bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elicitation of superinfection exclusion by p28 of turnip crinkle virus is separable from its replication function with mutations at specific amino acid residues
Authors: Guo Qin , Zhang Shaoyan , Sun Rong , Yao Xiaolong , Zhang Xiao-Feng , Tatineni Satyanarayana , Meulia Tea , Qu Feng 
Published: April 2019

ABSTRACTWe recently reported that the p28 auxiliary replication protein encoded by turnip crinkle virus (TCV) is also responsible for eliciting superinfection exclusion (SIE) against superinfecting TCV. However, it remains unresolved whether the replication function of p28 could be separated from its ability to elicit SIE. Here we report the identification of two single amino acid (aa) mutations that decouple these two functions. Using an Agrobacterium infiltration-based delivery system, we transiently expressed a series of p28 deletion and point mutants, and tested their ability to elicit SIE against a co-introduced TCV replicon. We found that substituting alanine (A) for valine (V) and phenylalanine (F) at p28 positions 181 and 182, respectively, modestly compromised SIE in transiently expressed p28 derivatives. Upon incorporation into TCV replicons, V181A and F182A decoupled TCV replication and SIE diametrically. While V181A impaired SIE without detectably compromising replication, F182A abolished TCV replication but had no effect on SIE once the replication of the defective replicon was restored through complementation. Both mutations diminished accumulation of p28 protein, suggesting that p28 must reach a concentration threshold in order to elicit a strong SIE. Importantly, the severe reduction of F182A protein levels correlated with a dramatic loss in the number of intracellular p28 foci formed by p28-p28 interactions. Together these findings not only decouples the replication and SIE functions of p28, but also unveils a concentration dependence for p28 coalescence and SIE elicitation. These data further highlight the role of p28 multimerization in driving the exclusion of secondary TCV infections.IMPORTANCESuperinfection exclusion (SIE) insulates virus-infected cells from subsequent invasion by the same or closely related viruses. SIE has been observed in both animal and plant virus-infected cells. Therefore, a thorough understanding of how SIE is achieved at the molecular level is expected to inspire novel strategies for combating virus infections in humans, animals, and plants. Our group has been using turnip crinkle virus (TCV) to elucidate the molecular interactions critical for SIE elicitation. The current study builds on the previous observation that TCV SIE is elicited by one single TCV-encoded protein (p28), and further identifies key regions and amino acids that are needed for SIE. We unravel key amino acid changes that decouple the replication and SIE functions of p28, and provides novel mechanistic insights of SIE.
A roadmap to mammalian oral microbiome evolution with dental calculus
Authors: Brealey Jaelle C. , Leitão Henrique G. , van der Valk Tom , Xu Wenbo , Bougiouri Katia , Dalén Love , Guschanski Katerina 
Published: April 2019

AbstractAnimals and their associated microbiomes share a long evolutionary history, influenced by a complex interplay between extrinsic environmental and intrinsic host factors. However, we know little about microbiome responses to long-lasting environmental and host-centred processes, which require studying microbiome changes through time. Here, we apply a temporal metagenomics approach to dental calculus, the calcified oral microbial biofilm. We establish dental calculus as a valuable tool for the study of host microbiome evolution by characterising the taxonomic and functional composition of the oral microbiome in a variety of wild mammals. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterise antibiotic resistance genes even before the advent of industrial antibiotic production, reconstruct components of the host diet and recover host genetic profiles. Our work demonstrates how dental calculus can be used in the future to study the evolution of oral microbiomes and pathogens, and the impact of anthropogenic changes on wildlife and the environment.
A new massively-parallel transposon mutagenesis approach comparing multiple datasets identifies novel mechanisms of action and resistance to triclosan
Authors: Yasir Muhammad , Turner A. Keith , Bastkowski Sarah , Page Andrew J. , Telatin Andrea , Phan Minh-Duy , Monahan Leigh G. , Darling Aaron E. , Webber Mark A. , Charles Ian G. 
Published: April 2019

AbstractThe mechanisms by which antimicrobials exert inhibitory effects against bacterial cells and by which bacteria display resistance vary under different conditions. Our understanding of the full complement of genes which can influence sensitivity to many antimicrobials is limited and often informed by experiments completed in a small set of exposure conditions. Capturing a broader suite of genes which contribute to survival under antimicrobial stress will improve our understanding of how antimicrobials work and how resistance can evolve. Here, we apply a new version of ‘TraDIS’ (Transposon Directed Insert Sequencing); a massively parallel transposon mutagenesis approach to identify different responses to the common biocide triclosan across a 125-fold range of concentrations. We have developed a new bioinformatic tool ‘AlbaTraDIS’ allowing both predictions of the impacts of individual transposon inserts on gene function to be made and comparisons across multiple TraDIS data sets. This new TraDIS approach allows essential genes as well as non-essential genes to be assayed for their contribution to bacterial survival and growth by modulating their expression. Our results demonstrate that different sets of genes are involved in survival following exposure to triclosan under a wide range of concentrations spanning bacteriostatic to bactericidal. The identified genes include those previously reported to have a role in triclosan resistance as well as a new set of genes not previously implicated in triclosan sensitivity. Amongst these novel genes are those involved in barrier function, small molecule uptake and integrity of transcription and translation. These data provide new insights into potential routes of triclosan entry and bactericidal mechanisms of action. Our data also helps to put recent work which has demonstrated the ubiquitous nature of triclosan in people and the built environment into context in terms of how different triclosan exposures may influence evolution of bacteria. We anticipate the approach we show here that allows comparisons across multiple experimental conditions of TraDIS data will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.
Influenza Classification from Short Reads with VAPOR Facilitates Robust Mapping Pipelines and Zoonotic Strain Detection for Routine Surveillance Applications
Authors: Southgate J. A. , Bull M. J. , Brown C. M. , Watkins J. , Corden S. , Southgate B. , Moore C. , Connor T. R. 
Published: April 2019

BackgroundInfluenza viruses are associated with a significant global public health burden. The segmented RNA genome of influenza changes continually due to mutation, and the accumulation of these changes within the antigenic recognition sites of haemagglutinin (HA) and neuraminidase (NA) in turn leads to annual epidemics. Influenza A is also zoonotic, allowing for exchange of segments between human and non-human viruses, resulting in new strains with pandemic potential. These processes necessitate a global surveillance system for influenza monitoring. To this end, whole-genome sequencing (WGS) has begun to emerge as a useful tool. However, due to the diversity and mutability of the influenza genome, and noise in short-read data, bioinformatics processing can present challenges.ResultsConventional mapping approaches can be insufficient when a sub-optimal reference strain is chosen. For short-read datasets simulated from influenza H1N1 HA sequences, read recovery after single-reference mapping was routinely as low as 90% for human-origin influenza sequences, and often lower than 10% for those from avian hosts. To this end, we developed adeBruijn Graph (DBG)-based classifier of influenza WGS datasets: VAPOR. In real data benchmarking using 257 WGS read sets with correspondingde novoassemblies, VAPOR provided classifications for all samples with a mean of >99.8% identity to assembled contigs. This resulted in an increase in the number of mapped reads by 6.8% on average, up to a maximum of 13.3%. Additionally, using simulations, we demonstrate that classification from reads may be applied to detection of reassorted strains.ConclusionsVAPOR has potential to simplify bioinformatics pipelines for surveillance, providing a novel method for detection of influenza strains of human and non-human origin directly from reads, minimization of potential data loss and bias associated with conventional mapping, and allowing visualization of alignments that would otherwise require slowde novoassembly. Whilst with expertise and time these pitfalls can largely be avoided, with pre-classification they are remedied in a single step. Furthermore, our algorithm could be adapted in future to surveillance of other RNA viruses. VAPOR is available athttps://github.com/connor-lab/vapor.
Computational design of a protein family that adopts two well-defined and structurally divergent de novo folds
Authors: Wei Kathy Y. , Moschidi Danai , Bick Matthew J. , Nerli Santrupti , McShan Andrew C. , Carter Lauren P. , Huang Po-Ssu , Fletcher Daniel A. , Sgourakis Nikolaos G. , Boyken Scott E. , Baker David 
Published: April 2019

AbstractThe plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used to de novo design proteins that fold to a single state with a deep free energy minima (Huang et al., 2016), and to reengineer natural proteins to alter their dynamics (Davey et al., 2017) or fold (Alexander et al., 2009), the de novo design of closely related sequences which adopt well-defined, but structurally divergent structures remains an outstanding challenge. Here, we design closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations -- one short (∼66 Å height) and the other long (∼100 Å height) -- reminiscent of the conformational transition of viral fusion proteins (Ivanovic et al., 2013; Podbilewicz, 2014; Skehel and Wiley, 2000). Crystallographic and NMR spectroscopic characterization show that both the short and long state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large scale conformational switches between structurally divergent forms.
Structure and Functional Binding Epitope of V-domain Ig Suppressor of T-cell Activation (VISTA)
Authors: Mehta Nishant , Maddineni Sainiteesh , Mathews Irimpan I. , Sperberg Andres Parra , Huang Po-Ssu , Cochran Jennifer R. 
Published: April 2019

AbstractV-domain Ig Suppressor of T cell Activation (VISTA) is an immune checkpoint protein that inhibits the T - cell response against cancer. Similar to PD-1 and CTLA-4, antibodies that block VISTA signaling can release the brakes of the immune system and promote tumor clearance. VISTA has an Ig-like fold, but little is known about its structure and mechanism of action. Here, we report a 1.85 Å crystal structure of the human VISTA extracellular domain and highlight structural features that make VISTA unique among B7 family members. Through fine-epitope mapping, we also identify solvent-exposed residues that underlie binding to a clinically relevant anti-VISTA antibody. This antibody-binding region is also shown to interact with V-set and Ig domain-containing 3 (VSIG3), the recently proposed functional binding partner of VISTA. The structure and functional epitope determined here will help guide future drug development efforts against this important checkpoint target.
Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin
Authors: Neparáczki Endre , Maróti Zoltán , Kalmár Tibor , Maár Kitti , Nagy István , Latinovics Dóra , Kustár Ágnes , Pálfi György , Molnár Erika , Marcsik Antónia , Balogh Csilla , Lőrinczy Gábor , Gál Szilárd Sándor , Tomka Péter , Kovacsóczy Bernadett , Kovács László , Raskó István , Török Tibor 
Published: April 2019

AbstractHun, Avar and conquering Hungarian nomadic groups arrived into the Carpathian Basin from the Eurasian Steppes and significantly influenced its political and ethnical landscape. In order to shed light on the genetic affinity of above groups we have determined Y chromosomal haplogroups and autosomal loci, from 49 individuals, supposed to represent military leaders. Haplogroups from the Hun-age are consistent with Xiongnu ancestry of European Huns. Most of the Avar-age individuals carry east Eurasian Y haplogroups typical for modern north-eastern Siberian and Buryat populations and their autosomal loci indicate mostly unmixed Asian characteristics. In contrast the conquering Hungarians seem to be a recently assembled population incorporating pure European, Asian and admixed components. Their heterogeneous paternal and maternal lineages indicate similar phylogeographic origin of males and females, derived from Central-Inner Asian and European Pontic Steppe sources. Composition of conquering Hungarian paternal lineages is very similar to that of Baskhirs, supporting historical sources that report identity of the two groups.
Brain imaging correlates of general intelligence in UK Biobank
Authors: Cox SR , Ritchie SJ , Fawns-Ritchie C , Tucker-Drob EM , Deary IJ 
Published: April 2019

AbstractThe associations between indices of brain structure and measured intelligence are not clear. In part, this is because the evidence to date comes from mostly small and heterogenous studies. Here, we report brain structure-intelligence associations on a large sample from the UK Biobank study. The overall N = 29,004, with N = 18,363 participants providing both brain MRI and cognitive data, and a minimum N = 7318 providing the MRI data alongside a complete four-test battery. Participants’ age range was 44-81 years (M = 63.13, SD = 7.48). A general factor of intelligence (g) was extracted from four varied cognitive tests, accounting for one third of the variance in the cognitive test scores. The association between (age-and sex-corrected) total brain volume and a latent factor of general intelligence is r = 0.275, 95% C.I. = [0.252, 0.299]. A model that incorporated multiple global measures of grey and white matter macro-and microstructure accounted for more than double the g variance in older participants compared to those in middle-age (13.4% and 5.9%, respectively). There were no sex differences in the magnitude of associations between g and total brain volume or other global aspects of brain structure. The largest brain regional correlates of g were volumes of the insula, frontal, anterior/superior and medial temporal, posterior and paracingulate, lateral occipital cortices, thalamic volume, and the white matter microstructure of thalamic and association fibres, and of the forceps minor.
The Long-run Effects of Secondary School Track Assignment
Authors: Borghans Lex , Diris Ron , Smits Wendy , de Vries Jannes 
Published: April 2019

AbstractThis study analyzes the long-run effects of secondary school track assignment for students at the achievement margin. Theoretically, track assignment maximizes individual outcomes when thresholds between tracks are set at the level of the indifferent student, and any other thresholds would imply that students at or around the margin are better off by switching tracks. We exploit non-linearities in the probability of track assignment across achievement to empirically identify the effect of track assignment on educational attainment and wages of students in the Netherlands, who can be assigned to four different tracks. We find that attending higher tracks leads to increases in years of schooling by around 1.5 years for students at the lowest and the highest choice margin, and wage gains of around 15% and 5%, respectively. Results at the margin of the two medium tracks show no effect on educational attainment, and decreases in wage of around 12% from attending the higher track. The negative returns for the medium margin and the relatively low returns for the higher margin (compared to the required educational investments) are partly mediated by motivation and study choice.
NF-YA Transcriptionally Activates the Expression of SOX2 in Cervical Cancer Stem Cells
Authors: Yang Wen-Ting , Zhao Zong-Xia , Li Bin , Zheng Peng-Sheng 
Published: April 2019

AbstractRoles for SOX2 have been extensively studied in several types of cancer, including colorectal cancer, glioblastoma and breast cancer, with particular emphasis placed on the roles of SOX2 in cancer stem cell. Our previous study identified SOX2 as a marker in cervical cancer stem cells driven by a full promoter element of SOX2 EGFP reporter. Here, dual-luciferase reporter and mutagenesis analyses were employed, identifying key cis-elements in the SOX2 promoter, including binding sites for SOX2, OCT4 and NF-YA factors in SOX2 promoter. Mutagenesis analysis provided additional evidence to show that one high affinity-binding domain CCAAT box was precisely recognized and bound by the transcription factor NF-YA. Furthermore, overexpression of NF-YA in primitive cervical cancer cells SiHa and C33A significantly activated the transcription and the protein expression of SOX2. Collectively, our data identified NF-YA box CCAAT as a key cis-element in the SOX2 promoter, suggesting that NF-YA is a potent cellular regulator in the maintenance of SOX2-positive cervical cancer stem cell by specific transcriptional activation of SOX2.
How the liver contributes to stomach warming in the endothermic white sharkCarcharodon carcharias
Authors: Bernvi David C. , Cliff Geremy 
Published: April 2019

BackgroundWhite sharks and other lamnids are able to elevate their stomach temperature. The ability to heat large amounts of food to the recorded levels of up to 17°C above the ambient water temperature can’t be explained only by the heat generated by catabolism and the endothermic adaptions of the suprahepatic rete. This rete has two shunts that regulates the volume of blood flowing from the liver to the sinus venosus, thereby providing a temperature control mechanism for the GIT. The liver’s function in this temperature regulation is unknown. White shark stomach volume is well above 135 l in sub-adults to accommodate large prey items, including marine mammals. The simultaneous ingestion of large volumes of cold water during feeding will result in marked cooling of the stomach. Our study investigated the role of the liver in relation to warming the gastro-intestinal tract and the retention of elevated core temperatures.Materials and methodsThe liver morphology and its position relative to the gastro-intestinal tract were investigated in 13 white sharksCarcharodon carcharias. Stomach volume and the thickness of the abdominal wall were also measured to give a comparative estimate of heat insulation by white muscles.ResultsIn all white sharks examined the two liver lobes completely enveloped the entire gastrointestinal tract, with the anterio-ventral margins of the liver almost interlocking around the stomach. A large, conspicuous, flattened vascular system was only present on the inner surfaces of both liver lobes. The thickness of the ventral abdominal body wall is only 12% of that of the dorso-lateral body wall, so the potential for heat loss from the GIT via the belly region is high.ConclusionOur study builds on the findings of other researchers which revealed that the liver and digestive tract receive a major portion of their blood supply through the suprahepatic rete, which is a heat exchanger aimed at retaining metabolic heat generated by the red locomotory muscles. This heat is not only transferred to the stomach via its supply of warm blood but also via thermal conduction from the vessels on the inside of the liver, which envelopes the digestive tract and serves as a large reservoir of venous blood. The liver is rich in lipids, with insulatory properties to retain the heat which would otherwise be rapidly lost through the extremely thin ventral abdominal wall in temperate waters, where white sharks commonly occur. These findings provide insight into the hitherto unknown role played by the liver in the highly elevated stomach temperatures reported, thereby providing this endothermic top predator with enhanced rates of digestion.
Bone regeneration in Ds-Red pig calvarial defect using allogenic transplantation of EGFP-pMSCs – a comparison of host cells and seeding cells in the scaffold
Authors: Hsieh Ming-Kai , Wu Chia-Jung , Su Xuan-Chun , Chen Yi-Chen , Tsai Tsung-Ting , Niu Chi-Chien , Lai Po-Liang , Wu Shinn-Chih 
Published: April 2019

AbstractBackgroundCells, scaffolds, and factors are the triad of regenerative engineering; however, it is difficult to distinguish whether cells in the regenerative construct are from the seeded cells or host cells via the host blood supply. We performed a novel in vivo study to transplant enhanced green fluorescent pig mesenchymal stem cells (EGFP-pMSCs) into calvarial defect of DsRed pigs. The cell distribution and proportion were distinguished by the different fluorescent colors through the whole regenerative period.Method/ResultsEight adult domestic Ds-Red pigs were treated with five modalities: empty defects without scaffold (group 1); defects ﬁlled only with scaffold (group 2); defects ﬁlled with osteoinduction medium-loaded scaffold (group 3); defects filled with 5 × 103 cells/scaffold (group 4); and defects filled with 5 × 104 cells/scaffold (group 5). The in vitro cell distribution, morphology, osteogenic differentiation, and ﬂuorescence images of groups 4 and 5 were analyzed. Two animals were sacriﬁced at 1, 2, 3, and 4 weeks after transplantation. The in vivo ﬂuorescence imaging and quantification data showed that EGFP-pMSCs were represented in the scaffolds in groups 4 and 5 throughout the whole regenerative period. A higher seeded cell density resulted in more sustained seeded cells in bone regeneration compared to a lower seeded cell density. Host cells were recruited by seeded cells if enough space was available in the scaffold. Host cells in groups 1 to 3 did not change from the 1st week to 4th week, which indicates that the scaffold without seeded cells cannot recruit host cells even when enough space is available for cell ingrowth. The histological and immunohistochemical data showed that more cells were involved in osteogenesis in scaffolds with seeded cells.ConclusionOur in vivo results showed that more seeded cells recruit more host cells and that both cell types participate in osteogenesis. These results suggest that scaffolds without seeded cells may not be effective in bone transplantation.