bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit
Authors: Sirén Jouni , Monlong Jean , Chang Xian , Novak Adam M. , Eizenga Jordan M. , Markello Charles , Sibbesen Jonas A. , Hickey Glenn , Chang Pi-Chuan , Carroll Andrew , Gupta Namrata , Gabriel Stacey , Blackwell Thomas W. , Ratan Aakrosh , Taylor Kent D. , Rich Stephen S. , Rotter Jerome I. , Haussler David , Garrison Erik , Paten Benedict 
Published: December 2020

ABSTRACTWe introduce Giraffe, a pangenome short read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe, part of the variation graph toolkit (vg)1, maps reads to thousands of human genomes at around the same speed BWA-MEM2maps reads to a single reference genome, while maintaining comparable accuracy to VG-MAP, vg’s original mapper. We have developed efficient genotyping pipelines using Giraffe. We demonstrate improvements in genotyping for single-nucleotide variants (SNVs), small insertions and deletions (indels) and structural variations (SVs) genome-wide. We use Giraffe to genotype about 167 thousand structural variants ascertained from long read studies in 5,202 human genomes sequenced with short reads, including the complete 1000 Genomes Project dataset, at an average cost of $1.50 per sample. We determine the frequency of these variations in diverse human populations, characterize their complex allelic variations and identify thousands of expression quantitative trait loci (eQTLs) driven by these variations.
The aging whole blood transcriptome reveals a potential role of FASLG in COVID-19
Authors: de Almeida Chuffa Luiz Gustavo , Souza Jeferson dos Santos , de Mello Mariana Costa , de Oliveira Neto Mario , Carvalho Robson Francisco 
Published: December 2020

AbstractThe risk for severe illness from COVID-19 increases with age as older patients are at the highest risk. Although it is still unclear whether the virus is blood-transmitted, the viral RNA is detected in serum. Identifying how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interacts with specific blood components during aging is expected to guide proper therapies. Considering that all human coronavirus require host cellular molecules to promote infection, we investigated the aging whole blood transcriptome from the Genotype-Tissue Expression (GTEx) database to explore differentially expressed genes (DEGs) translated into proteins potentially interacting with viral proteins. From a total of 22 DEGs in aged blood, five genes (FASLG, CTSW, CTSE, VCAM1, andBAG3) changed expression during aging. These age-related genes are involved in immune response, inflammation, cell component and cell adhesion, and platelet activation/aggregation. Both males and females older than 50 overexpressFASLGcompared with younger adults (20-30 years old), possibly inducing a hyper-inflammatory cascade that activates specific immune cells. Furthermore, the expression of cathepsins (CTSWandCTSE) and the anti-apoptotic co-chaperone moleculeBAG3was significantly increased throughout aging in both gender. By exploring publicly available Single-Cell RNA-Sequencing (scRNA-Seq) data on peripheral blood of SARS-CoV-2-infected patients, we foundFASLGandCTSWexpressed mainly in natural killer (NK) cells and CD8+ (cytotoxic) T lymphocytes whereasBAG3was expressed in CD4+ T cells, naive T cells, and CD14+ monocytes. The increased expression ofFASLGin blood during aging may explain why older patients are more prone to severe acute viral infection complications. These results indicateFASLGas a prognostic candidate and potential therapeutic target for more aggressive clinical manifestation of COVID-19.
The pan-cancer lncRNA PLANE regulates an alternative splicing program to promote cancer pathogenesis
Authors: Teng Liu , Feng Yu Chen , Guo Su Tang , Wang Pei Lin , Wang Shi Xing , Zhang Sheng Nan , Qi Teng Fei , La Ting , Zhang Yuan Yuan , Zhao Xiao Hong , Zhang Didi , Wang Jenny Y , Shi Yujie , Li Jin Ming , Cao Huixia , Liu Tao , Thorne Rick F. , Jin Lei , Shao Feng-Min , Zhang Xu Dong 
Published: December 2020

ABSTRACTGenomic amplification of the distal portion of chromosome 3q, which encodes a number of oncogenic proteins, is one of the most frequent chromosomal abnormalities in malignancy. Here we functionally characterise a non-protein product of the 3q region, the long noncoding RNA (lncRNA) PLANE, which is upregulated in diverse cancer types through copy number gain as well as E2F1-mediated transcriptional activation. PLANE forms an RNA-RNA duplex with the nuclear receptor co-repressor 2 (NCOR2) pre-mRNA at intron 45, binds to heterogeneous ribonucleoprotein M (hnRNPM) and facilitates the association of hnRNPM with the intron, thus leading to repression of the alternative splicing (AS) event generating NCOR2-202, a major protein-coding NCOR2 AS variant. In consequence, PLANE promotes cancer cell proliferation and tumorigenicity and its upregulation is associated with poor patient outcomes. These results uncover the function and regulation of PLANE and suggest that PLANE may constitute a therapeutic target in the pan-cancer context.
The ascending arousal system promotes optimal performance through meso-scale network integration in a visuospatial attentional task
Authors: Wainstein Gabriel , Rojas-Libano Daniel , Medel Vicente , Alnæs Dag , Kolskår Knut K. , Endestad Tor , Laeng Bruno , Ossandon Tomas , Crossley Nicolás , Matar Elie , Shine James M. 
Published: December 2020

AbstractPrevious research has shown that the autonomic nervous system provides essential constraints over ongoing cognitive function. However, there is currently a relative lack of direct empirical evidence for how this interaction manifests in the brain at the macro-scale level. Here, we examine the role of ascending arousal and attentional load on large-scale network dynamics by combining pupillometry, functional MRI and graph theoretical analysis to analyze data from a visual motion-tracking task with a parametric load manipulation. We found that attentional load effects were observable in measures of pupil diameter and in a set of brain regions that parametrically modulated their BOLD activity and meso-scale network-level integration. In addition, the regional patterns of network reconfiguration were correlated with the spatial distribution of theα2a adrenergic receptor. Our results further solidify the relationship between ascending noradrenergic activity, large-scale network integration, and cognitive task performance.Author SummaryIn our daily lives, it is usual to encounter highly demanding cognitive tasks. They have been traditionally regarded as challenges that are solved mainly through cerebral activity, specifically via information-processing steps carried by neurons in the cerebral cortex. Activity in cortical networks thus constitutes a key factor for improving our understanding cognitive processes. However, recent evidence has shown that evolutionary older players in the central nervous system, such as brainstem’s ascending modulatory systems, might play an equally important role in diverse cognitive mechanisms. Our article examines the role of the ascending arousal system on large-scale network dynamics by combining pupillometry, functional MRI and graph theoretical analysis.
Deletion of PI3-Kinase Promotes Myelodysplasia Through Dysregulation of Autophagy in Hematopoietic Stem Cells
Authors: Ames Kristina , Kaur Imit , Shi Yang , Tong Meng , Sinclair Taneisha , Hemmati Shayda , Glushakow-Smith Shira G. , Tein Ellen , Gurska Lindsay , Dubin Robert , Shan Jidong , Pradhan Kith , Verma Amit , Montagna Cristina , Gritsman Kira 
Published: December 2020

AbstractHematopoietic stem cells (HSCs) maintain the blood system through a delicate equilibrium between self-renewal and differentiation. Most hematopoietic growth factors and cytokines signal through phosphoinositide 3-kinase (PI3K) via three Class IA catalytic PI3K isoforms (P110α, β, and δ), encoded byPik3ca, Pik3cb, andPik3cd, respectively. The PI3K/AKT pathway is commonly activated in acute myeloid leukemia (AML), and PI3K is a common therapeutic target in cancer. However, it is not known whether PI3K is required for HSC differentiation or self-renewal. We previously demonstrated that individual PI3K isoforms are dispensable in HSCs1,2. To determine the redundant roles of PI3K isoforms in HSCs, we generated a triple knockout (TKO) mouse model with deletion of all three Class IA PI3K isoforms in the hematopoietic system. Surprisingly, we observed significant expansion of TKO HSCs after transplantation, with decreased differentiation capacity and impaired multilineage repopulation. Additionally, the bone marrow of TKO mice exhibited myelodysplastic features with chromosomal abnormalities. Interestingly, we found that macroautophagy (thereafter autophagy) is impaired in TKO HSCs, and that pharmacologic induction of autophagy improves their differentiation. Therefore, we have uncovered important roles for PI3K in autophagy regulation in HSCs to maintain the balance between self-renewal and differentiation.
Strain specific persistence in the murine lung ofAspergillus fumigatusconidia causes an Allergic Broncho-Pulmonary Aspergillosis-like disease phenotype
Authors: Jones Jane T. , Liu Ko-Wei , Wang Xi , Kowalski Caitlin H. , Ross Brandon S. , Mills Kathleen A. M. , Kerkaert Joshua D. , Hohl Tobias M. , Lofgren Lotus A. , Stajich Jason E. , Obar Joshua J. , Cramer Robert A. 
Published: December 2020

ABSTRACTAspergillus fumigatusis a filamentous fungus which can cause multiple diseases in humans. Allergic Broncho-pulmonary Aspergillosis (ABPA) is a disease diagnosed primarily in Cystic Fibrosis patients caused by a severe allergic response often to long-termA. fumigatuscolonization in the lungs. Mice develop an allergic response to repeated inhalation ofA. fumigatusspores; however, no strains have been identified that can survive long-term in the mouse lung and cause ABPA-like disease. We characterizedA. fumigatusstrain W72310 by whole genome sequencing andin vitroandin vivoviability assays in comparison to a common reference strain, CEA10. W72310 was resistant to leukocyte-mediated killing and persisted in the mouse lung longer than CEA10, a phenotype that correlated with greater resistance to oxidative stressors, hydrogen peroxide and menadione,in vitro. In animals both sensitized and challenged with W72310, conidia, but not hyphae, were viable in the lungs for up to 21 days in association with eosinophilic airway inflammation, airway leakage, serum IgE, and mucus production. W72310-sensitized mice that were recall-challenged with conidia had increased inflammation, Th1 and Th2 cytokines, and airway leakage compared to controls. Collectively, our studies demonstrate that a unique strain ofA. fumigatusresistant to leukocyte killing can persist in the mouse lung in conidial form and elicit features of ABPA-like disease.IMPORTANCEAllergic Broncho-pulmonary Aspergillosis (ABPA) patients often present with long-term colonization ofAspergillus fumigatus. Current understanding of ABPA pathogenesis has been complicated by a lack of long-termin vivofungal persistence models. We have identified a clinical isolate ofA. fumigatus, W72310, which persists in the murine lung and causes an ABPA-like disease phenotype. Surprisingly, while viable, W72310 showed little to no growth beyond the conidial stage in the lung. This indicates that it is possible thatA. fumigatuscan cause allergic disease in the lung without any significant hyphal growth. The identification of this strain ofA. fumigatuscan not only be used to better understand disease pathogenesis of ABPA and potential anti-fungal treatments, but also to identify features of fungal strains that drive long-term fungal persistence in the lung. Consequently, these observations are a step toward helping resolve the long-standing question when to utilize antifungal therapies in patients with ABPA and fungal allergic type diseases.
Host-age prediction from fecal microbiome composition in laboratory mice
Authors: Low Adrian , Soh Melissa , Miyake Sou , Seedorf Henning 
Published: December 2020

ABSTRACTThe life-long relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Changes in microbiome composition throughout the lifespan of a host remain, however, largely understudied. In this study, the fecal microbiome of conventionally raised C57BL/6J mice was analyzed throughout almost the entire expected lifespan, from ‘maturing’ (9 weeks) until ‘very old’ age (112 weeks). Analysis of alpha and beta diversity suggests that gradual microbiome changes occur throughout the entire murine life but appear to be more pronounced in ‘maturing’ to ‘middle-aged’ phases. Phylum-level analysis indicates a shift in the Firmicutes/Bacteroidetes ratio in favor of the Firmicutes in the second year of adulthood. Varying successional patterns throughout life were observed for many Firmicutes OTUs, while relative abundances of Bacteroidetes OTUs varied primarily in the early life phases. Microbiome configurations at given time points were used as training sets in a Bayesian model, which in turn effectively enabled the prediction of host age. The fecal microbiome composition may therefore serve as an accurate biomarker for aging. This study further suggests that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies.ImportanceThe life-long relationship between microorganisms and hosts has a profound impact on the overall physiology of the holobiont. Understanding the extent of gut microbiome compositional changes over the expected mouse lifespan may allow to better understand the interplay of microbiome and the host at the different life stages. In this study, we performed a two-year longitudinal study of murine fecal microbiome. Using fine-scale microbiome profiling we were able to predict the host age from the fecal microbiome composition. Moreover, we observed that the rate of compositional change appears to slow with age. The description of the compositional changes in commonly used C57BL/6J mice can be used to optimize selection of age-associated mouse models and highlights the use of microbiome-profiling as biomarker for aging.
NGLY1 knockdown or pharmacological inhibition induces cellular autophagy
Authors: Needs Sarah H , Bootman Martin D , Grotzke Jeff E , Kramer Holger B , Allman Sarah A 
Published: December 2020

SummaryPan-caspase inhibitor Z-VAD-fmk acts as an inhibitor of peptide:N-glycanase (NGLY1); an endoglycosidase which cleavesN-linked glycans from glycoproteins exported from the endoplasmic reticulum during ER-associated degradation (ERAD). PharmacologicalN-glycanase inhibition by Z-VAD-fmk or siRNA knockdown (KD) induces GFP-LC3 positive puncta in HEK 293 cells. Activation of ER stress markers or reactive oxygen species (ROS) induction are not observed. In NGLY1 inhibition or KD, upregulation of autophagosome formation without impairment of autophagic flux are observed. Enrichment and proteomics analysis of autophagosomes after Z-VAD-fmk treatment or NGLY1 KD reveals comparable autophagosomal protein content. Upregulation of autophagy represents a cellular adaptation to NGLY1 inhibition or KD, and ATG13-deficient mouse embryonic fibroblasts (MEFs) show reduced viability under these conditions. In contrast, treatment with pan-caspase inhibitor, Q-VD-OPh does not induce cellular autophagy. Therefore, experiments with Z-VAD-fmk are complicated by the effects of NGLY1 inhibition and Q-VD-OPh represents an alternative caspase inhibitor free from this limitation.
ProbingE. coliSSB Protein-DNA topology by reversing DNA backbone polarity
Authors: Kozlov Alexander G. , Lohman Timothy M. 
Published: December 2020

AbstractE. colisingle strand (ss) DNA binding protein (SSB) is an essential protein that binds ssDNA intermediates formed during genome maintenance. SSB homo-tetramers bind ssDNA in two major modes differing in occluded site size and cooperativity. The (SSB)35mode in which ssDNA wraps on average around two subunits is favored at low [NaCl] and high SSB to DNA ratios and displays high “unlimited”, nearest-neighbor cooperativity forming long protein clusters. The (SSB)65mode, in which ssDNA wraps completely around four subunits of the tetramer, is favored at higher [NaCl] (> 200 mM) and displays “limited” low cooperativity. Crystal structures ofE. coliSSB andP. falciparumSSB show ssDNA bound to the SSB subunits (OB-folds) with opposite polarities of the sugar phosphate backbones. To investigate whether SSB subunits show a polarity preference for binding ssDNA, we examinedEcSSB andPfSSB binding to a series of (dT)70constructs in which the backbone polarity was switched in the middle of the DNA by incorporating a reverse polarity (RP) phosphodiester linkage, either 3’-3’ or 5’-5’. We find only minor effects on the DNA binding properties for these RP constructs, although (dT)70with a 3’-3’ polarity switch shows decreased affinity forEcSSB in the (SSB)65mode and lower cooperativity in the (SSB)35mode. However, (dT)70in which every phosphodiester linkage is reversed, does not form a completely wrapped (SSB)65mode, but rather bindsEcSSB in the (SSB)35mode, with little cooperativity. In contrast,PfSSB, which binds ssDNA only in an (SSB)65mode and with opposite backbone polarity and different topology, shows little effect of backbone polarity on its DNA binding properties. We present structural models suggesting that strict backbone polarity can be maintained for ssDNA binding to the individual OB-folds if there is a change in ssDNA wrapping topology of the RP ssDNA.Statement of SignificanceSingle stranded (ss) DNA binding (SSB) proteins are essential for genome maintenance. Usually homo-tetrameric, bacterial SSBs bind ssDNA in multiple modes, one of which involves wrapping 65 nucleotides of ssDNA around all four subunits. Crystal structures ofE. coliandP. falciparumSSB-ssDNA complexes show ssDNA bound with different backbone polarity orientations raising the question of whether these SSBs maintain strict backbone polarity in binding ssDNA. We show that bothE. coliandP. falciparumSSBs can still form high affinity fully wrapped complexes with non-natural DNA containing internal reversals of the backbone polarity. These results suggest that both proteins maintain a strict backbone polarity preference, but adopt an alternate ssDNA wrapping topology.
Structural basis of FANCD2 deubiquitination by USP1-UAF1
Authors: Rennie Martin L. , Arkinson Connor , Chaugule Viduth K. , Toth Rachel , Walden Helen 
Published: December 2020

AbstractUbiquitin-Specific Protease 1 (USP1), together with the cofactor UAF1, acts during DNA repair processes to specifically to remove mono-ubiquitin signals. The mono-ubiquitinated FANCI-FANCD2 heterodimer is one such substrate and is involved in the repair of DNA interstrand crosslinks via the Fanconi Anemia pathway. Here we determine structures of human USP1-UAF1 with and without ubiquitin, and bound to mono-ubiquitinated FANCI-FANCD2 substrate. Crystal structures of USP1-UAF1 reveal plasticity in USP1 and key differences to USP12-UAF1 and USP46-UAF1. A cryoEM reconstruction of USP1-UAF1 in complex mono-ubiquitinated FANCI-FANCD2, highlights a highly orchestrated deubiquitination process with USP1-UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for their requirement despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1-UAF1 regulation and substrate recognition.
Distinct temporal expression of GW182 in neurons regulates dendritic arborization
Authors: Nawalpuri Bharti , Muddashetty Ravi 
Published: December 2020

AbstractPrecise development of the dendritic architecture is a critical determinant of mature neuronal circuitry. MicroRNA-mediated regulation of protein synthesis plays a crucial role in dendritic morphogenesis but the role of miRISC protein components in this process is less studied. Here, we show an important role of a key miRISC protein GW182 in the regulation of dendritic growth. We have identified a distinct brain region specific Spatio-temporal expression pattern of GW182 during rat postnatal development. We found that the window of peak GW182 expression coincides with the period of extensive dendritic growth, both in the hippocampus and cerebellum. Perturbation of GW182 function during a specific temporal window resulted in reduced dendritic growth of cultured hippocampal neurons. Mechanistically, we show that GW182 modulates dendritic growth by regulating global somato-dendritic translation, and actin cytoskeletal dynamics of developing neurons. Furthermore, we found that GW182 affects dendritic architecture by regulating the expression of actin modulator LIMK1. Taken together, our data reveal a previously undescribed neurodevelopmental expression pattern of GW182 and its role in dendritic morphogenesis, through both translational control and actin cytoskeletal rearrangement.SummaryGW182 is a key component of miRNA induced silencing complex (miRISC). Nawalpuri et al. show that GW182 has a unique temporal expression profile during neuronal development. The developmentally controlled expression of GW182 influences dendritic morphology by regulating the expression of actin modulator LIMK1.
Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor
Authors: Uberoi Aayushi , Bartow-McKenney Casey , Zheng Qi , Flowers Laurice , Campbell Amy , Knight Simon A.B. , Chan Neal , Wei Monica , Lovins Victoria , Bugayev Julia , Horwinski Joseph , Bradley Charles , Meyer Jason , Crumrine Debra , Sutter Carrie Hayes , Elias Peter , Mauldin Elizabeth , Sutter Thomas R. , Grice Elizabeth A. 
Published: December 2020

SUMMARYThe epidermis forms a barrier that defends the body from desiccation and entry of harmful substances, while sensing and integrating environmental signals. The tightly orchestrated cellular changes required for the proper formation and maintenance of this epidermal barrier occur in the context of the skin microbiome. Using germ free mice, we demonstrate the microbiota is necessary for proper differentiation and repair of the epidermal barrier. These effects were mediated by the aryl hydrocarbon receptor (AHR) in keratinocytes, a xenobiotic receptor also implicated in epidermal differentiation. Murine skin lacking keratinocyte AHR was more susceptible to barrier damage and infection, during steady state and epicutaneous sensitization. Colonization with a defined consortium of human skin isolates restored barrier competence in an AHR-dependent manner. We reveal a fundamental mechanism whereby the microbiota regulates skin barrier formation and repair, with far-reaching implications for the numerous skin disorders characterized by epidermal barrier dysfunction.