bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescence Microscopy Datasets for Training Deep Neural Networks
Authors: Hagen Guy M. , Bendesky Justin , Machado Rosa , Nguyen Tram-Anh , Kumar Tanmay , Ventura Jonathan 
Published: June 2020

AbstractBackgroundFluorescence microscopy is an important technique in many areas of biological research. Two factors which limit the usefulness and performance of fluorescence microscopy are photobleaching of fluorescent probes during imaging, and, when imaging live cells, phototoxicity caused by light exposure. Recently developed methods in machine learning are able to greatly improve the signal to noise ratio of acquired images. This allows researchers to record images with much shorter exposure times, which in turn minimizes photobleaching and phototoxicity by reducing the dose of light reaching the sample.FindingsTo employ deep learning methods, a large amount of data is needed to train the underlying convolutional neural network. One way to do this involves use of pairs of fluorescence microscopy images acquired with long and short exposure times. We provide high quality data sets which can be used to train and evaluate deep learning methods under development.ConclusionThe availability of high quality data is vital for training convolutional neural networks which are used in current machine learning approaches.
The novel, recurrent mutation in theTOP2Agene results in the enhanced topoisomerase activity and transcription deregulation in glioblastoma
Authors: Gielniewski Bartlomiej , Poleszak Katarzyna , Roura Adria-Jaume , Szadkowska Paulina , Krol Sylwia K. , Guzik Rafal , Wiechecka Paulina , Maleszewska Marta , Kaza Beata , Marchel Andrzej , Czernicki Tomasz , Koziarski Andrzej , Zielinski Grzegorz , Styk Andrzej , Kawecki Maciej , Szczylik Cezary , Czepko Ryszard , Banach Mariusz , Kaspera Wojciech , Szopa Wojciech , Bujko Mateusz , Czapski Bartosz , Zabek Miroslaw , Izycka-Swieszewska Ewa , Kloc Wojciech , Nauman Pawel , Cieslewicz Joanna , Wojtas Bartosz , Kaminska Bozena 
Published: June 2020

AbstractBackgroundHigh grade gliomas (HGGs) are aggressive, primary brain tumors with poor clinical outcomes. We aim to better understand glioma pathobiology and find potential therapeutic susceptibilities.MethodsWe designed a custom panel of 664 cancer- and epigenetics-related genes, and employed targeted next generation sequencing to study the genomic landscape of somatic and germline variants in 182 gliomas of different malignancy grades. mRNA sequencing was performed to detect transcriptomic abnormalities.ResultsIn addition to known alterations inTP53,IDH1,ATRX,EGFRgenes found in this cohort, we identified a novel, recurrent mutation in theTOP2Agene coding for Topoisomerase 2A occurring only in glioblastomas (GBM, WHO grade IV gliomas). Biochemical assays with recombinant proteins demonstrated stronger DNA binding and DNA supercoil relaxation activities of the variant proteins. GBM patients carrying the mutatedTOP2Ahad shorter overall survival than those with the wild typeTOP2A. Computational analyses of transcriptomic data showed that GBMs with the mutatedTOP2Ahave different transcriptomic patterns suggesting higher transcriptomic activity.ConclusionWe identified a novel TOP2A E948Q variant that strongly binds to DNA and is more active than the wild type protein. Our findings suggest that the discoveredTOP2Avariant is gain–of-function mutation.Key pointsThe most frequent genetic alterations in high grade gliomas are reported.A new mutation in theTOP2Agene was found in 4 patients from Polish population.A E948Q substitution changes TOP2A activities towards DNA.The recurrentTOP2Avariant is a gain-of-function mutation.Importance of the studyGlioblastoma is a deadly disease. Despite recent advancements in genomics and innovative targeted therapies, glioblastoma therapy has not shown improvements. Insights into glioblastoma biology may improve diagnosis, prognosis, and treatment prediction, directing to a better outcome. We performed targeted sequencing of 664 cancer genes, and identified a new variant of theTOP2Agene encoding topoisomerase 2A in glioblastomas. The TOP2A protein variant shows a higher affinity towards DNA and causes transcriptional alterations, suggesting a higherde novotranscription rate.
Investigation of Compatibility of SARS-CoV-2 RT-PCR Kits Containing Different Gene Targets During COVID-19 Pandemic
Authors: Sarıgul Figen , Doluca Osman , Akhan Sıla , Sayan Murat 
Published: June 2020

ABSTRACTAimIn the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reverse transcriptase-polymerase chain reaction (RT-PCR) technique is often used. We evaluated the compatibility of SARS-CoV-2 RT-PCR kits containing different gene targets during the pandemic.Materials & methodsSamples were tested by Bio-Speddy® (RdRp gene) and Diagnovital® (RdRp+E genes). The correlation between two assays were determined by Deming regression and chi-square heatmap analyses.ResultsDiagnovital PCR kit showed in a constricted range and conveniently exponential amplification curves than Bio-Speedy PCR kit. While the correlation increased when a secondary biomarker was added to the kit.ConclusionIn an unknown sample, using together different PCR kits that target different genes during the pandemic situation may provide a more accurate diagnosis of SARS-CoV-2.
Variant analysis of SARS-CoV-2 strains in Middle Eastern countries
Authors: Bindayna Khalid Mubarak , Crinion Shane 
Published: June 2020

AbstractBackgroundSARS-CoV-2 is diverging from the initial Wuhan serotype, and different variants of the virus are reported. Mapping the variant strains and studying their pattern of evolution will provide better insights into the pandemic spreadMethodsData on different SARS-CoV2 for WHO EMRO countries were obtained from the Chinese National Genomics Data Center (NGDC), Genbank and the Global Initiative on Sharing All Influenza Data (GISAID). Multiple sequence alignments (MSA) was performed to study the evolutionary relationship between the genomes. Variant calling, genome and variant alignment were performed to track the strains in each country. Evolutionary and phylogenetic analysis is used to explore the evolutionary hypothesis.FindingsOf the total 50 samples, 4 samples did not contain any variants. Variant calling identified 379 variants. Earliest strains are found in Iranian samples. Variant alignment indicates Iran samples have a low variant frequency. Saudi Arabia has formed an outgroup. Saudi Arabia, Qatar and Kuwait were the most evolved genomes and are the countries with the highest number of cases per million.InterpretationIran was exposed to the virus earlier than other countries in the Eastern Mediterranean Region.FundingNone
Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles
Authors: Laufer Benjamin I. , Hwang Hyeyeon , Jianu Julia M. , Mordaunt Charles E. , Korf Ian F. , Hertz-Picciotto Irva , LaSalle Janine M. 
Published: June 2020

AbstractNeonatal dried blood spots (NDBS) are a widely banked sample source that enable retrospective investigation into early-life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early-life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q< 0.05) DMRs that distinguished DS from typical development (TD) and idiopathic developmental delay (DD) were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons to previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q< 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q< 0.05) enriched for blood-specific chromatin states. A ∼28 kb block of hypermethylation was observed on chromosome 21 in theRUNX1locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q< 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early-life mechanisms of epigenomic dysregulation resulting from trisomy 21.
Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses
Authors: Banerjee Arinjay , El-Sayes Nader , Budylowski Patrick , Richard Daniel , Maan Hassaan , Aguiar Jennifer A. , Baid Kaushal , D’Agostino Michael R. , Ang Jann Catherine , Tremblay Benjamin J.-M. , Afkhami Sam , Karimzadeh Mehran , Irving Aaron T. , Yip Lily , Ostrowski Mario , Hirota Jeremy A. , Kozak Robert , Capellini Terence D. , Miller Matthew S. , Wang Bo , Mubareka Samira , McGeer Allison J. , McArthur Andrew G. , Doxey Andrew C. , Mossman Karen 
Published: June 2020

SUMMARYType I interferons (IFNs) are our first line of defence against a virus. Protein over-expression studies have suggested the ability of SARS-CoV-2 proteins to block IFN responses. Emerging data also suggest that timing and extent of IFN production is associated with manifestation of COVID-19 severity. In spite of progress in understanding how SARS-CoV-2 activates antiviral responses, mechanistic studies into wildtype SARS-CoV-2-mediated induction and inhibition of human type I IFN responses are lacking. Here we demonstrate that SARS-CoV-2 infection induces a mild type I IFN responsein vitroand in moderate cases of COVID-19.In vitrostimulation of type I IFN expression and signaling in human airway epithelial cells is associated with activation of canonical transcriptions factors, and SARS-CoV-2 is unable to inhibit exogenous induction of these responses. Our data demonstrate that SARS-CoV-2 is not adept in blocking type I IFN responses and provide support for ongoing IFN clinical trials.
Reconstitution of an intact clock that generates circadian DNA binding in vitro
Authors: Chavan Archana G. , Ernst Dustin C. , Fang Mingxu , Sancar Cigdem , Partch Carrie L. , Golden Susan S. , LiWang Andy 
Published: June 2020

AbstractCircadian clocks control gene expression in the complex milieu of cells. Here, we reconstituted under defined conditions in vitro the cyanobacterial circadian clock system which includes an oscillator, signal-transduction pathways, transcription factor, and promoter DNA. The system oscillates autonomously with a near 24 h period, remains phase coherent for many days, and allows real-time observation of each component simultaneously without user intervention. This reassembled clock system provides new insights into how a circadian clock exerts control over gene expression and can serve in the area of synthetic biology as a new platform upon which to build even more complexity.One Sentence SummaryAn autonomously oscillating circadian clock-controlled gene regulatory circuit is studied in vitro using a real-time high-throughput assay.
Structure-based modelling and dynamics of MurM, aStreptococcus pneumoniaepenicillin resistance determinant that functions at the cytoplasmic membrane interface
Authors: York Anna , Lloyd Adrian. J. , del Genio Charo I. , Shearer Jonathan , Hinxman Karen. J. , Fritz Konstantin , Fulop Vilmos , Khalid Syma , Dowson Christopher. G. , Roper David. I. 
Published: June 2020

AbstractMurM is an aminoacyl-tRNA dependant ligase that aminoacylates the Lipid II peptidoglycan precursor, in the human pathogenStreptococcus pneumoniae. MurM is required for the generation of branched peptidoglycan precursors enabling indirect cross-links in the peptidoglycan and is found to be essential for penicillin resistance. In this study we have solved the X-ray crystal structure ofStaphylococcus aureusFemX, an isofunctional homologue of MurM, and used this as a template to generate a homology model of MurM. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of the protein with the phospholipid bilayer and the membrane embedded Lipid II substrate of MurM. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and we confirm this with experimental evidence that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. This suggests that the spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may be a critical to the final architecture of the peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
Microscope-AOtools: A generalised adaptive optics implementation
Authors: Hall Nicholas , Titlow Josh , Booth Martin J. , Dobbie Ian M. 
Published: June 2020

AbstractMicroscope-AOtools is a software package which allows for a simple, robust and generalised implementation of adaptive optics (AO) elements. It contains all the necessary methods for set-up, calibration, and aberration correction which are simple to use and function in a robust manner. Aberrations arising from sources such as sample hetero-geneity and refractive index mismatches are constant problems in biological imaging. These aberrations reduce image quality and the achievable depth of imaging, particularly in super-resolution microscopy techniques. AO technology has been proven to be effective in correcting for these aberrations and thereby improving the image quality. However, it has not been widely adopted by the biological imaging community due, in part, to difficulty in set-up and operation of AO, particularly by non-specialist users. Microscope-AOtools offers a robust, easy-to-use implementation of the essential methods for set-up and use of AO techniques. These methods are constructed in a generalised manner that can utilise a range of adaptive optics elements, wavefront sensing techniques and sensorless AO correction methods. Furthermore, the methods are designed to be easily extensible as new techniques arise, leading to a streamlined pipeline for new AO technology and techniques to be adopted by the wider microscopy community.
Beyond Plug and Pray: Context Sensitivity andin silicoDesign of Artificial Neomycin Riboswitches
Authors: Günzel Christian , Kühnl Felix , Arnold Katharina , Findeiß Sven , Weinberg Christina , Stadler Peter F , Mörl Mario 
Published: June 2020

AbstractGene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5’ untranslated region of mRNA. Rearrangements of the RNA structure in response, e. g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modeling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviorin vivocritically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developedin silicomethods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyze the influence of 5’ hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free license on Github.1
Rub1/NEDD8, a ubiquitin-like modifier, is also a ubiquitin modifier
Authors: Gurevich Sylvia Zerath , Sinha Abhishek , Longworth Joseph , Singh Rajesh K. , Lemma Betsegaw E. , Thakur Anita , Popp Oliver , Kornitzer Daniel , Reis Noa , Scheffner Martin , Dittmar Gunnar , Pick Elah , Fushman David , Glickman Michael H. 
Published: June 2020

ABSTRACTOf all ubiquitin-like small protein modifiers, Rub1/NEDD8 is the closest kin of ubiquitin in sequence and in structure. Despite their profound similarities, prevalence of ubiquitin and of Rub1 is starkly different: targets of ubiquitin modification reach into the thousands, whereas unique targets of Rub1/NEDD8 appear limited to one family of proteins, Cullins. This distinction is likely due to dedicated E1 activating enzymes that select either one or the other and relay the modifier until it is covalently attached to a target. To convert typical neddylation targets for modification by ubiquitin, and vice versa, we designed reciprocal substitutions at position 72 of Rub1 and of ubiquitin to render them substrates for activation by their non-cognate E1 activating enzymes. We found that this single amino acid is sufficient to distinguish between Ub and Rub1 in living cells, and determine their targets. Thus, modification of Cullins by UbR72Tcould compensate for loss of Rub1, even as it maintained its ability to polymerize and direct conjugates for degradation. Conversely, Rub1T72Ractivated by ubiquitin-activating enzyme entered into the ubiquitination cascade, however was not efficiently polymerized, essentially capping polyubiquitin chains. Upon shortage of free ubiquitin under stress, even native Rub1 spilled-over into the ubiquitinome suppressing polyubiquitination. By contrast, the need to maintain monomeric modifications on unique targets is a likely explanation for why the Rub1-activating enzyme strictly discriminates against ubiquitin. Swapping Rub1 and ubiquitin signals uncovered a reason for maintaining two separate pathways across eukaryotic kingdom.
ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Authors: Trincado Juan L. , Reixachs-Sole Marina , Pérez-Granado Judith , Fugmann Tim , Sanz Ferran , Yokota Jun , Eyras Eduardo 
Published: June 2020

AbstractImmunotherapies provide effective treatments for previously untreatable tumors and identifying tumor-specific epitopes can help elucidate the molecular determinants of therapy response. Here, we describe a pipeline, ISOTOPE (ISOform-guided prediction of epiTOPEs In Cancer), for the comprehensive identification of tumor-specific splicing-derived epitopes. Using RNA sequencing and mass spectrometry for MHC-I associated proteins, ISOTOPE identified neoepitopes from tumor-specific splicing events that are potentially presented by MHC-I complexes. Analysis of multiple samples indicates that splicing alterations may affect the production of self-epitopes and generate more candidate neoepitopes than somatic mutations. Although there was no difference in the number of splicing-derived neoepitopes between responders and non-responders to immune therapy, higher MHC-I binding affinity was associated with a positive response. Our analyses highlight the diversity of the immunogenic impacts of tumor-specific splicing alterations and the importance of studying splicing alterations to fully characterize tumors in the context of immunotherapies. ISOTOPE is available at https://github.com/comprna/ISOTOPEAuthor summaryImmune cells have the ability to attack tumor cells upon the identification of tumor-specific peptides, i.e., epitopes, that are presented by the major histocompatibility complex (MHC). New cancer immunotherapies that help trigger this process provide a promising therapeutic strategy. One crucial aspect for their success is the ability to determine the molecular properties of a tumor that are informative about the effectiveness of the therapy. Alterations in the way genes are processed to express RNA molecules could lead to the production of new peptides, with some of them potentially being presented as tumor epitopes and facilitate the attack of immune cells. It is therefore essential to facilitate the identification of these splicing-derived epitopes. In this work, we describe a computational pipeline that performs a comprehensive identification of splicing alterations in a tumor and the potential epitopes that they would produce. Analysis of tumor samples with our pipeline show that responders and non-responders to immune therapy do not show differences in the number of splicing-derived epitopes, but splicing neoepitopes have higher affinity to the MHC complex in responders. Our new pipeline facilitates the genome-scale analysis of the role of splicing alterations in shaping the molecular properties that influence response to immunotherapy.
A multi-enhancerRETregulatory code is disrupted in Hirschsprung disease
Authors: Chatterjee Sumantra , Karasaki Kameko M , Fries Lauren E , Kapoor Ashish , Chakravarti Aravinda 
Published: June 2020

AbstractThe major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms withincisregulatory elements (CREs) of theRETreceptor tyrosine kinase gene that reduce its gene expression during enteric nervous system (ENS) development. These variants have synergistic effects onRETgene expression and additionally dysregulate other ENS and HSCR genes in theRET-EDNRBgene regulatory network (GRN). Here, we use siRNA, ChIP and CRISPR/Cas9 deletion analyses in the SK-N-SH cell line to ask, how many HSCR-associated risk variants reside in CREs and affectRETgene expression? We demonstrate that 31 HSCR-associated variants reside in candidateRETCREs, ten with differential allele-specificin vitroenhancer activity and seven affectingRETgene expression; of these, five bind the transcription factors PAX3, RARB, GATA2 and SOX10. These and our prior results demonstrate that common sequence variants in at least 10RETenhancers affect HSCR risk, extending the knownRET-EDNRBGRN to reveal an extensive regulatory code modulating disease risk even at a single gene.
A sweep of earth’s virome reveals host-guided viral protein structural mimicry; with implications for human disease
Authors: Lasso Gorka , Honig Barry , Shapira Sagi D. 
Published: June 2020

SUMMARYViruses deploy an array of genetically encoded strategies to coopt host machinery and support viral replicative cycles. Molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, allow viruses to harness or disrupt cellular functions including nucleic acid metabolism and modulation of immune responses. Here, we use protein structure similarity to scan for virally encoded structure mimics across thousands of catalogued viruses and hosts spanning broad ecological niches and taxonomic range, including bacteria, plants and fungi, invertebrates and vertebrates. Our survey identified over 6,000,000 instances of structural mimicry, the vast majority of which (>70%) cannot be discerned through protein sequence. The results point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. Interrogation of proteins mimicked by human-infecting viruses points to broad diversification of cellular pathways targeted via structural mimicry, identifies biological processes that may underly autoimmune disorders, and reveals virally encoded mimics that may be leveraged to engineer synthetic metabolic circuits or may serve as targets for therapeutics. Moreover, the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type, with ssRNA viruses circumventing limitations of their small genomes by mimicking human proteins to a greater extent than their large dsDNA counterparts. Finally, we identified over 140 cellular proteins that are mimicked by CoV, providing clues about cellular processes driving the pathogenesis of the ongoing COVID-19 pandemic.