bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bee and Flowering Plant Communities in a Riparian Corridor of the Lower Rio Grande River (Texas, USA)
Authors: Rubio Amede , Wright Karen , Longing Scott 
Published: January 2020

AbstractThe Rio Grande in Texas serves as the geo-political boundary between the United States and Mexico. It is considered one of the world’s most at-risk rivers and has been the subject of intensified management by the inhabitants of both countries lining its banks. Additionally, invasion by non-native Arundo donax (Linnaeus) (Cyperales: Poaceae), giant reed, has been extensive in the riparian corridor, with potential impacts to native wildlife. Locally, there remains a significant lack of ecological community data of riparian and upland habitats parallel to the river. We sampled bee and flowering plant communities monthly over two years, along a 3.22 km stretch of the lower Rio Grande in Webb County, TX. Data show that bee and plant richness and abundance was highest during March-April and September among both habitat types. Analysis of bee communities showed low spatial and temporal variation at the habitat level. Although common bee taxa (Halictidae and Apidae) were numerically dominant, NMS and ISA found key bee species driving community patterns. This included higher abundances of two species in the riparian habitat Anthophora occidentalis (Cresson) (Hymenoptera: Apidae) and Lasioglossum sp.L (Curtis) (Hymenoptera: Apidae) and one showing affinity for the upland habitat Halictus ligatus (Say) (Hymenoptera: Halictidae). Additionally, ISA analysis of plant data revealed that three species were significant indicator taxa in riparian habitats. Further analysis showed a positive correlation between bee generic richness and abundance with various climate attributes. Management of the riparian corridor and associated watershed could include significant areas for ecological restoration to assist pollinators.
ZEAMAP, a comprehensive database adapted to the maize multi-omics era
Authors: Gui Songtao , Yang Linfeng , Li Jianbo , Luo Jingyun , Xu Xiaokai , Yuan Jianyu , Chen Lu , Li Wenqiang , Yang Xin , Wu Shenshen , Li Shuyan , Wang Yuebin , Zhu Yabing , Gao Qiang , Yang Ning , Yan Jianbing 
Published: January 2020

AbstractAs one of the most extensively cultivated crops, maize (Zea maysL.) has been extensively studied by researchers and breeders for over a century. With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte. Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits. To this end, we constructed ZEAMAP (http://www.zeamap.com), a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions, high-quality genetic variants, phenotypes, metabolomics, genetic maps, genetic mapping loci, population structures and domestication selection signals between teosinte and maize. ZEAMAP is user-friendly, with the ability to interactively integrate, visualize and cross-reference multiple different omics datasets.
Subcortical magnocellular visual system facilities object recognition by processing topological property
Authors: Wang Wenbo , Zhou Tiangang , Zhuo Yan , Chen Lin , Huang Yan 
Published: January 2020

AbstractThe Magnocellular (M) visual pathway is known as a fast route to convey coarse information and facilitates object recognition by initiating top-down processes. It is unclear what exact properties M pathway conveys to accelerate visual object processing. Previous studies suggest that visual systems are highly sensitive to the perception of topological property (TP), which remains unchanged under various shape changes, and the TP is probably processed through a fast subcortical pathway. Here we hypothesize that a subcortical M system contributes to the fast object recognition by processing TP first. We first demonstrate that the facilitation effect of TP processing on object perception occurs mainly in the M visual system, and then support the subcortical M hypothesis of TP processing by the evidence that the early processing of TP was not affected when cortical function was temporarily damaged by the transcranial magnetic stimulation and when stimuli were biased to M system.
A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair
Authors: van den Heuvel Diana , Spruijt Cornelia G. , González-Prieto Román , Kragten Angela , Paulsen Michelle T. , Zhou Di , Wu Haoyu , Apelt Katja , van der Weegen Yana , Yang Kevin , Dijk Madelon , Daxinger Lucia , Marteijn Jurgen A. , Vertegaal Alfred C.O. , Ljungman Mats , Vermeulen Michiel , Luijsterburg Martijn S. 
Published: January 2020

AbstractThe coordinated transcription of genes involves the regulated release of RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but this is not sufficient to resume transcription. Through proteomics screens, we find that the TCR-specific CSB protein loads the evolutionary conserved PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. PAF1C is dispensable for TCR-mediated repair, but is essential for recovery of RNA synthesis after UV irradiation, suggesting an uncoupling between DNA repair and transcription recovery. Moreover, we find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.
1-[(4-Nitrophenyl)sulfonyl]-4-phenylpiperazine Treatment After Brain Irradiation Preserves Cognitive Function in Mice
Authors: Bhat Kruttika , Medina Paul , He Ling , Zhang Le , Saki Mohammad , Ioannidis Angeliki , Nguyen Nhan T. , Sodhi Sirajbir S. , Sung David , Magyar Clara E. , Liau Linda M. , Kornblum Harley I. , Pajonk Frank 
Published: January 2020

AbstractBackgroundNormal tissue toxicity to the CNS is an inevitable consequence of a successful radiotherapy of brain tumors or cancer metastases to the CNS. Cranial irradiation commonly leads to neurocognitive deficits that manifest months or years after treatment. Mechanistically, radiation-induced loss of neural stem/progenitor cells, neuro-inflammation and de-myelinization are contributing factors that lead to progressive cognitive decline.MethodsThe effects of Compound #5 on irradiated murine neurospheres, microglia cells and patients-derived gliomaspheres were assessed in sphere-formation assays, flow cytometry and IL-6 ELISAs, Activation of the Hedgehog pathway was studied by qRT-PCR. Thein vivoeffects of Compound #5 were analyzed using flow cytometry, sphere-formation assays, immune-histochemistry, behavioral testing and an intracranial mouse model of glioblastoma.ResultsWe report that 1-[(4-Nitrophenyl)sulfonyl]-4-phenylpiperazine (Compound #5) mitigates radiation-induced normal tissue toxicity in the brains of mice. Compound #5 treatment significantly increased the number of neural stem/progenitor cells after brain irradiation in female animals, inhibited radiation-induced microglia activation and expression of the pro-inflammatory cytokine interleukin-6. Behavioral testing revealed that treatment with Compound #5 after radiotherapy successfully mitigates radiation-induced decline in motor, sensory and memory function of the brain. In mouse models of glioblastoma, Compound #5 showed no toxicity and did not interfere with the growth-delaying effects of radiation.ConclusionsWe conclude that Compound #5 has the potential to mitigate cognitive decline in patients undergoing partial or whole brain irradiation without promoting tumor growth and that the use of this compound as a radiation mitigator of radiation late effects on the CNS warrants further investigation.Importance of the StudySuccessful radiotherapy of CNS malignancies inevitably lead to cognitive decline in cancer survivors and treatment options to mitigate this side effect are limited. We present evidence that a piperazine compound can prevent cognitive decline in mice after total brain irradiation without compromising the antitumor effect of radiation, suggesting that this compound could be used to mitigate radiation side effects in brain tumor patients undergoing radiotherapy.
In vivocommensal control ofClostridioides difficilevirulence
Authors: Girinathan Brintha P. , DiBenedetto Nicholas , Worley Jay N. , Peltier Johann , Arrieta-Ortiz Mario L. , Immanuel Rupa , Lavin Richard , Delaney Mary L. , Cummins Christopher , Hoffmann Maria , Luo Yan , Escalona Narjol Gonzalez , Allard Marc , Onderdonk Andrew B. , Gerber Georg K. , Sonenshein Abraham L. , Baliga Nitin , Dupuy Bruno , Bry Lynn 
Published: January 2020

SummaryWe define multiple mechanisms by which commensals protect against or worsenClostridioides difficileinfection. Leveraging new systems-level models we show how metabolically distinct species ofClostridiamodulate the pathogen’s colonization, growth, and virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenterParaclostridium bifermentanssurvived infection while mice colonized with the butyrate- producer,Clostridium sardiniense,more rapidly succumbed. Systematicin vivoanalyses revealed how each commensal altered the gut nutrient environment, modulating the pathogen’s metabolism, regulatory networks, and toxin production. Oral administration ofP. bifermentansrescued conventional mice from lethalC. difficileinfection via mechanisms identified in specifically colonized mice. Our findings lay the foundation for mechanistically informed therapies to counterC. difficileinfections using systems biologic approaches to define host-commensal-pathogen interactionsin vivo.Graphical Abstract
Monitoring the production of high diffraction-quality crystals of two enzymes in real time usingin situdynamic light scattering
Authors: de Wijn Raphaël , Rollet Kévin , Engilberge Sylvain , McEwen Alastair G. , Hennig Oliver , Betat Heike , Mörl Mario , Riobé François , Maury Olivier , Girard Eric , Bénas Philippe , Lorber Bernard , Sauter Claude 
Published: January 2020

ABSTRACTThe reproducible preparation of well diffracting crystals is a prerequisite for every structural study based on crystallography. An instrument called the XtalController has recently been designed that allows the monitoring of crystallization assays using dynamic light scattering and microscopy, and integrates piezo pumps to alter the composition of the mother liquor during the experiment. We have applied this technology to study the crystallization of two enzymes, the CCA-adding enzyme of the psychrophilic bacteriumPlanococcus halocryophilusand the hen egg white lysozyme in the presence of a synthetic chemical nucleant. We were able to i) detect early nucleation events and ii) drive the crystallization system (through cycles of dissolution/crystallization) towards growth conditions yielding crystals with excellent diffraction properties. This technology opens a way to the rational production of samples for crystallography, ranging from nanocrystals for electron diffraction, microcrystals for serial or conventional X-ray diffraction, to larger crystals for neutron diffraction.
Co-option ofPlasmodium falciparumPP1 for egress from host erythrocytes
Authors: Paul Aditya S. , Miliu Alexandra , Paulo Joao A. , Goldberg Jonathan M. , Bonilla Arianna M. , Berry Laurence , Séveno Marie , Braun-Breton Catherine , Kosber Aziz L. , Elsworth Brendan , Arriola Jose S.N. , Lebrun Maryse , Gygi Steven P. , Lamarque Mauld H. , Duraisingh Manoj T. 
Published: January 2020

AbstractAsexual proliferation of thePlasmodiumparasites that cause malaria follow a developmental program that alternates non-canonical intraerythrocytic replication with dissemination to new host cells. We carried out a functional analysis of thePlasmodium falciparumhomolog of Protein Phosphatase 1 (PfPP1), a universally conserved cell cycle factor in eukaryotes, to investigate regulation of parasite proliferation.PfPP1 is indeed required for efficient replication, but is absolutely essential for egress of parasites from host red blood cells. A phosphoproteomic screen and chemical-genetic analysis provided evidence for a HECT E3 protein-ubiquitin ligase, as well as a fusion protein with guanylyl cyclase and phospholipid transporter domains, as functional targets ofPfPP1. Extracellular phosphatidylcholine stimulatesPfPP1-dependent egress. ParasitePfPP1 acts as a master regulator that can integrate multiple cell-intrinsic pathways with external signals to direct parasite egress from host cells.
Synaptic vesicles dynamics in neocortical epilepsy
Authors: Vannini Eleonora , Restani Laura , Dilillo Marialaura , McDonnell Liam , Caleo Matteo , Marra Vincenzo 
Published: January 2020

AbstractNeuronal hyperexcitability often results from an unbalance between excitatory and inhibitory neurotransmission, but the synaptic alterations leading to enhanced seizure propensity are only partly understood. Taking advantage of a mouse model of neocortical epilepsy, we used a combination of photoconversion and electron microscopy to assess changes in synaptic vesicles poolsin vivo. Our analyses reveal that epileptic networks show an early onset lengthening of active zones at inhibitory synapses, together with a delayed spatial reorganization of recycled vesicles at excitatory synapses. Proteomics of synaptic content indicate that specific proteins were increased in epileptic mice. Altogether, our data reveal a complex landscape of nanoscale changes affecting the epileptic synaptic release machinery. In particular, our findings show that an altered positioning of release-competent vesicles represent a novel signature of epileptic networks.
The landscape of mouse epididymal cells defined by the single-cell RNA-Seq
Authors: Shi Jianwu , Sang Mengmeng , Xie Gangcai , Chen Hao 
Published: January 2020

ABSTRACTSpermatozoa acquire their fertilizing ability and forward motility properties during epididymal transit. Although lots of attempts elucidating the functions of different cell types in epididymis, the composition of epididymal tubal and cell types are still largely unknown. Using single-cell RNA sequence, we analyzed the cell constitutions and their gene expression profiles of adult epididymis derived from caput, corpus and cauda epididymis with a total of 12,597 cells. This allowed us to elucidate the full range of gene expression changes during epididymis and derive region-specific gene expression signatures along the epididymis. A total of 7 cell populations were identified with all known constituent cells of mouse epididymis, as well as two novel cell types. Our analyses revealed a segment to segment variation of the same cell type in the three different part of epididymis and generated a reference dataset of epididymal cell gene expression. Focused analyses uncovered nine subtypes of principal cell. Two subtypes of principal cell, c0.3 and c.6 respectively, in our results supported with previous finding that they mainly located in the caput of mouse epididymis and play important roles during sperm maturation. We also showed unique gene expression signatures of each cell population and key pathways that may concert epididymal epithelial cell-sperm interactions. Overall, our single-cell RNA seq datasets of epididymis provide a comprehensive potential cell types and information-rich resource for the studies of epididymal composition, epididymal microenvironment regulation by the specific cell type, or contraceptive development, as well as a gene expression roadmap to be emulated in efforts to achieve sperm maturation regulation in the epididymis.
A sample preparation protocol for high throughput immunofluorescence of suspension cells
Authors: Bäckström Anna , Kugel Laura , Gnann Christian , Xu Hao , Aslan Joseph E. , Lundberg Emma , Stadler Charlotte 
Published: January 2020

AbstractImaging is a powerful approach for studying protein expression and has the advantage over other methodologies in providing spatial informationin situat single cell level. Using immunofluorescence and confocal microscopy, detailed information of subcellular distribution of proteins can be obtained. While adherent cells of different tissue origin are relatively easy to prepare for imaging applications, nonadherent cells from hematopoietic origin, present a challenge due to their poor attachment to surfaces and subsequent loss of a substantial fraction of the cells. Still, these cell types represent an important part of the human proteome and express genes that are not expressed in adherent cell types. In the era of cell mapping efforts, overcoming the challenge with suspension cells for imaging applications would enable systematic profiling of hematopoietic cells. In this work, we successfully established an immunofluorescence protocol for preparation of suspension cell lines and peripheral blood mononucleated cells (PBMC) and human platelets. The protocol is based on a multi-well plate format with automated sample preparation, allowing for robust high throughput imaging applications. In combination with confocal microscopy, the protocol enables systematic exploration of protein localization to all major subcellular structures.
TGF-β-driven downregulation of the Wnt/β-Catenin transcription factor TCF7L2/TCF4 in PDGFRα+fibroblasts
Authors: Contreras Osvaldo , Soliman Hesham , Theret Marine , Rossi Fabio M.V. , Brandan Enrique 
Published: January 2020

ABSTRACTMesenchymal stromal/stem cells (MSCs) are multipotent progenitors essential ororganogenesis, tissue homeostasis, regeneration, and scar formation. Tissue injury upregulates TGF-β signaling, which modulates myofibroblast fate, extracellular matrix remodeling, and fibrosis. However, the molecular determinants of MSCs differentiation and survival remain poorly understood. The canonical Wnt Tcf/Lef transcription factors regulate development and stemness, but the mechanisms by which injury-induced cues modulate their expression remain underexplored. Here, we studied the cell-specific gene expression of Tcf/Lef and, more specifically, we investigated whether damage-induced TGF-β impairs the expression and function of TCF7L2, using several models of MSCs, including skeletal muscle fibro-adipogenic progenitors. We show that Tcf/Lefs are differentially expressed and that TGF-β reduces the expression of TCF7L2 in MSCs but not in myoblasts. We also found that the ubiquitin-proteasome system regulates TCF7L2 proteostasis and participates in TGF-β-mediated TCF7L2 protein downregulation. Finally, we show that TGF-β requires HDACs activity to repress the expression of TCF7L2. Thus, our work found a novel interplay between TGF-β and Wnt canonical signaling cascades in PDGFRα+fibroblasts and suggests that this mechanism could be targeted in tissue repa ir and regeneration.Summary statementTGF-β signaling suppresses the expression of the Wnt transcription factor TCF7L2 and compromises TCF7L2-dependent functions in tissue-resident PDGFRα+fibroblasts.
GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline
Authors: Guerra-Assunção José Afonso , Conde Lucia , Moghul Ismail , Webster Amy P. , Ecker Simone , Chervova Olga , Chatzipantsiou Christina , Prieto Pablo P. , Beck Stephan , Herrero Javier 
Published: January 2020

AbstractIn recent years, there has been a significant increase in whole genome sequencing data of individual genomes produced by research projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner.GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation.GenomeChronicler can be used with data from whole genome or whole exome sequencing, producing a genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalgenomes.org.uk/data).The objective of this method is to leverage existing resources to find known phenotypes associated with the genotypes detected in each sample. The provided trait data is based primarily upon information available in SNPedia, but also collates data from ClinVar, GETevidence and gnomAD to provide additional details on potential health implications, presence of genotype in other PGP participants and population frequency of each genotype.The analysis can be run in a self-contained environment without requiring internet access, making it a good choice for cases where privacy is essential or desired: any third party project can embed GenomeChronicler within their off-line safe-haven environments. GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager.The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. Users without access to computational resources to run GenomeChronicler can access the software from the Lifebit CloudOS platform (https://lifebit.ai/cloudos) enabling the production of reports and variant calls from raw sequencing data in a scalable fashion.
Spatial accumulation of salicylic acid is regulated by RBOHD in potato immunity against viruses
Authors: Lukan Tjaša , Pompe-Novak Maruša , Baebler Špela , Tušek-Žnidarič Magda , Kladnik Aleš , Križnik Maja , Blejec Andrej , Zagorščak Maja , Stare Katja , Dušak Barbara , Coll Anna , Pollmann Stephan , Morgiewicz Karolina , Hennig Jacek , Gruden Kristina 
Published: January 2020

AbstractWhile activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to restriction of pathogen remain mostly unknown. We studied the immunity network response conditioned by the potatoNy-1gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels to reveal spatiotemporal regulation of immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes, spatiotemporal regulation is completely lost in SA-deficient line, while the others show different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during resistance response. In plants with silenced RBOHD, the functionality of resistance response is perturbed and virus spread is not arrested at the site of infection. RBOHD is required for spatial accumulation of SA, and conversely RBOHD is under transcriptional regulation of SA signaling. Using spatially resolved RNA-Seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.