bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chagas disease serological test performance in United States blood donor specimens
Authors: Whitman Jeffrey D. , Bulman Christina A. , Gunderson Emma L. , Irish Amanda M. , Townsend Rebecca L. , Stramer Susan L. , Sakanari Judy A. , Bern Caryn 
Published: August 2019

ABSTRACTBackgroundChagas disease affects an estimated 300,000 individuals in the US. Diagnosis in the chronic phase requires positive results by two different IgG serological tests. Three ELISAs (Hemagen, Ortho, Wiener) and one rapid test (InBios) are FDA-cleared, but comparative data in US populations are sparse.MethodsWe evaluated 500 seropositive and 300 seronegative blood donor plasma samples. Country of birth was known for 255 seropositive specimens and grouped into regions: Mexico (n=94), Central America (n=88) and South America (n=73). Specimens were tested by the four FDA-cleared IgG serological assays. Test performance was evaluated by two comparators and latent class analysis.ResultsInBios had the highest sensitivity (97.4-99.3%), but lowest specificity (87.5-92.3%). Hemagen had the lowest sensitivity (88.0-92.0%), but high specificity (99.0-100.0%). Sensitivity was intermediate for Ortho (92.4-96.5%) and Wiener (94.0-97.1%); both had high specificity (98.8-100.0% and 96.7-99.3%, respectively). Antibody reactivity and clinical sensitivity was lowest in donors from Mexico, intermediate in those from Central America and highest in those from South America.ConclusionsOur findings provide an initial evidence base to improve laboratory diagnosis of Chagas disease in the US. The best current testing algorithm would employ a high sensitivity screening test followed by a high specificity confirmatory test.
Efficient CRISPR/Cas9 gene ablation in uncultured naïve mouse T cells for in vivo studies
Authors: Nüssing Simone , House Imran G. , Kearney Conor J. , Vervoort Stephin J. , Beavis Paul A. , Oliaro Jane , Johnstone Ricky W. , Trapani Joseph A. , Parish Ian A. 
Published: August 2019

AbstractCRISPR/Cas9 technologies have revolutionised our understanding of gene function in complex biological settings, including T cell immunology. Current CRISPR-mediated gene deletion strategies in T cells require in vitro stimulation or culture that can both preclude studies of gene function within unmanipulated naïve T cells and can alter subsequent differentiation. Here we demonstrate highly efficient gene deletion within uncultured primary naïve murine CD8+ T cells by electroporation of recombinant Cas9/sgRNA ribonucleoprotein immediately prior to in vivo adoptive transfer. Using this approach, we generated single and double gene knock-out cells within multiple mouse infection models. Strikingly, gene deletion occurred even when the transferred cells were left in a naïve state, suggesting that gene deletion occurs independent of T cell activation. This protocol thus expands CRISPR-based probing of gene function beyond models of robust T cell activation, to encompass both naïve T cell homeostasis and models of weak activation, such as tolerance and tumour models.
Conidial melanin of the human pathogenic fungusAspergillus fumigatusdisrupts cell autonomous defenses in amoebae
Authors: Ferling Iuliia , Dunn Joe Dan , Ferling Alexander , Soldati Thierry , Hillmann Falk 
Published: August 2019

AbstractThe human pathogenic fungusAspergillus fumigatusis a ubiquitous saprophyte that causes fatal infections in immunocompromised individuals. Following inhalation, conidia are ingested by innate immune cells and can arrest phagolysosome maturation. How such general virulence traits could have been selected for in natural environments is unknown. Here, we used the model amoebaDictyostelium discoideumto follow the antagonistic interaction ofA. fumigatusconidia with environmental phagocytes in real time. We found that conidia covered with the green pigment 1,8-dihydroxynaphthalene-(DHN)-melanin were internalized at far lower rates when compared to those lacking the pigment, despite high rates of initial attachment. Immediately after uptake of the fungal conidia, nascent phagosomes were formed through sequential membrane fusion and fission events. Using single-cell assays supported by a computational model integrating the differential dynamics of internalization and phagolysosome maturation, we could show that acidification of phagolysosomes was transient and was followed by neutralization and, finally, exocytosis of the conidium. For unpigmented conidia, the cycle was completed in less than 1 h, while the process was delayed for conidia covered with DHN-melanin. At later stages of infection, damage to infected phagocytes triggered the ESCRT membrane repair machinery, whose recruitment was also attenuated by DHN-melanin, favoring prolonged persistence and the establishment of an intracellular germination niche in this environmental phagocyte. Increased exposure of DHN-melanin on the conidial surface also improved fungal survival when confronted with the fungivorous predatorProtostelium aurantium, demonstrating its universal antiphagocytic properties.
Population genomics of the widespread African savannah treesAfzelia africanaandAfzelia quanzensis(Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges
Authors: Donkpegan Armel S.L. , Piñeiro Rosalía , Heuertz Myriam , Duminil Jérôme , Daïnou Kasso , Doucet Jean-Louis , Hardy Olivier J. 
Published: August 2019

ABSTRACTFew studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region).Afzelia(Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs:A. africanain the Sudanian region andA. quanzensisin the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241A. africanaand 113A. quanzensisindividuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30A. africanaand 12A. quanzensisindividuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005and −0.007andbLd (SNP)= −0.008and −0.006 forA. africanaandA. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.
Natural genetic variation underlying tiller development in barley (Hordeum vulgareL)
Authors: Haaning Allison M. , Smith Kevin P. , Brown-Guedira Gina L. , Chao Shiaoman , Tyagi Priyanka , Muehlbauer Gary J. 
Published: August 2019

ABSTRACTIn barley (Hordeum vulgareL.), lateral branches called tillers contribute to grain yield and define shoot architecture, but genetic control of tiller number and developmental rate are not well characterized. The primary objectives of this work were to examine relationships between tiller number and other agronomic and morphological traits and identify natural genetic variation associated with tiller number and rate, and related traits. We grew 768 lines from the USDA National Small Grain Core Collection in the field and collected data over two years for tiller number and rate, and agronomic and morphological traits. Our results confirmed that spike row-type and days to heading are correlated with tiller number, and as much as 28% of tiller number variance is attributed to these traits. In addition, negative correlations between tiller number and leaf width and stem diameter were observed, indicating trade-offs between tiller development and other vegetative growth. Thirty-three quantitative trait loci (QTL) were associated with tiller number or rate. Of these, 40% overlapped QTL associated with days to heading and 22% overlapped QTL associated with spike row-type, further supporting that tiller development is influenced by these traits. Despite this, some QTL associated with tiller number or rate, including the major QTL on chromosome 3H, were not associated with any other traits, suggesting that tiller number can be modified independently of other important agronomic traits. These results enhance our knowledge of the genetic control of tiller development in barley, which is important for optimizing tiller number and rate for yield improvement.
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
Authors: Wang Shu , Lin Jia-Ren , Sontag Eduardo D. , Sorger Peter K. 
Published: August 2019

AbstractThe goal of many single-cell studies on eukaryotic cells is to gain insight into the biochemical reactions that control cell fate and state. In this paper we introduce the concept of effective stoichiometric space (ESS) to guide the reconstruction of biochemical networks from multiplexed, fixed time-point, single-cell data. In contrast to methods based solely on statistical models of data, the ESS method leverages the power of the geometric theory of toric varieties to begin unraveling the structure of chemical reaction networks (CRN). This application of toric theory enables a data-driven mapping of covariance relationships in single cell measurements into stoichiometric information, one in which each cell subpopulation has its associated ESS interpreted in terms of CRN theory. In the development of ESS we reframe certain aspects of the theory of CRN to better match data analysis. As an application of our approach we process cytomery- and image-based single-cell datasets and identify differences in cells treated with kinase inhibitors. Our approach is directly applicable to data acquired using readily accessible experimental methods such as Fluorescence Activated Cell Sorting (FACS) and multiplex immunofluorescence.Author summaryWe introduce a new notion, which we call the effective stoichiometric space (ESS), that elucidates network structure from the covariances of single-cell multiplexed data. The ESS approach differs from methods that are based on purely statistical models of data: it allows a completely new and data-driven translation of the theory of toric varieties in geometry and specifically their role in chemical reaction networks (CRN). In the process, we reframe certain aspects of the theory of CRN. As illustrations of our approach, we find stoichiometry in different single-cell datasets, and pinpoint dose-dependence of network perturbations in drug-treated cells.
Immunomodulatory activity of Momordica charantia L. (Cucurbitaceae) leaf diethyl ether and methanol extracts on Salmonella typhi infected mice and LPS-induced phagocytic activities of macrophages and neutrophils
Authors: Mahamat Oumar , Flora Hakoueu N. , Christopher Tume , Albert Kamanyi 
Published: August 2019

AbstractInfections due to salmonella strains constitute one of the major health problems in humans, particularly in Africa. Use of traditional herbs has proven effective in reducing the incidence of infection in some high-risk groups. To assess the effects of Momordica charantia leaf extracts that influence blood infestation, in vitro study of the effect on macrophages and neutrophils, and treatment of mouse model of S. typhi infection was done. Methanol and diethyl ether extracts were concerned by this study. In vitro study was to assess the effects of extracts on phagocytosis and related intracellular killing mechanisms of macrophages were examined. Later, mobilization of leukocytes and production of antibodies against S. typhi were measured followed by quantitating cultures evaluation of the blood infestation of orally inoculated mice with S. thyphi. Ingestion or attachment of carbon particles, production of superoxide anion, nitric oxide and that of lysosomal acid phosphatase by macrophages and neutrophils were significantly increased by methanol and diethyl extracts at concentrations ranging from 40 μg/ml to 640 μg/ml. Antibody titer and mobilization of leukocytes, particularly lymphocytes against S. typhi were highly increased by both methanol and diethyl extracts at concentrations of 500 and 1000 mg/kg. In the same the extracts have reduced the rate of blood infestation in mice inoculated with 108 CFU of S. typhi for 28 days. Reduction in blood infestation rates was similar for levamisole mice group. Results of this study should prove useful of leave of Momordica charantia for treatment of infections by salmonella strains and for assessment of drugs for therapeutic intervention.
Mechanical reinforcement of protein L fromFinegoldia magnapoints to a new bind-and-search mechanism
Authors: Dahal Narayan R. , Nowitzke Joel , Eis Annie , Popa Ionel 
Published: August 2019

AbstractSeveral significant bacterial pathogens in humans secrete surface proteins that bind antibodies in order to protect themselves from the adaptive immune response and have evolved to operate under the mechanical sheer generated by mucus flow, coughing or urination. Protein L is secreted byFinegoldia magnaand has several antibody-binding domains. These domains have two antibody-binding sites with vastly different avidity and the function of the second weaker binding interface is currently unknown. Here we use magnetic tweezers and covalent attachment via HaloTag and SpyTag to expose Protein L to unfolding forces in the absence and presence of antibody-ligands. We find that antibody binding increases the mechanical stability of protein L. Using the change in mechanical stability as a binding reporter, we determined that the low-avidity binding site is acting as a mechano-sensor. We propose a novel mechanism where the high-avidity binding site engages the tether, while the low-avidity binding site acts as a mechano-sensor, allowing bacteria to sample the antibody surface concentration and localize its search during successful binding under strain.SignificanceIt is well known that bacteria have an arsenal of tools to invade and to avoid dislocation. Based on the molecular response of a protein used by anaerobic bacteria to attach to antibodies and disrupt the immune system, here we report on a force-sensor-like behavior, triggered by antibody clusters and force. This pseudo-catch bond between bacteria and antibodies is activated through a second binding site which has lower avidity to antibodies, and which acts as a mechanical sensor, potentially regulating the search radii of the bacterium. Understanding of the bacteria attachment mechanism is of great importance toward developing new antibiotics and mechano-active drugs.
Heritable gene expression variability governs clonal heterogeneity in circadian period
Authors: Nikhil K.L. , Korge Sandra , Achim Kramer 
Published: August 2019

ABSTRACTA ubiquitous feature of circadian clocks across life forms is its organization as a network of coupled cellular oscillators. Individual cellular oscillators of the network often exhibit a considerable degree of heterogeneity in their intrinsic periods. While the interaction of coupling and heterogeneity in circadian clock networks is hypothesized to influence clock’s entrainability, our knowledge of mechanisms governing network heterogeneity remains elusive. In this study, we aimed to explore the principles that underlie inter-cellular period variation in circadian clock networks (clonal period-heterogeneity). To this end, we employed a laboratory selection approach and derived a panel of 25 clonal cell populations exhibiting circadian periods ranging from 22 h to 28 h. We report that while a single parent clone can produce progeny clones with a wide distribution of circadian periods, heterogeneity is not entirely stochastically driven but has a strong heritable component. By quantifying the expression of 20 circadian clock and clock-associated genes across our panel, we found that inheritance of different expression patterns in at least three clock genes might govern clonal period-heterogeneity in circadian clock networks. Furthermore, we provide preliminary evidence suggesting that epigenetic variation might underlie such gene expression variation.
Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes
Authors: Garg Sriram G. , Kapust Nils , Lin Weili , Tria Fernando D. K. , Nelson-Sathi Shijulal , Gould Sven B. , Fan Lu , Zhu Ruixin , Zhang Chuanlun , Martin William F. 
Published: August 2019

SummaryMetagenomic studies have claimed the existence of novel lineages with unprecedented properties never before observed in prokaryotes. Such lineages include Asgard archaea1–3, which are purported to represent archaea with eukaryotic cell complexity, and the Candidate Phyla Radiation (CPR), a novel domain level taxon erected solely on the basis of metagenomic data4. However, it has escaped the attention of most biologists that these metagenomic sequences are not assembled into genomes by sequence overlap, as for cultured archaea and bacteria. Instead, short contigs are sorted into computer files by a process called binning in which they receive taxonomic assignment on the basis of sequence properties like GC content, dinucleotide frequencies, and stoichiometric co-occurrence across samples. Consequently, they are not genome sequences as we know them, reflecting the gene content of real organisms. Rather they are metagenome assembled genomes (MAGs). Debates that Asgard data are contaminated with individual eukaryotic sequences5–7are overshadowed by the more pressing issue that no evidence exists to indicate that any sequences in binned Asgard MAGs actually stem from the same chromosome, as opposed to simply stemming from the same environment. Here we show that Asgard and CPR MAGs fail spectacularly to meet the most basic phylogenetic criterion8fulfilled by genome sequences of all cultured prokaryotes investigated to date: the ribosomal proteins of Asgard and CPR MAGs do not share common evolutionary histories. Their phylogenetic behavior is anomalous to a degree never observed with genomes of real organisms. CPR and Asgard MAGs are binning artefacts, assembled from environments where up to 90% of the DNA is from dead cells9–12. Asgard and CPR MAGs are unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning.
Does Vision Extract Absolute Distance from Vergence?
Authors: Linton Paul 
Published: August 2019

AbstractSince Kepler (1604) and Descartes (1638), ‘vergence’ (the angular rotation of the eyes) has been thought of as one of our most important absolute distance cues. But vergence has never been tested as an absolute distance cue divorced from obvious confounding cues such as binocular disparity. In this article we control for these confounding cues for the first time by gradually manipulating vergence, and find that observers fail to accurately judge distance from vergence. We consider a number of different interpretations of these results, and argue that the most principled response to these results is to question the general effectiveness of vergence as an absolute distance cue. Given other absolute distance cues (such as motion parallax and vertical disparities) are limited in application, this poses a real challenge to our contemporary understanding of visual scale.
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations
Authors: Pietrek Lisa M. , Stelzl Lukas S. , Hummer Gerhard 
Published: August 2019

AbstractIntrinsically disordered proteins (IDPs) constitute a large fraction of the human proteome and are critical in the regulation of cellular processes. A detailed understanding of the conformational dynamics of IDPs could help to elucidate their roles in health and disease. However the inherent flexibility of IDPs makes structural studies and their interpretation challenging. Molecular dynamics (MD) simulations could address this challenge in principle, but inaccuracies in the simulation models and the need for long simulations have stymied progress. To overcome these limitations, we adopt an hierarchical approach that builds on the “flexible meccano” model of Bernadó et al. (J. Am. Chem. Soc. 2005, 127, 17968-17969). First, we exhaustively sample small IDP fragments in all-atom simulations to capture local structure. Then, we assemble the fragments into full-length IDPs to explore the stereochemically possible global structures of IDPs. The resulting ensembles of three-dimensional structures of full-length IDPs are highly diverse, much more so than in standard MD simulation. For the paradigmatic IDPα-synuclein, our ensemble captures both local structure, as probed by nuclear magnetic resonance (NMR) spectroscopy, and its overall dimension, as obtained from small-angle X-ray scattering (SAXS) in solution. By generating representative and meaningful starting ensembles, we can begin to exploit the massive parallelism afforded by current and future high-performance computing resources for atomic-resolution characterization of IDPs.
CRISPR-Cas systems in the plant pathogenXanthomonasspp. and their impact on genome plasticity
Authors: Martins Paula Maria Moreira , da Silva Xavier Andre , Takita Marco Aurelio , Alfemas-Zerbini Poliane , de Souza Alessandra Alves 
Published: August 2019

AbstractXanthomonasis one of the most important bacterial genera of plant pathogens causing economic losses in crop production worldwide. Despite its importance, many aspects of basicXanthomonasbiology remain unknown or understudied. Here, we present the first genus-wide analysis of CRISPR-Cas inXanthomonasand describe specific aspects of its occurrence. Our results show thatXanthomonasgenomes harbour subtype I-C and I-F CRISPR-Cas systems and that species belonging to distantlyXanthomonas-related genera inXanthomonadaceaeexhibit the same configuration of coexistence of the I-C and I-F CRISPR subtypes. Additionally, phylogenetic analysis using Cas proteins indicated that the CRISPR systems present inXanthomonasspp. are the result of an ancient acquisition. Despite the close phylogeny of these systems, they present significant variation in both the number and targets of spacers. An interesting characteristic observed in this study was that the identified plasmid-targeting spacers were always driven toward plasmids found in otherXanthomonasstrains, indicating that CRISPR-Cas systems could be very effective in coping with plasmidial infections. Since many effectors are plasmid encoded, CRISPR-Cas might be driving specific characteristics of plant-pathogen interactions.