bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysregulation of M segment gene expression contributes to influenza A virus host restriction
Authors: Calderon Brenda M. , Danzy Shamika , Delima Gabrielle K. , Jacobs Nathan T. , Ganti Ketaki , Hockman Megan R. , Conn Graeme L. , Lowen Anice C. , Steel John 
Published: April 2019

AbstractThe M segment of the 2009 pandemic influenza A virus (IAV) has been implicated in its emergence into human populations. To elucidate the genetic contributions of the M segment to host adaptation, and the underlying mechanisms, we examined a panel of isogenic viruses that carry avian- or human-derived M segments. Avian, but not human, M segments restricted viral growth and transmission in mammalian model systems, and the restricted growth correlated with increased expression of M2 relative to M1. M2 overexpression was associated with intracellular accumulation of autophagosomes, which was alleviated by interference of the viral proton channel activity by amantadine treatment. As M1 and M2 are expressed from the M mRNA through alternative splicing, we separated synonymous and non-synonymous changes that differentiate human and avian M segments and found that dysregulation of gene expression leading to M2 overexpression diminished replication, irrespective of amino acid composition of M1 or M2. Moreover, in spite of efficient replication, virus possessing a human M segment that expressed avian M2 protein at low level did not transmit efficiently. We conclude that (i) determinants of transmission reside in the IAV M2 protein, and that (ii) control of M segment gene expression is a critical aspect of IAV host adaptation needed to prevent M2-mediated dysregulation of vesicular homeostasis.Author summaryInfluenza A virus (IAV) pandemics arise when a virus adapted to a non-human host overcomes species barriers to successfully infect humans and sustain human-to-human transmission. To gauge the adaptive potential and therefore pandemic risk posed by a particular IAV, it is critical to understand the mechanisms underlying viral adaptation to human hosts. Here, we focused on the role of one of IAV’s eight gene segments, the M segment, in host adaptation. Comparing the growth of IAVs with avian- and human-derived M segments in avian and mammalian systems revealed that the avian M segment restricts viral growth specifically in mammalian cells. We show that the mechanism underlying this host range phenotype is a dysregulation of viral gene expression when the avian IAV M segment is transcribed in mammalian cells. In particular, excess production of the M2 protein results in viral interference with cellular functions on which the virus relies. Our results therefore reveal that the use of cellular machinery to control viral gene expression leaves the virus vulnerable to over- or under-production of critical viral gene products in a new host species.
Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record
Authors: Hughey Jacob J. , Rhoades Seth D. , Fu Darwin Y. , Bastarache Lisa , Denny Joshua C. , Chen Qingxia 
Published: April 2019

AbstractBackgroundThe growth of DNA biobanks linked to data from electronic health records (EHRs) has enabled the discovery of numerous associations between genomic variants and clinical phenotypes. Nonetheless, although clinical data are generally longitudinal, standard approaches for detecting genotype-phenotype associations in such linked data, notably logistic regression, do not naturally account for the times at which events occur. Here we explored the advantages of quantifying associations using Cox proportional hazards regression, which can account for the age at which a patient first visited the healthcare system (left truncation) and the age at which a patient either last visited the healthcare system or acquired a particular phenotype (right censoring).ResultsUsing simulated data, we found that, compared to logistic regression, Cox regression had greater power at equivalent Type I error. We then scanned for genotype-phenotype associations using logistic regression and Cox regression on 50 phenotypes derived from the electronic health records of 49 792 genotyped individuals. In terms of effect sizes, the hazard ratios estimated by Cox regression were nearly identical to the odds ratios estimated by logistic regression. Consistent with the findings from our simulations, Cox regression had approximately 10% greater relative sensitivity for detecting known associations from the NHGRI-EBI GWAS Catalog.ConclusionsAs longitudinal health-related data continue to grow, Cox regression may improve our ability to identify the genetic basis for a wide range of human phenotypes.
The Draft Genome ofKochia scopariaand the Mechanism of Glyphosate Resistance via Transposon-MediatedEPSPSTandem Gene Duplication
Authors: Patterson Eric L. , Saski Christopher A. , Sloan Daniel B. , Tranel Patrick J. , Westra Philip , Gaines Todd A. 
Published: April 2019

ABSTRACTIncreased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world’s most-used herbicide. There are typically three to eightEPSPScopies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled theEPSPSlocus from a glyphosate-resistant kochia plant by sequencing a kochia bacterial artificial chromosome library. These resources helped reconstruct the history of duplication in the structurally complexEPSPSlocus and uncover the genes that are co-duplicated withEPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. We discovered a FHY3/FAR1-like mobile genetic element that is associated with the duplicatedEPSPSgene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of theEPSPSgene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.
Tumor-targeted delivery of childhood vaccine recall antigens by attenuatedListeriareduces pancreatic cancer
Authors: Selvanesan Benson Chellakkan , Chandra Dinesh , Quispe-Tintaya Wilber , Jahangir Arthee , Patel Ankur , Meena Kiran , Alves Da Silva Rodrigo Alberto , Friedman Madeline , Libutti Steven K , Yuan Ziqiang , Li Jenny , Siddiqui Sarah , Beck Amanda , Tesfa Lydia , Koba Wade , Chuy Jennifer , McAuliffe John C. , Jafari Rojin , Entenberg David , Wang Yarong , Condeelis John , DesMarais Vera , Balachandran Vinod , Zhang Xusheng , Gravekamp Claudia 
Published: April 2019

ABSTRACTPancreatic ductal adenocarcinoma is highly metastatic, poorly immunogenic, and immune suppression prevents T cell activation in the tumor microenvironment. We developed a microbial-based immunotherapeutic concept for selective delivery of a highly immunogenic tetanus toxoid protein (TT856-1313), into tumor cells by attenuatedListeria monocytogenes, and reactivation of pre-existing TT-specific memory T cells (generated during childhood) to kill infected tumor cells. Thus, TT here functions as an alternative for neoantigens. Treatment of KPC mice withListeria-TT resulted in TT accumulation in tumors and inside tumor cells, and attraction of predominantly TT-specific memory CD4 T cells. Moreover, gemcitabine (GEM) combined withListeria-TTsignificantly improved the migration of CD4 T cells into tumors and the production of perforin and granzyme B, turning cold tumors into immunological hot tumors.In vivodepletion of T cells in Listeria-TT+GEM-treated mice demonstrated CD4 T cell-mediated eradication of tumors and metastases (Mann-Whitney p<0.05). In addition, peritumoral lymph node like structures (LNS) were observed in close contact with the pancreatic tumors displaying CD4 T cells and CD8 T cells of KPC mice treated withListeria-TT orListeria-TT+GEM. The production of perforin and granzyme B was observed in LNS of KPC mice that receivedListeria-TT+GEM. This combination not only reduced tumor burden (80%) and metastases (87%) significantly (p<0.05, Mann-Whitney), but also improved the survival time of KPC mice with advanced pancreatic cancer substantially (Mantel-Cox p<0.0001). Our results unveil new mechanisms ofListeriaand GEM improving immunotherapy for PDAC.
A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer
Authors: Lee Brian H. , Kelly Geoffrey , Bradford Shermineh , Davila Melanie , Guo Xinzheng V. , Amir El-ad David , Thrash Emily M. , Solga Michael D. , Lannigan Joanne , Sellers Brian , Candia Julian , Tsang John , Montgomery Ruth R. , Tamaki Stanley J. , Sigdel Tara K. , Sarwal Minnie M. , Lanier Lewis L. , Tian Yuan , Kim Cheryl , Hinz Denise , Peters Bjoern , Sette Alessandro , Rahman Adeeb H. 
Published: April 2019

AbstractMass cytometry is a powerful tool for high dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. Fluidigm’s 3rd-generation Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median signal intensities and higher coefficients of variation in antibody expression. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multi-site study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces inter-instrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multi-center studies.
Loss of Ku’s DNA end binding activity affects telomere length via destabilizing telomere-bound Est1 rather than altering TLC1 homeostasis
Authors: Lemon Laramie D. , Morris Danna K. , Bertuch Alison A. 
Published: April 2019

ABSTRACTSaccharomyces cerevisiaetelomerase, which maintains telomere length, is comprised of an RNA component, TLC1, the reverse transcriptase, Est2, and regulatory subunits, including Est1. The Yku70/Yku80 (Ku) heterodimer, a DNA end binding (DEB) protein, also contributes to telomere length maintenance. Ku binds TLC1 and telomere ends in a mutually exclusive fashion, and is required to maintain levels and nuclear localization of TLC1. Ku also interacts with Sir4, which localizes to telomeres. Here we sought to determine the role of Ku’s DEB activity in telomere length maintenance by utilizingyku70-R456Emutant strains, in which Ku has reduced DEB and telomere association but proficiency in TLC1 and Sir4 binding, and TLC1 nuclear retention. Telomere lengths in ayku70-R456Estrain were nearly as short as those inykuΔstrains and shorter than in strains lacking either Sir4, Ku:Sir4 interaction, or Ku:TLC1 interaction. TLC1 levels were decreased in theyku70-R456Emutant, yet overexpression of TLC1 failed to restore telomere length. Reduced DEB activity did not impact Est1’s ability to associate with telomerase but did result in decreased association of Est1 with the telomere. These findings suggest Ku’s DEB activity maintains telomere length homeostasis by preserving Est1’s interaction at the telomere rather than altering TLC1 levels.
DeeplyTough: Learning Structural Comparison of Protein Binding Sites
Authors: Simonovsky Martin , Meyers Joshua 
Published: April 2019

AbstractMotivationProtein binding site comparison (pocket matching) is of importance in drug discovery. Identification of similar binding sites can help guide efforts for hit finding, understanding polypharmacology and characterization of protein function. The design of pocket matching methods has traditionally involved much intuition, and has employed a broad variety of algorithms and representations of the input protein structures. We regard the high heterogeneity of past work and the recent availability of large-scale benchmarks as an indicator that a data-driven approach may provide a new perspective.ResultsWe propose DeeplyTough, a convolutional neural network that encodes a three-dimensional representation of protein binding sites into descriptor vectors that may be compared efficiently in an alignment-free manner by computing pairwise Euclidean distances. The network is trained with supervision: (i) to provide similar pockets with similar descriptors, (ii) to separate the descriptors of dissimilar pockets by a minimum margin, and (iii) to achieve robustness to nuisance variations. We evaluate our method using three large-scale benchmark datasets, on which it demonstrates excellent performance for held-out data coming from the training distribution and competitive performance when the trained network is required to generalize to datasets constructed independently.Availabilityhttps://github.com/BenevolentAI/DeeplyToughContactmartin.simonovsky@enpc.fr,joshua.meyers@benevolent.ai
Separate domains of G3BP promote efficient clustering of alphavirus replication complexes and recruitment of the translation initiation machinery
Authors: Götte Benjamin , Panas Marc D , Hellström Kirsi , Liu Lifeng , Samreen Baila , Larsson Ola , Ahola Tero , McInerney Gerald M 
Published: April 2019

AbstractG3BP-1 and -2 (hereafter referred to as G3BP) are multifunctional RNA-binding proteins involved in stress granule (SG) assembly. Viruses from diverse families target G3BP for recruitment to replication or transcription complexes in order to block SG assembly but also to acquire pro-viral effects via other unknown functions of G3BP. The Old World alphaviruses, including Semliki Forest virus (SFV) and chikungunya virus (CHIKV) recruit G3BP into viral replication complexes, via an interaction between FGDF motifs in the C-terminus of the viral non-structural protein 3 (nsP3) and the NTF2-like domain of G3BP. To study potential proviral roles of G3BP, we used human osteosarcoma (U2OS) cell lines lacking endogenous G3BP generated using CRISPR-Cas9 and reconstituted with a panel of G3BP1 mutants and truncation variants. While SFV replicated with varying efficiency in all cell lines, CHIKV could only replicate in cells expressing G3BP1 variants containing both the NTF2-like and the RGG domains. The ability of SFV to replicate in the absence of G3BP allowed us to study effects of different domains of the protein. We used immunoprecipitation to demonstrate that that both NTF2- like and RGG domains are necessary for the formation a complex between nsP3, G3BP1 and the 40S ribosomal subunit. Electron microscopy of SFV-infected cells revealed that formation of nsP3:G3BP1 complexes via the NTF2-like domain was necessary for clustering of cytopathic vacuoles (CPVs) and that the presence of the RGG domain was necessary for accumulation of electron dense material containing G3BP1 and nsP3 surrounding the CPV clusters. Clustered CPVs also exhibited localised high levels of translation of viral mRNAs as detected by ribopuromycylation staining. These data confirm that G3BP is a ribosomal binding protein and reveal that alphaviral nsP3 uses G3BP to concentrate viral replication complexes and to recruit the translation initiation machinery, promoting the efficient translation of viral mRNAs.
ERASE: Extended Randomization for assessment of annotation enrichment in ASE datasets
Authors: D’Sa Karishma , Reynolds Regina H. , Guelfi Sebastian , Zhang David , Ruiz Sonia Garcia ,   International Parkinson’s Disease Genomics Consortium (IPDGC),   System Genomics of Parkinson’s Disease (SGPD), Hardy John , Gagliano Taliun Sarah A. , Small Kerrin S. , Ryten Mina , Botía Juan A. 
Published: April 2019

AbstractGenome-wide association studies (GWAS) have identified thousands of genetic variants associated with various human phenotypes and many of these loci are thought to act at a molecular level by regulating gene expression. Detection of allele specific expression (ASE), namely preferential usage of an allele at a transcribed locus, is an increasingly important means of studying the genetic regulation of gene expression. However, there are currently a paucity of tools available to link ASE sites with GWAS risk loci. Existing integration methods first use ASE sites to infer cis-acting expression quantitative trait loci (eQTL) and then apply eQTL-based approaches. ERASE is a method that assesses the enrichment of risk loci amongst ASE sites directly. Furthermore, ERASE enables additional biological insights to be made through the addition of other SNP level annotations. ERASE is based on a randomization approach and controls for read depth, a significant confounder in ASE analyses. In this paper, we demonstrate that ERASE can efficiently detect the enrichment of eQTLs and risk loci within ASE data and that it remains sensitive even when used with underpowered GWAS datasets. Finally, using ERASE in combination with GWAS data for Parkinson’s disease and data on the splicing potential of individual SNPs, we provide evidence to suggest that risk loci for Parkinson’s disease are enriched amongst ASEs likely to affect splicing. Thus, we show that ERASE is an important new tool for the integration of ASE and GWAS data, capable of providing novel insights into the pathophysiology of complex diseases.
The Role of CD147 in Leukocyte Aggregation in Liver Injury
Authors: Yee Christine , Main Nathan , Terry Alexandra , Stevanovski Igor , Maczurek Annette , Morgan Alison J. , Calabro Sarah , Potter Alison J. , Iemma Tina L. , Bowen David G. , Ahlenstiel Golo , Warner Fiona J. , McCaughan Geoffrey W. , McLennan Susan V. , Shackel Nicholas A. 
Published: April 2019

AbstractBackgroundChronic inflammation is the driver of liver injury resulting in progressive fibrosis and eventual cirrhosis. The consequences include both liver failure and liver cancer. We have previously described increased expression of the highly multifunctional glycoprotein CD147 in liver injury. This work describes a novel role of CD147 in liver inflammation and the importance of leukocyte aggregates in determining the extent of liver injury.MethodsNon-diseased, progressive injury and cirrhotic liver from humans and mice were examined using mAb targeting CD147. Inflammatory cell subsets were assessed by multicolor flow cytometry.ResultsIn liver injury, we observe abundant intrahepatic leukocyte clusters defined as ≥5 adjacent CD45+cells which we have labelled “leukocyte aggregates”. We have shown that these leukocyte aggregates are significant in determining the extent of liver injury. If CD147 is blockedin vivo,these leukocyte aggregates diminish in size and number together with a marked significant reduction in liver injury including fibrosis. This accompanied by no change in overall intrahepatic leukocyte numbers. Further, blocking aggregation formation occurs prior to an appreciable increase in inflammatory markers or fibrosis. Additionally, there were no observed, “off-target” or unpredicted effects in targeting CD147.ConclusionCD147 mediates leukocyte aggregation which is associated with the development of liver injury. This is not a secondary effect, but a cause of injury as aggregate formation proceeds other markers of injury. Leukocyte aggregation has been previously described in inflammation dating back over many decades but till now been shown to determine the extent of injury.
Isolation of persisters enabled by ß-lactam-induced filamentation reveals their single-cell awakening characteristics
Authors: Windels Etthel M. , Meriem Zacchari Ben , Zahir Taiyeb , Verstrepen Kevin J. , Hersen Pascal , Van den Bergh Bram , Michiels Jan 
Published: April 2019

AbstractWhen exposed to lethal doses of antibiotics, bacterial populations are most often not completely eradicated. A small number of phenotypic variants, defined as ‘persisters’, are refractory to antibiotics and survive treatment. Despite their involvement in relapsing infections caused by major pathogens, processes determining phenotypic switches from and to the persister state largely remain elusive. This is mainly due to the low frequency of persisters in a population and the lack of reliable persistence markers, both hampering studies of persistence at the single-cell level. Problematically, existing methods to enrich for persisters result in samples with very low persister densities and/or a too high abundance of other cell types. Here we present a novel and highly effective persister isolation method involving cephalexin, an antibiotic that induces extensive filamentation of susceptible cells. We show that antibiotic-tolerant cells can easily be separated by size after a short cephalexin treatment, and that the isolated cells are genuine persisters. We used our isolation method to monitor persister outgrowth at the single-cell level in a microfluidic device, thereby conclusively demonstrating that awakening is a stochastic phenomenon. We anticipate that our novel approach can have far-reaching consequences in the persistence field, by allowing single-cell studies at a much higher throughput than previously reported.
Optical induction of autophagy viaTranscription factor EB(TFEB) reduces pathological tau in neurons
Authors: Binder JL , Deretic V , Weick JP , Bhaskar K 
Published: April 2019

AbstractAggregation and accumulation of microtubule associated protein tau in neurons is major neuropathological hallmark of Alzheimer’s disease (AD) and related tauopathies. Attempts have been made to promote clearance of pathological tau (p-Tau) from neurons via autophagy. Over expression of transcription factor EB (TFEB), has shown to clear pTau from neurons via autophagy. However, sustained TFEB activation and/or autophagy can create burden on cellular bioenergetics and can be deleterious. Thus, we engineered a minimally invasive optical system that could transiently alter autophagic flux. We optimized and tested an optogenetic gene expression system derived from a previously engineered bacterial transcription factor, EL222. For the first time, our group utilized this system not only to spatial-temporally control nuclear TFEB expression, we also show light-induced TFEB has the capacity to reduce p-Tau burden in AD patient-derived human iPSC-neurons. Together, these results suggest that optically-regulatable gene expression of TFEB unlocks opto-therapeutics to treat AD and other dementias.