bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioContainers Registry: searching for bioinformatics tools, packages and containers
Authors: Bai Jingwen , Bandla Chakradhar , Guo Jiaxin , Alvarez Roberto Vera , Vizcaíno Juan Antonio , Bai Mingze , Moreno Pablo , Grüning Björn A. , Sallou Olivier , Perez-Riverol Yasset 
Published: July 2020

1AbstractBioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize the software containers including the metadata, versions, licenses, and/or software dependencies. BioContainers supports multiple packaging and containers technologies such as Conda, Docker, and Singularity. Here, we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). BioContainers registry provides a fast and convenient way to find and retrieve bioinformatics tools packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.
Neural Stem Cells Secreting Bispecific T Cell Engager to Induce Selective Anti-Glioma Activity
Authors: Pituch Katarzyna C. , Zanikou Markella , Ilut Liliana , Xiao Ting , Chastkofsky Michael , Sukhanova Madina , Bertolino Nicola , Procissi Daniele , Amidei Christina , Horbinski Craig M. , Aboody Karen S. , James Charles D. , Lesniak Maciej S. , Balyasnikova Irina V. 
Published: July 2020

AbstractGlioblastoma (GBM) is the most lethal primary brain tumor in adults. There is no treatment that provides durable relief for the vast majority of GBM patients. In this study, we’ve tested a bispecific antibody comprised of single-chain variable regions (scFvs) against T cell CD3ε and GBM cell interleukin 13 receptor alpha 2 (IL13Rα2). We demonstrate that this BiTE (BiTELLON) engages peripheral and tumor-infiltrating lymphocytes harvested from patient’s tumors, and in so doing exerts anti-GBM activityex vivo. The interaction of BiTELLONwith T cells and engagement of IL13Rα2-expressing GBM cells stimulates T cell proliferation as well as production of pro-inflammatory cytokines INFγ and TNFα. We have modified neural stem cells (NSCs) to produce and secrete the BiTE (NSCsLLON). When injected intracranially in mice with brain tumor, NSCsLLONshow tropism for tumor, secrete BiTELLON, and remain viable for several days. When injected directly into tumor, NSCLLONprovide significant survival benefit to mice bearing IL13Rα2+ GBM. Our results support further investigation and development of this therapeutic for clinical translation.
rTASSEL: an R interface to TASSEL for association mapping of complex traits
Authors: Monier Brandon , Casstevens Terry M. , Bradbury Peter J. , Buckler Edward S. 
Published: July 2020

AbstractSummaryThe need for efficient tools and applications for analyzing genomic diversity is essential for any genetics research program. One such tool, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), provides many core methods for genomic analyses. Despite its efficiency, TASSEL has limited means to use scripting languages for reproducible research and interacting with other analytical tools. Here we present an R package rTASSEL, a front-end to connect to a variety of highly used TASSEL methods and analytical tools. The goal of this package is to create a unified scripting workflow that exploits the analytical prowess of TASSEL in conjunction with R’s popular data handling and parsing capabilities without ever having the user to switch between these two environments. By implementing this workflow, we can achieve performances ranging from approximately 2 to 20 times faster than other widely used R packages for various functionalities.Availability and implementationrTASSEL is implemented in R using core TASSEL methods written in Java. The source code for rTASSEL can be found athttps://bitbucket.org/bucklerlab/rtassel/src/master/. The source code for TASSEL can be found athttps://bitbucket.org/tasseladmin/tassel-5-source/src/master/.Supplemental informationThe rTASSEL user manual and tutorials are freely available athttps://maize-genetics.github.io/rTASSEL/. Supplemental material for this manuscript regarding performance metrics can be found in the attached file.
T cells are present in non-diabetic islets and accumulate during aging
Authors: Denroche Heather C. , Miard Stéphanie , Sallé-Lefort Sandrine , Picard Frédéric , Verchere C. Bruce 
Published: July 2020

ABSTRACTBackgroundThe resident immune population of pancreatic islets has roles in islet development, beta cell physiology, and the pathology of diabetes. These roles have largely been attributed to islet macrophages, comprising 90% of islet immune cells (in the absence of islet autoimmunity), and, in the case of type 1 diabetes, to infiltrating autoreactive T cells. In adipose, tissue-resident and recruited T and B cells have been implicated in the development of insulin resistance during diet-induced obesity and aging, but whether this is paralleled in the pancreatic islets is not known. Here, we investigated the non-macrophage component of resident islet immune cells in islets isolated from C57BL/6J male mice during aging (3 to 24 months of age) and following diet-induced obesity (12 weeks 60% high fat diet). Immune cells were also examined by flow cytometry in cadaveric non-diabetic human islets.ResultsImmune cells comprised 2.7 ± 1.3% of total islet cells in non-diabetic mouse islets, and 2.3 ± 1.7% of total islet cells in non-diabetic human islets. In 3-month old mice on standard diet, B and T cells each comprised approximately 2-4% of the total islet immune cell compartment, and approximately 0.1% of total islet cells. A similar amount of T cells were present in non-diabetic human islets. Islet T cells were comprised of CD8-positive, CD4-positive, and regulatory T cells. Interestingly, while islet B cells and macrophage numbers were unaltered by age, the number of islet T cells increased linearly (R2=0.9902) with age from 0.10 ± 0.05% (3 months) to 0.38 ±0.11% (24 months) of islet cells. This increase was uncoupled from body weight, and was not phenocopied by a degree similar weight gain induced by high fat diet in mice.ConclusionsThis study reveals that T cells are a part of the normal islet immune population in mouse and human islets, and that they accumulate in islets during aging in a body weight-independent manner. Though comprising only a small subset of the immune cells within islets, islet T cells may play a role in the physiology of islet aging.
Neuronal SKN-1B Modulates Nutritional Signalling Pathways and Mitochondrial Networks to Control Satiety
Authors: Tataridas-Pallas Nikolaos , Thompson Maximillian , Howard Alexander , Brown Ian , Ezcurra Marina , Wu Ziyun , Keurten Timo , Silva Isabel Goncalves , Blackwell T. Keith , Tullet Jennifer 
Published: July 2020

AbstractThe feeling of hunger or satiety results from integration of the sensory nervous system with other physiological and metabolic cues. This regulates food intake, maintains homeostasis and prevents disease. InC. elegans, chemosensory neurons sense food and relay information to the rest of the animal via hormones to control food-related behaviour and physiology. Here we identify a new component of this system, SKN-1B which acts as a central food-responsive node, ultimately controlling satiety and metabolic homeostasis. SKN-1B, an ortholog of mammalian NF-E2 related transcription factors (Nrfs), has previously been implicated with metabolism and respiration, because can mediate the increased lifespan incurred by dietary restriction. We show that actually SKN-1B is not essential for dietary restriction longevity and instead, controls a variety of food-related behaviours. It acts in two hypothalamus-like ASI neurons to sense food, communicate nutritional status to the organism, and control satiety and exploratory behaviours. This is achieved by SKN-1B modulating endocrine signalling pathways (IIS and TGF-β), and by promoting a robust mitochondrial network. Our data suggest a food-sensing and satiety role for mammalian Nrf proteins.
Structure of Macrolide Efflux Protein (MefA/E) inStreptococcus pneumoniae: An in silico approach
Authors: Peela Sreeram Chandra Murthy , Sharma Jyoti , Sistla Sujatha 
Published: July 2020

AbstractBackgroundMacrolides are one of the commonest antibiotics used to treat bacterial respiratory tract infections. Resistance to this class of antibiotics is on the rise and is mediated by macrolide efflux (MefA/E) protein as one of the mechanisms. Despite its importance, the structure of this protein is not known yet.MethodsThe publicly available MefA/E protein sequence was used to model the structure. Modelling was performed in I-TASSER, and the model was further refined. Its orientation in a membrane was studied using OPM server.Results and conclusionsThe structure of MefA/E resembled that of Major Facilitator Superfamily (MFS) proteins, with 13 transmembrane helices. It had a V-shaped conformation, with the wider part towards the outer membrane layer.
Mitochondrial and insulin gene expression in single cells shape pancreatic beta cells’ population divergence
Authors: Medini H. , Cohen T. , Mishmar D. 
Published: July 2020

AbstractMitochondrial gene expression is pivotal to cell metabolism. Nevertheless, it is unknown whether it diverges within a given cell type. Here, we analysed single-cell RNA-seq experiments from ∼4600 human pancreatic alpha and beta cells, as well as ∼900 mouse beta cells. Cluster analysis revealed two distinct human beta cells populations, which diverged by mitochondrial (mtDNA) and nuclear DNA (nDNA)-encoded oxidative phosphorylation (OXPHOS) gene expression in healthy and diabetic individuals, and in newborn but not in adult mice. Insulin gene expression was elevated in beta cells with higher mtDNA gene expression in humans and in young mice. Such human beta cell populations also diverged in mt-RNA mutational repertoire, and in their selective signature, thus implying the existence of two previously overlooked distinct and conserved beta cell populations. While applying our approach to alpha cells, two sub-populations of cells were identified which diverged in mtDNA gene expression, yet these cellular populations did not consistently diverge in nDNA OXPHOS genes expression, nor did they correlate with the expression of glucagon, the hallmark of alpha cells. Thus, pancreatic beta cells within an individual are divided into distinct groups with unique metabolic-mitochondrial signature.
New mechanisms of radioiodide uptake revealed via a novel high throughput drug screening approach in thyroid cancer
Authors: Read Martin L. , Brookes Katie , Thornton Caitlin E.M. , Fletcher Alice , Alshahrani Mohammed , Khan Rashida , Nieto Hannah R. , Borges de Souza Patricia , Webster Jamie R.M. , Alderwick Luke J. , Boelaert Kristien , Smith Vicki E. , McCabe Christopher J. 
Published: July 2020

ABSTRACTNew combinatorial drug strategies are urgently needed to improve radioiodide (RAI) uptake and efficiently ablate thyroid cancer cells, thereby addressing recurrent and metastatic disease. Cellular iodide uptake is accomplished solely by the sodium iodide symporter (NIS), but the complexity of NIS functional regulation and a lack of amenable high-throughput screening assays has impeded progress. We utilised mutated yellow fluorescent protein (YFP) as a surrogate biosensor of intracellular iodide for ∼1200 FDA-approved drugs, allowing us to appraise the impact of 73 leading compounds at 10 doses on125I uptake in thyroid cancer cell lines. Subsequent mechanistic analysis suggests three predominant modes of drug action: Firstly, a number of drugs inhibited specific regulation of NIS function by the protein VCP. Secondly, some drugs enhanced transcriptional or post-transcriptional regulation of NIS expression. Thirdly, several drugs strongly implicated proteasomal degradation and the unfolded protein response in the cellular processing of NIS. Exploiting these mechanistic insights, multiple compounds gave striking increases in radioiodide uptake when combined with the drug SAHA. Importantly, our new drug combination strategies were also effective in human primary thyrocytes, suggesting they target endogenous NIS physiology. In patients with papillary thyroid cancer, genes involved in proteostasis were remarkably altered and predicted significantly worse outcome, but only in those patients who received RAI therapy. Collectively, we therefore propose a new model of intracellular NIS processing, and identify key nodes which may now be druggable in patients with aggressive thyroid cancer.SUMMARYOur data identify FDA-approved drugs that enhance radioiodide uptake outside of the canonical pathways of NIS processing, leading to a new mechanistic understanding of endogenous NIS function which is subverted in cancer.
UV-A/B radiation rapidly activates photoprotective mechanisms inChlamydomonas reinhardtii
Authors: Tokutsu Ryutaro , Fujimura-Kamada Konomi , Yamasaki Tomohito , Okajima Keisuke , Minagawa Jun 
Published: July 2020

AbstractConversion of light energy into chemical energy through photosynthesis in the chloroplasts of photosynthetic organisms is essential for photoautotrophic growth. However, the conversion of excess light energy into thermal energy by non-photochemical quenching (NPQ) is important for avoiding the generation of reactive oxygen species and maintaining efficient photosynthesis. In the unicellular green algaChlamydomonas reinhardtii, NPQ is activated as a photoprotective mechanism through wavelength-specific light signaling pathways mediated by the phototropin (blue light) and UVR8 (ultra-violet light, UV) photoreceptors. NPQ-dependent photoprotection improves cell survival under high-light conditions; however, the biological significance of photoprotection being activated by light with different qualities remains poorly understood. Here, we demonstrate that NPQ-dependent photoprotection is activated more rapidly by UV than by visible light. We found that induction of gene expression and protein accumulation related to photoprotection was significantly faster and greater in magnitude under UV treatment compared to that under blue- or red-light treatment. Furthermore, the action spectrum of UV-dependent induction of photoprotective factors implied that Chlamydomonas sense relatively long-wavelength UV (including UV-A/B), whereas the model dicot plantArabidopsis thalianapreferentially senses relatively short-wavelength UV (mainly UV-B/C) for induction of photoprotective responses. Therefore, we hypothesize that Chlamydomonas developed a UV response distinct from that of land plants.One-sentence summaryIn contrast to land plants, which sense short-wave UV light, the unicellular green alga Chlamydomonas senses long-wavelength UV light for photoprotective responses.
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes
Authors: Hleap Jose S. , Littlefair Joanne E. , Steinke Dirk , Hebert Paul D. N. , Cristescu Melania E. 
Published: July 2020

ABSTRACTThe effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need to generate accurate taxonomic assignments. The assignment of sequences to a generic or species level is critical for biodiversity surveys and biomonitoring, but it is particularly challenging. Researchers must select the approach that best recovers information on species composition. This study evaluates the performance and accuracy of seven methods in recovering the species composition of mock communities which vary in species number and specimen abundance, while holding upstream molecular and bioinformatic variables constant. It also evaluates the impact of parameter optimization on the quality of the predictions. Despite the general belief that BLAST top hit underperforms newer methods, our results indicate that it competes well with more complex approaches if optimized for the mock community under study. For example, the two machine learning methods that were benchmarked proved more sensitive to the reference database heterogeneity and completeness than methods based on sequence similarity. The accuracy of assignments was impacted by both species and specimen counts which will influence the selection of appropriate software. We urge the usage of realistic mock communities to allow optimization of parameters, regardless of the taxonomic assignment method used.
In SituUnzipping of Long, High Molecular Weight DNA in Solid State Nanopores
Authors: Losakul R. , Tobar D. E. , Pfeffer A.M. , Gutierrez A. , Schipper R. , Jehle W. A. , Postma H.W.Ch. 
Published: July 2020

AbstractNanopores are an established paradigm in genome sequencing technology, with remarkable advances still being made today. All efforts continually address the challenges associated with rapid, accurate, high-throughput, and low cost detection, particularly with long-read length DNA. We report on thein situmelting and unzipping oflong, high molecular weightDNA. At varying salt concentration, we directly compare the translocation conductance and speeds between SiN and graphene nanopores at sub-10 nm pore diameters. We observe the force-induced unzipping of dsDNA at higher salt concentrations than previously reported in literature. We observe free running translocation without secondary structures of ssDNA that is an order of magnitude longer than reported before. We hypothesize that the frayed single strands at the molecule’s end get captured with a higher likelihood than both ends together. In understanding this phenomena for long-read lengths, we continue to address the challenges revolving around future generations of sequencing technology.Statement of SignificanceGenome sequencing is an advancing field with applications in clinical diagnostics. However, the challenges of providing accurate identification of longer DNA molecules at low cost are still developing. While detection of long DNA molecules is established, the identification of its individual nucleotides presents its own set of challenges. By separating the hydrogen bonds between the two strands, individual nucleotides are made directly measurable. However, identification is hindered from the formation of secondary structures, where the single-stranded DNA sticks to itself. Previous studies only included short DNA molecules. We report in situ force-induced unzipping and translocation of long DNA without secondary structures almost an order of magnitude longer than reported before. Our findings present new experimental conditions and insights that progress the field towards high accuracy sequencing of individual long molecules.
Full-length annotation with multi-strategy RNA-seq uncovers transcriptional regulation of lncRNAs in diploid cottonG. arboreum1
Authors: Zheng Xiaomin , Chen Yanjun , Zhou Yifan , Li Danyang , Shi Keke , Hu Xiao , Ye Hanzhe , Zhou Yu , Wang Kun 
Published: July 2020

AbstractLong noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. High-throughput and accurate identification of lncRNAs is still lacking in plants. To build an accurate atlas of lncRNA in cotton, we combined Isoform-sequencing (Iso-seq), strand-specific RNA-seq (ssRNA-seq), cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA (PULL) to integrate multi-omics data. A total of 9240 lncRNAs from 21 tissue samples of the diploid cottonGossypium arboreumwere identified. We revealed that alternative usage of transcription start site (TSS) and transcription end site (TES) of lncRNAs occurs pervasively during plant growth and responses to stress. We identified the lncRNAs which co-expressed or be linked to the protein coding genes (PCGs) or GWAS studied SNPs associated with ovule and fiber development. We also mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing (ChIRP-seq) and validated thetranstranscriptional regulation oflnc-Ga13g0352via virus induced gene suppression (VIGS) assay. These findings provide valuable research resources for plant community and broaden our understandings of biogenesis and regulation function of plant lncRNAs.One sentence summaryThe full-length annotation and transcriptional regulation of long noncoding RNAs in cotton.
Experimental evidence for the role of natural radioactivity in influencing viability of commensal microorganisms
Authors: Ruggiero Marco 
Published: July 2020

AbstractThe role of natural radioactivity in influencing viability of commensal microorganisms, with particular reference to those pertaining to the human microbiota, has not been investigated in detail. The results of experiments culturing a diversified array of microorganims - probiotics - in naturally radioactive mineral water or deuterium-depleted water are here described. Culturing microorganisms in naturally radioactive mineral water yielded one order of magnitude more live microbial cells in comparison with culturing in deuterium-depleted water. Based on these experimental results, a method for co-culturing prebiotic microorganisms (cyanobacteria) that are extremely resistant to the harmful effects of radiations, together with the probiotics mentioned above, is described. The goal of this co-culture in naturally radioactive mineral water is to transfer the information from the radiation-resistant microorganisms to the probiotics whose viability is enhanced by natural radioactivity. Expression of DNA repair genes in cyanobacteria is induced by co-culturing in a medium of carbonated mineral water naturally containing the radioactive isotopes228U and226Ra. The culture medium, in addition to naturally radioactive water, contains silica from vegetal origin to enhance horizontal gene transfer. Finally, it is described the transfer of resistance to the harmful effects of radiations to human cells through a Lactococcus phage-encoded protein, ORF252, that is the evolutionary precursor of human proteins involved in DNA repair and cancer protection.
Spatial patterns in phage-Rhizobiumcoevolutionary interactions across regions of common bean domestication
Authors: Van Cauwenberghe Jannick , Santamaría Rosa I. , Bustos Patricia , Juárez Soledad , Ducci Maria Antonella , Fleming Trinidad Figueroa , Etcheverry Angela Virginia , González Víctor 
Published: July 2020

AbstractBacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respectiveRhizobiumpopulations is lacking. Here, through the study of four phage-Rhizobiumcommunities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.