reference genome (CtarK1) based on PacBio HiFi reads from a single male. Using theCx. tarsalistranscriptome and protein sequences fromCulex quinquefasciatus, approximately 17,456 protein-coding genes, including theparainsecticide resistance gene, were annotated in the CtarK1 genome. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. The CtarK1 assembly is 790Mb with an N50 of 58kb. Using full mitochondrial genome alignments with other sequenced mosquito genomes we present a Bayesian phylogeny, which estimates that the divergence ofCx. tarsalisfromCulex quinquefasciatus, the most closely related mosquito species with a genome, occurred 15.8-22.2 million years ago.
A transcriptome for the early-branching fernBotrychium lunariaenables fine-grained resolution of population structure
Authors: Mossion Vinciane , Dauphin Benjamin , Grant Jason , Zemp Niklaus , Croll Daniel 
Published: February 2020

AbstractFerns are the second most dominant group of land plants after angiosperms. Extant species occupy an extensive range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources. The genusBotrychiumbelongs to the family Ophioglossaceae, one of the earliest divergent lineages of vascular plants, and has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome forBotrychium lunaria, a diploid species with an extremely large genome with a 1C value of 12.10 pg. We assembled 25,701 high-quality transcripts with an average length of 1,332 bp based on deep RNA-sequencing of a single individual. We sequenced an additional 11 transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,510 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kb. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 90 taxa representing all fern orders to ascertain the placement of the genusBotrychium. The high-quality transcriptomic resources enable powerful population and phylogenomic studies in an important group of ferns.Significance statementFerns pose substantial puzzles in terms of lifestyles, genome organization and population structure. Progress has been significantly hampered by the lack of genomic resources. Here, we present a transcriptome forBotrychium lunaria, a phylogenetically early-branching fern with an extremely large genome. We show that the new transcriptome improves phylogenetic resolution among early-branching ferns. Based on an additional 11 transcriptomes of the same species, we identify unexpected variation in population-level heterozygosity.
Vaccinia Virus Infection Inhibits Skin Dendritic Cell Migration to Draining Lymph Node
Authors: Aggio Juliana Bernardi , Krmeská Veronika , Ferguson Brian J. , Wowk Pryscilla Fanini , Rothfuchs Antonio Gigliotti 
Published: February 2020

AbstractDespite the success of Vaccinia virus (VACV) against smallpox there remains a paucity of information on Dendritic cell (DC) responses to the virus, especially on the traffic of DCs and VACV to draining LN (dLN). Herein we studied skin DC migration in response to VACV and compared it to the tuberculosis vaccineMycobacterium bovisBacille Calmette-Guérin (BCG), another live-attenuated vaccine administered via the skin. In stark contrast to BCG, skin DCs did not relocate to dLN in response to VACV. This happened in spite of virus-induced accumulation of several other innate-immune cell populations in the dLN. UV inactivation of VACV or use of the Modified Vaccinia virus Ankara (MVA) strain promoted DC movement to dLN, indicating that the virus actively interferes with skin DC migration. This active immune suppression by VACV was potent enough to ablate the mobilization of skin DCs in response to BCG, and to reduce the transport of BCG to dLN. Expression of inflammatory mediators associated with BCG-triggered DC migration were absent from virus-injected skin, suggesting that other pathways provoke DC movement in response to replication-deficient VACV. Despite viral suppression of DC migration, VACV was detected in dLN much earlier than BCG, indicating a rapid, alternative route of viral traffic to dLN despite marked blockade of skin DC mobilization from the site of infection.
Contribution of CTCF binding to transcriptional activity at theHOXAlocus inNPM1-mutant AML cells
Authors: Ghasemi Reza , Struthers Heidi , Wilson Elisabeth R. , Spencer David H. 
Published: February 2020

AbstractTranscriptional regulation of theHOXAgenes is thought to involve CTCF-mediated chromatin loops and the opposing actions of the COMPASS and Polycomb epigenetic complexes. We investigated the role of these mechanisms at theHOXAcluster in AML cells with the common NPM1c mutation, which express bothHOXAandHOXBgenes. CTCF binding at theHOXAlocus is conserved across primary AML samples, regardless ofHOXAgene expression, and defines a continuous chromatin domain marked by COMPASS-associated histone H3 trimethylation inNPM1-mutant primary AML samples. Profiling of the three-dimensional chromatin architecture ofNPM1-mutant OCI-AML3 cells identified chromatin loops between the activeHOXA9-HOXA11genes and loci in theSNX10gene and an intergenic region located 1.4Mbp upstream of theHOXAlocus. Deletion of CTCF binding sites in OCI-AML3 cells reduced these interactions, but resulted in new, CTCF-independent loops with regions in theSKAP2gene that were marked by enhancer-associated histone modifications in primary AML samples.HOXAgene expression was maintained in the CTCF deletion mutants, indicating that transcriptional activity at theHOXAlocus inNPM1-mutant AML cells does not require long-range CTCF-mediated chromatin interactions, and instead may be driven by intrinsic factors within theHOXAgene cluster.
TGF-β inhibitor accelerates BMP4-induced cochlear gap junction formation duringin vitrodifferentiation of embryonic stem cells
Authors: Fukunaga Ichiro , Chen Cheng , Oe Yoko , Danzaki Keiko , Ohta Sayaka , Koike Akito , Fujimoto Ayumi , Ikeda Katsuhisa , Kamiya Kazusaku 
Published: February 2020

AbstractMutations in the connexin 26 (CX26)/gap junction beta-2 (GJB2) gene are the most frequent cause of hereditary deafness worldwide. Using mouse induced pluripotent stem cells (iPSCs) and a BMP4 signal-based floating and adherent culture system, we recently producedin vitroresponsible forGJB2-related deafness (CX26-gap junction plaque-forming cells, CX26GJCs). However, to use these cells as a disease model platform for high-throughput drug screening or regenerative therapy, cell yields must be substantially increased. In addition to BMP4, presently uncharacterized factors may also induce CX26 gap junction (GJ) formation. A floating culture with embryonic stem cell (ESC) treatment and BMP4/TGF-β inhibitor (SB431542:SB) has been shown to result in greater production of isolatable CX26-positive small vesicles (CX26+ vesicles) and higherGjb2mRNA levels than BMP4 treatment alone, suggesting that SB may promote BMP4-mediated production of CX26+ vesicles in a dose-dependent manner, thereby increasing the yield of highly purified CX26GJCs.In the present study, we first demonstrated that SB accelerates BMP4 induced GJ formation during stem cell differentiation. By controlling the concentration and timing of SB supplementation with CX26+ vesicle purification, large-scale production of highly purified CX26GJCs suitable for high-throughput drug screening or regenerative therapy forGJB2-related deafness may be possible.
Generation of multi-transgenic pigs using PiggyBac transposons co-expressing pectinase, xylanase, cellulase, β-1.3-1.4-glucanase and phytase
Authors: Wang Haoqiang , Li Guoling , Zhong Cuili , Mo Jianxin , Sun Yue , Shi Junsong , Zhou Rong , Li Zicong , Yang Huaqiang , Wu Zhenfang , Liu Dewu , Zhang Xianwei 
Published: February 2020

AbstractThe current challenges facing the pork industry are to maximize feed efficiency and minimize fecal emissions. Unlike ruminants, pigs lack a number of digestive enzymes like pectinase, xylanase, cellulase, β-1.3-1.4-glucanase and phytase to hydrolyze the cell walls of grains to release endocellular nutrients into their digestive tracts. Herein, we synthesized multiple cellulase and pectinase genes derived from lower organisms and then codon optimized these genes to be expressed in pigs. These genes were then cloned into our previously optimizedXynB(xylanase)-EsAPPA(phytase) bicistronic construct. We then successfully generated transgenic pigs that expressed four enzymes (Pg7fn(pectinase),XynB(xylanase),EsAPPA(phytase) andTeEGI(cellulase and β-glucanase)) using somatic cell cloning. Expression of these genes was parotid gland specific. Enzymatic assays using the saliva of these founders demonstrated high levels of phytase (2.0~3.4 U/mL) and xylanase (0.25~0.42 U/mL) activity, but low levels of pectinase (0.06~0.08 U/mL) activity. These multi-transgenic pigs are expected to contribute to enhance feed utilization and reduce environmental impact.
BARTweb: a web server for transcription factor association analysis
Authors: Ma Wenjing , Wang Zhenjia , Zhang Yifan , Magee Neal E. , Chen Yang , Zang Chongzhi 
Published: February 2020

ABSTRACTIdentifying active transcription factors (TFs) that bind to cis-regulatory regions in the genome to regulate differential gene expression is a key task in gene regulation research. TF binding profiles from numerous existing ChIP-seq data can be utilized for association analysis with query data for TF identification, as alternative to DNA sequence motif analysis. Here, we present BARTweb, an interactive webserver for identifying TFs whose genomic binding patterns associate with input genomic features, by leveraging over 13,000 public ChIP-seq datasets for human and mouse. Using an updated Binding Analysis for Regulation of Transcription (BART) algorithm, BARTweb can identify functional TFs that regulate a gene set, or have a binding profile correlated with a ChIP-seq profile or enriched in a genomic region set, without a priori information of the cell type. Compared with the original BART package, BARTweb substantially reduces the execution time of a typical job by two orders of magnitude. We also show that BARTweb outperforms other existing tools in identifying true TFs from collected experimental data. BARTweb is a useful webserver for performing functional analysis of gene regulation. BARTweb is freely available athttp://bartweb.org.
Cell substrate patterns driven by curvature-sensitive actin polymerization: waves and podosomes
Authors: Naoz Moshe , Gov Nir S. 
Published: February 2020

AbstractCells adhered to an external solid substrate are observed to exhibit rich dynamics of actin structures on the basal membrane, which are distinct from those observed on the dorsal (free) membrane. Here we explore the dynamics of curved membrane proteins, or protein complexes, that recruit actin polymerization when the membrane is confined by the solid substrate. Such curved proteins can induce the spontaneous formation of membrane protrusions on the dorsal side of cells. However, on the basal side of the cells, such protrusions can only extend as far as the solid substrate and this constraint can convert such protrusions into propagating wave-like structures. We also demonstrate that adhesion molecules can stabilize localized protrusions, that resemble some features of podosomes. This coupling of curvature and actin forces may underlie the differences in the observed actin-membrane dynamics between the basal and dorsal sides of adhered cells.