bluuebunny/crossref_metadata_2025_split huggingface dataset:
REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats
Authors: Dolzhenko Egor , Weisburd Ben , Garikano Kristina Ibanez , Rajan Babu Indhu Shree , Bennett Mark F , Billingsley Kimberley , Carroll Ashley , Danzi Matt C. , Deshpande Viraj , Ding Jinhui , Fazal Sarah , Halman Andreas , Jadhav Bharati , Qiu Yunjiang , Richmond Phillip , Scheffler Konrad , van Vugt Joke J.F.A , Zwamborn Ramona R.A.J. ,   Genomics England Research Consortium, Chong Samuel S. , Friedman Jan M. , Tucci Arianna , Rehm Heidi L. , Eberle Michael A 
Published: October 2021

AbstractBackgroundExpansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely-recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads.ResultsWe implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in STR research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically-relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR.ConclusionsRead pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions.
Cryo-EM structures of pentameric autoinducer-2 exporter from E. coli reveal its transport mechanism
Authors: Khera Radhika , Mehdipour Ahmad Reza , Bolla Jani R , Kahnt Joerg , Welsch Sonja , Ermler Ulrich , Muenke Cornelia , Robinson Carol V , Hummer Gerhard , Xie Hao , Michel Hartmut 
Published: October 2021

AbstractBacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from E. coli, which belongs to a large underexplored membrane transporter family, the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism. This study emphasizes the structural distinctiveness of this family of pentameric transporters and provides fundamental insights for the ensuing studies.
Yn-situ: a robust single RNA molecule in situ detection method
Authors: Wu Yunming , Xu Wenjing , Ma Limei , Yu Zulin , Wang Yongfu , Yu C. Ron 
Published: October 2021

AbstractWe describe a cost-effective, highly sensitive, and quantitative method for in situ detection of single RNA molecules in tissue sections. This method, dubbed Yn situ, standing for Y-branched probe in situ hybridization, uses a single-strand DNA preamplifier with multiple initiation sites that trigger hybridization chain reaction (HCR) to detect polynucleotide. We characterized the performance of this method and compared it to other approaches in the postnatal mouse olfactory epithelia. We find that the Yn situ method, in conjunction with an improved fixation step, is sensitive enough to allow detection of single molecules using a single pair of probes targeting a short nucleotide sequence. A set of 5-probes can produce quantitative results with smaller puncta and higher signal-to-noise ratio than the 20-probe sets commonly required for HCR and RNA-Scope. We show that the high sensitivity and wide dynamic range allow quantification of genes expressed at different levels in the olfactory sensory neurons. We describe key steps of this method to enable broad utility by individual laboratories.
Structural Basis for the Inhibition of IAPP Fibril Formation by the Hsp60 Co-Chaperonin Prefoldin
Authors: Törner Ricarda , Kupreichyk Tatsiana , Gremer Lothar , Debled Elisa Colas , Fenel Daphna , Gans Pierre , Willbold Dieter , Schoehn Guy , Hoyer Wolfgang , Boisbouvier Jerome 
Published: October 2021

AbstractChaperones, as modulators of protein conformational states, are key cellular actors to prevent the accumulation of fibrillar aggregates. Here, we integrated kinetic investigations with structural studies to elucidate how the ubiquitous co-chaperonin prefoldin (PFD) inhibits diabetes associated islet amyloid polypeptide (IAPP) fibril formation. We demonstrated that both human and archaeal PFD interfere similarly with the IAPP fibril elongation and secondary nucleation pathways. Using archaeal prefoldin model, we combined NMR spectroscopy with EM to establish that the inhibition of fibril formation is mediated by the binding of prefoldin’s coiled-coil helices to the flexible IAPP N-terminal segment accessible on the fibril surface and fibril ends. AFM demonstrates that binding of prefoldin to IAPP leads to the formation of lower amounts of aggregates, composed of shorter fibrils, clustered together. Linking structural models with observed fibrillation inhibition processes opens new perspectives for understanding the interference between natural chaperones and formation of disease-associated amyloids.
A Network-based Deep Learning Framework Catalyzes GWAS and Multi-Omics Findings to Biology and Drug Repurposing for Alzheimer’s Disease
Authors: Xu Jielin , Hou Yuan , Zhou Yadi , Hu Ming , Cheng Feixiong 
Published: October 2021

AbstractHuman genome sequencing studies have identified numerous loci associated with complex diseases, including Alzheimer’s disease (AD). Translating human genetic findings (i.e., genome-wide association studies [GWAS]) to pathobiology and therapeutic discovery, however, remains a major challenge. To address this critical problem, we present anetworktopology-based deep learning framework to identify disease-associatedgenes (NETTAG). NETTAG is capable of integrating multigenomics data along with the protein-protein interactome to infer putative risk genes and drug targets impacted by GWAS loci. Specifically, we leverage non-coding GWAS loci effects on expression quantitative trait loci (eQTLs), histone-QTLs, and transcription factor binding-QTLs, enhancers and CpG islands, promoter regions, open chromatin, and promoter flanking regions. The key premises of NETTAG are that the disease risk genes exhibit distinct functional characteristics compared to non-risk genes and therefore can be distinguished by their aggregated genomic features under the human protein interactome. Applying NETTAG to the latest AD GWAS data, we identified 156 putative AD-risk genes (i.e.,APOE,BIN1,GSK3B,MARK4, andPICALM). We showed that predicted risk genes are: 1) significantly enriched in AD-related pathobiological pathways, 2) more likely to be differentially expressed regarding transcriptome and proteome of AD brains, and 3) enriched in druggable targets with approved medicines (i.e., choline and ibudilast). In summary, our findings suggest that understanding of human pathobiology and therapeutic development could benefit from a network-based deep learning methodology that utilizes GWAS findings under the multimodal genomic analyses.
Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells
Authors: Robinson Philip S. , Thomas Laura E. , Abascal Federico , Jung Hyunchul , Harvey Luke M.R. , West Hannah D. , Olafsson Sigurgeir , Lee Bernard C. H. , Coorens Tim H.H. , Lee-Six Henry , Butlin Laura , Lander Nicola , Sanders Mathijs A. , Lensing Stefanie V. , Buczacki Simon J.A. , ten Hoopen Rogier , Coleman Nicholas , Brunton-Sim Roxanne , Rushbrook Simon , Saeb-Parsy Kourosh , Lalloo Fiona , Campbell Peter J. , Martincorena Iñigo , Sampson Julian R. , Stratton Michael R. 
Published: October 2021

ABSTRACTCellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequenced normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 5-fold in all individuals, except for one showing a 33-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C>A changes. Different mutation rates and signatures between individuals were likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.Summary
CRISPR-Cas9 mediated knockout of SagD gene for overexpression of streptokinase in Streptococcus equisimilis
Authors: Chaudhari Armi M. , Vyas Sachin , Patel Amrutlal , Singh Vijai , Joshi Chaitanya G. , Joshi Madhvi 
Published: October 2021

AbstractStreptokinase is an enzyme that can break down the blood clots in some cases of myocardial infarction (Heart attack), pulmonary embolism, and arterial thromboembolism. Demand for streptokinase is high globally than the production due to increased incidences of various heart conditions. The main source of streptokinase is from various strains of Streptococcus. Expression of streptokinase in native strain Streptococcus equisimilis is limited due to the SagD inhibitor gene for production of streptokinase that needs to be knocked out in order to increase it expression. However, FasX is a small RNA (sRNA) present in group A Streptococcus species which is responsible for post-transcriptional regulation of streptokinase (ska) gene by binding at the 5’ end of ska mRNA. S. equisimilis is a β-hemolysin producing streptococcus bacterium (group C) containing the orthologue of FasX and natively expresses a clinically important thrombolytic streptokinase. In order to improve the stability of mRNA and increasing the expression of streptokinase which is inhibited by SagD. We used CRISPR-Cas9 to successfully knock-out of SagD gene and observed a 13.58-fold relative quantification of streptokinase expression in the mutant strain as compared to wild type. We have also demonstrated the successful target gene knockout using CRISPR-Cas9 in S. equisimilis that engineered strain can be used further for overexpression of streptokinase for therapeutic applications.Graphical Abstract
Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex
Authors: Greenrod Samuel T. E. , Stoycheva Martina , Elphinstone John , Friman Ville-Petri 
Published: October 2021

AbstractRalstonia solanacearum is a destructive plant pathogenic bacterium and the causative agent of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, its virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape R. solanacearum virulence, the global diversity, distribution, and wider functional gene content of R. solanacearum prophages is unknown. In this study, prophages were identified in a diverse collection of 192 R. solanacearum draft genome assemblies originating from six continents. Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distribution was characterised using metadata on R. solanacearum geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 343 intact prophages were identified, forming ten genetically distinct clusters. These included five prophage clusters belonging to the Inoviridae, Myoviridae, and Siphoviridae phage families, and five uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distribution being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained a myriad of auxiliary genes involved in metabolism and virulence of both phage and bacteria. Our results show that while R. solanacearum prophages are highly diverse globally, they make lineage-specific contributions to the R. solanacearum accessory genome, which could have resulted from shared coevolutionary history.
Cholesterol biosynthetic pathway induces cellular senescence through ERRα
Authors: Ziegler Dorian V. , Vernier Mathieu , Czarnecka-Herok Joanna , Scholtes Charlotte , Machon Christelle , Guitton Jérôme , Rieusset Jennifer , Giguère Vincent , Martin Nadine , Bernard David 
Published: October 2021

AbstractCellular senescence is a cell program induced by various stresses that leads to a stable proliferation arrest and to a senescence-associated secretory phenotype. Accumulation of senescent cells during age-related diseases participates in these pathologies and regulates healthy lifespan. Recent evidences point out a global dysregulated intracellular metabolism associated to senescence phenotype. Nonetheless, the functional contribution of metabolic homeostasis in regulating senescence is barely understood. In this work, we describe how the mevalonate pathway, an anabolic pathway leading to the endogenous biosynthesis of poly-isoprenoids, such as cholesterol, acts as a positive regulator of cellular senescence in normal human cells. Mechanistically, this mevalonate-induced senescence is partly mediated by the downstream cholesterol biosynthetic pathway. This pathway promotes transcriptional activity of ERRα leading to dysfunctional mitochondria, ROS production, DNA damage and a p53-dependent senescence. Supporting the relevance of these observations, increase of senescence in liver due to a high-fat diet regimen is abrogated in ERRα knockout mouse. Overall, this work unravels the role of cholesterol biosynthesis in the induction of an ERRα-dependent mitochondrial program leading to cellular senescence and related pathological alterations.
A Tissue-Bioengineering Strategy for Modeling Rare Human Kidney Diseases In Vivo
Authors: Hernandez J.O.R. , Wang X. , Vazquez-Segoviano M. , Sobral-Reyes M.F. , Moran-Horowich A. , Sundberg M. , Lopez-Marfil M. , Lopez-Cantu D.O. , Probst C.K. , Ruiz-Esparza G.U , Giannikou K. , Henske E.P. , Kwiatkowski D.J. , Sahin M. , Lemos D.R. 
Published: October 2021

ABSTRACTThe lack of animal models for certain human diseases precludes our understanding of disease mechanisms and our ability to test new therapies in vivo. Here we generated kidney organoids from Tuberous Sclerosis Complex (TSC) patient-derived-hiPSCs to recapitulate a rare kidney tumor called angiomylipoma (AML). Organoids derived from TSC2-/- hiPSCs but not from isogenic TSC2+/- or TSC2+/+ hiPSCs shared a common transcriptional signature and a myomelanocytic cell phenotype with kidney AMLs, and developed epithelial cysts, replicating two major TSC-associated kidney lesions driven by genetic mechanisms that cannot be robustly and consistently recapitulated with transgenic mice. Transplantation of multiple TSC2-/- kidney organoids into the kidneys of immunodeficient rats allowed us to recapitulate AML and cystic kidney disease in vivo, in a scalable fashion and with fidelity, and to test the efficiency of rapamycin-loaded nanoparticles as a novel approach to ablate AMLs by inducing apoptosis triggered by mTOR-inhibition. Collectively, these methods represent a novel tissue-bioengineering strategy for rare disease modeling in vivo.
Persistent synaptic inhibition of the subthalamic nucleus by high frequency stimulation
Authors: Steiner Leon A , Kühn Andrea A , Geiger Jörg RP , Alle Henrik , Popovic Milos R , Kalia Suneil K , Hodaie Mojgan , Lozano Andres M , Hutchison William D , Milosevic Luka 
Published: October 2021

AbstractBackgroundDeep brain stimulation (DBS) provides symptomatic relief in a growing number of neurological indications, but local synaptic dynamics in response to electrical stimulation that may relate to its mechanism of action have not been fully characterized.ObjectiveThe objectives of this study were to (1) study local synaptic dynamics during high frequency extracellular stimulation of the subthalamic nucleus (STN), and (2) compare STN synaptic dynamics with those of the neighboring substantia nigra pars reticulata (SNr).MethodsTwo microelectrodes were advanced into the STN and SNr of patients undergoing DBS surgery for PD. Neuronal firing and evoked field potentials (fEPs) were recorded with one microelectrode during stimulation from an adjacent microelectrode.ResultsExcitatory and inhibitory fEPs could be discerned within the STN and their amplitudes predicted bidirectional effects on neuronal firing (p = .007). There were no differences between STN and SNr inhibitory fEP dynamics at low stimulation frequencies (p > .999). However, inhibitory neuronal responses were sustained over time in STN during high frequency stimulation, but not SNr (p < .001) where depression of inhibitory input was coupled with a return of neuronal firing (p = .003).InterpretationPersistent inhibitory input to the STN suggests a local synaptic mechanism for the suppression of subthalamic firing during high frequency stimulation. Moreover, differences in the resiliency versus vulnerability of inhibitory inputs to the STN and SNr suggest a projection source- and frequency-specificity for this mechanism. The feasibility of targeting electrophysiologically-identified neural structures may provide insight into how DBS achieves frequency-specific modulation of neuronal projections.
Dual domestication, diversity, and differential introgression in Old World cotton diploids
Authors: Grover Corrinne E. , Arick Mark A. , Thrash Adam , Sharbrough Joel , Hu Guanjing , Yuan Daojun , Miller Emma R. , Ramaraj Thiruvarangan , Peterson Daniel G. , Udall Joshua A. , Wendel Jonathan F. 
Published: October 2021

AbstractDomestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and G. arboreum, because of the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we confirm their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 2.3×10-3) within species is similar, and that divergence between species is modest (weighted FST=0.4430). Individual accessions were homozygous for ancestral SNPs at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated in introgression analyses. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces influencing diversity and divergence in the diploid cultivated species, and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.Significance statementThe cotton genus (Gossypium) contains four different species that were independently domesticated at least 4,000 years ago. Relatively little is understood about diversity and evolution in the two diploid African-Asian sister-species G. herbaceum and G. arboreum, despite their historical importance in the region and contemporary cultivation, largely in the Indian subcontinent. Here we address questions regarding the relationship between the two species, their contemporary levels of diversity, and their patterns of interspecific gene flow accompanying their several millennia history of human-mediated dispersal and contact. We validate independent domestication of the two species and document the genomic distribution of interspecific genetic exchange.
The Polo kinase Cdc5 is regulated at multiple levels in the adaptation response to telomere dysfunction
Authors: Coutelier Héloïse , Ilioaia Oana , Peillet Jeanne Le , Hamon Marion , D’Amours Damien , Teixeira Maria Teresa , Xu Zhou 
Published: October 2021

AbstractTelomere dysfunction activates the DNA damage checkpoint to induce a cell cycle arrest. After an extended period of time, however, cells can bypass the arrest and undergo cell division despite the persistence of the initial damage, a process called adaptation to DNA damage. The Polo kinase Cdc5 inSaccharomyces cerevisiaeis essential for adaptation and for many other cell-cycle processes. How the regulation of Cdc5 in response to telomere dysfunction relates to adaptation is not clear. Here, we report that Cdc5 protein level decreases after telomere dysfunction in a Mec1-, Rad53- and Ndd1-dependent manner. This regulation of Cdc5 is important to maintain long-term cell cycle arrest but not for the initial checkpoint arrest. We find that both Cdc5 and the adaptation-deficient mutant protein Cdc5-ad are heavily phosphorylated and several phosphorylation sites modulate adaptation efficiency. The PP2A phosphatases are involved in Cdc5-ad phosphorylation status and contribute to adaptation mechanisms. We finally propose that Cdc5 orchestrates multiple cell cycle pathways to promote adaptation.