bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytotoxic efficiency of human CD8+T cell memory subtypes
Authors: Knörck Arne , Schwär Gertrud , Alansary Dalia , Thurner Lorenz , Hoth Markus , Schwarz Eva C. 
Published: March 2021

AbstractImmunological memory is an important concept to protect humans against recurring diseases. Memory CD8+T cells are required for quick expansion into effector cells but also provide immediate cytotoxicity against their targets. Whereas many functions of the two main cytotoxic subtypes, effector memory CD8+T cells (TEM) and central memory CD8+T cells (TCM), are relatively well defined, single TEMand TCMcell cytotoxicity has not been quantified. Here, we analyze human CD8+subtype distribution following SEA stimulation and quantify the expression of death mediators, including perforin, granzyme B, FasL and TRAIL. We find higher perforin, granzyme B and FasL expression in TEMand compared to TCM. To quantify single TEMand TCMcytotoxicity, we develop a FRET-based fluorescent assay with NALM6 target cells stably transfected with a GFP-RFP FRET construct based on a caspase-cleavage sequence (apoptosis sensor Casper-GR). Applying this assay, TEMor TCMinduced target cell apoptosis or necrosis can be quantified. We find that single TEMare much more effective than TCMin killing their targets mainly by apoptosis and secondary necrosis. The reason for this is the higher perforin expression and on a more efficient lytic immunological synapse during TEM-target contact compared to TCM-target contact. Defining and quantifying single TEMand TCMcytotoxicity and the respective mechanism should be helpful to optimize future subset-based immune therapies.
SPIRO – the automated Petri plate imaging platform designed by biologists, for biologists
Authors: Ohlsson Jonas A , Leong Jia Xuan , Elander Pernilla H , Ballhaus Florentine , Holla Sanjana , Dauphinee Adrian N , Johansson Johan , Lommel Mark , Hofmann Gero , Betnér Staffan , Sandgren Mats , Schumacher Karin , Bozhkov Peter V , Minina Elena A 
Published: March 2021

AbstractPhenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists.Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photos of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists’ needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO’s excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses.Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared to manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing and photoblastic response.
Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics
Authors: Ge Fei , Qu Jingtao , Liu Peng , Pan Lang , Zou Chaoying , Yuan Guangsheng , Yang Cong , Gao Shibin , Pan Guangtang , Huang Jianwei , Ma Langlang , Shen Yaou 
Published: March 2021

AbstractHeretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ∼30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.HighlightOur manuscript presents a high-quality reference genome of the inbred line A188, and provides new insights into candidate genes underlying maize embryonic callus induction and other maize agronomic traits.
oCEM: Automatic detection and analysis of overlapping co-expressed gene modules
Authors: Nguyen Quang-Huy , Le Duc-Hau 
Published: March 2021

ABSTRACTBackgroundWhen it comes to the co-expressed gene module detection, its typical challenges consist of overlap between identified modules and local co-expression in a subset of biological samples. The nature of module detection is the use of unsupervised clustering approaches and algorithms. Those methods are advanced undoubtedly, but the selection of a certain clustering method for sample- and gene-clustering tasks is separate, in which the latter task is often more complicated.ResultsThis study presented an R-package, Overlapping CoExpressed gene Module (oCEM), armed with the decomposition methods to solve the challenges above. We also developed a novel auxiliary statistical approach to select the optimal number of principal components using a permutation procedure. We showed that oCEM outperformed state-of-the-art techniques in the ability to detect biologically relevant modules additionally.ConclusionsoCEM helped non-technical users easily perform complicated statistical analyses and then gain robust results. oCEM and its applications, along with example data, were freely provided athttps://github.com/huynguyen250896/oCEM.
tbg - a new file format for genomic data
Authors: Schönnenbeck Philipp , Schell Tilman , Gerber Susanne , Pfenninger Markus 
Published: March 2021

AbstractMotivationThe question of determining whether a Single-Nucleotide Polymorphism (SNP) or a variant in general leads to a change in the amino acid sequence of a protein coding gene is often a laborious and time-consuming challenge. Here, we introduce the tbg file format for storing genomic data and tbg-tools, a user-friendly toolbox for the faster analysis of SNPs. The file format stores information for each nucleotide in each gene, allowing to predict which change in the amino acid sequence will be caused by a variant in the nucleotide sequence. Our new tool therefore has the potential to make biological sense of the unprecedented amount of genome-wide genetic variation that researchers currently face.ResultsThe new tab-separated file for storing the nucleotide data can be easily analyzed and used for a wide variety of biological research. It is also possible to automate some of these analyses using the additional analysis tools fromtbg-toolsAvailabilitytbg-toolsis written in Python and allows the installation from the command line. It can be found onhttps://github.com/Croxa/tbg-tools.Contactpschoenn@students.uni-mainz.de
Causal inference on microbiome-metabolome relations viain silico in vivoassociation pattern analyses
Authors: Hertel Johannes , Heinken Almut , Thiele Ines 
Published: March 2021

AbstractThe effects of the microbiome on the host’s metabolism are core to understanding the role of the microbiome in health and disease. Herein, we develop the paradigm ofin silico in vivoassociation pattern analyses, entailing a methodology to combine microbiome metabolome association studies within silicoconstraint-based microbial community modelling. By dissecting confounding and causal paths, we show thatin silico in vivoassociation pattern analyses allows for causal inference on microbiome-metabolome relations in observational data. Then, we demonstrate the feasibility and validity of our approach on a published multi-omics dataset (n=346), demonstrating causal microbiome-metabolite relations for 43 out of 53 metabolites from faeces. Finally, we utilise the identifiedin silico in vivoassociation pattern to estimate the microbial component of the faecal metabolome, revealing that the retrieved metabolite prediction scores correlate with the measured metabolite concentrations, and they also reflect the multivariate structure of the faecal metabolome. Concluding, we integrate with hypothesis free screening association studies and knowledge-basedin silicomodelling two major paradigms of systems biology, generating a promising new paradigm for causal inference in metabolic host-microbe interactions.
Genome-wide association study of gastric cancer- and duodenal ulcer-derivedHelicobacter pyloristrains reveals discriminatory amino acid differences and novel oncoprotein candidates
Authors: Tuan Vo Phuoc , Yahara Koji , Quy Dung Ho Dang , Binh Tran Thanh , Tung Pham Huu , Tri Tran Dinh , Minh Thuan Ngo Phuong , Khien Vu Van , Huyen Trang Tran Thi , Phuc Bui Hoang , Tshibangu-Kabamba Evariste , Matsumoto Takashi , Akada Junko , Suzuki Rumiko , Okimoto Tadayoshi , Kodama Masaaki , Murakami Kazunari , Yano Hirokazu , Fukuyo Masaki , Takahashi Noriko , Kato Mototsugu , Nishiumi Shin , Azuma Takeshi , Ogura Yoshitoshi , Hayashi Tetsuya , Toyoda Atsushi , Kobayashi Ichizo , Yamaoka Yoshio 
Published: March 2021

AbstractGenome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such asHelicobacter pylori, which causes gastric cancer (GC). We conducted a GWAS followed by regression-based prediction of GC and duodenal ulcerH. pyloristrains. We identified 14 single nucleotide polymorphisms (11 amino acid changes) that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into GC pathogenesis and a basis for identifying a set of biomarkers for application in clinical settings.
Morphometry of newborn piglets and its relevance at weaning
Authors: Silva Lucas M. , Fidelis Pedro H. S. , Gomes Lígia V. L. , Santos Gleyson A. , Oliveira Amanda M. A. , Medeiros Elias S. , Araújo Marcelle S. , Moreira Rennan H. R. 
Published: March 2021

AbstractThis study aimed to evaluate the development of suckling piglets using morphometric parameters. Different models were created to predict the probability to occur any of the three weight classes (light, medium, and heavy) based on the piglets’ weaning weight. The variables in this research were birth weight (PWB), lactation length (Lac), and morphometric parameters– body length (BL), heart girth (HG), body mass index (BMI), ponderal index (PI), surface-mass ratio (SM), and birth order (BO). An adjustment of the ordinal regression was proposed to predict the weight classifications. The model with a significant effect of the Lac variables was selected. The light and heavy piglets, regardless of their morphometry, have a high chance of staying in the same weight class at weaning. However, this does not occur in medium piglets with diverse morphometry.Summary statementThis manuscript demonstrates how morphometry can influence the development of animals, even with similar weights.
phastSim: efficient simulation of sequence evolution for pandemic-scale datasets
Authors: De Maio Nicola , Boulton William , Weilguny Lukas , Walker Conor R. , Turakhia Yatish , Corbett-Detig Russell , Goldman Nick 
Published: March 2021

AbstractSequence simulators are fundamental tools in bioinformatics, as they allow us to test data processing and inference tools, as well as being part of some inference methods. The ongoing surge in available sequence data is however testing the limits of our bioinformatics software. One example is the large number of SARS-CoV-2 genomes available, which are beyond the processing power of many methods, and simulating such large datasets is also proving difficult. Here we present a new algorithm and software for efficiently simulating sequence evolution along extremely large trees (e.g. < 100, 000 tips) when the branches of the tree are short, as is typical in genomic epidemiology. Our algorithm is based on the Gillespie approach, and implements an efficient multi-layered search tree structure that provides high computational efficiency by taking advantage of the fact that only a small proportion of the genome is likely to mutate at each branch of the considered phylogeny. Our open source software is available fromhttps://github.com/NicolaDM/phastSimand allows easy integration with other Python packages as well as a variety of evolutionary models, including indel models and new hypermutatability models that we developed to more realistically represent SARS-CoV-2 genome evolution.Author summaryOne of the most influential responses to the SARS-CoV-2 pandemic has been the widespread adoption of genome sequencing to keep track of viral spread and evolution. This has resulted in vast availability of genomic sequence data, that, while extremely useful and promising, is also increasingly hard to store and process efficiently. An important task in the processing of this genetic data is simulation, that is, recreating potential histories of past and future virus evolution, to benchmark data analysis methods and make statistical inference. Here, we address the problem of efficiently simulating large numbers of closely related genomes, similar to those sequenced during SARS-CoV-2 pandemic, or indeed to most scenarios in genomic epidemiology. We develop a new algorithm to perform this task, that provides not only computational efficiency, but also extreme flexibility in terms of possible evolutionary models, allowing variation in mutation rates, non-stationary evolution, and indels; all phenomena that play an important role in SARS-CoV-2 evolution, as well as many other real-life epidemiological scenarios.
A NEW CASE OF DIPLOIDY WITHIN A HAPLOID GENUS OF ENTOMOPATHOGENIC FUNGI
Authors: Nielsen Knud Nor , Salgado João Felipe Moreira , Natsopoulou Myrsini Eirini , Stajich Jason E , De Fine Licht Henrik H. 
Published: March 2021

ABSTRACTFungi in the genusMetarhiziumare soil-borne plant-root endophytes and rhizosphere colonisers, but also potent insect pathogens with highly variable host ranges. These ascomycete fungi are predominantly asexually reproducing and ancestrally haploid, but two independent origins of persistent diploidy within the Coleoptera-infectingM. majusspecies complex are known and has been attributed to incomplete chromosomal segregation following meiosis during the sexual cycle. There is also evidence for infrequent sexual cycles in the locust-specific pathogenic fungusMetarhizium acridum(Hypocreales: Clavicipitaceae), which is an important entomopathogenic biocontrol agent used for the control of grasshoppers in agricultural systems as an alternative to chemical control. Here, we show that the genome of theM. acridumisolate ARSEF 324, which is formulated and commercially utilised under the name ‘Green Guard’, is functionally diploid. We used single-molecule real-time (SMRT) sequencing technology to complete a high-quality assembly of ARSEF 324. Kmer frequencies, intragenomic collinearity between contigs and single nucleotide variant read depths across the genome revealed the first incidence of diploidy described within the speciesM. acridum. The haploid assembly of 44.7 Mb consisting of 20.8% repetitive elements, which is the highest proportion described of anyMetarhiziumspecies. The genome assembly and the inferred diploid state, can shed light on past research on this strain and could fuel future investigation into the fitness landscape of aberrant ploidy levels, not least in the contest of biocontrol agents.
Deletion of Rap-Phr systems inBacillus subtilisinfluencesin vitrobiofilm formation and plant root colonization
Authors: Christensen Mathilde Nordgaard , Mortensen Rasmus Møller Rosenbek , Kirk Nikolaj Kaae , Gallegos-Monterrosa Ramses , Kovács Ákos T. 
Published: March 2021

SummaryNatural isolates of the soil-dwelling bacteriumBacillus subtilisform robust biofilms under laboratory conditions and colonize plant roots.B. subtilisbiofilm gene expression displays phenotypic heterogeneity that is influenced by a family of Rap-Phr regulatory systems. Most Rap-Phr systems inB. subtilishave been studied independently, in different genetic backgrounds and under distinct conditions, hampering true comparison of the Rap-Phr systems’ impact on bacterial differentiation. Here, we investigated each of the 12 Rap-Phr systems ofB. subtilisNCIB 3610 for their effect on biofilm formation. By studying single Δrap-phrmutants, we show that despite redundancy between the cell-cell communication systems, deletion of each of the 12 Rap-Phr systems influences matrix gene expression, which could possibly enable fine-tuning of the timing and level of matrix production in response to specific conditions. Furthermore, some of the Δrap-phrmutants demonstrated altered biofilm formationin vitroand colonization ofArabidopsis thalianaroots, but not necessarily similarly in both processes, indicating that the pathways regulating matrix gene expression and other factors important for biofilm formation may be differently regulated under these distinct conditions.Significance StatementNatural isolates ofBacillus subtilisform robust biofilmsin vitroand on plant roots. The formation of these heterogeneous populations is regulated by diverse Rap-Phr systems. However, most Rap-Phr systems inB. subtilishave been studied independently and in different genetic backgrounds. Here, we report that all 12 Rap-Phr systems affect matrix gene expression, while some of them affect development ofin vitrobiofilms and plant root colonization. Our study highlights the importance of the Rap-Phr systems in environmental adaptation ofB. subtilis, specifically during biofilm formation in the rhizosphere.
Twenty years of change in benthic communities across the Belizean Barrier Reef
Authors: Alves Catherine , Aronson Richard B. , Bood Nadia , Castillo Karl D. , Cox Courtney , Fieseler Clare , Locklear Zachary , McField Melanie , Mudge Laura , Umbanhowar James , Valdivia Abel , Bruno John F. 
Published: March 2021

AbstractDisease, ocean warming, and pollution have caused catastrophic declines in the cover of living coral on reefs across the Caribbean. Subsequently, reef-building corals have been replaced by invertebrates and macroalgae, leading to changes in ecological functioning. We describe changes in benthic community composition and cover at 15 sites across the Belizean Barrier Reef (BBR) following numerous major disturbances—bleaching, storms, and disease outbreaks—over the 20-year period 1997–2016. We tested the role of potential drivers of change on coral reefs, including local human impacts and ocean temperature. From 1997 to 2016, mean coral cover significantly declined from 26.3% to 10.7%, while macroalgal cover significantly increased from 12.9% to 39.7%. We documented a significant decline over time of the reef-building coralsOrbicellaspp. and described a major shift in benthic composition between early sampling years (1997–2005) and later years (2009–2016). The covers of hard-coral taxa, includingAcroporaspp.,M. cavernosa, Orbicellaspp., andPoritesspp., were negatively related to marine heatwave frequency. Only gorgonian cover was related, negatively, to our metric of the magnitude of local impacts (the Human Influence Index). Changes in benthic composition and cover were not associated with local protection or fishing. This result is concordant with studies throughout the Caribbean that have documented living coral decline and shifts in reef-community composition following disturbances, regardless of local fisheries restrictions. Our results suggest that benthic communities along the BBR have experienced disturbances that are beyond the capacity of the current management structure to mitigate. We recommend that managers devote greater resources and capacity to enforce and expand existing marine protected areas and that government, industry, and the public act to reduce global carbon emissions.
A biomechanical comparison of the jerk, back jerk, vertical jump and jump squat
Authors: Liu Jiatian 
Published: March 2021

AbstractAlthough weightlifting exercises and their pulling and catching derivatives have been well studied, less is known about the group of weightlifting overhead pressing derivatives (WOPDs). There were two purposes of the present study. Above all, it was to compare WOPDs (i.e. jerk and back jerk) with jump squat in enhancing sport performance such as vertical jump in the perspective of biomechanics. Furthermore, it was to gain a better understanding of the biomechanical difference between jerk and back jerk. The study compared the kinetics, kinematics, and muscle activation of the jerk, back jerk, vertical jump and jump squat. Ground reaction forces, joint angle data and electromyography were collected from 20 track and field athletes while they performed the four movements. The joint coordination pattern and EMG characters of the jump squat were more similar to those of the vertical jump. WOPDs, especially jerk, exhibited less similarity with vertical jump in joint coordination, as well as the subsequent peak activation. The electromyography data demonstrated significant differences in rectus femoris and gluteus maximus in the relative timing of peak activations and the maximum activation. Jump squat was greater in peak force (2211N) than jerk (P < .005), greater peak power (4749W) than jerk and back jerk (P < .001) and no significant difference with WOPDs in rate of force development. Back jerk produced a greater peak force (2223 N), peak power (3767W) and eccentric RFD (15965 N·s−1) than jerk (2061N)(P < .001) (3364W)(P < .05) (12280 N·s−1)(P < .01)and the opposite in concentric RFD that jerk (7702 N·s−1) was greater than back jerk (5972 N·s−1)(P < .05). We can conclude that for runner and jumpers, jump squat was better for improving vertical jump than WOPDs and back jerk is better than jerk in power training.