bluuebunny/crossref_metadata_2025_split huggingface dataset:
OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons
Authors: Willforss Jakob , Siino Valentina , Levander Fredrik 
Published: October 2020

AbstractVisual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. The OmicLoupe software was developed to facilitate such exploration and provides more than 15 interactive cross-dataset visualizations for omic data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three diverse studies, including an analysis of SARS-CoV-2 infection across omic layers, based on previously published proteomics and transcriptomics studies. OmicLoupe is available at quantitativeproteomics.org/omicloupe
Quantifying growth perturbations over the fattening period in swine via mathematical modelling
Authors: Manuel Revilla , Guillaume Lenoir , Loïc Flatres-Grall , Rafael Muñoz-Tamayo , Friggens Nicolas C 
Published: October 2020

AbstractBackgroundResilience can be defined as the capacity of animals to cope with short-term perturbations in their environment and return rapidly to their pre-challenge status. In a perspective of precision livestock farming, it is key to create informative indicators for general resilience and therefore incorporate this concept in breeding goals. In the modern swine breeding industry, new technologies such as automatic feeding system are increasingly common and can be used to capture useful data to monitor animal phenotypes such as feed efficiency. This automatic and longitudinal data collection integrated with mathematical modelling has a great potential to determine accurate resilience indicators, for example by measuring the deviation from expected production levels over a period of time.ResultsThis work aimed at developing a modelling approach for facilitating the quantification of pig resilience during the fattening period, from approximately 34 kg to 105 kg of body weight. A total of 13 093 pigs, belonging to three different genetic lines were monitored (Pietrain, Pietrain NN and Duroc) since 2015, and body weight measures registered (approximately 11.1 million of weightings) with automatic feeding systems. We used the Gompertz model and linear interpolation on body weight data to quantify individual deviations from expected production, thereby creating a resilience index (ABC). The estimated heritabilities ofABCare low but not zero from 0.03 to 0.04 (± 0.01) depending on the breed.ConclusionsOur model-based approach can be useful to quantify pig responses to perturbations using exclusively the growth curves and should contribute to the genetic improvement of resilience of fattening pigs by providing a resilience index.
Selection of internal references for transcriptomics and RT-qPCR assays in Neurofibromatosis type 1 (NF1) related Schwann cell lines
Authors: Gu Yi-Hui , Cui Xi-Wei , Ren Jie-Yi , Long Man-Mei , Wang Wei , Wei Cheng-Jiang , Aimaier Rehanguli , Li Yue-Hua , Chung Man-Hon , Gu Bin , Li Qing-Feng , Wang Zhi-Chao 
Published: October 2020

AbstractTranscriptomics has been widely applied in uncovering disease mechanisms and screening potential biomarkers. Internal reference selection determines the accuracy and reproducibility of data analyses. The aim of this study was to identify the most qualified reference genes for the relative quantitation analysis of transcriptomics and real-time quantitative reverse-transcription PCR in fourteen NF1 related cell lines, including non-tumor, benign and malignant Schwann cell lines. The expression characteristics of eleven candidate reference genes (RPS18, ACTB, B2M, GAPDH, PPIA, HPRT1, TBP, UBC, RPLP0, TFRC and RPL32) were screened and analyzed by four software programs: geNorm, NormFinder, BestKeeper and RefFinder. Results showed that GAPDH, the most used internal reference gene, was significantly unstable. The combinational use of two reference genes (PPIA and TBP) was optimal in malignant Schwann cell lines and the use of single reference genes (PPIA or PRLP0) alone or in combination was optimal in benign Schwann cell lines. Our recommended internal reference genes may improve the accuracy and reproducibility of the results of transcriptomics and real-time quantitative reverse-transcription PCR in further gene expression analyses of NF1 related tumors.
Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant coniferPinus sylvestris
Authors: Cervantes Sandra , Vuosku Jaana , Paczesniak Dorota , Pyhäjärvi Tanja 
Published: October 2020

AbstractDespite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome.Here we provide an atlas of gene expression patterns for coniferPinus sylvestrisacross five tissues: embryo, megagametophyte, needle, phloem, and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics, and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.
Discovering the drivers of clonal hematopoiesis
Authors: Pich Oriol , Reyes-Salazar Iker , Gonzalez-Perez Abel , Lopez-Bigas Nuria 
Published: October 2020

AbstractMutations in genes that confer a selective advantage to hematopoietic stem cells (HSCs) in certain conditions drive clonal hematopoiesis (CH). While some CH drivers have been identified experimentally or through epidemiological studies, the compendium of all genes able to drive CH upon mutations in HSCs is far from complete. We propose that identifying signals of positive selection in blood somatic mutations may be an effective way to identify CH driver genes, similarly as done to identify cancer genes. Using a reverse somatic variant calling approach, we repurposed whole-genome and whole-exome blood/tumor paired samples of more than 12,000 donors from two large cancer genomics cohorts to identify blood somatic mutations. The application of IntOGen, a robust driver discovery pipeline, to blood somatic mutations across both cohorts, and more than 24,000 targeted sequenced samples yielded a list of close to 70 genes with signals of positive selection in CH, available athttp://www.intogen.org/ch. This approach recovers all known CH genes, and discovers novel candidates. Generating this compendium is an essential step to understand the molecular mechanisms of CH and to accurately detect individuals with CH to ascertain their risk to develop related diseases.
SARS-CoV-2 Variants Reveal Features Critical for Replication in Primary Human Cells
Authors: Pohl Marie O. , Busnadiego Idoia , Kufner Verena , Glas Irina , Karakus Umut , Schmutz Stefan , Zaheri Maryam , Abela Irene , Trkola Alexandra , Huber Michael , Stertz Silke , Hale Benjamin G. 
Published: October 2020

ABSTRACTSince entering the human population, SARS-CoV-2 (the causative agent of COVID-19) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from non-human Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally-occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E, and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin-cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific virus replication, and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants-of-concern.
Configurable Digital Virus Counter on Robust Universal DNA Chips
Authors: Seymour Elif , Ünlü Nese Lortlar , Carter Eric P. , Connor John H. , Ünlü M. Selim 
Published: October 2020

ABSTRACTHere, we demonstrate real-time multiplexed virus detection by applying DNA-directed antibody immobilization technique to a single-particle interferometric reflectance imaging sensor (SP-IRIS). In this technique, the biosensor chip surface spotted with different DNA sequences is converted to a multiplexed antibody array by flowing antibody-DNA conjugates and allowing specific DNA-DNA hybridization. The resulting antibody array is shown to detect three different recombinant Vesicular Stomatitis Viruses (rVSVs) genetically engineered to express surface glycoproteins of Ebola, Marburg, and Lassa viruses in real-time in a disposable microfluidic cartridge. We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in solution phase prior to flowing in the microfluidic cartridge, eliminating the antibody immobilization step. This homogenous approach achieved detection of the model Ebola virus, rVSV-EBOV, at a concentration of 100 PFU/ml in 1 hour. Finally, we demonstrate the feasibility of this homogeneous technique as a rapid test using a passive microfluidic cartridge. A concentration of 104PFU/ml was detectable under 10 minutes for the rVSV-Ebola virus. Utilizing DNA microarrays for antibody-based diagnostics is an alternative approach to antibody microarrays and offers advantages such as configurable sensor surface, long-term storage ability, and decreased antibody use. We believe these properties will make SP-IRIS a versatile and robust platform for point-of-care diagnostics applications.
Loss of coordinated expression between ribosomal and mitochondrial genes revealed by comprehensive characterization of a large family with a rare mendelian disorder
Authors: Panici Brendan , Nakajima Hosei , Carlston Colleen M. , Ozadam Hakan , Cenik Can , Cenik Elif Sarinay 
Published: October 2020

ABSTRACTNon-canonical intronic variants are a poorly characterized yet highly prevalent class of alterations associated with Mendelian disorders. Here, we report the first RNA expression and splicing analysis from a family whose members carry a non-canonical splice variant in an intron of RPL11 (c.396+3A>G). This mutation is causative for Diamond Blackfan Anemia (DBA) in this family despite incomplete penetrance and variable expressivity. Our analyses revealed a complex pattern of disruptions with many novel junctions of RPL11. These include an RPL11 transcript that is translated with a late stop codon in the 3’ untranslated region (3’UTR) of the main isoform. We observed that RPL11 transcript abundance is comparable among carriers regardless of symptom severity. Interestingly, both the small and large ribosomal subunit transcripts were significantly overexpressed in individuals with a history of anemia in addition to congenital abnormalities. Finally, we discovered that coordinated expression between mitochondrial components and RPL11 was lost in all carriers, which may lead to variable expressivity. Overall, this study highlights the importance of RNA splicing and expression analyses in families for molecular characterization of Mendelian diseases.
Asymmetric directed functional connectivity within the frontoparietal motor network during motor imagery and execution
Authors: Ogawa Takeshi , Shimobayashi Hideki , Hirayama Jun-ichiro , Kawanabe Motoaki 
Published: October 2020

AbstractBoth imagery and execution of motor controls consist of interactions within a neuronal network, including frontal motor-related regions and posterior parietal regions. To reveal neural representation in the frontoparietal motor network, two approaches have been proposed thus far: one is decoding of actions/modes related to motor control from the spatial pattern of brain activity; another is to estimate directed functional connectivity, which means a directed association between two brain regions within motor regions. However, directed connectivity among multiple regions of the motor network during motor imagery (MI) or motor execution (ME) has not been investigated. Here, we attempted to characterize the directed functional connectivity within the frontoparietal motor-related networks between the MI and ME conditions. We developed a delayed sequential movement and imagery task to evoke brain activity associated with data under ME and MI via functional magnetic resonance imaging scanning. We applied a causal discovery approach, linear non-Gaussian acyclic causal model, to identify directed functional connectivity among the frontoparietal motor-related brain regions for each condition. We demonstrated higher directed functional connectivity from the contralateral dorsal premotor cortex (dPMC) to the primary motor cortex (M1) in ME than in MI. We mainly identified significant direct effects of the dPMC and ventral premotor cortex (vPMC) to the parietal regions. In particular, connectivity from the dPMC to the superior parietal lobule in the same hemisphere showed significant positive effects across all conditions. Contrastingly, interlateral connectivities from the vPMC to the superior parietal lobule showed significantly negative effects across all conditions. Finally, we found positive effects from A1 to M1 in the same hemisphere, such as the audio-motor pathway. These results indicated that the sources of motor command originated in d/vPMC influenced M1 and parietal regions as achieving ME and MI. Additionally, sequential sounds may functionally facilitate temporal motor processes.
Membrane Shape Remodeling by Protein Crowding
Authors: Liese Susanne , Carlson Andreas 
Published: October 2020

AbstractThe steric repulsion between proteins on biological membranes is one of the most generic mechanisms that cause membrane shape changes. We present a minimal model where a spontaneous curvature is induced by steric repulsion between membrane-associated proteins. Our results show that the interplay between the induced spontaneous curvature and the membrane tension determine the energy minimizing shapes, which describe the wide range of experimentally observed membrane shapes,i.e. flat membranes, spherical vesicles, elongated tubular protrusions, and pearling structures.
Cell group analysis reveals changes in upper-layer neurons associated with schizophrenia
Authors: Dai Rujia , Chen Lulu , Liu Sihan , Wu Chiung-Ting , Chen Yu , Jiang Yi , Dai Jiacheng , Wang Qihang , Kopp Richard , Yu Guoqiang , Wang Yue , Chen Chao , Liu Chunyu 
Published: October 2020

AbstractGenome-wide association studies (GWAS) of schizophrenia (SCZ) have revealed over 100 risk loci. We investigated whether these SCZ-associated variants regulate gene expression by cell type. Using a fully unsupervised deconvolution method, we calculated gene expression by clusters of estimated cell types (cell-groups, CGs). Five CGs emerged in the dorsolateral prefrontal cortices (DLPFC) of 341 donors with and without SCZ. By mapping expression quantitative trait loci (eQTL) per CG, we partitioned the heritability of SCZ risk in GWAS by CGs. CG-specific expressions and eQTLs were replicated in both a deconvoluted bulk tissue data set with a different method and also in sorted-cell expression data. Further, we characterized CG-specific gene differential expression and cell proportion changes in SCZ brains. We found upper-layer neurons in the DLPFC to be associated with SCZ based on enrichment of SCZ heritability in eQTLs, disease-related transcriptional signatures, and decreased cell proportion. Our study suggests that neurons and related anomalous circuits in the upper layers of the DLPFC may have a major contribution to SCZ risk.
Single cell transcriptional profiling reveals helper, effector, and regulatory MAIT cell populations enriched during homeostasis and activation
Authors: Vorkas Charles Kyriakos , Krishna Chirag , Li Kelin , Aubé Jeffrey , Fitzgerald Daniel W. , Mazutis Linas , Leslie Christina S. , Glickman Michael S. 
Published: October 2020

AbstractMucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that recognize microbial vitamin B metabolites and have emerging roles in infectious disease, autoimmunity, and cancer. Although MAIT cells are identified by a semi-invariant T cell receptor, their phenotypic and functional heterogeneity is not well understood. Here we present an integrated single cell transcriptomic analysis of over 76,000 human MAIT cells during acute and chronic antigen-specific activation with the MR1 ligand 5-OP-RU and non-specific TCR stimulation. We show that MAIT cells span a broad range of homeostatic, effector, helper, tissue-infiltrating, regulatory, and exhausted phenotypes, with distinct gene expression programs associated with CD4+or CD8+co-expression. During acute activation, MAIT cells rapidly adopt a cytotoxic phenotype characterized by high expression ofGZMB,IFNGandTNF. In contrast, chronic stimulation induces heterogeneous states defined by proliferation, cytotoxicity, immune modulation, and exhaustion. These scRNAseq-defined MAIT cell subtypes were also detected in individuals recently exposed toMycobacterium tuberculosisinfection, confirming their presence during human infection. Our study provides the first comprehensive atlas of human MAIT cells in activation conditions and defines substantial functional heterogeneity, suggesting complex roles in health and disease.
Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase
Authors: Levine Zebulon G. , Potter Sarah C. , Joiner Cassandra M. , Fei George Q. , Nabet Behnam , Sonnett Matthew , Zachara Natasha E. , Gray Nathanael S. , Paulo Joao A. , Walker Suzanne 
Published: October 2020

AbstractO-GlcNAc transferase (OGT), found in the nucleus and cytoplasm of all mammalian cell types, is essential for cell proliferation. Why OGT is required for cell growth is not known. OGT performs two enzymatic reactions in the same active site. In one, it glycosylates thousands of different proteins, and in the other, it proteolytically cleaves another essential protein involved in gene expression. Deconvoluting OGT’s myriad cellular roles has been challenging because genetic deletion is lethal; complementation methods have not been established. Here, we developed approaches to replace endogenous OGT with separation-of-function variants to investigate the importance of OGT’s enzymatic activities for cell viability. Using genetic complementation, we found that OGT’s glycosyltransferase function is required for cell growth but its protease function is dispensable. We next used complementation to construct a cell line with degron-tagged wild-type OGT. When OGT was degraded to very low levels, cells stopped proliferating but remained viable. Adding back catalytically-inactive OGT rescued growth. Therefore, OGT has an essential noncatalytic role that is necessary for cell proliferation. By developing a method to quantify how OGT’s catalytic and noncatalytic activities affect protein abundance, we found that OGT’s noncatalytic functions often affect different proteins from its catalytic functions. Proteins involved in oxidative phosphorylation and the actin cytoskeleton were especially impacted by the noncatalytic functions. We conclude that OGT integrates both catalytic and noncatalytic functions to control cell physiology.SignificanceMammalian cells contain only one glycosyltransferase, OGT, that operates in the nucleus and cytoplasm rather than the secretory pathway. OGT is required for cell proliferation, but a basic unanswered question is what OGT functions are essential. This question is challenging to address because OGT has thousands of glycosylation substrates, two different enzymatic activities, and a large number of binding partners. Here, by establishing genetic tools to replace endogenous OGT with variants that preserve only a subset of its activities, we show that only a low level of glycosylation activity is required to maintain cell viability; however, cell proliferation requires noncatalytic OGT function(s). The ability to replace OGT with variants provides a path to identifying its essential substrates and binding partners.
Genome-wide CRISPR screens reveal multitiered mechanisms through which mTORC1 senses mitochondrial dysfunction
Authors: Condon Kendall J. , Orozco Jose M. , Adelmann Charles H. , Spinelli Jessica B. , van der Helm Pim W. , Roberts Justin M. , Kunchok Tenzin , Sabatini David M. 
Published: October 2020

AbstractIn mammalian cells, nutrients and growth factors signal through an array of upstream proteins to regulate the mTORC1 growth control pathway. Because the full complement of these proteins has not been systematically identified, we developed a FACS-based CRISPR-Cas9 genetic screening strategy to pinpoint genes that regulate mTORC1 activity. Along with almost all known positive components of the mTORC1 pathway, we identified many new genes that impact mTORC1 activity, includingDCAF7, CSNK2B, SRSF2, IRS4, CCDC43, andHSD17B10. Using the genome-wide screening data, we generated a focused sublibrary containing single guide RNAs (sgRNAs) targeting hundreds of genes and carried out epistasis screens in cells lacking nutrient- and stress-responsive mTORC1 modulators, including GATOR1, AMPK, GCN2, and ATF4. From these data, we pinpointed mitochondrial function as a particularly important input into mTORC1 signaling. While it is well appreciated that mitochondria signal to mTORC1, the mechanisms are not completely clear. We find that the kinases AMPK and HRI signal, with varying kinetics, mitochondrial distress to mTORC1, and that HRI acts through the ATF4-dependent upregulation of both Sestrin2 and Redd1. Loss of both AMPK and HRI is sufficient to make mTORC1 largely resistant to mitochondrial dysfunction. Taken together, our data reveal a catalog of genes that impact the mTORC1 pathway and clarify the multifaceted ways in which mTORC1 senses mitochondrial dysfunction.