{"messages":[{"status":"ok","interval":"2020-03-01:2020-03-30","cursor":"5","count":100,"total":"1527"}], "collection":[{"preprint_doi":"10.1101\/793471","published_doi":"10.1111\/1462-2920.14968","published_journal":"Environmental Microbiology","preprint_platform":"bioRxiv","preprint_title":"The biogeography and biodiversity of endophytes--how far have we come and where do we go from here?","preprint_authors":"Harrison, J. G.; Griffin, E. A.","preprint_category":"ecology","preprint_date":"2019-10-09","published_date":"2020-03-02","preprint_abstract":"The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from [~]600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the seventeen biomes encompassed by our survey, seven were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.\n\nOriginality-Significance StatementMuch remains to be learned regarding the biodiversity and distribution of the microbes that colonize the interiors of plants. Here, we surveyed approximately 600 publications to characterize gaps in knowledge and provide a roadmap for future research. We compared biomes, plant families, and geographical regions in terms of the research interest that they have garnered. Additionally, we synthesized published results and report that variation in endophyte richness among plant tissue types is a function of host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. We hope to inspire research to fill the gaps in knowledge that we uncovered.","preprint_author_corresponding":"Joshua G Harrison","preprint_author_corresponding_institution":"University of Wyoming"},{"preprint_doi":"10.1101\/776609","published_doi":"10.1111\/eva.12939","published_journal":"Evolutionary Applications","preprint_platform":"bioRxiv","preprint_title":"Evaluating the Probability of CRISPR-based Gene Drive Contaminating Another Species","preprint_authors":"Courtier-Orgogozo, V.; Danchin, A.; Gouyon, P.-H.; Boete, C.","preprint_category":"genetics","preprint_date":"2019-09-19","published_date":"2020-03-02","preprint_abstract":"The probability D that a given CRISPR-based gene drive element contaminates another, non-target species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = (hyb+transf).express.cut.flank.immune.nonextinct with\\nhyb = probability of hybridization between the target species and a non-target species\\ntransf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a non-target species (with no hybridization)\\nexpress = probability that the Cas9 and guide RNA genes are expressed\\ncut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host\\nflank = probability that the gene drive cassette inserts at the cut site\\nimmune = probability that the immune system does not reject Cas9-expressing cells\\nnonextinct = probability of invasion of the drive within the population\\n\\n\\nWe discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.","preprint_author_corresponding":"Virginie  Courtier-Orgogozo","preprint_author_corresponding_institution":"Institut Jacques Monod \/ CNRS \/ Universite de Paris"},{"preprint_doi":"10.1101\/2020.01.14.906859","published_doi":"10.1002\/ecy.3029","published_journal":"Ecology","preprint_platform":"bioRxiv","preprint_title":"Species-specific, age-varying plant traits affect herbivore growth and survival","preprint_authors":"Yang, L. H.; Cenzer, M. L.; Morgan, L. J.; Hall, G. W.","preprint_category":"ecology","preprint_date":"2020-01-14","published_date":"2020-03-02","preprint_abstract":"Seasonal windows of opportunity represent intervals of time within a year during which organisms have improved prospects of achieving life history aims such as growth or reproduction, and may be commonly structured by temporal variation in abiotic factors, bottom-up factors, and top-down factors. Although seasonal windows of opportunity are likely to be common, few studies have examined the factors that structure seasonal windows of opportunity in time. Here, we experimentally manipulated host plant age in two milkweed species (Asclepias fascicularis and Asclepias speciosa) in order to investigate the role of plant species-specific and plant age-varying traits on the survival and growth of monarch caterpillars (Danaus plexippus). We show that the two plant species showed diverging trajectories of defense traits with increasing age. These species-specific and age-varying host plant traits significantly affected the growth and survival of monarch caterpillars through both resource quality- and resource quantity-based constraints. The effects of plant age on monarch developmental success were comparable to and sometimes larger than those of plant species identity. We conclude that species-specific and age-varying plant traits are likely to be important factors with the potential to structure seasonal windows of opportunity for monarch development, and examine the implications of these findings for both broader patterns in the ontogeny of plant defense traits and the specific ecology of milkweed-monarch interactions in a changing world.","preprint_author_corresponding":"Louie H. Yang","preprint_author_corresponding_institution":"University of California, Davis"},{"preprint_doi":"10.1101\/697409","published_doi":"10.1038\/s41598-020-60873-y","published_journal":"Scientific Reports","preprint_platform":"bioRxiv","preprint_title":"64-Channel Carbon Fiber Electrode Arrays for Chronic Electrophysiology","preprint_authors":"Guitchounts, G.; Cox, D. D.","preprint_category":"neuroscience","preprint_date":"2019-07-09","published_date":"2020-03-02","preprint_abstract":"A chief goal in neuroscience is to understand how neuronal activity relates to behavior, perception, and cognition. However, monitoring neuronal activity over long periods of time is technically challenging, and limited, in part, by the invasive nature of recording tools. While electrodes allow for recording in freely-behaving animals, they tend to be bulky and stiff, causing damage to the tissue they are implanted in. One solution to this invasiveness problem may be probes that are small enough to fly under the immune systems radar. Carbon fiber (CF) electrodes are thinner and more flexible than typical metal or silicon electrodes, but the arrays described in previous reports had low channel counts and required time-consuming manual assembly. Here we report the design of an expanded-channel-count carbon fiber electrode array (CFEA) as well as a method for fast preparation of the recording sites using acid etching and electroplating with PEDOT-TFB, and demonstrate the ability of the 64-channel CFEA to record from rat visual cortex. We include designs for interfacing the system with micro-drives or flex-PCB cables for recording from multiple brain regions, as well as a facilitated method for coating CFs with the insulator Parylene-C. High-channel-count CFEAs may thus be an alternative to traditional microwire-based electrodes and a practical tool for exploring the neural code.","preprint_author_corresponding":"Grigori  Guitchounts","preprint_author_corresponding_institution":"Harvard University"},{"preprint_doi":"10.1101\/2020.01.13.903906","published_doi":"10.1038\/s41598-020-60733-9","published_journal":"Scientific Reports","preprint_platform":"bioRxiv","preprint_title":"Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes","preprint_authors":"Mutte, S.; Weijers, D.","preprint_category":"evolutionary biology","preprint_date":"2020-01-14","published_date":"2020-03-02","preprint_abstract":"Protein oligomerization is a fundamental process to build complex functional modules. Domains that facilitate the oligomerization process are diverse and widespread in nature across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is functionally (relatively) well understood in the animal kingdom. However, beyond animals, neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. While PB1 domain proteins have been found in other kingdoms, including plants, it is unclear how these relate to animal PB1 proteins.\n\nTo address this question, we utilized large transcriptome datasets along with the proteomes of a broad range of species. We discovered eight PB1 domain-containing protein families in plants, along with three each in Protozoa and Chromista and four families in Fungi. Studying the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. Tertiary structural models of these plant PB1 families, combined with Random Forest based classification, indicated family-specific differences attributed to the length of PB1 domain and the proportion of {beta}-sheets.\n\nThis study identifies novel PB1 families and reveals considerable complexity in the protein oligomerization potential at the origin of eukaryotes. The newly identified relationships provide an evolutionary basis to understand the diverse functional interactions of key regulatory proteins carrying PB1 domains across eukaryotic life.","preprint_author_corresponding":"Dolf  Weijers","preprint_author_corresponding_institution":"Wageningen University"},{"preprint_doi":"10.1101\/2020.01.06.894147","published_doi":"10.1039\/D0LC00009D","published_journal":"Lab on a Chip","preprint_platform":"bioRxiv","preprint_title":"Low-cost microphysiological systems: Feasibility study of a tape-based barrier-on-chip system for small intestine modeling","preprint_authors":"Winkler, T. E.; Feil, M.; Stronkman, E. F.; Matthiesen, I.; Herland, A.","preprint_category":"bioengineering","preprint_date":"2020-01-06","published_date":"2020-03-02","preprint_abstract":"We see affordability as a key challenge in making organs-on-chips accessible to a wider range of users, particularly outside the highest-resource environments. Here, we present an approach to barrier-on-a-chip fabrication based on double-sided pressure-sensitive adhesive tape and off-the-shelf polycarbonate. Besides a low materials cost, common also to PDMS or thermoplastics, it requires minimal ({euro} 100) investment in laboratory equipment, yet at the same time is suitable for upscaling to industrial roll-to-roll manufacture. We evaluate our microhpysiological system with an epithelial (C2BBe1) barrier model of the small intestine, studying the biological effects of permeable support pore size, as well as stimulation with a common food compound (chili pepper-derived capsaicinoids). The cells form tight and continuous barrier layers inside our systems, with comparable permeability but superior epithelial polarization compared to Transwell culture, in line with other perfused microphysiological models. Permeable support pore size is shown to weakly impact barrier layer integrity as well as the metabolic cell profile. Capsaicinoid response proves distinct between culture systems, but we show that impacted metabolic pathways are partly conserved, and that cytoskeletal changes align with previous studies. Overall, our tape-based microphysiolgical system proves to be a robust and reproducible approach to studying physiological barriers, in spite of its low cost.","preprint_author_corresponding":"Thomas E Winkler","preprint_author_corresponding_institution":"Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden"},{"preprint_doi":"10.1101\/842831","published_doi":"10.1016\/j.cma.2020.112935","published_journal":"Computer Methods in Applied Mechanics and Engineering","preprint_platform":"bioRxiv","preprint_title":"Three-dimensional traction microscopy accounting for cell-induced matrix degradation","preprint_authors":"Song, D.; Seidl, D. T.; Oberai, A. A.","preprint_category":"biophysics","preprint_date":"2019-11-15","published_date":"2020-03-02","preprint_abstract":"Tractions exerted by cells on the extracellular matrix (ECM) are critical in many important physiological and pathological processes such as embryonic morpho-genesis, wound healing, and cancer metastasis. Three-dimensional Traction Microscopy (3DTM) is a tool to quantify cellular tractions by first measuring the displacement field in the ECM in response to these tractions, and then using this measurement to infer tractions. Most applications of 3DTM have assumed that the ECM has spatially-uniform mechanical properties, but cells secrete enzymes that can locally degrade the ECM. In this work, a novel computational method is developed to quantify both cellular tractions and ECM degradation. In particular, the ECM is modeled as a hyperelastic, Neo-Hookean solid, whose material parameters are corrupted by a single degradation parameter. The feasibility of determining both the traction and the degradation parameter is first demonstrated by showing the existence and uniqueness of the solution. An inverse problem is then formulated to determine the nodal values of the traction vector and the degradation parameter, with the objective of minimizing the difference between a predicted and measured displacement field, under the constraint that the predicted displacement field satisfies the equation of equilibrium. The inverse problem is solved by means of a gradient-based optimization approach, and the gradient is computed efficiently using appropriately derived adjoint fields. The computational method is validated in-silico using a geometrically accurate neuronal cell model and synthetic traction and degradation fields. It is found that the method accurately recovers both the traction and degradation fields. Moreover, it is found that neglecting ECM degradation can yield significant errors in traction measurements. Our method can extend the range of applicability of 3DTM.","preprint_author_corresponding":"Dawei  Song","preprint_author_corresponding_institution":"University of Southern California"},{"preprint_doi":"10.1101\/2020.01.27.921312","published_doi":"10.3390\/cancers12030577","published_journal":"Cancers","preprint_platform":"bioRxiv","preprint_title":"Testing of the survivin suppressant YM155 in a large panel of drug-resistant neuroblastoma cell lines","preprint_authors":"Michaelis, M.; Voges, Y.; Rothweiler, F.; Weipert, F.; Zhia-Amad, A.; Cinatl, J.; von Deimling, A.; Westermann, F.; Roedel, F.; Wass, M. N.; Cinatl, J.","preprint_category":"pharmacology and toxicology","preprint_date":"2020-01-28","published_date":"2020-03-02","preprint_abstract":"The survivin suppressant YM155 is a drug candidate for neuroblastoma. Here, we tested YM155 in 101 neuroblastoma cell lines (19 parental cell lines, 82 drug-adapted sublines). 77 cell lines displayed YM155 IC50s in the range of clinical YM155 concentrations. ABCB1 was an important determinant of YM155 resistance. The activity of the ABCB1 inhibitor zosuquidar ranged from being similar to that of the structurally different ABCB1 inhibitor verapamil to being 65-fold higher. ABCB1 sequence variations may be responsible for this, suggesting that the design of variant-specific ABCB1 inhibitors may be possible. Further, we showed that ABCC1 confers YM155 resistance. Previously, p53 depletion had resulted in decreased YM155 sensitivity. However, TP53-mutant cells were not generally less sensitive to YM155 than TP53 wild-type cells in this study. Finally, YM155 cross-resistance profiles differed between cells adapted to drugs as similar as cisplatin and carboplatin. In conclusion, the large cell line panel was necessary to reveal an unanticipated complexity of the YM155 response in neuroblastoma cell lines with acquired drug resistance. Novel findings include that ABCC1 mediates YM155 resistance and that YM155 cross-resistance profiles differ between cell lines adapted to drugs as similar as cisplatin and carboplatin.","preprint_author_corresponding":"Jindrich  Cinatl","preprint_author_corresponding_institution":"Klinikum der Goethe-Universitaet"},{"preprint_doi":"10.1101\/452250","published_doi":"10.1111\/evo.13946","published_journal":"Evolution","preprint_platform":"bioRxiv","preprint_title":"Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints","preprint_authors":"Kontopoulos, D. - G.; van Sebille, E.; Lange, M.; Yvon-Durocher, G.; Barraclough, T. G.; Pawar, S.","preprint_category":"evolutionary biology","preprint_date":"2018-10-25","published_date":"2020-03-02","preprint_abstract":"To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness-related traits to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can--at least partly--overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta-analysis of the thermal performance curves of growth rate of phytoplankton--a globally important functional group--, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak \"hotter-is-better\" constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.","preprint_author_corresponding":"Dimitrios - Georgios  Kontopoulos","preprint_author_corresponding_institution":"Department of Life Sciences, Imperial College London, Silwood Park"},{"preprint_doi":"10.1101\/804591","published_doi":"10.1038\/s41477-020-0613-7","published_journal":"Nature Plants","preprint_platform":"bioRxiv","preprint_title":"An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses","preprint_authors":"Radhakrishnan, G. V.; Keller, J.; Rich, M. K.; Vernie, T.; Mbadinga Mbadinga, D. L.; Vigneron, N.; Cottret, L.; San Clemente, H.; Libourel, C.; Cheemah, J.; Linde, A.-M.; Eklund, D. M.; Cheng, S.; Wong, G. K.-S.; Lagercrantz, U.; Li, F.-W.; Oldroyd, G. E.; Delaux, P.-M.","preprint_category":"plant biology","preprint_date":"2019-10-16","published_date":"2020-03-02","preprint_abstract":"Plants are the foundation of terrestrial ecosystems and their colonization of land was facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following that founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Through analysis of 271 transcriptomes and 122 plant genomes, we demonstrate that the common symbiosis signalling pathway controlling the association with arbuscular mycorrhizal fungi and with nitrogen-fixing bacteria specifically co-evolved with intracellular endosymbioses, including ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. In contrast, species forming exclusively extracellular symbioses like ectomycorrhizae or associations with cyanobacteria have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million years of plant diversification.","preprint_author_corresponding":"Pierre-Marc  Delaux","preprint_author_corresponding_institution":"LRSV, Universite de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France"},{"preprint_doi":"10.1101\/2020.01.15.907766","published_doi":"10.1038\/s41556-020-0472-5","published_journal":"Nature Cell Biology","preprint_platform":"bioRxiv","preprint_title":"Fast and efficient generation of knock-in human organoids using homology-independent CRISPR\/Cas9 precision genome editing","preprint_authors":"Artegiani, B.; Hendriks, D.; Beumer, J.; Kok, R.; Zheng, X.; Joore, I.; Chuva de Sousa Lopes, S.; van Zon, J.; Tans, S.; Clevers, H.","preprint_category":"cell biology","preprint_date":"2020-01-15","published_date":"2020-03-02","preprint_abstract":"CRISPR\/Cas9 technology has revolutionized genome editing and is applicable to the organoid field. However, precise integration of exogenous DNA sequences in human organoids awaits robust knock-in approaches. Here, we describe CRISPR\/Cas9-mediated Homology-independent Organoid Transgenesis (CRISPR-HOT), which allows efficient generation of knock-in human organoids representing different tissues. CRISPR-HOT avoids extensive cloning and outperforms homology directed repair (HDR) in achieving precise integration of exogenous DNA sequences at desired loci, without the necessity to inactivate TP53 in untransformed cells, previously used to increase HDR-mediated knock-in. CRISPR-HOT was employed to fluorescently tag and visualize subcellular structural molecules and to generate reporter lines for rare intestinal cell types. A double reporter labelling the mitotic spindle by tagged tubulin and the cell membrane by tagged E-cadherin uncovered modes of human hepatocyte division. Combining tubulin tagging with TP53 knock-out revealed TP53 involvement in controlling hepatocyte ploidy and mitotic spindle fidelity. CRISPR-HOT simplifies genome editing in human organoids.","preprint_author_corresponding":"Hans  Clevers","preprint_author_corresponding_institution":"Hubrecht Institute"},{"preprint_doi":"10.1101\/682955","published_doi":"10.1038\/s41559-020-1125-6","published_journal":"Nature Ecology & Evolution","preprint_platform":"bioRxiv","preprint_title":"A hydrogen dependent geochemical analogue of primordial carbon and energy metabolism","preprint_authors":"Preiner, M.; Igarashi, K.; Muchowska, K. B.; Yu, M.; Varma, S. J.; Kleinermanns, K.; Nobu, M. K.; Kamagata, Y.; Tu\u0308ysu\u0308z, H.; Moran, J.; Martin, W. F.","preprint_category":"evolutionary biology","preprint_date":"2019-06-27","published_date":"2020-03-02","preprint_abstract":"Hydrogen gas, H2, is generated in alkaline hydrothermal vents from reactions of iron containing minerals with water during a geological process called serpentinization. It has been a source of electrons and energy since there was liquid water on the early Earth, and it fuelled early anaerobic ecosystems in the Earths crust1-3. H2 is the electron donor for the most ancient route of biological CO2 fixation, the acetyl-CoA (or Wood-Ljungdahl) pathway, which unlike any other autotrophic pathway simultaneously supplies three key requirements for life: reduced carbon in the form of acetyl groups, electrons in the form of reduced ferredoxin, and ion gradients for energy conservation in the form of ATP4,5. The pathway is linear, not cyclic, it releases energy rather than requiring energy input, its enzymes are replete with primordial metal cofactors6,7, it traces to the last universal common ancestor8 and abiotic, geochemical organic syntheses resembling segments of the pathway occur in hydrothermal vents today9,10. Laboratory simulations of the acetyl-CoA pathways reactions include the nonenzymatic synthesis of thioesters from CO and methylsulfide11, the synthesis of acetate12 and pyruvate13 from CO2 using native iron or external electrochemical potentials14 as the electron source. However, a full abiotic analogue of the acetyl-CoA pathway from H2 and CO2 as it occurs in life has not been reported to date. Here we show that three hydrothermal minerals -- awaruite (Ni3Fe), magnetite (Fe3O4) and greigite (Fe3S4) -- catalyse the fixation of CO2 with H2 at 100 {degrees}C under alkaline aqueous conditions. The product spectrum includes formate (100 mM), acetate (100 M), pyruvate (10 M), methanol (100 M), and methane. With these simple catalysts, the overall exergonic reaction of the acetyl-CoA pathway is facile, shedding light on both the geochemical origin of microbial metabolism and on the nature of abiotic formate and methane synthesis in modern hydrothermal vents.","preprint_author_corresponding":"William F Martin","preprint_author_corresponding_institution":"Institute for Molecular Evolution, Heinrich-Heine-University"},{"preprint_doi":"10.1101\/697573","published_doi":"10.1038\/s41564-020-0673-5","published_journal":"Nature Microbiology","preprint_platform":"bioRxiv","preprint_title":"Inflammasome-mediated antagonism of type I interferon enhances Rickettsia pathogenesis","preprint_authors":"Burke, T. P.; Engstro\u0308m, P.; Chavez, R. A.; Fonbuena, J. A.; Vance, R. E.; Welch, M. D.","preprint_category":"immunology","preprint_date":"2019-07-11","published_date":"2020-03-02","preprint_abstract":"Inflammasomes and interferons constitute two critical arms of innate immunity. Most facultative bacterial pathogens that inhabit the host cell cytosol avoid activating inflammasomes and are often resistant to killing by type I interferon (IFN-I). We report that the human pathogen Rickettsia parkeri, an obligate intracellular pathogen that resides in the cytosol, is sensitive to IFN-I. The mechanism of IFN-I-dependent restriction requires the transcription factor IRF5, which upregulates anti-rickettsial factors including guanylate-binding proteins and iNOS. However, R. parkeri curtails cGAS-dependent IFN-I production by causing caspase-11-dependent pyroptosis. In vivo, inflammasome activation antagonizes IFN-I production, enhancing R. parkeri abundance in the spleen. Mice lacking either IFN-I or IFN-{gamma} signaling are resistant to infection, but mice lacking both rapidly succumb, revealing that both interferons are required to control R. parkeri. This study illuminates how an obligate cytosolic pathogen exploits the intrinsic trade-off between cell death and cytokine production to escape killing by innate immunity.\\n\\nHighlightsO_LIRickettsia killed by GBPs activates caspase-11 and GSDMD, promoting pyroptosis\\nC_LIO_LIRickettsia exploits pyroptosis to avoid cGAS-dependent type I interferon\\nC_LIO_LIIRF5, GBPs, and iNOS contribute to controlling R. parkeri infection\\nC_LIO_LIIfnar-\/-Ifngr-\/- mice succumb to infection, uncovering a mouse model to study R. parkeri\\nC_LI","preprint_author_corresponding":"Matthew D Welch","preprint_author_corresponding_institution":"University of California, Berkeley"},{"preprint_doi":"10.1101\/519660","published_doi":"10.1038\/s41592-020-0748-5","published_journal":"Nature Methods","preprint_platform":"bioRxiv","preprint_title":"TooManyCells identifies and visualizes relationships of single-cell clades","preprint_authors":"Schwartz, G. W.; Petrovic, J.; Fasolino, M.; Zhou, Y.; Cai, S.; Xu, L.; Pear, W. S.; Vahedi, G.; Faryabi, R. B.","preprint_category":"bioinformatics","preprint_date":"2019-01-13","published_date":"2020-03-02","preprint_abstract":"Transcriptional programs contribute to phenotypic and functional cell states. While elucidation of cell state heterogeneity and its role in biology and pathobiology has been advanced by studying single cell level measurements, the underlying assumptions of current analytical methods limit the identification and exploration of cell clades. Unlike other methods, which produce a single uni-layer partition of cells ignoring echelons of cell states, we present TooManyCells, a software consisting of a suite of graph-based tools for efficient, global, and unbiased identification and visualization of cell clades while maintaining and presenting the relationship between cell states. TooManyCells provides a set of tools based on a matrix-free efficient divisive hierarchical spectral clustering algorithm wholly different from the prevalent Louvain-based methods. BirchBeer, the visualization component of TooManyCells, introduces a new approach for single cell analysis that is built on a concept intentionally orthogonal to the widely used dimensionality reduction methods. Together, this suite of tools provide a paradigm shift in the analysis and interpretation of single cell data by enabling simultaneous comparisons of cell states at context-and application-dependent scales. A byproduct of this shift is the immediate detection and visualization of rare populations that outperforms previous algorithms as demonstrated by applying these tools to existing single cell RNA-seq data sets from various mouse organs.","preprint_author_corresponding":"Robert B Faryabi","preprint_author_corresponding_institution":"Department of Pathology and Laboratory Medicine, University of Pennsylvania"},{"preprint_doi":"10.1101\/869370","published_doi":"10.1099\/mgen.0.000339","published_journal":"Microbial Genomics","preprint_platform":"bioRxiv","preprint_title":"Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive","preprint_authors":"Wyres, K. L.; Cahill, S. M.; Holt, K. E.; Hall, R. M.; Kenyon, J. J.","preprint_category":"microbiology","preprint_date":"2019-12-10","published_date":"2020-03-02","preprint_abstract":"Multiply antibiotic resistant Acinetobacter baumannii infections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological marker. The outer core (OC) of lipooligosaccharide also exhibits variation. To take better advantage of the untapped information available in whole genome sequences, we have created a curated reference database of the 92 publicly available gene clusters at the locus encoding proteins responsible for biosynthesis and export of CPS (K locus), and a second database for the 12 gene clusters at the locus for outer core biosynthesis (OC locus). Each entry has been assigned a unique KL or OCL number, and is fully annotated using a simple, transparent and standardised nomenclature. These databases are compatible with Kaptive, a tool for in silico typing of bacterial surface polysaccharide loci, and their utility was validated using a) >630 assembled A. baumannii draft genomes for which the KL and OCL regions had been previously typed manually, and b) 3386 A. baumannii genome assemblies downloaded from NCBI. Among the previously typed genomes, Kaptive was able to confidently assign KL and OCL types with 100% accuracy. Among the genomes retrieved from NCBI, Kaptive detected known KL and OCL in 87% and 90% of genomes, respectively indicating that the majority of common KL and OCL types are captured within the databases; 13 KL were not detected in any public genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multi-locus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the two predominant globally-distributed clones, ST1 of GC1 and ST2 of GC2, and in collections of other clones comprising >20 isolates each (ST10, ST25, and ST140), indicating extensive within-clone replacement of these loci. The databases are available at https:\/\/github.com\/katholt\/Kaptive and will be updated as further locus types become available.\n\nData Summary1. Databases including fully annotated gene cluster sequences for A. baumannii K loci and OC loci are available for download at https:\/\/github.com\/katholt\/Kaptive\n\n2. The Kaptive software, which can be used to screen new genomes against the K and O locus database is available at https:\/\/github.com\/katholt\/Kaptive (command-line code) and http:\/\/kaptive.holtlab.net\/ (interactive web service).\n\n3. Details of the Kaptive search results validating in silico serotyping of K and O loci using our approach are provided as supplementary files, Dataset 1 (92 KL reference sequences and 12 OCL reference sequences), Dataset 2 (642 genomes assembled from reads available in NCBI SRA) and Dataset 3 (3415 genome assemblies downloaded from NCBI GenBank).\n\nImpact statementThe ability to identify and track closely related isolates is key to understanding, and ultimately controlling, the spread of multiply antibiotic resistant A. baumannii causing difficult to treat infections, which are an urgent public health threat. Extensive variation in the KL and OCL gene clusters responsible for biosynthesis of capsule and the outer core of lipooligosaccharide, respectively, are potentially highly informative epidemiological markers. However, clear, well-documented identification of each variant and simple-to-use tools and procedures are needed to reliably identify them in genome sequence data. Here, we present curated databases compatible with the available web-based and command-line Kaptive tool to make KL and OCL typing readily accessible to assist epidemiological surveillance of this species. As many bacteriophage recognise specific properties of the capsule and attach to it, capsule typing is also important in assessing the potential of specific phage for therapy on a case by case basis.","preprint_author_corresponding":"Johanna J Kenyon","preprint_author_corresponding_institution":"Queensland University of Technology"},{"preprint_doi":"10.1101\/612390","published_doi":"10.1371\/journal.pmed.1003031","published_journal":"PLOS Medicine","preprint_platform":"bioRxiv","preprint_title":"Adverse childhood experiences: associations with educational attainment and adolescent health, and the role of family and socioeconomic factors. Analysis of a prospective cohort study.","preprint_authors":"Houtepen, L.; Heron, J.; Suderman, M.; Fraser, A.; Chittleborough, C. R.; Howe, L.","preprint_category":"epidemiology","preprint_date":"2019-04-19","published_date":"2020-03-02","preprint_abstract":"BackgroundExperiencing multiple adverse childhood experiences (ACE) is a risk factor for many adverse outcomes. However, the role of family and socioeconomic factors in these associations is often overlooked.\\n\\nMethods and findingsUsing data from the Avon Longitudinal Study of Parents and Children, we assess associations of ACE between birth and 16 years (sexual, physical or emotional abuse, emotional neglect, parental substance abuse, parental mental illness or suicide attempt, violence between parents, parental separation, bullying, and parental criminal conviction) with educational attainment at 16 years (n=9,959) and health at age 17 years (depression, obesity, harmful alcohol use, smoking and illicit drug use, n=4,917). We explore the extent to which associations are robust to adjustment for family and socioeconomic factors, whether associations differ according to socioeconomic factors, and estimate the proportion of adverse educational and health outcomes attributable to ACE, family or socioeconomic measures.\\n\\nThere were strong associations of ACE with lower educational attainment and higher risk of depression, drug use and smoking. Associations with educational attainment attenuated after adjustment but remained strong. Associations with depression, drug use and smoking were not altered by adjustment. Associations of ACE with harmful alcohol use and obesity were weak. We found no evidence that associations differed by socioeconomic factors. Between 5-15% of the cases of adverse educational and health outcomes occur amongst people experiencing 4+ ACE, and between 1-19% occur in people whose mothers have a low level of education.\\n\\nConclusionsThis study demonstrates strong associations between ACE and lower educational attainment and worse health that are independent of family and socioeconomic factors. Our findings imply that interventions that focus solely on ACE or solely on socioeconomic deprivation, whilst beneficial, would miss most cases of adverse educational and health outcomes. Intervention strategies should therefore target a wide range of relevant factors, including ACE, socioeconomic deprivation, parental substance use and mental health.","preprint_author_corresponding":"Laura  Howe","preprint_author_corresponding_institution":"University of Bristol"},{"preprint_doi":"10.1101\/871426","published_doi":"10.1371\/journal.pone.0226860","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"Voluntary wheel running has no impact on brain and liver mitochondrial DNA copy number or mutation measures in the PolG mouse model of aging","preprint_authors":"Maclaine, K. D.; Stebbings, K. A.; Llano, D. A.; Rhodes, J. S.","preprint_category":"cell biology","preprint_date":"2019-12-10","published_date":"2020-03-02","preprint_abstract":"The mitochondrial theory of aging attributes much of the aging process to mitochondrial DNA damage. The PolGAD257A\/D257A (PolG) mutant mouse was created to explore the mitochondrial theory of aging and carries a mutated proofreading region of polymerase gamma, which exclusively transcribes the mitochondrial genome. As a result, PolG mice accumulate mitochondrial DNA (mtDNA) mutations which leads to premature aging including hair loss, weight loss, kyphosis, increased rates of apoptosis, organ damage, and eventually, an early death at around 12 months. Exercise has been reported to decrease skeletal muscle mtDNA mutations and normalize protein levels in PolG mice. However, brain mtDNA changes with exercise in PolG mice have not been explored. We found no effects of exercise on mtDNA mutations or copy number in brain or liver in PolG mice, despite effects on body mass. Our results suggest that mitochondrial mutations play little role in exercise-brain interactions in the PolG model of accelerated aging. In addition to evaluating the effect of exercise on mtDNA outcomes, we also implemented novel methods for mtDNA extraction and measuring mtDNA mutations to improve efficiency and accuracy.","preprint_author_corresponding":"Justin  S  Rhodes","preprint_author_corresponding_institution":"University of Illinois at Urbana-Champaign"},{"preprint_doi":"10.1101\/768929","published_doi":"10.1371\/journal.pone.0223030","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"Discontinuous transcription of ribosomal DNA in human cells","preprint_authors":"Smirnov, E.; Trosan, P.; de Sousa Cabral, J. V.; Studeny, P.; Kerei\u0308che, S.; Jirsova, K.; Cmarko, D.","preprint_category":"cell biology","preprint_date":"2019-09-16","published_date":"2020-03-02","preprint_abstract":"Numerous studies show that various genes in all kinds of organisms are transcribed discontinuously, i.e. in short bursts or pulses with periods of inactivity between them. But it remains unclear whether ribosomal DNA (rDNA), represented by multiple copies in every cell, is also expressed in such manner. In this work, we synchronized the pol I activity in the populations of tumour derived as well as normal human cells by cold block and release. Then using special software for analysis of the microscopic images, we measured the intensity of transcription signal revealed by incorporated 5-fluorouridine (FU) in the nucleoli at different time points after the release. We found that the ribosomal genes in the human cells are transcribed discontinuously with periods ranging from 45 min to 75 min. Our data indicate that the dynamics of rDNA transcription follows the undulating pattern, in which the bursts are alternated by periods of rare transcription events.","preprint_author_corresponding":"Eugene  Smirnov","preprint_author_corresponding_institution":"Univerzita Karlova 1 lekarska fakulta"},{"preprint_doi":"10.1101\/714311","published_doi":"10.1371\/journal.pbio.3000625","published_journal":"PLOS Biology","preprint_platform":"bioRxiv","preprint_title":"Drifting codes within a stable coding scheme for working memory","preprint_authors":"Wolff, M. J.; Jochim, J.; Akyurek, E. G.; Buschman, T. J.; Stokes, M. G.","preprint_category":"neuroscience","preprint_date":"2019-07-25","published_date":"2020-03-02","preprint_abstract":"Working memory (WM) is important to maintain information over short time periods to provide some stability in a constantly changing environment. However, brain activity is inherently dynamic, raising a challenge for maintaining stable mental states. To investigate the relationship between WM stability and neural dynamics, we used electroencephalography to measure the neural response to impulse stimuli during a WM delay. Multivariate pattern analysis revealed representations were both stable and dynamic: there was a clear difference in neural states between time-specific impulse responses, reflecting dynamic changes, yet the coding scheme for memorized orientations was stable. This suggests that a stable subcomponent in WM enables stable maintenance within a dynamic system. A stable coding scheme simplifies readout for WM-guided behaviour, whereas the low-dimensional dynamic component could provide additional temporal information. Despite having a stable subspace, WM is clearly not perfect - memory performance still degrades over time. Indeed, we find that even within the stable coding scheme, memories drift during maintenance. When averaged across trials, such drift contributes to the width of the error distribution.","preprint_author_corresponding":"Michael J. Wolff","preprint_author_corresponding_institution":"University of Oxford"},{"preprint_doi":"10.1101\/723387","published_doi":"10.1371\/journal.pntd.0007675","published_journal":"PLOS Neglected Tropical Diseases","preprint_platform":"bioRxiv","preprint_title":"Polarized Lung Inflammation and Tie2\/Angiopoietin-Mediated Endothelial Dysfunction during Severe Orientia tsutsugamushi Infection","preprint_authors":"Trent, B.; Liang, Y.; Xing, Y.; Esqueda, M.; Wei, Y.; Cho, N.-H.; Kim, H.-I.; Kim, Y.-S.; Shelite, T.; Cai, J.; Sun, J.; Bouyer, D.; Liu, J.; Soong, L.","preprint_category":"microbiology","preprint_date":"2019-08-02","published_date":"2020-03-02","preprint_abstract":"Orientia tsutsugamushi infection can cause acute lung injury and high mortality in humans; however, the underlying mechanisms are unclear. Here, we tested a hypothesis that dysregulated pulmonary inflammation and Tie2-mediated endothelial malfunction contribute to lung damage. Using a murine model of lethal O. tsutsugamushi infection, we demonstrated pathological characteristics of vascular activation and tissue damage: 1) a significant increase of ICAM-1, VEGFR2, and angiopoietin-2 (Ang2) proteins in inflamed tissues and lung-derived endothelial cells (EC), 2) a progressive loss of endothelial quiescent and junction proteins (Ang1, VE-cadherin\/CD144, occuludin), and 3) a profound impairment of Tie2 receptor at the transcriptional and functional levels. In vitro infection of primary human EC cultures and serum Ang2 proteins in scrub typhus patients support our animal studies, implying endothelial dysfunction in severe scrub typhus. Flow cytometric analyses of lung-recovered cells further revealed that pulmonary macrophages (M{Phi}) were polarized toward an M1-like phenotype (CD80+CD64+CD11b+Ly6G-) during the onset of disease and prior to host death, which correlated with the significant loss of CD31+CD45- ECs and M2-like (CD206+CD64+CD11b+Ly6G-) cells. In vitro studies indicated extensive bacterial replication in M2-type, but not M1-type, M{Phi}s, implying the protective and pathogenic roles of M1-skewed responses. This is the first detailed investigation of lung cellular immune responses during acute O. tsutsugamushi infection. It uncovers specific biomarkers for vascular dysfunction and M1-skewed inflammatory responses, highlighting future therapeutic research for the control of this neglected tropical disease.\\n\\nAuthor SummaryScrub typhus is a life-threatening disease, infecting an estimated one million people yearly. Acute lung injury is the most common clinical observation; however, its pathogenic biomarkers and mechanisms of progression remain unknown. Here, we used a lethal infection mouse model that parallels certain aspects of severe scrub typhus, primary human endothelial cell cultures, and patient sera to define pathogenic biomarkers following Orientia tsutsugamushi infections. We found a significant increase in the levels of endothelial activation\/stress markers (angiopoietins and ICAM-1) in infected mouse lungs and in patient sera, but a progressive loss of endothelium-specific Tie2 receptor and junction proteins (VE-cadherin), at severe stages of disease. These signs of vasculature disruption positively correlated with the timing and magnitude of recruitment\/activation of proinflammatory M{Phi} subsets in infected lungs. Bacterial growth in vitro was favored in M2-like, but not in M1-like, M{Phi}s. This study, for the first time, reveals endothelial malfunction and dysregulated inflammatory responses, suggesting potential therapeutic targets to ameliorate tissue damage and pathogenesis.","preprint_author_corresponding":"Lynn  Soong","preprint_author_corresponding_institution":"University of Texas Medical Branch"},{"preprint_doi":"10.1101\/415687","published_doi":"10.1371\/journal.pcbi.1007605","published_journal":"PLOS Computational Biology","preprint_platform":"bioRxiv","preprint_title":"Interplay scenarios between CatSper and CaV channels in sea urchin sperm flagellum signaling cascades triggered by egg peptides: a mathematical modelling approach","preprint_authors":"Priego-Espinosa, D. A.; Darszon, A.; Guerrero, A.; Gonzalez-Cota, A. L.; Nishigaki, T.; Martinez-Mekler, G.; Carneiro, J.","preprint_category":"developmental biology","preprint_date":"2018-09-13","published_date":"2020-03-02","preprint_abstract":"Intracellular calcium ([Ca2+]i) is a basic, versatile and ubiquitous cellular signal controlling a wide variety of biological processes. A remarkable example is the steering of sea urchin spermatozoa towards the conspecific egg by a spatially and temporally orchestrated series of cytosolic [Ca2+]i spikes. Although this process has been an experimental paradigm for reproduction and sperm chemotaxis studies, the composition and regulation of the signalling network underlying the cytosolic calcium fluctuations are hitherto not fully understood. Here, we used a differential equations model of the signalling network to assess which set of channels can explain the characteristic envelop and temporal organisation of the [Ca2+]i-spike trains. The signalling network comprises an initial membrane hyperpolarisation\/repolarisation produced by an upstream module triggered by the egg-released chemoattractant peptide, via receptor activation, cGMP synthesis and decay. Followed by downstream modules leading to pHi, voltage and [Ca2+]i fluctuations. The upstream module outputs were fitted to kinetic data on cGMP activity and early membrane potential changes measured in bulk cell populations. Two candidate modules featuring voltage-dependent Ca2+-channels link these outputs to the downstream dynamics and can independently explain the typical decaying envelop and the progressive spacing of the spikes. In the first module, [Ca2+]i-spike trains require the concerted action of a classical CaV-like channel and a potassium channel, BK (Slo1), whereas the second module relies on pHi-dependent, [Ca2+]i-inactivated CatSper dynamics alone. The model predicts that these two modules interfere with each other and produce unreasonable dynamics when present at similar proportions, which suggests that one may predominate over the other in vivo. To assess these alternatives, several quantitative predictions were derived from each module and confronted to experimental observations. We show that the [Ca2+]I dynamics observed experimentally after sustained alkalinisation can be reproduced by a model featuring the CatSper module but not by one including the pH-independent CaV and BK module. We conclude in favour of the module containing CatSper.","preprint_author_corresponding":"Jorge  Carneiro","preprint_author_corresponding_institution":"Instituto Gulbenkian de Ci\u00eancia"},{"preprint_doi":"10.1101\/519116","published_doi":"10.1371\/journal.pcbi.1007630","published_journal":"PLOS Computational Biology","preprint_platform":"bioRxiv","preprint_title":"Characterizing and inferring epistasis via direct evolutionary couplings in models of allostery","preprint_authors":"Bravi, B.; Ravasio, R.; Brito, C.; Wyart, M.","preprint_category":"biophysics","preprint_date":"2019-01-13","published_date":"2020-03-02","preprint_abstract":"In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such al-losteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well mutation costs but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in agreement with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects.\\n\\nAuthor summaryAllostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy and we propose neural networks as more promising tool to measure epistasis.","preprint_author_corresponding":"Barbara  Bravi","preprint_author_corresponding_institution":"Ecole Polytechnique Federale de Lausanne"},{"preprint_doi":"10.1101\/639864","published_doi":"10.1371\/journal.pgen.1008198","published_journal":"PLOS Genetics","preprint_platform":"bioRxiv","preprint_title":"Bayesian network analysis complements Mendelian randomization approaches for exploratory analysis of causal relationships in complex data","preprint_authors":"Howey, R.; Shin, S.-Y.; Relton, C.; Davey Smith, G.; Cordell, H. J.","preprint_category":"genetics","preprint_date":"2019-05-15","published_date":"2020-03-02","preprint_abstract":"Mendelian randomization (MR) implemented through instrumental variables analysis is an increasingly popular causal inference tool used in genetic epidemiology. But it can have limitations for evaluating simultaneous causal relationships in complex data sets that include, for example, multiple genetic predictors and multiple potential risk factors associated with the same genetic variant. Here we use real and simulated data to investigate Bayesian network analysis (BN) with the incorporation of directed arcs, representing genetic anchors, as an alternative approach. A Bayesian network describes the conditional dependencies\/independencies of variables using a graphical model (a directed acyclic graph) with an accompanying joint probability. In real data, we found BN could be used to infer simultaneous causal relationships that confirmed the individual causal relationships suggested by bi-directional MR, while allowing for the existence of potential horizontal pleiotropy (that would violate MR assumptions). In simulated data, BN with two directional anchors (mimicking genetic instruments) had greater power for a fixed type 1 error than bi-directional MR, while BN with a single directional anchor performed better than or as well as bi-directional MR. Both BN and MR could be adversely affected by violations of their underlying assumptions (such as genetic confounding due to unmeasured horizontal pleiotropy). BN with no directional anchor generated inference that was no better than by chance, emphasizing the importance of directional anchors in BN (as in MR). Under highly pleiotropic simulated scenarios, BN outperformed both MR (and its recent extensions) and two recently-proposed alternative approaches: a multi-SNP mediation intersection-union test (SMUT) and a latent causal variable (LCV) test. We conclude that BN incorporating genetic anchors is a useful complementary method to conventional MR for exploring causal relationships in complex data sets such as those generated from modern \"omics\" technologies\n\nAuthor summaryMendelian randomization (MR) is a popular method for inferring causal relationships between variables (such as between an intermediate biological factor and a disease outcome). However, MR relies on a number of assumptions that may be hard to verify, and it is not ideally suited to comparing different underlying causal scenarios. Here we propose the use of an alternative approach, Bayesian network analysis (BN), as a complementary tool to conventional MR. We use real and simulated data to investigate the performance of MR, BN and several other recently-proposed methods, and find that BN performs as well as, or better than, the other methods, particularly under complex scenarios. We conclude that BN is a useful complementary approach to conventional MR for exploring causal relationships in complex data sets.","preprint_author_corresponding":"Heather  J  Cordell","preprint_author_corresponding_institution":"Newcastle University"},{"preprint_doi":"10.1101\/581520","published_doi":"10.1371\/journal.pbio.3000207","published_journal":"PLOS Biology","preprint_platform":"bioRxiv","preprint_title":"Asymmetric sampling in human auditory cortex reveals spectral processing hierarchy","preprint_authors":"Giroud, J.; Trebuchon, A.; Scho\u0308n, D.; Marquis, P.; Liegeois-Chauvel, C.; Poeppel, D.; Morillon, B.","preprint_category":"neuroscience","preprint_date":"2019-03-18","published_date":"2020-03-02","preprint_abstract":"Speech perception is mediated by both left and right auditory cortices, but with differential sensitivity to specific acoustic information contained in the speech signal. A detailed description of this functional asymmetry is missing, and the underlying models are widely debated. We analyzed cortical responses from 96 epilepsy patients with electrode implantation in left or right primary, secondary, and\/or association auditory cortex. We presented short acoustic transients to reveal the stereotyped spectro-spatial oscillatory response profile of the auditory cortical hierarchy. We show remarkably similar bimodal spectral response profiles in left and right primary and secondary regions, with preferred processing modes in the theta ([~]4-8 Hz) and low gamma ([~]25-50 Hz) ranges. These results highlight that the human auditory system employs a two-timescale processing mode. Beyond these first cortical levels of auditory processing, a hemispheric asymmetry emerged, with delta and beta band ([~]3\/15 Hz) responsivity prevailing in the right hemisphere and theta and gamma band ([~]6\/40 Hz) activity in the left. These intracranial data provide a more fine-grained and nuanced characterization of cortical auditory processing in the two hemispheres, shedding light on the neural dynamics that potentially shape auditory and speech processing at different levels of the cortical hierarchy.\\n\\nAuthor summarySpeech processing is now known to be distributed across the two hemispheres, but the origin and function of lateralization continues to be vigorously debated. The asymmetric sampling in time (AST) hypothesis predicts that (1) the auditory system employs a two-timescales processing mode, (2) present in both hemispheres but with a different ratio of fast and slow timescales, (3) that emerges outside of primary cortical regions. Capitalizing on intracranial data from 96 epileptic patients we sensitively validated each of these predictions and provide a precise estimate of the processing timescales. In particular, we reveal that asymmetric sampling in associative areas is subtended by distinct two-timescales processing modes. Overall, our results shed light on the neurofunctional architecture of cortical auditory processing.","preprint_author_corresponding":"Benjamin  Morillon","preprint_author_corresponding_institution":"Aix-Marseille University"},{"preprint_doi":"10.1101\/641217","published_doi":"10.1371\/journal.ppat.1008278","published_journal":"PLOS Pathogens","preprint_platform":"bioRxiv","preprint_title":"Antibiotic interactions shape short-term evolution of resistance in  E. faecalis","preprint_authors":"Dean, Z.; Maltas, J.; Wood, K. B.","preprint_category":"evolutionary biology","preprint_date":"2019-05-17","published_date":"2020-03-02","preprint_abstract":"Antibiotic combinations are increasingly used to combat bacterial infections. Multidrug therapies are a particularly important treatment option for E. faecalis, an opportunistic pathogen that contributes to high-inoculum infections such as infective endocarditis. While numerous synergistic drug combinations for E. faecalis have been identified, much less is known about how different combinations impact the rate of resistance evolution. In this work, we use high-throughput laboratory evolution experiments to quantify adaptation in growth rate and drug resistance of E. faecalis exposed to drug combinations exhibiting different classes of interactions, ranging from synergistic to suppressive. We identify a wide range of evolutionary behavior, including both increased and decreased rates of growth adaptation, depending on the specific interplay between drug interaction and cross resistance. For example, selection in a dual-lactam combination leads to accelerated growth adaptation compared to selection with the individual drugs, even though the resulting resistance profiles are nearly identical. On the other hand, populations evolved in an aminoglycoside and -lactam combination exhibit decreased growth adaptation and resistant profiles that depend on the specific drug concentrations. We show that the main qualitative features of these evolutionary trajectories can be explained by simple rescaling arguments that correspond to geometric transformations of the two-drug growth response surfaces measured in ancestral cells. The analysis also reveals multiple examples where resistance profiles selected by drug combinations correspond to (nearly) optimized linear combinations of those selected by the component drugs. Our results highlight trade-offs between drug interactions and collateral effects during the evolution of multi-drug resistance and emphasize evolutionary benefits and disadvantages of particular drug pairs targeting enterococci.","preprint_author_corresponding":"Kevin B Wood","preprint_author_corresponding_institution":"University of Michigan"},{"preprint_doi":"10.1101\/656967","published_doi":"10.1371\/journal.pcbi.1007147","published_journal":"PLOS Computational Biology","preprint_platform":"bioRxiv","preprint_title":"Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines","preprint_authors":"Raimundez, E.; Keller, S.; Zwingenberger, G.; Ebert, K.; Hug, S.; Theis, F. J.; Maier, D.; Luber, B.; Hasenauer, J.","preprint_category":"systems biology","preprint_date":"2019-05-31","published_date":"2020-03-02","preprint_abstract":"Targeted cancer therapies are powerful alternatives to chemotherapies or can be used complementary to these. Yet, the response to targeted treatments depends on a variety of factors, including mutations and expression levels, and therefore their outcome is difficult to predict. Here, we develop a mechanistic model of gastric cancer to study response and resistance factors for cetuximab treatment. The model captures the EGFR, ERK and AKT signaling pathways in two gastric cancer cell lines with different mutation patterns. We train the model using a comprehensive selection of time and dose response measurements, and provide an assessment of parameter and prediction uncertainties. We demonstrate that the proposed model facilitates the identification of causal differences between the cell lines. Furthermore, our study shows that the model provides accurate predictions for the responses to different perturbations, such as knockdown and knockout experiments. Among other results, the model predicted the effect of MET mutations on cetuximab sensitivity. These predictive capabilities render the model a powerful basis for the assessment of gastric cancer signaling and for the development and discovery of predictive biomarkers.\\n\\nAuthor SummaryUnraveling the causal differences between drug responders and non-responders is an important challenge. The information can help to understand molecular mechanisms and to guide the selection and design of targeted therapies. Here, we approach this problem for cetuximab treatment for gastric cancer using mechanistic mathematical modeling. The proposed model describes multiple gastric cancer cell lines and can accurately predict the response in several validation experiments. Our analysis provides a differentiated view on mutations and explains, for instance, the relevance of MET mutations and the insignificance of PIK3CA mutation in the considered cell lines. The model might provide the basis for understanding the recent failure of several clinical studies.","preprint_author_corresponding":"Jan  Hasenauer","preprint_author_corresponding_institution":"University of Bonn"},{"preprint_doi":"10.1101\/795237","published_doi":"10.1186\/s12864-020-6568-2","published_journal":"BMC Genomics","preprint_platform":"bioRxiv","preprint_title":"GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations","preprint_authors":"Manchanda, N.; Lawrence-Dill, C. J.; Hufford, M.; Andorf, C. M.; Woodhouse, M. R.; Seetharam, A.; Portwood, J. L.","preprint_category":"bioinformatics","preprint_date":"2019-10-07","published_date":"2020-03-02","preprint_abstract":"BackgroundGenome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.\\n\\nFindingsOur application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.\\n\\nConclusionsThe GenomeQC web application is implemented in R\/Shiny version 1.5.9 and Python 3.6 and is freely available at https:\/\/genomeqc.maizegdb.org\/ under the GPL license.\\n\\nAll source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https:\/\/github.com\/HuffordLab\/GenomeQC.","preprint_author_corresponding":"Matthew  Hufford","preprint_author_corresponding_institution":"Iowa State University"},{"preprint_doi":"10.1101\/763573","published_doi":"10.1002\/glia.23812","published_journal":"Glia","preprint_platform":"bioRxiv","preprint_title":"An alternative mechanism of early nodal clustering and myelination onset in GABAergic neurons of the central nervous system","preprint_authors":"Thetiot, M.; Freeman, S. A.; Roux, T.; Dubessy, A.-L.; Aigrot, M.-S.; Rappeneau, Q.; Lejeune, F.-X.; Tailleur, J.; Sol-Foulon, N.; Lubetzki, C.; Desmazieres, A.","preprint_category":"neuroscience","preprint_date":"2019-09-09","published_date":"2020-03-02","preprint_abstract":"In vertebrates, fast saltatory conduction along myelinated axons relies on the node of Ranvier. How nodes assemble on CNS neurons is not yet fully understood. We recently highlighted that clusters similar to nodes can form prior to myelin deposition in hippocampal GABAergic neurons and are associated with increased conduction velocity. Here, we used a live imaging approach to characterize the intrinsic mechanisms underlying the assembly of these early clusters. We first demonstrated that their components can partially pre-assemble prior to membrane targeting and determined the molecular motors involved in their trafficking. We then demonstrated the key role of the protein {beta}2Nav for clustering initiation. We further unraveled the fate of these early clusters, by showing that they participate in node formation, but also have an unexpected role in guiding oligodendrocyte processes prior to myelin deposition. Altogether our results shed light on an alternative mechanism of nodal clustering and myelination onset.","preprint_author_corresponding":"Anne  Desmazieres","preprint_author_corresponding_institution":"Sorbonne Universite, Inserm, CNRS, Institut du Cerveau et de la Moelle epiniere, ICM-GH Pitie-Salpetriere, F-75013, Paris, France"},{"preprint_doi":"10.1101\/585604","published_doi":"10.1074\/mcp.RA119.001909","published_journal":"Molecular & Cellular Proteomics","preprint_platform":"bioRxiv","preprint_title":"Human Hepatocyte Nuclear Factor 4-\u03b1 encodes isoforms with distinct transcriptional functions","preprint_authors":"Lambert, E.; Babeu, J.-P.; Simoneau, J.; Levesque, D.; Jolibois, E.; Scott, M. S.; Boudreau, F.; Boisvert, F.-M.","preprint_category":"cell biology","preprint_date":"2019-03-21","published_date":"2020-03-02","preprint_abstract":"HNF4 is a nuclear receptor produced as 12 isoforms from two promoters by alternative splicing. In order to characterize the transcriptional capacities of all 12 HNF4 isoforms, stable lines expressing each isoform were generated. The entire transcriptome associated with each isoform was analyzed as well as their respective interacting proteome. Major differences were noted in the transcriptional function of these isoforms. The 1 and 2 isoforms were the most potent regulators of gene expression while the 3 isoform exhibited significantly reduced activity. The 4, 5 and 6 isoforms, which use an alternative first exon, were characterized for the first time, and showed a greatly reduced transcriptional potential with an inability to recognize the consensus response element of HNF4. Several transcription factors and coregulators were identified as potential specific partners for certain HNF4 isoforms. An analysis integrating the vast amount of omics data enabled the identification of transcriptional regulatory mechanisms specific to certain HNF4 isoforms, hence demonstrating the importance of considering all isoforms given their seemingly diverse functions.","preprint_author_corresponding":"Francois-Michel  Boisvert","preprint_author_corresponding_institution":"Universit\u00e9 de Sherbrooke"},{"preprint_doi":"10.1101\/693804","published_doi":"10.1186\/s12870-020-2299-4","published_journal":"BMC Plant Biology","preprint_platform":"bioRxiv","preprint_title":"Barley ROP-INTERACTIVE PARTNER-a organizes into RAC1- and MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1-dependent membrane domains","preprint_authors":"Hoefle, C.; McCollum, C.; Huckelhoven, R.","preprint_category":"plant biology","preprint_date":"2019-07-09","published_date":"2020-03-02","preprint_abstract":"Small ROP (also called RAC) GTPases are key factors in polar cell development and in interaction with the environment. ROP-Interactive Partner (RIP) proteins are predicted scaffold or ROP-effector proteins, which function downstream of activated GTP-loaded ROP proteins in establishing membrane heterogeneity and cellular organization. Grass ROP proteins function in cell polarity, resistance and susceptibility to fungal pathogens but grass RIP proteins are little understood.\\n\\nWe found that the barley (Hordeum vulgare L.) RIPa protein can interact with barley ROPs in yeast. Fluorescent-tagged RIPa, when co-expressed with the constitutively activated ROP protein CA RAC1, accumulates at the cell periphery or plasma membrane. Additionally, RIPa, locates into membrane domains, which are laterally restricted by microtubules, when co-expressed with RAC1 and MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1. Both structural integrity of MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1 and microtubule stability are key to maintenance of RIPa-labeled membrane domains. In this context, RIPa also accumulates at the interface of barley and invading hyphae of the powdery mildew fungus Blumeria graminis f.sp. hordei.\\n\\nData suggest that barley RIPa interacts with barley ROPs and specifies RAC1 activity-associated membrane domains with potential signaling capacity. Lateral diffusion of this RAC1 signaling capacity is restricted the resulting membrane heterogeneity requires intact microtubules and MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1. Focal accumulation of RIPa at sites of fungal attack may indicate locally restricted ROP activity at sites of fungal invasion.","preprint_author_corresponding":"Ralph  Huckelhoven","preprint_author_corresponding_institution":"Technical University of Munich"},{"preprint_doi":"10.1101\/571687","published_doi":"10.1103\/PhysRevE.101.022420","published_journal":"Physical Review E","preprint_platform":"bioRxiv","preprint_title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","preprint_authors":"Davis, L. K.; Ford, I. J.; Saric, A.; Hoogenboom, B.","preprint_category":"biophysics","preprint_date":"2019-03-08","published_date":"2020-03-02","preprint_abstract":"In the nuclear pore complex (NPC), intrinsically disordered nuclear pore proteins (FG nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG nup behaviour has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.","preprint_author_corresponding":"Bart  Hoogenboom","preprint_author_corresponding_institution":"University College London"},{"preprint_doi":"10.1101\/2020.02.24.963447","published_doi":"10.1016\/j.jneumeth.2020.108671","published_journal":"Journal of Neuroscience Methods","preprint_platform":"bioRxiv","preprint_title":"A self-initiated cue-reward learning procedure for neural recording in rodents","preprint_authors":"Reverte, I.; Volz, S.; Alhazmi, F. H.; Kang, M.; Kaufman, K.; Chan, S.; Jou, C.; Iordanova, M. D.; Esber, G. R.","preprint_category":"neuroscience","preprint_date":"2020-02-25","published_date":"2020-03-02","preprint_abstract":"BackgroundSingle-unit recording in Pavlovian conditioning tasks requires the use of within-subject designs as well as sampling a considerable number of trials per trial type and session, which increases the total trial count. Pavlovian conditioning, on the other hand, requires a long average intertrial interval (ITI) relative to cue duration for cue-specific learning to occur. These requirements combined can make the session duration unfeasibly long.\n\nNew MethodTo circumvent this issue, we developed a self-initiated variant of the Pavlovian magazine-approach procedure in rodents. Unlike the standard procedure, where the animals passively receive the trials, the self-initiated procedure grants animals agency to self-administer and self-pace trials from a predetermined, pseudorandomized list. Critically, whereas in the standard procedure the typical ITI is in the order of minutes, our procedure uses a much shorter ITI (10 s).\n\nResultsDespite such a short ITI, discrimination learning in the self-initiated procedure is comparable to that observed in the standard procedure with a typical ITI, and superior to that observed in the standard procedure with an equally short ITI.\n\nComparison with Existing Method(s)The self-initiated procedure permits delivering 100 trials in a [~]1-h session, almost doubling the number of trials safely attainable over that period with the standard procedure.\n\nConclusionsThe self-initiated procedure enhances the collection of neural correlates of cue-reward learning while producing good discrimination performance. Other advantages for neural recording studies include ensuring that at the start of each trial the animal is engaged, attentive and in the same location within the conditioning chamber.","preprint_author_corresponding":"Guillem R Esber","preprint_author_corresponding_institution":"Brooklyn College, City University of New York"},{"preprint_doi":"10.1101\/429605","published_doi":"10.1186\/s12898-020-00281-y","published_journal":"BMC Ecology","preprint_platform":"bioRxiv","preprint_title":"Coexistence and cooperation in structured habitats","preprint_authors":"Geyrhofer, L.; Brenner, N.","preprint_category":"evolutionary biology","preprint_date":"2018-09-28","published_date":"2020-03-02","preprint_abstract":"Many natural habitats are structured, which imposes certain environmental conditions on extant populations. Which conditions are important for coexistence of diverse communities, and how social traits in such populations stabilize, have been important ecological and evolutionary questions. We investigate a minimal ecological model of microbial population dynamics, that exhibits crucial features to show coexistence: Populations are repeatedly separated into compartmentalized habitats on a timescale typically longer than growth. In this framework, we consider several scenarios for possible interactions between different strains and their environments, which includes sharing a common nutrient source or expression of public goods that potentially increase population size. Examples for these public good dynamics are collective resistance against antibiotics, and enhanced iron-availability due to pyoverdine. We show that the two features of a long mixing timescale and spatial compartmentalization are already enough to enable coexisting strains. In the case of public goods, stable coexistence immediately entails cooperation.","preprint_author_corresponding":"Lukas  Geyrhofer","preprint_author_corresponding_institution":"Network Biology Research Labs, and Department of Chemical Engineering, Technion, Haifa, Israel"},{"preprint_doi":"10.1101\/824946","published_doi":"10.7554\/eLife.52539","published_journal":"eLife","preprint_platform":"bioRxiv","preprint_title":"SLAMF6 deficiency augments tumor killing and skews towards an effector phenotype revealing it as a new T cell checkpoint","preprint_authors":"Hajaj, E.; Eisenberg, G.; Klein, S.; Frankenburg, S.; Merims, S.; Ben David, I.; Eisenhaure, T.; Henrickson, S. E.; Villani, A. C.; Hacohen, N.; Abudi, N.; Abramovich, R.; Cohen, J. E.; Peretz, T.; Veillette, A.; Lotem, M.","preprint_category":"physiology","preprint_date":"2019-10-31","published_date":"2020-03-03","preprint_abstract":"SLAMF6 is a homotypic receptor of the Ig-superfamily whose exact role in immune modulation has remained elusive. Its constitutive expression on resting and activated T cells precludes it from being a bona fide exhaustion marker. By breeding Pmel-1 mice with SLAMF6 KO mice, we generated donors for T cells lacking SLAMF6 and expressing a transgenic TCR for gp100-melanoma antigen. Activated Pmel-1xSLAMF6 KO CD8 T cells displayed improved polyfunctionality and strong tumor cytolysis. T-bet was the dominant transcription factor in Pmel-1xSLAMF6 KO cells, and upon activation, they acquired an effector-memory phenotype. Blocking LAG-3 improved the function of SLAMF6 deficient T cells even further. Finally, adoptive transfer of Pmel-1xSLAMF6 KO T cells into melanoma-bearing mice resulted in lasting tumor regression in contrast to temporary responses achieved with Pmel-1 T cells. These results support the notion that SLAMF6 is an inhibitory immune receptor whose absence enables powerful CD8 T cells to eradicate tumors.","preprint_author_corresponding":"Emma  Hajaj","preprint_author_corresponding_institution":"Hadassah Hebrew University Hospital"},{"preprint_doi":"10.1101\/537936","published_doi":"10.1186\/s12864-020-6542-z","published_journal":"BMC Genomics","preprint_platform":"bioRxiv","preprint_title":"Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets","preprint_authors":"Ozaki, H.; Hayashi, T.; Mana, U.; Nikaido, I.","preprint_category":"bioinformatics","preprint_date":"2019-02-01","published_date":"2020-03-03","preprint_abstract":"BackgroundRead coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly \"full-length\" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking.\n\nResultsHere, we have developed Millefy, a tool for visualizing read coverage of scRNA-seq data in genomic contexts. Millefy is designed to show read coverage of all individual cells at once in genomic contexts and to highlight cell-to-cell heterogeneity in read coverage. By visualizing read coverage of all cells as a heat map and dynamically reordering cells based on diffusion maps, Millefy facilitates discovery of \"local\" region-specific, cell-to-cell heterogeneity in read coverage, including variability of transcribed regions.\n\nConclusionsMillefy simplifies the examination of cellular heterogeneity in RNA transcription and processing events using scRNA-seq data. Millefy is available as an R package (https:\/\/github.com\/yuifu\/millefy) and a Docker image to help use Millefy on the Jupyter notebook (https:\/\/hub.docker.com\/r\/yuifu\/datascience-notebook-millefy).","preprint_author_corresponding":"Haruka  Ozaki","preprint_author_corresponding_institution":"Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba"},{"preprint_doi":"10.1101\/690198","published_doi":"10.1534\/genetics.119.302471","published_journal":"Genetics","preprint_platform":"bioRxiv","preprint_title":"Regulation of nucleolar dominance in Drosophila melanogaster","preprint_authors":"Yamashita, Y.; Warsinger-Pepe, N.; Li, D.","preprint_category":"developmental biology","preprint_date":"2019-07-02","published_date":"2020-03-03","preprint_abstract":"In eukaryotic genomes, ribosomal RNA (rRNA) genes exist as tandemly repeated clusters, forming ribosomal DNA (rDNA) loci. Each rDNA locus typically contains hundreds of rRNA genes to meet the high demand of ribosome biogenesis. Nucleolar dominance is a phenomenon, whereby individual rDNA loci are entirely silenced or transcribed, and is believed to be a mechanism to control rRNA dosage. Nucleolar dominance was originally noted to occur in interspecies hybrids, and has been shown to occur within a species (i.e. non-hybrid contexts). However, studying nucleolar dominance within a species has been challenging due to the highly homogenous sequence across rDNA loci. By utilizing single nucleotide polymorphisms (SNPs) between X rDNA vs. Y rDNA loci in males, as well as sequence variations between two X rDNA loci in females, we conducted a thorough characterization of nucleolar dominance throughout development of D. melanogaster. We demonstrate that nucleolar dominance is a developmentally-regulated program, where Y rDNA dominance is established during male embryogenesis, whereas females normally do not exhibit dominance between two X rDNA loci. By utilizing various chromosomal complements (e.g. X\/Y, X\/X, X\/X\/Y) and a chromosome rearrangement, we show that Y chromosome rDNA likely contains cis elements that dictate its dominance over the X chromosome rDNA. Our study begins to reveal the mechanisms underlying the selection of rDNA loci for activation\/silencing in nucleolar dominance.","preprint_author_corresponding":"Yukiko  Yamashita","preprint_author_corresponding_institution":"University of Michigan, HHMI"},{"preprint_doi":"10.1101\/847707","published_doi":"10.1534\/genetics.120.303147","published_journal":"Genetics","preprint_platform":"bioRxiv","preprint_title":"Pits and CtBP control tissue growth in Drosophila melanogaster with the Hippo pathway transcription repressor, Tgi.","preprint_authors":"Vissers, J. H.; Dent, L. G.; House, C. M.; Kondo, S.; Harvey, K. F.","preprint_category":"developmental biology","preprint_date":"2019-11-20","published_date":"2020-03-03","preprint_abstract":"The Hippo pathway is an evolutionary conserved signalling network that regulates organ size, cell fate control and tumorigenesis. In the context of organ size control, the pathway incorporates a large variety of cellular cues such as cell polarity and adhesion into an integrated transcriptional response. The central Hippo signalling effector is the transcriptional co-activator Yorkie, which controls gene expression in partnership with different transcription factors, most notably Scalloped. When it is not activated by Yorkie, Scalloped can act as a repressor of transcription, at least in part due to its interaction with the corepressor protein Tgi. The mechanism by which Tgi represses transcription is incompletely understood and therefore we sought to identify proteins that potentially operate together with it. Using an affinity purification and mass-spectrometry approach we identified Pits and CtBP as Tgi-interacting proteins, both of which have been linked to transcriptional repression. Both Pits and CtBP were required for Tgi to suppress the growth of the D. melanogaster eye and CtBP loss suppressed the undergrowth of yorkie mutant eye tissue. Furthermore, as reported previously for Tgi, overexpression of Pits suppressed transcription of Hippo pathway target genes. These findings suggest that Tgi might operate together with Pits and CtBP to repress transcription of genes that normally promote tissue growth. The human orthologues of Tgi, CtBP and Pits (VGLL4, CTBP2 and IRF2BP2) physically and functionally interact to control transcription, implying that the mechanism by which these proteins control transcriptional repression is conserved throughout evolution.","preprint_author_corresponding":"Kieran F Harvey","preprint_author_corresponding_institution":"Peter MacCallum Cancer Centre"},{"preprint_doi":"10.1101\/714022","published_doi":"10.1016\/j.bpj.2020.02.022","published_journal":"Biophysical Journal","preprint_platform":"bioRxiv","preprint_title":"Exon definition facilitates reliable control of alternative splicing","preprint_authors":"Enculescu, M.; Braun, S.; Setty, S. T.; Zarnack, K.; Koenig, J.; Legewie, S.","preprint_category":"systems biology","preprint_date":"2019-07-24","published_date":"2020-03-03","preprint_abstract":"Alternative splicing is a key step in eukaryotic gene expression that allows the production of multiple protein isoforms from the same gene. Even though splicing is perturbed in many diseases, we currently lack insights into regulatory mechanisms promoting its precision and efficiency. We analyse high-throughput mutagenesis data obtained for an alternatively spliced exon in the proto-oncogene RON and determine the functional units that control this splicing event. Using mathematical modeling of distinct splicing mechanisms, we show that alternative splicing is based in RON on a so-called  exon definition mechanism. Here, the recognition of the adjacent exons by the spliceosome is required for removal of an intron. We use our model to analyze the differences between the exon and intron definition scenarios and find that exon definition is crucial to prevent the accumulation of deleterious, partially spliced retention products during alternative splicing regulation. Furthermore, it modularizes splicing control, as multiple regulatory inputs are integrated into a common net input, irrespective of the location and nature of the corresponding cis-regulatory elements in the pre-mRNA. Our analysis suggests that exon definition promotes robust and reliable splicing outcomes in RON splicing.\n\nSIGNIFICANCEDuring mRNA maturation, pieces of the pre-mRNA (introns) are removed during splicing, and remaining parts (exons) are joined together. In alternative splicing, certain exons are either included or excluded, resulting in different splice products. Inclusion of RON alternative exon 11 leads to a functional receptor tyrosine kinase, while skipping results in a constitutively active receptor that promotes epithelial-to-mesenchymal transition and contributes to tumour invasiveness. Intron retention results in to deleterious isoforms that cannot be translated properly. Using kinetic modeling, we investigate the combinatorial regulation of this important splicing decision, and find that the experimental data supports a so-called exon definition mechanism. We show that this mechanism enhances the precision of alternative splicing regulation and prevents the retention of introns in the mature mRNA.","preprint_author_corresponding":"Mihaela  Enculescu","preprint_author_corresponding_institution":"Institute of Molecular Biology"},{"preprint_doi":"10.1101\/756965","published_doi":"10.1016\/j.bpj.2020.02.020","published_journal":"Biophysical Journal","preprint_platform":"bioRxiv","preprint_title":"Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization","preprint_authors":"Shinkai, S.; Sugawara, T.; Miura, H.; Hiratani, I.; Onami, S.","preprint_category":"biophysics","preprint_date":"2019-09-05","published_date":"2020-03-03","preprint_abstract":"The 1-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in 3-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell imaging experiments have revealed the dynamic organization of chromatin domains caused by stochastic thermal fluctuations. However, the mechanism underlying the dynamic regulation of such hierarchical and structural chromatin units within the micro-scale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose, to our knowledge, a new microrheology for Hi-C data to analyze the compliance property as a barometer of rigidness and flexibility of genomic regions along with the time evolution. Our method allows conversion of a Hi-C matrix into the spectrum of the rheological property along the genomic coordinate of a single chromosome. To demonstrate the technique, we analyzed Hi-C data during the neural differentiation of mouse embryonic stem cells. We found that TAD boundaries behave as more rigid nodes than the intra-TAD region. The spectrum clearly shows the rheological property of the dynamic chromatin domain formations at an individual time scale. Furthermore, we characterized the appearance of synchronous and liquid-like inter-compartment interactions in differentiated cells. Together, our microrheology provides physical insights revealing the dynamic 3D genome organization from Hi-C data.\\n\\nSIGNIFICANCEGenomic DNA is hierarchically packed inside the eukaryotic cell nucleus, and the genome organization in 3D contributes to proper genome functions at the multiscale chromatin domains. Although thermal fluctuations inevitably drive movements of the genome molecules in the micro-scale cell environment, there is no method, as yet, to quantify such dynamic 3D genome organization of hierarchical and structural chromatin units. Here, we describe a method to calculate rheological properties as barometers of flexibility and liquid-like behavior of genomic regions. We show that biologically relevant boundaries between chromatin domains are more rigid than the inside at a particular time scale. Our method allows interpretation of static and population-averaged genome conformation data as dynamic and hierarchical 3D genome picture.","preprint_author_corresponding":"Soya  Shinkai","preprint_author_corresponding_institution":"RIKEN"},{"preprint_doi":"10.1101\/768648","published_doi":"10.1016\/j.ijpara.2020.01.002","published_journal":"International Journal for Parasitology","preprint_platform":"bioRxiv","preprint_title":"Screening the Medicines for Malaria Venture Pathogen Box for invasion and egress inhibitors of the blood stage of Plasmodium falciparum reveals several inhibitory compounds","preprint_authors":"Dans, M. G.; Weiss, G. E.; Wilson, D. W.; Sleebs, B. E.; Crabb, B.; de Koning-Ward, T. F.; Gilson, P. R.","preprint_category":"cell biology","preprint_date":"2019-09-13","published_date":"2020-03-03","preprint_abstract":"To identify potential inhibitors of egress and invasion in the asexual blood stage of Plasmodium falciparum, we screened the Medicines for Malaria Venture (MMV) Pathogen Box. This compound library comprises of 400 drugs against neglected tropical diseases, including 125 with antimalarial activity. For this screen, we utilised transgenic parasites expressing a bioluminescent reporter, Nanoluciferase (Nluc), to measure inhibition of parasite egress and invasion in the presence of the Pathogen Box compounds. At a concentration of 2 {micro}M, we found 15 compounds that inhibited parasite egress by >40% and 24 invasion-specific compounds that inhibited invasion by >90%. We further characterised 11 of these inhibitors through cell-based assays and live cell microscopy and found two compounds that inhibited merozoite maturation in schizonts, one compound that inhibited merozoite egress, one compound that directly inhibited parasite invasion and one compound that slowed down invasion and arrested ring formation. The remaining compounds were general growth inhibitors that acted during the egress and invasion phase of the cell cycle. We found the sulfonylpiperazine, MMV020291, to be the most invasion-specific inhibitor, blocking successful merozoite internalisation within human RBCs and having no substantial effect on other stages of the cell cycle. This has greater implications for the possible development of an invasion-specific inhibitor as an antimalarial in a combination based therapy, in addition to being a useful tool for studying the biology of the invading parasite.\\n\\nImportancePlasmodium falciparum causes the most severe form of malaria and with emerging resistance to frontline treatments, there is the need to identify new drug targets in the parasite. One of the most critical processes during the asexual blood stage in the parasites lifecycle is the egress from old red blood cells (RBCs) and subsequent invasion of new RBCs. Many unique parasite ligands, receptors and enzymes are employed during egress and invasion that are essential for parasite proliferation and survival, therefore making these processes druggable targets. Identifying novel compounds that inhibit these essential processes would further their development into possible antimalarials that would be highly effective at killing asexual RBC stage parasites when used in combination with drugs that target the intraerythrocytic growth phase. These compounds potentially may also be used as novel tools to study the complex biology of parasites to gain further insight into the mechanisms behind egress and invasion.","preprint_author_corresponding":"Madeline Grace  Dans","preprint_author_corresponding_institution":"Burnet Institute"},{"preprint_doi":"10.1101\/662163","published_doi":"10.1016\/j.bpj.2020.02.023","published_journal":"Biophysical Journal","preprint_platform":"bioRxiv","preprint_title":"Kindlin Assists Talin to Promote Integrin Activation","preprint_authors":"Haydari, Z.; Shams, H.; Jahed, Z.; Mofrad, M. R. K.","preprint_category":"biophysics","preprint_date":"2019-06-06","published_date":"2020-03-03","preprint_abstract":"Integrin IIb{beta}3 is a predominant type of integrin abundantly expressed on the surface of platelets and its activation regulates the process of thrombosis. Talin and kindlin are cytoplasmic proteins that bind to integrin and modulate its affinity for extracellular ligands. While the molecular details of talin-mediated integrin activation are known, the mechanism of kindlin involvement in this process remains elusive. Here, we demonstrate that the interplay between talin and kindlin promotes integrin activation. Our all-atomic molecular dynamics simulations on complete transmembrane and cytoplasmic domains of integrin IIb{beta}3, talin1 F2\/F3 subdomains, and kindlin2 FERM domain in an explicit lipid-water environment over microsecond timescale, unraveled the role of kindlin as an enhancer of the talin interaction with the membrane proximal region of {beta}-integrin. The cooperation of kindlin with talin results in a complete disruption of salt bridges between R995 on IIb and D723\/E726 on {beta}3. Furthermore, kindlin modifies the molecular mechanisms of inside-out activation by decreasing the crossing angle between transmembrane helices of integrin IIb-{beta}3, which eventually results in parallelization of integrin dimer. In addition, our control simulation featuring integrin in complex with kindlin reveals that kindlin binding is not sufficient for unclasping the inner membrane and outer membrane interactions of integrin dimer, thus ruling out the possibility of solitary action of kindlin in integrin activation.\\n\\nStatement of SignificanceUsing the newly solved crystal structure of kindlin, we investigated, for the first time, the molecular mechanism of kindlin-mediated integrin activation through simultaneous binding of talin and kindlin. We demonstrate in atomist details how kindlin cooperates with talin to promote the activation of integrin IIb-{beta}3.","preprint_author_corresponding":"Mohammad R. K.  Mofrad","preprint_author_corresponding_institution":"UC Berkeley Departments of Bioengineering and Mechanical Engineering"},{"preprint_doi":"10.1101\/571802","published_doi":"10.1073\/pnas.1908100117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Active Efficient Coding Explains the Development of Binocular Vision and its Failure in Amblyopia","preprint_authors":"Eckmann, S.; Klimmasch, L.; Shi, B. E.; Triesch, J.","preprint_category":"neuroscience","preprint_date":"2019-03-09","published_date":"2020-03-03","preprint_abstract":"The development of vision during the first months of life is an active process that comprises the learning of appropriate neural representations and the learning of accurate eye movements. While it has long been suspected that the two learning processes are coupled, there is still no widely accepted theoretical framework describing this joint development. Here we propose a computational model of the development of active binocular vision to fill this gap. The model is based on a new formulation of the Active Efficient Coding theory, which proposes that eye movements, as well as stimulus encoding, are jointly adapted to maximize the overall coding efficiency. Under healthy conditions, the model self-calibrates to perform accurate vergence and accommodation eye movements. It exploits disparity cues to deduce the direction of defocus, which leads to co-ordinated vergence and accommodation responses. In a simulated anisometropic case, where the refraction power of the two eyes differs, an amblyopia-like state develops, in which the foveal region of one eye is suppressed due to inputs from the other eye. After correcting for refractive errors, the model can only reach healthy performance levels if receptive fields are still plastic, in line with findings on a critical period for binocular vision development. Overall, our model offers a unifying conceptual framework for understanding the development of binocular vision.\n\nSignificance StatementBrains must operate in an energy-efficient manner. The efficient coding hypothesis states that sensory systems achieve this by adapting neural representations to the statistics of sensory input signals. Importantly, however, these statistics are shaped by the organisms behavior and how it samples information from the environment. Therefore, optimal performance requires jointly optimizing neural representations and behavior, a theory called Active Efficient Coding. Here we test the plausibility of this theory by proposing a computational model of the development of binocular vision. The model explains the development of accurate binocular vision under healthy conditions. In the case of refractive errors, however, the model develops an amblyopia-like state and suggests conditions for successful treatment.","preprint_author_corresponding":"Jochen  Triesch","preprint_author_corresponding_institution":"Frankfurt Institute for Advanced Studies"},{"preprint_doi":"10.1101\/746214","published_doi":"10.1073\/pnas.1915458117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin+ cortical interneurons","preprint_authors":"Vogt, K.; Pai, E. L.-L.; Bilinovich, S. M.; Stafford, A. M.; Nguyen, J. T.; Paul, A.; Rubenstein, J. L.; Vogt, D.","preprint_category":"neuroscience","preprint_date":"2019-08-24","published_date":"2020-03-03","preprint_abstract":"Neurofibromatosis-1 (NF-1) is a monogenic disorder caused by mutations in the NF1 gene, which encodes the protein, Neurofibromin, an inhibitor of Ras GTPase activity. While NF-1 is often characterized by cafe-au-lait skin spots and benign tumors, the mechanisms underlying cognitive changes in NF-1 are poorly understood. Cortical GABAergic interneurons (CINs) are implicated in NF-1 pathology but cellular and molecular changes to CINs are poorly understood. We deleted Nf1 from the medial ganglionic eminence (MGE), which gives rise to both oligodendrocytes and CINs that express somatostatin and parvalbumin. Loss of Nf1 led to a persistence of immature oligodendrocytes that prevented later born oligodendrocytes from occupying the cortex. Moreover, PV+ CINs were uniquely lost, without changes in SST+ CINs. We discovered that loss of Nf1 results in a graded decrease in Lhx6 expression, the transcription factor necessary to establish SST+ and PV+ CINs, revealing a mechanism whereby Nf1 regulates a critical CIN developmental milestone.","preprint_author_corresponding":"Daniel  Vogt","preprint_author_corresponding_institution":"Michigan State University"},{"preprint_doi":"10.1101\/764084","published_doi":"10.1073\/pnas.1917586117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Eye movements support behavioral pattern completion","preprint_authors":"Wynn, J. S.; Ryan, J. D.; Buchsbaum, B. R.","preprint_category":"neuroscience","preprint_date":"2019-09-12","published_date":"2020-03-03","preprint_abstract":"The ability to recall a detailed event from a simple reminder is supported by pattern completion, a cognitive operation performed by the hippocampus wherein existing mnemonic representations are retrieved from incomplete input. In behavioral studies, pattern completion is often inferred through the false endorsement of lure (i.e., similar) items as old. However, evidence that such a response is due to the specific retrieval of a similar, previously encoded item is severely lacking. We used eye movement (EM) monitoring during a partial-cue recognition memory task to index reinstatement of lure images behaviorally via the recapitulation of encoding-related EMs or, gaze reinstatement. Participants reinstated encoding-related EMs following degraded retrieval cues and this reinstatement was negatively correlated with accuracy for lure images, suggesting that retrieval of existing representations (i.e., pattern completion) underlies lure false alarms. Our findings provide novel evidence linking gaze reinstatement and pattern completion and advance a functional role for EMs in memory retrieval.","preprint_author_corresponding":"Jordana S. Wynn","preprint_author_corresponding_institution":"Rotman Research Institute"},{"preprint_doi":"10.1101\/2019.12.11.873281","published_doi":"10.1073\/pnas.1921630117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"An allosteric switch regulates Mycobacterium tuberculosis ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR","preprint_authors":"Vahidi, S.; Ripstein, Z. A.; Juravsky, J. B.; Rennella, E.; Goldberg, A. L.; Mittermaier, A. K.; Rubinstein, J. L.; Kay, L. E.","preprint_category":"biophysics","preprint_date":"2019-12-12","published_date":"2020-03-03","preprint_abstract":"The 300-kDa ClpP1P2 protease from Mycobacterium tuberculosis collaborates with the AAA+ (ATPases associated with a variety of cellular activities) unfoldases, ClpC1 and ClpX, to degrade substrate proteins. Unlike in other bacteria, all the components of the Clp system are essential for growth and virulence of mycobacteria, and their inhibitors show promise as novel antibiotics. MtClpP1P2 is unique in that it contains a pair of distinct ClpP1 and ClpP2 rings and also requires the presence of activator peptides, such as benzoyl-leucyl-leucine (Bz-LL), for function. Understanding the structural basis for this requirement has been elusive but is critical for the rational design and improvement of anti-TB therapeutics that target the Clp system. Here we present a combined biophysical and biochemical study to explore the structure-dynamics-function relationship in MtClpP1P2. Cryo-EM structures of apo and acyldepsipeptide-bound MtClpP1P2 explain their lack of activity by showing loss of a key {beta}-sheet in a sequence known as the handle region that is critical for the proper formation of the catalytic triad. Methyl transverse relaxation-optimized spectroscopy (TROSY)-based NMR, cryo-EM, and biochemical assays show that upon binding Bz-LL or covalent inhibitors, MtClpP1P2 undergoes a conformational change from an inactive compact state to an active extended structure that can be explained by a modified Monod-Wyman-Changeux model. Our study establishes a critical role for the handle region as an on\/off switch for function, and shows extensive allosteric interactions involving both intra- and inter-ring communication that regulate MtClpP1P2 activity and that can potentially be exploited by small molecules to target M. tuberculosis.\n\nSignificance StatementThe MtClpP1P2 protease is part of the essential protein degradation machinery that helps maintain protein homeostasis in Mycobacterium tuberculosis, the causative agent of TB. Antibiotics that selectively kill both dormant and growing drug-resistant populations of M. tuberculosis by disrupting MtClpP1P2 function have attracted recent attention. Here we characterize a switch that can control MtClpP1P2 activity through binding of small peptides, leading to a concerted conformational change that potentially can be exploited by drug molecules to interfere with MtClpP1P2 function. Overall, this work highlights the power of a combined NMR and cryo-EM approach to provide detailed insights into the structure-dynamics-function relationship of molecular machines critical to human health.","preprint_author_corresponding":"Lewis E Kay","preprint_author_corresponding_institution":"University of Toronto"},{"preprint_doi":"10.1101\/820845","published_doi":"10.1073\/pnas.1919893117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism","preprint_authors":"Cribbs, A. P.; Terlecki-Zaniewicz, S.; Philpott, M.; Baardman, J.; Ahern, D.; Lindow, M.; Obad, S.; Oerum, H.; Sampey, B.; Mander, P.; Penn, H.; Wordsworth, P.; Bowness, P.; Prinjha, R. K.; de Winther, M.; Feldmann, M.; Oppermann, U.","preprint_category":"immunology","preprint_date":"2019-10-30","published_date":"2020-03-03","preprint_abstract":"T helper (Th) cells are CD4+ effector T cells that play an instrumental role in immunity by shaping the inflammatory cytokine environment in a variety of physiological and pathological situations. Using a combined chemico-genetic approach we identify histone H3K27 demethylases KDM6A and KDM6B as central regulators of human Th subsets. The prototypic KDM6 inhibitor GSK-J4 increases genome-wide levels of the repressive H3K27me3 chromatin mark and leads to suppression of the key transcription factor ROR{gamma}t during Th17 differentiation, whereas in mature Th17 cells an altered transcriptional program leads to a profound metabolic reprogramming with concomitant suppression of IL-17 cytokine levels and reduced proliferation. Single cell analysis reveals a specific shift from highly inflammatory cell subsets towards a resting state upon demethylase inhibition. The root cause of the observed anti-inflammatory phenotype in stimulated Th17 cells is reduced expression of key metabolic transcription factors, such as PPRC1 and c-myc. Overall, this leads to reduced mitochondrial biogenesis resulting in a metabolic switch with concomitant anti-inflammatory effects. These data are consistent with an opposing effect of GSK-J4 on Th17 T-cell differentiation pathways directly related to proliferation and effector cytokine profiles.","preprint_author_corresponding":"Adam P Cribbs","preprint_author_corresponding_institution":"University of Oxford"},{"preprint_doi":"10.1101\/802744","published_doi":"10.1073\/pnas.1917849117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"The neural signature of numerosity: Separating numerical and continuous magnitude extraction in early visual cortex with frequency-tagged EEG","preprint_authors":"Van Rinsveld, A.; Guillaume, M.; Kohler, P. J.; Schiltz, C.; Gevers, W.; Content, A.","preprint_category":"neuroscience","preprint_date":"2019-10-13","published_date":"2020-03-03","preprint_abstract":"The ability to handle approximate quantities, or number sense, has been recurrently linked to mathematical skills, though the nature of the mechanism allowing to extract numerical information (i.e., numerosity) from environmental stimuli is still debated. A set of objects is indeed not only characterized by its numerosity but also by other features, such as the summed area occupied by the elements, which often covary with numerosity. These intrinsic relations between numerosity and non-numerical magnitudes led some authors to argue that numerosity is not independently processed but extracted through a weighting of continuous magnitudes. This view cannot be properly tested through classic behavioral and neuroimaging approaches due to these intrinsic correlations. The current study used a frequency-tagging EEG approach to separately measure responses to numerosity as well as to continuous magnitudes. We recorded occipital responses to numerosity, total area, and convex hull changes but not to density and dot size. We additionally applied a model predicting primary visual cortex responses to the set of stimuli. The model output was closely aligned with our electrophysiological data, since it predicted discrimination only for numerosity, total area, and convex hull. Our findings thus demonstrate that numerosity can be independently processed at an early stage in the visual cortex, even when completely isolated from other magnitude changes. The similar implicit discrimination for numerosity as for some continuous magnitudes, which correspond to basic visual percepts, shows that both can be extracted independently, hence substantiating the nature of numerosity as a primary feature of the visual scene.","preprint_author_corresponding":"Amandine  Van Rinsveld","preprint_author_corresponding_institution":"Universit\u00e9 Libre de Bruxelles"},{"preprint_doi":"10.1101\/748160","published_doi":"10.1073\/pnas.1920561117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation","preprint_authors":"Elledge, S. K.; Tran, H. L.; Christian, A. H.; Steri, V.; Hann, B.; Toste, F. D.; Chang, C. J.; Wells, J. A.","preprint_category":"bioengineering","preprint_date":"2019-08-28","published_date":"2020-03-03","preprint_abstract":"Chemical modification of antibodies is one of the most important bioconjugations utilized by biologists and biotechnology. To date, the field has been dominated by random modification of lysines or more site-specific labeling of cysteines, each with attendant challenges. Recently we have developed oxaziridine chemistry for highly selective and efficient sulfimide modification of methionine called redox-activated chemical tagging (ReACT). Here, we systematically scanned methionines throughout one of the most popular antibody scaffolds, trastuzumab, for antibody engineering and drug conjugation. We tested the expression, reactivities, and stabilities of 123 single engineered methionines distributed over the surface of the antibody when reacted with oxaziridine. We found uniformly high expression for these mutants and generally good reaction efficiencies with the panel of oxaziridines. Remarkably, the stability to hydrolysis of the sulfimide varied more than ten-fold depending on temperature and the site of the engineered methionine. Interestingly, the most stable and reactive sites were those that were partially buried, likely because of their reduced access to water. There was also a ten-fold variation in stability depending on the nature of the oxaziridine, which we determined was inversely correlated with the electrophilic nature of the sulfimide. Importantly, the stabilities of the best analogs and antibody drug conjugate potencies were comparable to those reported for cysteine-maleimide modifications of trastuzumab. We also found our antibody drug conjugates to be potent in a breast cancer mouse xenograft model. These studies provide a roadmap for broad application of ReACT for efficient, stable, and site-specific antibody and protein bioconjugation.","preprint_author_corresponding":"James A. Wells","preprint_author_corresponding_institution":"University of California, San Francisco"},{"preprint_doi":"10.1101\/755074","published_doi":"10.1073\/pnas.1915333117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Investigations of the Underlying Mechanisms of HIF-1\u03b1 and CITED2 Binding to TAZ1","preprint_authors":"Chu, W.-T.; Chu, X.; Wang, J.","preprint_category":"biophysics","preprint_date":"2019-09-02","published_date":"2020-03-03","preprint_abstract":"The TAZ1 domain of CREB binding protein is crucial for transcriptional regulation and recognizes multiple targets. The interactions between TAZ1 and its specific targets are related to the cellular hypoxic negative feedback regulation. Previous experiments reported that one of the TAZ1 targets CITED2 is an efficient competitor of another target HIF-1. Here by developing the structure-based models of TAZ1 complexes we have uncovered the underlying mechanisms of the competitions between HIF-1 and CITED2 binding to TAZ1. Our results are consistent with the experimental hypothesis on the competition mechanisms and the apparent affinity. In addition, the simulations prove the dominant position of forming TAZ1-CITED2 complex in both thermodynamics and kinetics. For thermodynamics, TAZ1-CITED2 is the lowest basin located on the free energy surface of binding in the ternary system. For kinetics, the results suggest that CITED2 binds to TAZ1 faster than HIF-1. Besides, the analysis of contact map and{phi} values in this study will be helpful for further experiments on TAZ1 systems.","preprint_author_corresponding":"Jin  Wang","preprint_author_corresponding_institution":"State University of New York at Stony Brook"},{"preprint_doi":"10.1101\/665463","published_doi":"10.1073\/pnas.1917820117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Class A PBPs have a distinct and unique role in the construction of the pneumococcal cell wall.","preprint_authors":"Straume, D.; Wiaroslawa Piechowiak, K.; Olsen, S.; Stamsas, G. A.; Berg, K. H.; Kjos, M.; Heggenhougen, M. V.; Alcorlo, M.; Hermoso, J. A.; Havarstein, L. S.","preprint_category":"microbiology","preprint_date":"2019-06-10","published_date":"2020-03-03","preprint_abstract":"In oval shaped Streptococcus pneumoniae, septal and longitudinal peptidoglycan synthesis is performed by independent functional complexes; the divisome and the elongasome. Penicillin binding proteins (PBPs) were long considered as the key peptidoglycan synthesizing enzymes in these complexes. Among these were the bifunctional class A PBPs, which are both glycosyltransferases and transpeptidases, and monofunctional class B PBPs with only transpeptidase activity. Recently, however, it was established that the monofunctional class B PBPs work together with non-PBP glycosyltransferases (FtsW and RodA) to make up the core peptidoglycan synthesizing machineries within the pneumococcal divisome (FtsW\/PBP2x) and elongasome (RodA\/PBP2b). The function of class A PBPs is therefore now an open question. Here we utilize the peptidoglycan hydrolase CbpD to show that class A PBPs have an autonomous role during cell wall synthesis in S. pneumoniae. Purified CbpD was shown to target the septum of S. pneumoniae cells. Using assays to specifically inhibit PBP2x, we demonstrate that CbpD specifically target nascent peptidoglycan synthesized by the divisome. Notably, class A PBPs could process this nascent peptidoglycan from a CbpD-sensitive to a CbpD-resistant form. The class A PBP mediated processing was independent of divisome and elongasome activities. Class A PBPs thus constitute an autonomous functional entity which processes or repairs nascent peptidoglycan synthesized by FtsW\/PBP2x. Our results support a model in which pneumococcal peptidoglycan is made by three functional entities, the divisome, the elongasome and a peptidoglycan-repairing or -remodelling complex consisting of bifunctional PBPs. To our knowledge this is the first time a specific function has been identified for class A PBPs in bacterial cell wall synthesis.","preprint_author_corresponding":"Leiv Sigve  H\u00e5varstein","preprint_author_corresponding_institution":"Norwegian University of Life Sciences"},{"preprint_doi":"10.1101\/809871","published_doi":"10.1073\/pnas.1918296117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Mechanophenotyping of 3D Multicellular Clusters using Displacement Arrays of Rendered Tractions","preprint_authors":"Leggett, S. E.; Patel, M.; Valentin, T. M.; Gamboa, L.; Khoo, A. S.; Williams, E. K.; Franck, C.; Wong, I. Y.","preprint_category":"bioengineering","preprint_date":"2019-10-21","published_date":"2020-03-03","preprint_abstract":"Epithelial tissues mechanically deform the surrounding extracellular matrix during embryonic development, wound repair, and tumor invasion. Ex vivo measurements of such multicellular tractions within three-dimensional (3D) biomaterials could elucidate collective dissemination during disease progression, and enable preclinical testing of targeted anti-migration therapies. However, past 3D traction measurements have been low throughput due to the challenges of imaging and analyzing information-rich 3D material deformations. Here, we demonstrate a method to profile multicellular clusters in a 96-well plate format based on spatially heterogeneous contractile, protrusive, and circumferential tractions. As a case study, we profile multicellular clusters across varying states of the epithelial-mesenchymal transition, revealing a successive loss of protrusive and circumferential tractions, as well as the formation of localized contractile tractions with elongated cluster morphologies. These cluster phenotypes were biochemically perturbed using drugs, biasing towards traction signatures of different epithelial or mesenchymal states. This higher-throughput analysis is promising to systematically interrogate and perturb aberrant mechanobiology, which could be utilized with human patient samples to guide personalized therapies.","preprint_author_corresponding":"Ian Y Wong","preprint_author_corresponding_institution":"Brown University"},{"preprint_doi":"10.1101\/825315","published_doi":"10.1073\/pnas.1919028117","published_journal":"Proceedings of the National Academy of Sciences","preprint_platform":"bioRxiv","preprint_title":"Caenorhabditis elegans ADAR editing and the ERI-6\/7\/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons","preprint_authors":"Fischer, S.; Ruvkun, G.","preprint_category":"genetics","preprint_date":"2019-10-31","published_date":"2020-03-03","preprint_abstract":"Endogenous retroviruses and LTR retrotransposons are mobile genetic elements that are closely related to retroviruses. Desilenced endogenous retroviruses are associated with human autoimmune disorders and neurodegenerative diseases. C. elegans and related Caenorhabdites contain LTR retrotransposons and, as described here, numerous integrated viral genes including viral envelope genes that are part of LTR retrotransposons. We found that both LTR retrotransposons and endogenous viral elements are silenced by ADARs (adenosine deaminases acting on double-stranded RNA (dsRNA)) together with the endogenous RNAi factor ERI-6\/7, a homolog of Mov10 helicase, a retrotransposon and retrovirus restriction factor in human. siRNAs corresponding to integrated viral genes and LTR retrotransposons, but not to DNA transposons, are dependent on the ADARs and ERI-6\/7; on the contrary, siRNAs corresponding to palindromic repeats are increased in adar-eri mutants because of an antiviral RNAi response to dsRNA. Silencing of LTR retrotransposons is dependent on downstream RNAi factors and P granule components but is independent of the viral sensor DRH-1\/RIG-I and the nuclear Argonaute NRDE-3. The activation of retrotransposons in the ADAR- and ERI-6\/7\/MOV10-defective mutant is associated with the induction of the Unfolded Protein Response (UPR), a common response to viral infection. The overlap between genes induced upon viral infection and infection with intracellular pathogens, and genes co-expressed with retrotransposons, suggests that there is a common response to different types of foreign elements that includes a response to proteotoxicity presumably caused by the burden of replicating pathogens and expressed retrotransposons.\\n\\nSIGNIFICANCESilencing of transposable elements and viruses is critical for the maintenance of genome integrity, cellular homeostasis and organismal health. Here we describe multiple factors that control different types of transposable elements, providing insight into how they are regulated. We also identify stress response pathways that are triggered upon mis-regulation of these transposable elements. The conservation of these factors and pathways in human suggests that our studies in C. elegans can provide general insight into the regulation of and response to transposable elements and viruses.","preprint_author_corresponding":"Gary  Ruvkun","preprint_author_corresponding_institution":"Massachusetts General Hospital and Harvard Medical School"},{"preprint_doi":"10.1101\/546879","published_doi":"10.1002\/ece3.6096","published_journal":"Ecology and Evolution","preprint_platform":"bioRxiv","preprint_title":"Predictor species: Improving assessments of rare species occurrence by modelling environmental co-responses","preprint_authors":"Thompson, P. R.; Fagan, W. F.; Staniczenko, P. P. A.","preprint_category":"ecology","preprint_date":"2019-02-11","published_date":"2020-03-03","preprint_abstract":"Designing an effective conservation strategy requires understanding where rare species are located. Although species distribution models are primarily used to identify patterns at large spatial scales, their general methodology is relevant for predicting the occurrence of individual species at specific locations. Here we present a new approach that uses Bayesian networks to improve predictions by modelling environmental co-responses among species. For species from a European peat bog community, our approach consistently performs better than single-species models, and better than conventional multi-species models for rare species when calibration data are limited. Furthermore, we identify a group of \"predictor species\" that are relatively common, insensitive to the presence of other species, and can be used to improve occurrence predictions of rare species. Predictor species are distinct from other categories of conservation surrogates such as umbrella or indicator species, which motivates focused data collection of predictor species to enhance conservation practices.","preprint_author_corresponding":"Phillip P.A. Staniczenko","preprint_author_corresponding_institution":"Brooklyn College, City University of New York"},{"preprint_doi":"10.1101\/686741","published_doi":"10.1534\/g3.119.400934","published_journal":"G3: Genes|Genomes|Genetics","preprint_platform":"bioRxiv","preprint_title":"Sexual selection does not increase the rate of compensatory adaptation to a mutation influencing a secondary sexual trait in Drosophila melanogaster","preprint_authors":"Chandler, C. H.; Mammel, A.; Dworkin, I.","preprint_category":"evolutionary biology","preprint_date":"2019-06-28","published_date":"2020-03-03","preprint_abstract":"Theoretical work predicts that sexual selection can enhance natural selection, increasing the rate of adaptation to new environments and helping purge harmful mutations. While some experiments support these predictions, remarkably little work has addressed the role of sexual selection on compensatory adaptation--populations ability to compensate for the costs of deleterious alleles that are already present. We tested whether sexual selection, as well as the degree of standing genetic variation, affect the rate of compensatory evolution via phenotypic suppression in experimental populations of Drosophila melanogaster. These populations were fixed for a spontaneous mutation causing mild abnormalities in the male sex comb, a structure important for mating success. We fine-mapped this mutation to an [~]85 kb region on the X chromosome containing three candidate genes, showed that the mutation is deleterious, and that its phenotypic expression and penetrance vary by genetic background. We then performed experimental evolution, including a treatment where opportunity for mate choice was limited by experimentally enforced monogamy. Although evolved populations did show some phenotypic suppression of the morphological abnormalities in the sex comb, the amount of suppression did not depend on the opportunity for sexual selection. Sexual selection, therefore, may not always enhance natural selection; instead, the interaction between these two forces may depend on additional factors.","preprint_author_corresponding":"Christopher H Chandler","preprint_author_corresponding_institution":"SUNY Oswego"},{"preprint_doi":"10.1101\/2020.01.08.898908","published_doi":"10.1534\/g3.120.401050","published_journal":"G3: Genes|Genomes|Genetics","preprint_platform":"bioRxiv","preprint_title":"The Gossypium longicalyx genome as a resource for cotton breeding and evolution","preprint_authors":"Grover, C. E.; Pan, M.; Yuan, D.; Arick, M. A.; Hu, G.; Brase, L.; Stelly, D. M.; Lu, Z.; Schmitz, R. J.; Peterson, D. G.; Wendel, J. F.; Udall, J. A.","preprint_category":"genomics","preprint_date":"2020-01-09","published_date":"2020-03-03","preprint_abstract":"Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.","preprint_author_corresponding":"Corrinne E.  Grover","preprint_author_corresponding_institution":"Iowa State University"},{"preprint_doi":"10.1101\/775312","published_doi":"10.1534\/g3.120.401133","published_journal":"G3: Genes|Genomes|Genetics","preprint_platform":"bioRxiv","preprint_title":"Cas9-mediated gene-editing in the malaria mosquito Anopheles stephensi by ReMOT Control","preprint_authors":"Macias, V. M.; McKeand, S.; Chaverra-Rodriguez, D.; Hughes, G. L.; Fazekas, A.; Pujhari, S.; Jasinskiene, N.; James, A. A.; Rasgon, J. L.","preprint_category":"genetics","preprint_date":"2019-09-19","published_date":"2020-03-03","preprint_abstract":"Innovative tool development is essential for continued advancement in malaria control and depends on a deeper understanding of the molecular mechanisms that govern transmission of malaria parasites by Anopheles mosquitoes. Targeted disruption of genes in mosquito vectors is a powerful method to uncover the underlying biology of vector-pathogen interactions, and genome manipulation technologies can themselves form the basis of mosquito and pathogen control strategies. However, the embryo injection methods used to genetically manipulate mosquitoes, and in particular Anopheles species, are difficult and inefficient, particularly for non-specialist laboratories. We have adapted a strategy called ReMOT Control (Receptor-mediated Ovary Transduction of Cargo) to deliver the Cas9 ribonucleoprotein complex to adult mosquito ovaries and generate targeted and heritable mutations in the malaria vector Anopheles stephensi. We found that gene editing by ReMOT Control in Anopheles mosquitoes was comparable to the technique in Ae. aegypti and as efficient in editing as standard embryo injections. The adaptation of this technology to Anopheles mosquitoes opens up the power of reverse genetics to malaria vector labs that do not have the equipment or technical expertise to perform embryo injections and establishes the flexibility of ReMOT Control for gene-editing in non-Aedes species.","preprint_author_corresponding":"Jason L Rasgon","preprint_author_corresponding_institution":"Penn State University"},{"preprint_doi":"10.1101\/162289","published_doi":"10.1002\/ece3.6136","published_journal":"Ecology and Evolution","preprint_platform":"bioRxiv","preprint_title":"Three Decades as an NSF REU Site: Lessons and Recommendations","preprint_authors":"McDevitt, A. L.; Patel, M. V.; Ellison, A.","preprint_category":"scientific communication and education","preprint_date":"2017-07-18","published_date":"2020-03-03","preprint_abstract":"NSFs Research Experiences for Undergraduates (REU) program supports thousands of undergraduate researchers annually. REU sites operate independently with regards to their research mission and structure, leading to a complex educational milieu distinct from traditional classrooms and labs. Overall, REU sites are perceived as providing highly formative experiences for developing researchers. However, given improved assessment practices over REUs three decades, best practices for student learning and evaluation of long-term impacts remain limited. To address this limitation, we recommend the use of systems-based theoretical frameworks when studying REU programs. We outline how one such framework, cultural-historical activity theory (CHAT), could inform the collection of assessment data. Among other strengths, CHAT guides collection of quantitative and qualitative information that can help characterize REU programs in an educationally meaningful context. Adoption of CHAT and similar approaches by REU Sites could improve dialogue among programs, encourage collaborations, and improve evidence-based practices.","preprint_author_corresponding":"Aaron  Ellison","preprint_author_corresponding_institution":"Harvard University"},{"preprint_doi":"10.1101\/2020.02.15.948976","published_doi":"10.1002\/nbm.4277","published_journal":"NMR in Biomedicine","preprint_platform":"bioRxiv","preprint_title":"Non-negative least squares computation for in vivo myelin mapping using simulated multi-echo spin-echo T2 decay data","preprint_authors":"Wiggermann, V.; Vavasour, I. M.; Kolind, S.; MacKay, A. L.; Helms, G.; Rauscher, A.","preprint_category":"biophysics","preprint_date":"2020-02-17","published_date":"2020-03-03","preprint_abstract":"Multi-compartment T2-mapping has gained particular relevance for the study of myelin water in brain. As a facilitator of rapid saltatory axonal signal transmission, myelin is a cornerstone indicator of white matter development and function. Regularized non-negative least squares fitting of multi-echo T2 data has been widely employed for the computation of the myelin water fraction (MWF) and the obtained MWF maps have been histopathologically validated. MWF measurements depend upon the quality of the data acquisition, B1+-homogeneity and a range of fitting parameters. In this special issue article, we discuss the relevance of these factors for the accurate computation of multi-compartment T2 and MWF maps. We generated multi-echo spin-echo T2 decay curves following the approach of CarrPurcell-Meiboom-Gill for various myelin concentrations and myelin T2 scenarios by simulating the evolution of the magnetization vector between echoes based on the Bloch equations. We demonstrated that noise and imperfect refocusing flip angles yield systematic underestimations in MWF and intra-\/extracellular water geometric mean (gm) T2. MWF estimates were more stable than myelin water gmT2 time across different settings of the T2 analysis. We observed that the lower limit of the T2 distribution grid should be slightly shorter than TE1. Both TE1 and the acquisition echo spacing also have to be sufficiently short to capture the rapidly decaying myelin water T2 signal. Among all parameters of interest, the estimated MWF and intra-\/extracellular water gmT2 differed by approximately 0.13-4 percentage points and 3-4 ms, respectively, from the true values, with larger deviations observed in the presence of greater B1+-inhomogeneities and at lower signal-to-noise ratio. Tailoring acquisition strategies may allow to better characterize the T2 distribution, including the myelin water, in vivo.","preprint_author_corresponding":"Vanessa  Wiggermann","preprint_author_corresponding_institution":"University of British Columbia, Vancouver, BC, Canada"},{"preprint_doi":"10.1101\/2020.01.12.903344","published_doi":"10.3389\/fpls.2020.00236","published_journal":"Frontiers in Plant Science","preprint_platform":"bioRxiv","preprint_title":"Beyond the forest-grassland dichotomy: the gradient-like organization of habitats in forest-steppes","preprint_authors":"Erdos, L.; Torok, P.; Szitar, K.; Batori, Z.; Tolgyesi, C.; Kiss, P. J.; Bede-Fazekas, A.; Kroel-Dulay, G.","preprint_category":"plant biology","preprint_date":"2020-01-13","published_date":"2020-03-03","preprint_abstract":"Featuring a transitional zone between closed forests and treeless steppes, forest-steppes cover vast areas and have outstanding conservation importance. The components of this mosaic ecosystem can conveniently be classified into two basic types, forests and grasslands. However, this dichotomic classification may not fit reality as habitat organization can be much more complex. In this study, our aim was to find out if the main habitat types can be grouped into two distinct habitat categories (which would support the dichotomic description), or a different paradigm better fits this complex ecosystem. We selected six main habitats of sandy forest-steppes, and, using 176 releves, we compared their vegetation based on species composition (NMDS ordination, number of common species of the studied habitats), relative ecological indicator values (mean indicators for temperature, soil moisture, and light availability), and functional species groups (life-form categories, geoelement types, and phytosociological preference groups). According to the species composition, we found a well-defined gradient, with the following habitat order: large forest patches - medium forest patches - small forest patches - north-facing edges - south-facing edges - grasslands. A considerable number of species were shared among all habitats, while the number of species restricted to certain habitat types was also numerous, especially for north-facing edges. The total (i.e., pooled) number of species peaked near the middle of the gradient, in north-facing edges. The relative ecological indicator values and functional species groups showed mostly gradual changes from the large forest patches to the grasslands. Our results indicate that the widely used dichotomic categorization of forest-steppe habitats into forest and grassland patches is too simplistic, potentially resulting in a considerable loss of information. We suggest that forest-steppe vegetation better fits the gradient-based paradigm of landscape structure, which is able to reflect continuous variations.","preprint_author_corresponding":"Peter  Torok","preprint_author_corresponding_institution":"MTA-DE Lendulet Functional and Restoration Ecology Research Group"},{"preprint_doi":"10.1101\/403824","published_doi":"10.1186\/s12915-020-0748-z","published_journal":"BMC Biology","preprint_platform":"bioRxiv","preprint_title":"Pervasive contaminations in sequencing experiments are a major source of false genetic variability: a Mycobacterium tuberculosis meta-analysis","preprint_authors":"Goig, G. A.; Blanco, S.; Garcia-Basteiro, A.; Comas, I.","preprint_category":"genomics","preprint_date":"2018-08-29","published_date":"2020-03-02","preprint_abstract":"Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data usually neglect the errors introduced by potential contaminations. We performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS by analyzing more than 4,000 bacterial samples from 20 different studies. We found that contaminations are pervasive and can introduce large biases in variant analysis. We showed that these biases can translate in hundreds of false positive and negative SNPs, even for samples with slight contaminations. Studies investigating complex biological traits from sequencing data can be completely biased if contaminations are neglected during the bioinformatic analysis. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines. Our results urge for the implementation of such pipelines as sequencing technologies consolidate as a precision tool in the research and clinical context.","preprint_author_corresponding":"Inaki  Comas","preprint_author_corresponding_institution":"Institute of Biomedicine of Valencia"},{"preprint_doi":"10.1101\/867960","published_doi":"10.3389\/fpls.2020.00225","published_journal":"Frontiers in Plant Science","preprint_platform":"bioRxiv","preprint_title":"High resolution mapping of a Hordeum bulbosum-derived powdery mildew resistance locus in barley using distinct homologous introgression lines","preprint_authors":"Hoseinzadeh, P.; Ruge-Wehling, B.; Schweizer, P.; Stein, N.; Pidon, H.","preprint_category":"plant biology","preprint_date":"2019-12-06","published_date":"2020-03-03","preprint_abstract":"Powdery mildew caused by Blumeria graminis f.sp. hordei (Bgh) is one of the main foliar diseases in barley (Hordeum vulgare L.; Hv). Naturally occurring resistance genes used in barley breeding are a cost effective and environmentally sustainable strategy to minimize the impact of pathogens, however, the primary gene pool of H. vulgare contains limited diversity owing to recent domestication bottlenecks. To ensure durable resistance against this pathogen, more genes are required that could be unraveled by investigation of secondary barley gene-pool. A large set of Hordeum bulbosum (Hb) introgression lines (ILs) harboring a diverse set of desirable resistance traits have been developed and are being routinely used as source of novel diversity in gene mapping studies. Nevertheless, this strategy is often compromised by a lack of recombination between the introgressed fragment and the orthologous chromosome of the barley genome. In this study, we fine-mapped a Hb gene conferring resistance to barley powdery mildew. The initial genotyping of two Hb ILs mapping populations with differently sized 2HS introgressions revealed severely reduced interspecific recombination in the region of the introgressed segment, preventing precise localization of the gene. To overcome this difficulty, we developed an alternative strategy, exploiting intraspecific recombination by crossing two Hv\/Hb ILs with collinear Hb introgressions, one of which carries a powdery mildew resistance gene, while the other doesnt. The intraspecific recombination rate in the Hb-introgressed fragment of 2HS was approximately 20 times higher than it was in the initial simple ILs mapping populations. Using high-throughput genotyping-by-sequencing (GBS), we allocated the resistance gene to a 1.4 Mb interval, based on an estimate using the Hv genome as reference, in populations of only 103 and 146 individuals respectively, similar to what is expected at this locus in barley. The most likely candidate resistance gene within this interval encodes a legume-type lectin-receptor-like protein (LecRLP). Like other LecRLPs that have been implicated in resistance, this gene could be a good candidate for Hb resistance. The reported strategy can be applied as a general strategic approach for identifying genes underlying traits of interest in crop wild relatives.","preprint_author_corresponding":"H\u00e9l\u00e8ne  Pidon","preprint_author_corresponding_institution":"Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)"},{"preprint_doi":"10.1101\/847368","published_doi":"10.1038\/s41375-020-0785-1","published_journal":"Leukemia","preprint_platform":"bioRxiv","preprint_title":"Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis","preprint_authors":"Sarin, V.; Yu, K.; Ferguson, I. D.; Gugliemini, O.; Nix, M. A.; Hann, B. C.; Sirota, M.; Wiita, A. P.","preprint_category":"cancer biology","preprint_date":"2019-11-20","published_date":"2020-03-02","preprint_abstract":"Multiple myeloma (MM) cell lines are routinely used to model the disease. However, a long-standing question is how well these cell lines truly represent tumor cells in patients. Here, we employ a recently-described method of transcriptional correlation profiling to compare similarity of 66 MM cell lines to 779 newly-diagnosed MM patient tumors. We found that individual MM lines differ significantly with respect to patient tumor representation, with median R ranging from 0.35-0.54. ANBL-6 was the \"best\" line, markedly exceeding all others (p < 2.2e-16). Notably, some widely-used cell lines (RPMI-8226, U-266) scored poorly in our patient similarity ranking (48 and 52 of 66, respectively). Lines cultured with interleukin-6 showed significantly improved correlations with patient tumor (p = 9.5e-4). When common MM genomic features were matched between cell lines and patients, only t(4;14) and t(14;16) led to increased transcriptional correlation. To demonstrate utility of our top-ranked line for preclinical studies, we showed that intravenously-implanted ANBL-6 proliferates in hematopoietic organs in immunocompromised mice. Overall, our large-scale quantitative correlation analysis, utilizing emerging datasets, provides a resource informing the MM community of cell lines that may be most reliable for modeling patient disease while also elucidating biological differences between cell lines and tumors.","preprint_author_corresponding":"Arun P. Wiita","preprint_author_corresponding_institution":"University of California, San Francisco"},{"preprint_doi":"10.1101\/509802","published_doi":"10.1007\/s10548-020-00758-5","published_journal":"Brain Topography","preprint_platform":"bioRxiv","preprint_title":"Exploring Frequency-dependent Brain Networks from ongoing EEG using Spatial ICA during music listening","preprint_authors":"Zhu, Y.; Zhang, C.; Toiviainen, P.; Huotilainen, M.; Mathiak, K.; Ristaniemi, T.; Cong, F.","preprint_category":"neuroscience","preprint_date":"2019-01-02","published_date":"2020-03-02","preprint_abstract":"Recently, exploring brain activity based on functional networks during naturalistic stimuli especially music and video represents an attractive challenge because of the low signal-to-noise ratio in collected brain data. Although most efforts focusing on exploring the listening brain have been made through functional magnetic resonance imaging (fMRI), sensor-level electro- or magnetoencephalography (EEG\/MEG) technique, little is known about how neural rhythms are involved in the brain network activity under naturalistic stimuli. This study exploited cortical oscillations through analysis of ongoing EEG and musical feature during free-listening to music. We used a data-driven method that combined music information retrieval with spatial Independent Components Analysis (ICA) to probe the interplay between the spatial profiles and the spectral patterns. We projected the sensor data into cortical space using a minimum-norm estimate and applied the Short Time Fourier Transform (STFT) to obtain frequency information. Then, spatial ICA was made to extract spatial-spectral-temporal information of brain activity in source space and five long-term musical features were computationally extracted from the naturalistic stimuli. The spatial profiles of the components whose temporal courses were significantly correlated with musical feature time series were clustered to identify reproducible brain networks across the participants. Using the proposed approach, we found brain networks of musical feature processing are frequency-dependent and three plausible frequency-dependent networks were identified; the proposed method seems valuable for characterizing the large-scale frequency-dependent brain activity engaged in musical feature processing.","preprint_author_corresponding":"Yongjie  Zhu","preprint_author_corresponding_institution":"University of Jyvaskyla"},{"preprint_doi":"10.1101\/805721","published_doi":"10.1186\/s12864-020-6595-z","published_journal":"BMC Genomics","preprint_platform":"bioRxiv","preprint_title":"New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species","preprint_authors":"Roach, M. J.; Borneman, A. R.","preprint_category":"genomics","preprint_date":"2019-10-16","published_date":"2020-03-02","preprint_abstract":"BackgroundYeast of the genus Brettanomyces are of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. However, considerable variance exists in the depth of research and knowledgebase of the five currently known species of Brettanomyces. For instance, Brettanomyces bruxellensis has been heavily studied and many resources are available for this species, whereas Brettanomyces nanus is rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus.\\n\\nResultsStrains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B. bruxellensis, Brettanomyces custersianus, Brettanomyces naardenensis, and B. nanus) were sequenced using a combination of long- and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Sweeping and extensive structural variation between the species genomes were observed and gene expansions in fermentation-relevant genes (particularly in B. bruxellensis and B. nanus) were identified. Numerous horizontal gene transfer (HGT) events in all Brettanomyces species, including an HGT event that is probably responsible for allowing B. bruxellensis and B. anomalus to utilize sucrose were also observed.\\n\\nConclusionsGenomic adaptations and some evidence of domestication that have taken place in Brettanomycesare outlined. These new genome assemblies form a valuable resource for future research in Brettanomyces.","preprint_author_corresponding":"Anthony R Borneman","preprint_author_corresponding_institution":"Australian Wine Research Institute"},{"preprint_doi":"10.1101\/532457","published_doi":"10.3390\/pathogens9030176","published_journal":"Pathogens","preprint_platform":"bioRxiv","preprint_title":"Upscaling surveillance of tick-borne pathogens in the French Caribbean islands","preprint_authors":"Gondard, M.; Delannoy, S.; Pinarello, V.; Aprelon, R.; Devillers, E.; Galon, C.; Pradel, J.; Vayssier-Taussat, M.; Albina, E.; MOUTAILLER, S.","preprint_category":"epidemiology","preprint_date":"2019-02-01","published_date":"2020-03-03","preprint_abstract":"Despite the high burden of vector-borne disease in (sub)-tropical areas, few information are available regarding the diversity of tick and tick-borne pathogens circulating in the Caribbean. Management and control of vector-borne disease require actual epidemiological data to better assess and anticipate the risk of (re)-emergence of tick-borne diseases in the region. To simplify and reduce the costs of such large-scale surveys, we implemented a high-throughput microfluidic real-time PCR system suitable for the screening of the main bacterial and parasitic genera involved in tick-borne disease and potentially circulating in the area. We used the new screening tool to perform an exploratory epidemiological study on 132 specimens of Amblyomma variegatum and 446 of Rhipicephalus microplus collected in Guadeloupe and Martinique. Not only the system was able to detect the main pathogens of the area- Ehrlichia ruminantium, Rickettsia africae, Anaplasma marginale, Babesia bigemina, Babesia bovis- but the system also provided evidence of unsuspected microorganisms in Caribbean ticks, belonging to the Anaplasma, Ehrlichia, Borrelia and Leishmania genera. Our study demonstrated how high-throughput microfluidic real-time PCR technology can assist large-scale epidemiological studies, providing a rapid overview of tick-borne pathogen and microorganism diversity, and opening up new research perspectives for the epidemiology of tick-borne pathogens.","preprint_author_corresponding":"Sara  Moutailler","preprint_author_corresponding_institution":"UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons-Alfort, France"},{"preprint_doi":"10.1101\/722033","published_doi":"10.1214\/19-STS7561","published_journal":"Statistical Science","preprint_platform":"bioRxiv","preprint_title":"Statistical inference for the evolutionary history of cancer genomes","preprint_authors":"\u0110inh, K. N.; Jaksik, R.; Kimmel, M.; Lambert, A.; Tavare, S.","preprint_category":"cancer biology","preprint_date":"2019-08-01","published_date":"2020-03-03","preprint_abstract":"Recent years have produced a large amount of work on inference about cancer evolution from mutations identified in cancer samples. Much of the modeling work has been based on classical models of population genetics, generalized to accommodate time-varying cell population size. Reverse-time genealogical views of such models, commonly known as coalescents, have been used to infer aspects of the past of growing populations. Another approach is to use branching processes, the simplest scenario being the linear birth-death process (lbdp), a binary fission Markov age-dependent branching process. A genealogical view of such models is also available. The two approaches lead to similar but not identical results. Inference from evolutionary models of DNA often exploits summary statistics of the sequence data, a common one being the so-called Site Frequency Spectrum (SFS). In a sequencing experiment with a known number of sequences, we can estimate for each site at which a novel somatic mutation has arisen, the number of cells that carry that mutation. These numbers are then grouped into sites which have the same number of copies of the mutant. SFS can be computed from the statistics of mutations in a sample of cells, in which DNA has been sequenced. In this paper, examine how the SFS based on birth-death processes differ from those based on the coalescent model. This may stem from the different sampling mechanisms in the two approaches. However, we also show mathematically and computationally that despite this, they can be made quantitatively comparable at least for the range of parameters typical for tumor cell populations. We also present a model of tumor evolution with selective sweeps, based on coalescence, and demonstrate how it may help in understanding the past history of tumor as well the influence of data pre-processing. We illustrate the theory with applications to several examples of The Cancer Genome Atlas tumors.","preprint_author_corresponding":"Marek  Kimmel","preprint_author_corresponding_institution":"Rice University"},{"preprint_doi":"10.1101\/813584","published_doi":"10.7554\/eLife.52330","published_journal":"eLife","preprint_platform":"bioRxiv","preprint_title":"Tumors attenuating the mitochondrial activity in T cells escape from PD-1 blockade therapy","preprint_authors":"Honjo, T.; Kumar, A.; Chamoto, K.; Chowdhury, P. S.","preprint_category":"immunology","preprint_date":"2019-10-21","published_date":"2020-03-03","preprint_abstract":"PD-1 blockade therapy has revolutionized cancer treatments. However, a substantial population of patients is unresponsive. To rescue unresponsive patients, the mechanism of unresponsiveness to PD-1 blockade therapy must be elucidated. Using a  bilateral tumor model where responsive and unresponsive tumors were inoculated into different sides of the mouse belly, we demonstrated that unresponsive tumors can be categorized into two groups: with and without systemic immunosuppressive property (SIP). The SIP-positive tumors released uncharacterized, non-proteinaceous small molecules which inhibited T cell proliferation and mitochondrial activation. By contrast, the SIP-negative B16 tumor, escaped from immunity by losing MHC class I expression. Unresponsiveness of SIP-positive tumors was partially overcome by improving the mitochondrial function with a mitochondrial activator; this was not successful to B16, which employs immune ignorance. These results demonstrated that our  bilateral tumor model was useful for stratifying tumors to investigate the mechanism of unresponsiveness and develop strategy for proper combination therapy.","preprint_author_corresponding":"Tasuku  Honjo","preprint_author_corresponding_institution":"Kyoto University"},{"preprint_doi":"10.1101\/2020.02.18.955286","published_doi":"10.1093\/nsr\/nwaa033","published_journal":"National Science Review","preprint_platform":"bioRxiv","preprint_title":"CasRx-mediated RNA targeting prevents choroidal neovascularization in a mouse model of age-related macular degeneration","preprint_authors":"Zhou, C.; Hu, X.; Tang, C.; Liu, W.; Wang, S.; Zhou, Y.; Zhao, Q.; Bo, Q.; Shi, L.; Sun, X.; Zhou, H.; Yang, H.","preprint_category":"genetics","preprint_date":"2020-02-20","published_date":"2020-03-02","preprint_abstract":"The smallest Cas13 family protein, CasRx, has a high cleavage activity and targeting specificity, offering attractive opportunity for therapeutic applications. Here we report that delivery of CasRx by adeno-associated virus via intravitreal injection could efficiently knockdown Vegfa transcripts and significantly reduce the area of laser-induced choroidal neovascularization in a mouse model of age-related macular degeneration. Thus, RNA-targeting CRISPR system could be used for in vivo gene therapy.","preprint_author_corresponding":"Hui  Yang","preprint_author_corresponding_institution":"nstitute of Neuroscience, Chinese Academy of Sciences"},{"preprint_doi":"10.1101\/563056","published_doi":"10.1038\/s41467-020-14845-5","published_journal":"Nature Communications","preprint_platform":"bioRxiv","preprint_title":"Do direct nose-to-brain pathways underlie intranasal oxytocin-induced changes in regional cerebral blood flow in humans?","preprint_authors":"Martins, D.; Mazibuko, N.; Zelaya, F.; Vasilakopoulou, S.; Loveridge, J.; Oates, A.; Maltezos, S.; Mehta, M.; Howard, M.; McAlonan, G.; Murphy, D.; Williams, S.; Fotopoulou, A.; Schuschnig, U.; Paloyelis, Y.","preprint_category":"neuroscience","preprint_date":"2019-02-28","published_date":"2020-03-03","preprint_abstract":"Could nose-to-brain pathways mediate the effects of peptides such as oxytocin (OT) on brain physiology when delivered intranasally? We address this question by contrasting two methods of intranasal administration (a standard nasal spray, and a nebulizer expected to improve OT deposition in nasal areas putatively involved in direct nose-to-brain transport) to intravenous administration in terms of effects on regional cerebral blood flow during two hours post-dosing. We demonstrate that OT-induced decreases in amygdala perfusion, a key hub of the OT central circuitry, are explained entirely by OT increases in systemic circulation following both intranasal and intravenous OT administration. Yet we also provide robust evidence confirming the validity of the intranasal route to target specific brain regions. Our work has important translational implications and demonstrates the need to carefully consider the method of administration in our efforts to engage specific central oxytocinergic targets for the treatment of neuropsychiatric disorders.","preprint_author_corresponding":"Yannis  Paloyelis","preprint_author_corresponding_institution":"Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, KCL"},{"preprint_doi":"10.1101\/627505","published_doi":"10.1038\/s41467-020-14952-3","published_journal":"Nature Communications","preprint_platform":"bioRxiv","preprint_title":"Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons","preprint_authors":"Hodge, R. D.; Miller, J. A.; Novotny, M. D.; Kalmbach, B. D.; Ting, J. T.; Bakken, T. E.; Aevermann, B. D.; Barkan, E. R.; Berkowitz-Cerasano, M. L.; Cobbs, C.; Diez-Fuertes, F.; Ding, S.-L.; McCorrison, J.; Schork, N. J.; Shehata, S. I.; Smith, K. A.; Sunkin, S. M.; Tran, D. N.; Venepally, P.; Yanny, A. M.; Steemers, F. J.; Phillips, J. W.; Bernard, A.; Koch, C.; Lasken, R. S.; Scheuermann, R. H.; Lein, E. S.","preprint_category":"neuroscience","preprint_date":"2019-05-07","published_date":"2020-03-03","preprint_abstract":"von Economo neurons (VENs) are bipolar, spindle-shaped neurons restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear to be selectively vulnerable to neuropsychiatric and neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing of frontoinsula layer 5 identified a transcriptomically-defined cell cluster that contained VENs, but also fork cells and a subset of pyramidal neurons. Cross-species alignment of this cell cluster with a well-annotated mouse classification shows strong homology to extratelencephalic (ET) excitatory neurons that project to subcerebral targets. This cluster also shows strong homology to a putative ET cluster in human temporal cortex, but with a strikingly specific regional signature. Together these results predict VENs are a regionally distinctive type of ET neuron, and we additionally describe the first patch clamp recordings of VENs from neurosurgically-resected tissue that show distinctive intrinsic membrane properties relative to neighboring pyramidal neurons.","preprint_author_corresponding":"Ed S Lein","preprint_author_corresponding_institution":"Allen Institute for Brain Science"},{"preprint_doi":"10.1101\/666594","published_doi":"10.1038\/s41467-020-14965-y","published_journal":"Nature Communications","preprint_platform":"bioRxiv","preprint_title":"Molecular and cellular determinants of motor asymmetry in zebrafish","preprint_authors":"Horstick, E. J.; Bayleyen, Y.; Burgess, H. A.","preprint_category":"neuroscience","preprint_date":"2019-06-11","published_date":"2020-03-03","preprint_abstract":"Asymmetries in motor behavior, such as human hand preference, are observed throughout bilateria. However, neural substrates and developmental signaling pathways that impose underlying functional lateralization on a broadly symmetric nervous system are unknown. Here we report that in the absence of over-riding visual information, zebrafish larvae show intrinsic lateralized motor behavior that is mediated by a cluster of 60 posterior tuberculum (PT) neurons in the forebrain. PT neurons impose motor bias via a projection through the epithalamic commissure to the habenula. Acquisition of left\/right identity is disrupted by heterozygous mutations in mosaic eyes and mindbomb, genes that regulate Notch signaling. These results define the neuronal substrate for motor asymmetry in a vertebrate and support the idea that developmental pathways that establish visceral asymmetries also govern acquisition of left\/right identity.","preprint_author_corresponding":"Harold Antony Burgess","preprint_author_corresponding_institution":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"},{"preprint_doi":"10.1101\/809947","published_doi":"10.1038\/s41598-020-60943-1","published_journal":"Scientific Reports","preprint_platform":"bioRxiv","preprint_title":"Decomposing Simon task BOLD activation using a drift-diffusion model framework","preprint_authors":"McIntosh, J. R.; Sajda, P.","preprint_category":"neuroscience","preprint_date":"2019-10-21","published_date":"2020-03-03","preprint_abstract":"The Simon effect is observed in spatial conflict tasks where the response time of subjects is increased if stimuli are presented in a lateralized manner so that they are incongruous with the response information that they represent symbolically. Previous studies have used fMRI to investigate this phenomenon, and while some have been driven by considerations of an underlying model, none have attempted to directly tie model and BOLD response together. It is likely that this is due to Simon models having been predominantly descriptive of the phenomenon rather than capturing the full spectrum of behavior at the level of individual subjects. Sequential sampling models (SSM) which capture full response distributions for correct and incorrect responses have recently been extended to capture conflict tasks.\\n\\nIn this study we use our freely available framework for fitting and comparing non-standard SSM to fit the Simon effect SSM (SE-SSM) to behavioral data. This model extension includes specific estimates of automatic response bias and conflict monitoring based deployment of attention to individual subject behavioral data. We apply this approach in order to investigate whether our task specific model parameters have a correlate in BOLD response. Under the assumption that the SE-SSM reflects aspects of neural processing in this task, we go on to examine the BOLD correlates with the within trial expected decision-variable.\\n\\nWe find that the SE-SSM captures the behavioral data and that our two conflict specific model parameters have clear across subject BOLD correlates, while other model parameters, as well as more standard behavioral measures do not. We also find that examining BOLD in terms of the expected decision-variable leads to a specific pattern of activation that would not be otherwise possible to extract.","preprint_author_corresponding":"James R McIntosh","preprint_author_corresponding_institution":"Columbia University"},{"preprint_doi":"10.1101\/688697","published_doi":"10.3389\/fgene.2020.00138","published_journal":"Frontiers in Genetics","preprint_platform":"bioRxiv","preprint_title":"Functional analysis of KIT gene structural mutations causing porcine dominant white phenotype by using genome edited mouse models","preprint_authors":"Sun, G.; He, Z.; Liang, X.; Qin, K.; Qin, Y.; Shi, X.; Cong, P.; Mo, D.; Liu, X.; Chen, Y.","preprint_category":"molecular biology","preprint_date":"2019-07-01","published_date":"2020-03-03","preprint_abstract":"Dominant white phenotype in pigs is considered to be caused by two structural mutations in KIT gene, including a 450-kb duplication encompassing the entire KIT gene, and a splice mutation (G > A) at the first base in intron 17, which leads to the deletion of exon 17 in mature KIT mRNA, and the production of KIT protein lacking a critical catalytic domain of kinase. However, this speculation has not yet been validated by functional studies. Here, by using CRISPR\/Cas9 technology, we created two mouse models mimicing the structural mutations of KIT gene in dominant white pigs, including the splice mutation mouse model KIT D17\/+ with exon 17 of one allele of KIT gene deleted, and duplication mutation mouse model KIT Dup\/+ with one allele of KIT gene coding sequence (CDS) duplicated. We found that each mutation individually can not cause dominant white phenotype. Splice mutation homozygote is lethal and heterozygous mice present piebald coat. Inconsistent with previous speculation, we found KIT gene duplication mutation did not confer the patched phenotype, and had no obvious impact on coat color. Interestingly, combination of these two mutations lead to dominant white phenotype. Further molecular analysis revealed that combination of these two structural mutations could inhibit the kinase activity of the KIT protein, thus reduce the phosphorylation level of PI3K and MAPK pathway associated proteins, which may be related to the observed impaired migration of melanoblasts during embryonic development, and eventually lead to dominant white phenotype. Our study provides a further insight into the underlying genetic mechanisms of porcine dominant white coat colour.\\n\\nAuthor summaryKIT plays a critical role in control of coat colour in mammals. Two mutation coexistence in KIT are considered to be the cause of the Dominant white phenotype in pigs. One mutation is a 450-kb large duplication encompassing the entire KIT gene, another mutation is a splice mutation causing the skipping of KIT exon 17. The mechanism of these two mutations of KIT on coat color formation has not yet been validated. In this study, by using genome edited mouse models, we found each structural mutation individual does not lead dominant white phenotype, but combination of these two mutations could lead to a nearly complete white coat colour similar to pig dominant white phenotype, possibly due to the inhibition of the kinase activity of the KIT protein, thus its signalling function on PI3K and MAPK pathways, leading to impaired migration of melanoblasts during embryonic development, and eventually lead to dominant white phenotype. Our study provides a further insight into the underlying genetic mechanisms of porcine dominant white coat colour.","preprint_author_corresponding":"Zuyong  He","preprint_author_corresponding_institution":"Sun Yat-Sen University"},{"preprint_doi":"10.1101\/802926","published_doi":"10.1094\/PBIOMES-09-19-0055-FI","published_journal":"Phytobiomes Journal","preprint_platform":"bioRxiv","preprint_title":"Switchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen Availability","preprint_authors":"Smercina, D.; Bowsher, A. W.; Evans, S. E.; Friesen, M. L.; Eder, E. K.; Hoyt, D. W.; Tiemann, L. K.","preprint_category":"ecology","preprint_date":"2019-10-16","published_date":"2020-03-03","preprint_abstract":"Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. We found switchgrass root exudate chemistry to be more responsive to N availability than to diazotroph presence. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment suggesting a potential for switchgrass to respond or even recruit diazotrophs. However, we found little evidence of N treatment and inoculation interaction effects which suggests switchgrass response to diazotroph presence is not mediated by N availability.","preprint_author_corresponding":"Darian  Smercina","preprint_author_corresponding_institution":"Michigan State University"},{"preprint_doi":"10.1101\/662940","published_doi":"10.1186\/s13059-020-01968-7","published_journal":"Genome Biology","preprint_platform":"bioRxiv","preprint_title":"NanoVar: Accurate Characterization of Patients\u2019 Genomic Structural Variants Using Low-Depth Nanopore Sequencing","preprint_authors":"Tham, C. Y.; Tirado-Magallanes, R.; Goh, Y.; Fullwood, M. J.; Koh, B. T. H.; Wang, W.; Ng, C. H.; Chng, W. J.; Thiery, A.; Tenen, D. G.; Benoukraf, T.","preprint_category":"bioinformatics","preprint_date":"2019-06-17","published_date":"2020-03-03","preprint_abstract":"Despite the increasing relevance of structural variants (SV) in the development of many human diseases, progress in novel pathological SV discovery remains impeded, partly due to the challenges of accurate and routine SV characterization in patients. The recent advent of third-generation sequencing (3GS) technologies brings promise for better characterization of genomic aberrations by virtue of having longer reads. However, the applications of 3GS are restricted by their high sequencing error rates and low sequencing throughput. To overcome these limitations, we present NanoVar, an accurate, rapid and low-depth (4X) 3GS SV caller utilizing long-reads generated by Oxford Nanopore Technologies. NanoVar employs split-reads and hard-clipped reads for SV detection and utilizes a neural network classifier for true SV enrichment. In simulated data, NanoVar demonstrated the highest SV detection accuracy (F1 score = 0.91) amongst other long-read SV callers using 12 gigabases (4X) of sequencing data. In patient samples, besides the detection of genomic aberrations, NanoVar also uncovered many normal alternative sequences or alleles which were present in healthy individuals. The low sequencing depth requirements of NanoVar enable the use of Nanopore sequencing for accurate SV characterization at a lower sequencing cost, an approach compatible with clinical studies and large-scale SV-association research.","preprint_author_corresponding":"Touati  Benoukraf","preprint_author_corresponding_institution":"Memorial University of Newfoundland"},{"preprint_doi":"10.1101\/456491","published_doi":"10.15252\/embj.2019103949","published_journal":"The EMBO Journal","preprint_platform":"bioRxiv","preprint_title":"Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells","preprint_authors":"HIGASHIJIMA, Y.; MATSUI, Y.; SHIMAMURA, T.; TSUTSUMI, S.; NAKAKI, R.; ABE, Y.; LINK, V. M.; OSAKA, M.; YOSHIDA, M.; WATANABE, R.; TANAKA, T.; TAGUCHI, A.; MIURA, M.; INOUE, T.; NANGAKU, M.; KIMURA, H.; FURUKAWA, T.; ABURATANI, H.; WADA, Y.; GLASS, C. K.; KANKI, Y.","preprint_category":"molecular biology","preprint_date":"2018-11-11","published_date":"2020-03-03","preprint_abstract":"Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are generally linked to gene repression. However, the functions of repressive histone methylation dynamics during inflammatory responses remain enigmatic. We found that tumor necrosis factor (TNF)- rapidly induces the co-occupancy of lysine demethylases 7A (KDM7A) and 6A (UTX) with nuclear factor kappa-B (NF-{kappa}B) recruited elements in human endothelial cells. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and both are required for activation of NF-{kappa}B-dependent inflammatory genes. Chromosome conformation capture-based methods demonstrated increased interactions between TNF--induced super enhancers at NF-{kappa}B-relevant loci, coinciding with KDM7A- and UTX-recruitment. Simultaneous inhibition of KDM7A and UTX significantly reduced leukocyte adhesion in mice, establishing the biological and potential translational relevance of this mechanism. Collectively, these findings suggest that rapid erasure of repressive histone marks by KDM7A and UTX is essential for NF-{kappa}B-dependent regulation of genes that control inflammatory responses of endothelial cells.\\n\\nHIGHLIGHTSO_LIKDM7A and UTX cooperatively control NF-{kappa}B-dependent transcription in vascular endothelial cells.\\nC_LIO_LIDemethylation of repressive histone marks by KDM7A and UTX is critical for early inflammatory responses.\\nC_LIO_LIKDM7A and UTX are associated with TNF--induced looping of super enhancers.\\nC_LIO_LIPharmacological inhibition of KDM7A and UTX reduces leukocyte adhesive interactions with endothelial cells in mice.\\nC_LI","preprint_author_corresponding":"Yasuharu  KANKI","preprint_author_corresponding_institution":"Isotope Science Center, The University of Tokyo"},{"preprint_doi":"10.1101\/845420","published_doi":"10.1088\/1361-6528\/ab7a2b","published_journal":"Nanotechnology","preprint_platform":"bioRxiv","preprint_title":"Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites","preprint_authors":"Miller, H.; Contera, S. A.; Wollman, A. J. M.; Hirst, A.; Dunn, K.; Schroeter, S.; O'Connell, D.; Leake, M. C.","preprint_category":"biophysics","preprint_date":"2019-11-16","published_date":"2020-03-03","preprint_abstract":"Intercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.","preprint_author_corresponding":"Mark C Leake","preprint_author_corresponding_institution":"University of York"},{"preprint_doi":"10.1101\/572099","published_doi":"10.1083\/jcb.201908006","published_journal":"Journal of Cell Biology","preprint_platform":"bioRxiv","preprint_title":"Chromosomes function as a barrier to mitotic spindle bipolarity in polyploid cells","preprint_authors":"Goupil, A.; Nano, M.; Letort, G.; Gogendeau, D.; Pennetier, C.; Basto, R.","preprint_category":"cell biology","preprint_date":"2019-03-09","published_date":"2020-03-03","preprint_abstract":"Whole genome duplications (WGDs) are found in a variety of tumors and are associated with chromosomal instability (CIN) and poor prognosis [1,2]. When induced experimentally, through cytokinesis failure, polyploid cells generate tumors [3]. Cytokinesis failure results in the accumulation of double DNA content, but also of cytoplasmic organelles, such as centrosomes, which are the major microtubule (MT) organizing centers of animal cells. Importantly, even if there is a correlation between polyploidy and CIN [4], the underlying mechanisms generating error-prone mitosis in cells with extra DNA and extra centrosomes are not known. When considering polyploid mitosis, it is essential to take into account the increase in MT nucleation due to the presence of extra centrosomes and extra DNA. The presence of supernumerary centrosomes in a cell, centrosome amplification [5], is associated with mitotic spindle multipolarity and CIN [6-9]. Importantly, additional MTs can be nucleated from the chromatin (chromatin mediated pathway-CMP) or from pre-existing MTs-through the Augmin pathway. We hypothesized that the increase in DNA and centrosome content in a cell could lead to an increased MT mass, which might account for abnormal mitosis described in polyploid cells [4, 10, 11, 12]. Using genetics, live imaging and modeling approaches, we investigated the mechanisms establishing multipolarity in vivo in polyploid cells. We found that MT nucleation from the centrosomes is the major contributor to multipolarity, while other pathways seem to play minor roles. Unexpectedly, we found that even if Ncd\/HSET, plays an essential role in promoting centrosome clustering in early mitosis, the increase in chromosome mass associated with cytokinesis failure functions as a barrier to centrosome clustering into two main poles. Our work provides a mechanistic link between polyploidy and the generation of CIN.","preprint_author_corresponding":"Renata  Basto","preprint_author_corresponding_institution":"Institut Curie"},{"preprint_doi":"10.1101\/489674","published_doi":"10.1016\/j.cmet.2020.02.001","published_journal":"Cell Metabolism","preprint_platform":"bioRxiv","preprint_title":"Bacteria boost mammalian host NAD metabolism by engaging the deamidated biosynthesis pathway","preprint_authors":"Shats, I.; Liu, J.; Williams, J. G.; Deterding, L. J.; Lim, C.; Lee, E.; Fan, W.; Sokolsky, M.; Kabanov, A. V.; Locasale, J.; Li, X.","preprint_category":"biochemistry","preprint_date":"2018-12-07","published_date":"2020-03-03","preprint_abstract":"Nicotinamide adenine dinucleotide (NAD), a cofactor for hundreds of metabolic reactions in all cell types, plays an essential role in diverse cellular processes including metabolism, DNA repair, and aging 1. NAD metabolism is critical to maintain cellular homeostasis in response to the environment, and disruption of this homeostasis is associated with decreased cellular NAD levels in aging 2. Conversely, elevated NAD synthesis is required to sustain the increased metabolic rate of cancer cells 3,4. Consequently, therapeutic strategies aimed to both upregulate NAD (i.e. NAD-boosting nutriceuticals) or downregulate NAD (inhibitors of key NAD synthesis enzymes) are being actively investigated 5-10. However, how this essential metabolic pathway is impacted by the environment remains unclear. Here, we report an unexpected trans-kingdom cooperation between bacteria and mammalian cells wherein bacteria contribute to host NAD biosynthesis. Bacteria confer cancer cells with the resistance to inhibitors of NAMPT, the rate limiting enzyme in the main vertebrate NAD salvage pathway. Mechanistically, a microbial nicotinamidase (PncA) that converts nicotinamide to nicotinic acid, a key precursor in the alternative deamidated NAD salvage pathway, is necessary and sufficient for this protective effect. This bacteria-enabled resistance mechanism that allows the mammalian host to bypass the drug-induced metabolic block represents a novel paradigm in drug resistance. This host-microbe metabolic interaction also enables bacteria to dramatically enhance the NAD-boosting efficiency of nicotinamide supplementation in vitro and in vivo, demonstrating a crucial role of microbes, gut microbiota in particular, in organismal NAD metabolism.","preprint_author_corresponding":"Xiaoling  Li","preprint_author_corresponding_institution":"National Institute of Environmental Health Sciences"},{"preprint_doi":"10.1101\/2019.12.13.876110","published_doi":"10.1016\/j.celrep.2020.02.018","published_journal":"Cell Reports","preprint_platform":"bioRxiv","preprint_title":"Wss1 promotes replication stress tolerance by degrading histones.","preprint_authors":"Maddi, K.; Sam, D. K.; Bonn, F.; Prgomet, S.; Tulowetzke, E.; Akutsu, M.; Lopez-Mosqueda, J.; Dikic, I.","preprint_category":"cell biology","preprint_date":"2019-12-14","published_date":"2020-03-03","preprint_abstract":"Timely completion of DNA replication is central to accurate cell division and to the maintenance of genomic stability. However, certain DNA-protein interactions can physically impede DNA replication fork progression. Cells remove or bypass these physical impediments by different mechanisms to preserve DNA macromolecule integrity and genome stability. In Saccharomyces cerevisiae, Wss1, the DNA-protein crosslink repair protease, allows cells to tolerate hydroxyurea-induced replication stress but the underlying mechanism by which Wss1 promotes this function has remained unknown. Here we report that Wss1 provides cells tolerance to replication stress by directly degrading core histone subunits that non-specifically and non-covalently bind to single-stranded DNA. Unlike Wss1-dependent proteolysis of covalent DNA-protein crosslinks, proteolysis of histones does not require Cdc48 nor SUMO-binding activities. Wss1 thus acts as a multi-functional protease capable of targeting a broad range of covalent and non-covalent DNA-binding proteins to preserve genome stability during adverse conditions.","preprint_author_corresponding":"Ivan  Dikic","preprint_author_corresponding_institution":"Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern- Kai 7, 60590 Frankfurt am Main, Germany"},{"preprint_doi":"10.1101\/740902","published_doi":"10.1016\/j.celrep.2020.02.033","published_journal":"Cell Reports","preprint_platform":"bioRxiv","preprint_title":"Synthetic cassettes for pH-mediated sensing, counting and containment","preprint_authors":"Stirling, F.; Naydich, A.; Bramante, J.; Barocio, R.; Certo, M.; Wellington, H.; Redfield, E.; O'Keefe, S.; Gao, S.; Cusolito, A.; Way, J.; Silver, P. A.","preprint_category":"synthetic biology","preprint_date":"2019-08-20","published_date":"2020-03-03","preprint_abstract":"AbstractAs pH is fundamental to all biological processes, pH-responsive bacterial genetic circuits enable precise sensing in any environment. Where unintentional release of engineered bacteria poses a concern, coupling pH sensing to expression of a toxin creates an effective bacterial containment system. Here, we present a pH-sensitive kill switch (acidic Termination of Replicating Population; acidTRP), based on the E. coli asr promoter, with a survival ratio of less than 1 in 106. We integrate acidTRP with cryodeath to produce a two-factor containment system with a combined survival ratio of less than 1 in 1011 whilst maintaining evolutionary stability. We further develop a pulse-counting circuit with single cell readout for each administered stimulus pulse. We use this pulse-counter to record multiple pH changes and combine it with acidTRP to make a two-count acid-sensitive kill switch. These results demonstrate the ability to build complex genetic systems for biological containment.","preprint_author_corresponding":"Pamela A. Silver","preprint_author_corresponding_institution":"Harvard Medical School"},{"preprint_doi":"10.1101\/2019.12.23.885186","published_doi":"10.1016\/j.celrep.2020.02.028","published_journal":"Cell Reports","preprint_platform":"bioRxiv","preprint_title":"Microglial homeostasis requires balanced CSF-1\/CSF-2 receptor signaling","preprint_authors":"Chitu, V.; Biundo, F.; Shlager, G. G. L.; Park, E. S.; Wang, P.; Gulinello, M. E.; Gokhan, S.; Ketchum, H. C.; Saha, K.; DeTure, M. A.; Dickson, D. W.; Wszolek, Z. K.; Zheng, D.; Croxford, A. L.; Becher, B.; Sun, D.; Mehler, M. F.; Stanley, E. R.","preprint_category":"neuroscience","preprint_date":"2019-12-23","published_date":"2020-03-03","preprint_abstract":"CSF-1R haploinsufficiency causes adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP). Previous studies in the Csf1r+\/- mouse model of ALSP hypothesized a central role of elevated cerebral Csf2 expression. Here we show that monoallelic deletion of Csf2 rescues most behavioral deficits and histopathological changes in Csf1r+\/- mice by preventing microgliosis and eliminating most microglial transcriptomic alterations, including those indicative of oxidative stress and demyelination. We also show elevation of Csf2 transcripts and of several CSF-2 downstream targets in the brains of ALSP patients, demonstrating that the mechanisms identified in the mouse model are functional in man. Our data provide new insights into the mechanisms underlying ALSP. Since both increased CSF2 levels and decreased microglial Csf1r expression have also been reported in Alzheimers disease and multiple sclerosis, we suggest that the unbalanced CSF-1R\/CSF-2 signaling we describe in the present study may contribute to the pathogenesis of other neurodegenerative conditions.\n\nHighlightsO_LIALSP is a CSF1R-deficiency dementia associated with increased CSF2 expression\nC_LIO_LIIn Csf1r+\/- ALSP mice CSF-2 promotes microgliosis by direct signaling in microglia\nC_LIO_LITargeting Csf2 improves cognition, myelination and normalizes microglial function\nC_LIO_LICSF-2 is a therapeutic target in ALSP\nC_LI","preprint_author_corresponding":"E. Richard  Stanley","preprint_author_corresponding_institution":"Albert Einstein College of Medicine"},{"preprint_doi":"10.1101\/586081","published_doi":"10.1016\/j.celrep.2020.02.039","published_journal":"Cell Reports","preprint_platform":"bioRxiv","preprint_title":"Germline features associated with immune infiltration in solid tumors","preprint_authors":"Shahamatdar, S.; He, M. X.; Reyna, M.; Gusev, A.; AlDubayan, S. H.; Van Allen, E. M.; Ramachandran, S.","preprint_category":"genetics","preprint_date":"2019-03-24","published_date":"2020-03-03","preprint_abstract":"Given the clinical success of immune checkpoint blockade (ICB) across a diverse set of solid tumors, and the emerging role for different immune infiltrates in contributing to response to ICB, a comprehensive assessment of the properties that dictate immune infiltrations may reveal new biological insights and inform the development of new effective therapies. Multiple studies have examined somatic and functional immune properties associated with different tumor infiltrates; however, germline features that associate with specific immune infiltrates in cancers have been incompletely characterized. Here, we analyzed over 7 million autosomal germline variants in the TCGA cohort (5788 European-ancestry samples across 30 cancer types) and tested for pan-cancer association with established immune-related phenotypes that describe the tumor immune microenvironment. We identified: one SNP associated with the fraction of follicular helper T cells in bulk tumor; 77 unique candidate genes, some of which are involved in cytokine-mediated signaling (e.g. CNTF and TRIM34) and cancer pathogenesis (e.g. ATR and AKAP9); and subnetworks with genes that are part of DNA repair (RAD51 and XPC) and transcription elongation (CCNT2) pathways. We found a positive association between polygenic risk for rheumatoid arthritis and absolute fraction of infiltrating CD8 T cells. Overall, we identified multiple germline genetic features associated with specific tumor-immune phenotypes across cancer, and developed a framework for probing inherited features that contribute to variation in immune infiltration.","preprint_author_corresponding":"Sahar  Shahamatdar","preprint_author_corresponding_institution":"Center for Computational Molecular Biology, Brown University"},{"preprint_doi":"10.1101\/819961","published_doi":"10.1016\/j.chembiol.2020.02.003","published_journal":"Cell Chemical Biology","preprint_platform":"bioRxiv","preprint_title":"Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors","preprint_authors":"Sivakumaren, S. C.; Shim, H.; Zhang, T.; Ferguson, F. M.; Lundquist, M. R.; Browne, C. M.; Seo, H.-S.; Paddock, M. N.; Manz, T. D.; Jiang, B.; Hao, M.-F.; Krishnan, P.; Wang, D. G.; Yang, T. J.; Kwiatkowski, N. P.; Ficarro, S. B.; Cunningham, J. M.; Marto, J. A.; Dhe-Paganon, S.; Cantley, L. C.; Gray, N. S.","preprint_category":"cancer biology","preprint_date":"2019-10-25","published_date":"2020-03-03","preprint_abstract":"The PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here we present the discovery and characterization of a novel pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4K\/{beta}\/{gamma}. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML\/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4Ks reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.","preprint_author_corresponding":"Nathanael S  Gray","preprint_author_corresponding_institution":"Department of Cancer Biology, Dana Farber Cancer Institute"},{"preprint_doi":"10.1101\/611780","published_doi":"10.1016\/j.celrep.2020.02.030","published_journal":"Cell Reports","preprint_platform":"bioRxiv","preprint_title":"Single-cell analysis of Foxp1-driven mechanisms essential for striatal development","preprint_authors":"Anderson, A. G.; Kulkarni, A.; Harper, M.; Konopka, G.","preprint_category":"neuroscience","preprint_date":"2019-04-18","published_date":"2020-03-03","preprint_abstract":"The striatum is a critical forebrain structure for integrating cognitive, sensory, and motor information from diverse brain regions into meaningful behavioral output. However, the transcriptional mechanisms that underlie striatal development and organization at single-cell resolution remain unknown. Here, we show that Foxp1, a transcription factor strongly linked to autism and intellectual disability, regulates organizational features of striatal circuitry in a cell-type-dependent fashion. Using single-cell RNA-sequencing, we examine the cellular diversity of the early postnatal striatum and find that cell-type-specific deletion of Foxp1 in striatal projection neurons alters the cellular composition and neurochemical architecture of the striatum. Importantly, using this approach, we identify the non-cell autonomous effects produced by disrupting Foxp1 in one cell-type and the molecular compensation that occurs in other populations. Finally, we identify Foxp1-regulated target genes within distinct cell-types and connect these molecular changes to functional and behavioral deficits relevant to phenotypes described in patients with FOXP1 loss-of-function mutations. These data reveal cell-type-specific transcriptional mechanisms underlying distinct features of striatal circuitry and identify Foxp1 as a key regulator of striatal development.","preprint_author_corresponding":"Genevieve  Konopka","preprint_author_corresponding_institution":"UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER"},{"preprint_doi":"10.1101\/2019.12.20.883629","published_doi":"10.1016\/j.tpb.2020.01.002","published_journal":"Theoretical Population Biology","preprint_platform":"bioRxiv","preprint_title":"Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent","preprint_authors":"Uyenoyama, M. K.; Takebayashi, N.; Kumagai, S.","preprint_category":"evolutionary biology","preprint_date":"2019-12-26","published_date":"2020-03-03","preprint_abstract":"We address the effect of population structure on key properties of the Ewens sampling formula. We use our previously-introduced inductive method for determining exact allele frequency spectrum (AFS) probabilities under the infinite-allele model of mutation and population structure for samples of arbitrary size. Fundamental to the sampling distribution is the novel-allele probability, the probability that given the pattern of variation in the present sample, the next gene sampled belongs to an as-yet-unobserved allelic class. Unlike the case for panmictic populations, the novel-allele probability depends on the AFS of the present sample. We derive a recursion that directly provides the marginal novel-allele probability across AFSs, obviating the need first to determine the probability of each AFS. Our explorations suggest that the marginal novel-allele probability tends to be greater for initial samples comprising fewer alleles and for sampling configurations in which the next-observed gene derives from a deme different from that of the majority of the present sample. Comparison to the efficient importance sampling proposals developed by De Iorio and Griffiths and colleagues indicates that their approximation for the novel-allele probability generally agrees with the true marginal, although it may tend to overestimate the marginal in cases in which the novel-allele probability is high and migration rates are low.","preprint_author_corresponding":"Marcy K. Uyenoyama","preprint_author_corresponding_institution":"Duke University"},{"preprint_doi":"10.1101\/818690","published_doi":"10.3390\/epigenomes4010004","published_journal":"Epigenomes","preprint_platform":"bioRxiv","preprint_title":"Divergent DNA methylation signatures of juvenile seedlings grafts and adult apple trees","preprint_authors":"Perrin, A.; Daccord, N.; Roquis, D.; Celton, J.-M.; Vergne, E.; Bucher, E.","preprint_category":"plant biology","preprint_date":"2019-10-25","published_date":"2020-03-02","preprint_abstract":"Plants are continuously exposed to environmental perturbations. Outcrossing annual plants can adapt rapidly to these changes via sexual mating and DNA mutations. However, perennial and clonally reproducing plants may have developed particular mechanisms allowing them to adapt to these changes and transmit this information to their offspring. It has been proposed that the mechanisms allowing this plasticity of response could come in the form of epigenetic marks that would evolve throughout a plants lifetime and modulate gene expression. To study these mechanisms, we used apple (Malus domestica) as a model perennial and clonally propagated plant. First, we investigated the DNA methylation patterns of mature trees compared to juvenile seedlings. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear changes in DNA methylation patterns localized in regions enriched in genes involved in photosynthesis. Transcriptomic analysis showed that genes involved in this pathway were overexpressed in seedlings. Secondly, we compared global DNA methylation of a newly grafted plant to its mother tree to assess if acquired epigenomic marks were transmitted via grafting. We identified clear changes, albeit showing weaker DNA methylation differences. Our results show that a majority of DNA methylation patterns from the tree are transmitted to newly grafted plants albeit with specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their mother tree.","preprint_author_corresponding":"Adrien  Perrin","preprint_author_corresponding_institution":"IRHS"},{"preprint_doi":"10.1101\/812610","published_doi":"10.1016\/j.compbiomed.2020.103690","published_journal":"Computers in Biology and Medicine","preprint_platform":"bioRxiv","preprint_title":"Systematic identification of A-to-I editing associated regulators from multiple human cancers","preprint_authors":"Gu, T.; Fu, A. Q.; Bolt, M. J.; Zhao, X.","preprint_category":"bioinformatics","preprint_date":"2019-10-21","published_date":"2020-03-03","preprint_abstract":"A-to-I editing is the most common editing type in human that is catalyzed by ADAR family members (ADARs), ADAR1 and ADAR2. Millions of A-to-I editing sites have been discovered recently, however, the regulation mechanisms of the RNA editing process are still not clear. Here we developed a two-step logistic regression model to identify genes that are potentially involved in RNA editing process in four human cancers. The first step by classifying the editing sites into different categories assists the analysis at the second step. In the first step, ADAR1 was identified as the enzyme that associated with the majority of the A-to-I editing sites. Thus, ADAR1 was taken as a control gene in the second step to identify genes that have a stronger effect on editing sites than ADAR1. In addition, the detectable interferons and their receptors were used as covariates in the both steps to account for potential association caused by interferons. Using our advanced method, we successfully found a set of genes that were significantly positively or negatively associated (PA or NA) with specific sets of RNA editing sites. We highlighted two genes, SRSF5 and MIR22HG which were supported by multiple evidences. Most PA and NA genes were unique to each cancer, and only a few shared across two cancers. Pathway enrichment analysis showed that the PA genes from the four cancer types were enriched in Immune System, while the NA genes were enriched in two pathways: Metabolism of RNA, and Metabolism. The functional similarity of the PA and NA genes across all the four cancers indicates that even though most of the editing associated genes were unique to each cancer, they may impact on editing process through common pathways. Interestingly, the PA genes from kidney cancer were enriched for survival-associated genes while the NA genes were depleted of these genes, indicating that the PA genes may play more important roles in kidney cancer development.","preprint_author_corresponding":"Tongjun  Gu","preprint_author_corresponding_institution":"Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL"},{"preprint_doi":"10.1101\/801225","published_doi":"10.1371\/journal.pbio.3000614","published_journal":"PLOS Biology","preprint_platform":"bioRxiv","preprint_title":"A G-protein-coupled receptor mediates neuropeptide-induced oocyte maturation in the jellyfish Clytia","preprint_authors":"Quiroga Artigas, G.; Lapebie, P.; Leclere, L.; Bauknecht, P.; Uveira, J.; Chevalier, S.; Jekely, G.; Momose, T.; Houliston, E.","preprint_category":"developmental biology","preprint_date":"2019-10-10","published_date":"2020-03-03","preprint_abstract":"The reproductive hormones that trigger oocyte meiotic maturation and release from the ovary vary greatly between animal species. Identification of receptors for these Maturation Inducing Hormones (MIHs), and understanding how they initiate the largely conserved maturation process, remain important challenges. In hydrozoan cnidarians including the jellyfish Clytia hemisphaerica, MIH comprises neuropeptides released from somatic cells of the gonad. We identified the receptor (MIHR) for these MIH neuropeptides in Clytia using cell culture-based \\\"deorphanization\\\" of candidate oocyte-expressed GPCRs. MIHR mutant jellyfish generated using CRISPR-Cas9 had severe defects in gamete development or in spawning both in males and females. Female gonads, or oocytes isolated from MIHR mutants, failed to respond to synthetic MIH. Treatment with the cAMP analogue 5Br-cAMP to mimic cAMP rise at maturation onset rescued meiotic maturation and spawning. Injection of inhibitory antibodies to GS into wild type oocytes phenocopied the MIHR mutants. These results provide the molecular links between MIH stimulation and meiosis initiation in hydrozoan oocytes. Molecular phylogeny grouped Clytia MIHR with a subset of bilaterian neuropeptide receptors including Neuropeptide Y, Gonadotropin Inhibitory Hormone, pyroglutamylated RFamide and Luqin, all upstream regulators of sexual reproduction. This identification and functional characterisation of a cnidarian peptide GPCR advances our understanding of oocyte maturation initiation and sheds light on the evolution of neuropeptide-hormone systems.","preprint_author_corresponding":"Evelyn  Houliston","preprint_author_corresponding_institution":"Sorbonne University, CNRS"},{"preprint_doi":"10.1101\/679712","published_doi":"10.1371\/journal.pntd.0008014","published_journal":"PLOS Neglected Tropical Diseases","preprint_platform":"bioRxiv","preprint_title":"Distinct gene expression patterns in vector-residing Leishmania infantum identify parasite stage-enriched markers","preprint_authors":"Coutinho-Abreu, I. V.; Serafim, T. D.; Meneses, C.; Kamhawi, S.; Oliveira, F.; Valenzuela, J. G.","preprint_category":"microbiology","preprint_date":"2019-06-23","published_date":"2020-03-03","preprint_abstract":"Promastigotes of Leishmania infantum undergo a series of extracellular developmental stages inside the natural sand fly vector Lutzomyia longipalpis to reach the infectious stage, the metacyclic promastigote. There is limited information regarding the expression profile of L. infantum developmental stages inside the sand fly vector, and molecular markers that can distinguish the different parasite stages are lacking. We performed RNAseq on unaltered midguts of the sand fly Lutzomyia longipalpis after infection with L. infantum parasites. RNAseq was carried out at various time points throughout parasite development. Principal component analysis mapped the sequences corresponding to the procyclic, nectomonad, leptomonad or metacyclic promastigote stage into distinct positions, with the procyclic stage being the most divergent population. Transcriptional levels across genes varied on average between 10- to 100-fold. Comparison between procyclic and nectomonad promastigotes resulted in 836 differentially expressed (DE) genes; between nectomonad and leptomonad promastigotes in 113 DE genes; and between leptomonad and metacyclic promastigotes in 302 DE genes. Most of the DE genes do not overlap across stages, highlighting the uniqueness of each stage. Furthermore, the different stages of Leishmania parasites exhibited specific transcriptional enrichment across chromosomes. Using the transcriptional signatures exhibited by distinct Leishmania stages during their development in the sand fly midgut, we determined the genes predominantly enriched in each stage, identifying multiple stage-specific markers for L. Infantum. Leading stage-specific marker candidates include genes encoding a zinc transporter in procyclics, a beta-fructofuranidase in nectomonads, a surface antigen-like protein in leptomonads, and an amastin-like surface protein in metacyclics. Overall, these findings demonstrate the transcriptional plasticity of the Leishmania parasite inside the sand fly vector and provide a repertoire of stage-specific markers for further development as molecular tools for epidemiological studies.","preprint_author_corresponding":"Jesus G. Valenzuela","preprint_author_corresponding_institution":"National Institute of Allergy and Infectious Diseases"},{"preprint_doi":"10.1101\/804799","published_doi":"10.1371\/journal.pone.0224343","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"ADHD symptoms and their neurodevelopmental correlates in children born very preterm","preprint_authors":"Montagna, A.; Karolis, V.; Batalle, D.; Counsell, S.; Rutherford, M.; Arulkumaran, S.; Happe, F.; Edwards, D.; Nosarti, C.","preprint_category":"neuroscience","preprint_date":"2019-10-14","published_date":"2020-03-03","preprint_abstract":"This study investigated the association between attention-deficit\/hyperactivity disorder (ADHD) symptomatology in preschool-aged children who were born very preterm (<32 weeks) and cognitive outcomes, clinical risk and socio-demographic characteristics. 119 very preterm children who participated in the Evaluation of Preterm Imaging Study at term-equivalent age were assessed at a mean age of 4.5 years. Parents completed the ADHD Rating Scale IV, a norm-referenced checklist that evaluates ADHD symptomatology according to diagnostic criteria, and the Behavior Rating Inventory of Executive Function-Preschool version. Children completed the Wechsler Preschool and Primary Scales of Intelligence and the Forward Digit Span task. Longitudinal data including perinatal clinical, qualitative MRI classification, socio-demographic variables and neurodevelopmental disabilities were investigated in relation to ADHD symptomatology. All results were corrected for multiple comparisons using false discovery rate. Results showed that although the proportion of very preterm children with clinically significant ADHD did not differ from normative data after excluding those with neurodevelopmental disabilities, 32.7% met criteria for subthreshold ADHD inattentive type and 33.6% for combined type, which was higher than the expected 20% in normative samples. Higher ADHD symptom scores (all) were associated with greater executive dysfunction (inhibitory self-control, flexibility, and emergent metacognition, corrected p<0.001 for all tests). Higher inattentive ADHD symptom scores were associated with lower IQ ({rho}=-0.241, p=0.036) and higher perinatal clinical risk (more days on mechanical ventilation ({rho}=0.206, p=0.025) and more days on parenteral nutrition ({rho}=0.223, p=0.015)). Higher hyperactive ADHD symptom scores instead were associated with lower socio-economic status ({rho}=0.278, p=0.002). These results highlight the importance of monitoring and supporting the development of very preterm children throughout the school years, as subthreshold ADHD symptoms represent risk factors for psychosocial problems and for receiving a future clinical diagnosis of ADHD.","preprint_author_corresponding":"Chiara  Nosarti","preprint_author_corresponding_institution":"Institute of Psychiatry, Psychology & Neuroscience, King's College London"},{"preprint_doi":"10.1101\/760942","published_doi":"10.1371\/journal.pone.0222690","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"A method of back-calculating the log odds ratio and standard error of the log odds ratio from the reported group-level risk of disease","preprint_authors":"Hu, D.; Wang, C.; O'Connor, A.","preprint_category":"bioengineering","preprint_date":"2019-09-06","published_date":"2020-03-03","preprint_abstract":"In clinical trials and observational studies, the effect of an intervention or exposure can be reported as an absolute or relative comparative measure such as risk difference, odds ratio or risk ratio, or at the group level with the estimated risk of disease in each group. For meta-analysis of results with covariate adjustment, the log of the odds ratio (log odds ratio), with its standard error, is a commonly used measure of effect. However, extracting the adjusted log odds ratio from the reported estimates of disease risk in each group is not straightforward. Here, we propose a method to transform the adjusted probability of the event in each group to the log of the odds ratio and obtain the appropriate (approximate) standard error, which can then use used in a meta-analysis. We also use example data to compare our method with two other methods and show that our method is superior in calculating the standard error of the log odds ratio.","preprint_author_corresponding":"Chong  Wang","preprint_author_corresponding_institution":"Iowa State University"},{"preprint_doi":"10.1101\/718205","published_doi":"10.1371\/journal.pone.0220925","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"Automated recognition of functional compound-protein relationships in literature","preprint_authors":"Gu\u0308nther, S.; Do\u0308ring, K.; Qaseem, A.; Telukunta, K. K.; Becer, M.; Thomas, P.","preprint_category":"bioinformatics","preprint_date":"2019-07-29","published_date":"2020-03-03","preprint_abstract":"MotivationMuch effort has been invested in the identification of protein-protein interactions using text mining and machine learning methods. The extraction of functional relationships between chemical compounds and proteins from literature has received much less attention, and no ready-to-use open-source software is so far available for this task.\\n\\nMethodWe created a new benchmark dataset of 2,753 sentences from abstracts containing annotations of proteins, small molecules, and their relationships. Two kernel methods were applied to classify these relationships as functional or non-functional, named shallow linguistic and all-paths graph kernel. Furthermore, the benefit of interaction verbs in sentences was evaluated.\\n\\nResultsThe cross-validation of the all-paths graph kernel (AUC value: 84.2%, F1 score: 81.8%) shows slightly better results than the shallow linguistic kernel (AUC value: 81.6%, F1 score: 79.7%) on our benchmark dataset. Both models achieve state-of-the-art performance in the research area of relation extraction. Furthermore, the combination of shallow linguistic and all-paths graph kernel could further increase the overall performance. We used each of the two kernels to identify functional relationships in all PubMed abstracts (28 million) and provide the results, including recorded processing time.\\n\\nAvailabilityThe software for the tested kernels, the benchmark, the processed 28 million PubMed abstracts, all evaluation scripts, as well as the scripts for processing the complete PubMed database are freely available at https:\/\/github.com\/KerstenDoering\/CPI-Pipeline.\\n\\nAuthor summaryText mining aims at organizing large sets of unstructured text data to provide efficient information extraction. Particularly in the area of drug discovery, the knowledge about small molecules and their interactions with proteins is of crucial importance to understand the drug effects on cells, tissues, and organisms. This data is normally hidden in written articles, which are published in journals with a focus on life sciences. In this publication, we show how text mining methods can be used to extract data about functional interactions between small molecules and proteins from texts. We created a new dataset with annotated sentences of scientific abstracts for the purpose of training two diverse machine learning methods (kernels), and successfully classified compound-protein pairs as functional and non-functional relations, i.e. no interactions. Our newly developed benchmark dataset and the pipeline for information extraction are freely available for download. Furthermore, we show that the software can be easily up-scaled to process large datasets by applying the approach to 28 million abstracts.","preprint_author_corresponding":"Stefan  G\u00fcnther","preprint_author_corresponding_institution":"Albert-Ludwigs-University Freiburg"},{"preprint_doi":"10.1101\/714899","published_doi":"10.1371\/journal.pone.0219722","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"Pre-warming before general anesthesia with isoflurane delays the onset of hypothermia in rats","preprint_authors":"Rufiange, M.; Leung, V.; Simpson, K.; Pang, D.","preprint_category":"pharmacology and toxicology","preprint_date":"2019-07-26","published_date":"2020-03-03","preprint_abstract":"General anesthesia causes hypothermia by impairing normal thermoregulatory mechanisms. Redistribution of warm blood from the core to the periphery is the primary mechanism in the development of hypothermia and begins following induction of anesthesia. Raising skin temperature before anesthesia reduces the temperature gradient between core and periphery, decreasing the transfer of heat. This prospective, crossover study (n = 17 adult male and female SD rats) compared three treatment groups: PW1% (pre-warming to increase core temperature 1% over baseline), PW40 (pre-warming to increase core temperature to 40{degrees}C) and NW (no warming). The PW1% group was completed first to ensure tolerance of pre-warming. Treatment order was then randomized and alternated after a washout period. Once target temperature was achieved, anesthesia was induced and maintained with isoflurane in oxygen without further external temperature support. Pre-warming was effective at delaying the onset of hypothermia, with a significant difference between PW1% (11.2 minutes) and PW40 (14.7 minutes, p = 0.0044 (95%CI -12 to -2.2), PW40 and NW (6.0 minutes, p = 0.003 (95%CI 1.8 to 8.7) and PW1% and PW40 (p = 0.004, 95%CI -12 to -2.2). The rate of heat loss in the pre-warmed groups exceed that of the NW group: PW1% versus NW (p = 0.005, 95%CI 0.004 to 0.027), PW40 versus NW (p < 0.0001, 95%CI 0.014 to 0.036) and PW1% versus PW40 (p = 0.07, 95%CI -0.021 to 0.00066). Pre-warming alone confers a protective effect against hypothermia during volatile anesthesia; however, longer duration procedures would require additional heating support.","preprint_author_corresponding":"Daniel  Pang","preprint_author_corresponding_institution":"Universite de Montreal"},{"preprint_doi":"10.1101\/856302","published_doi":"10.1021\/acssynbio.9b00506","published_journal":"ACS Synthetic Biology","preprint_platform":"bioRxiv","preprint_title":"An Escherichia coli Chassis for Production of Electrically Conductive Protein Nanowires","preprint_authors":"Ueki, T.; Walker, D. J.; Woodard, T. L.; Nevin, K. P.; Nonnenmann, S. S.; Lovley, D. R.","preprint_category":"synthetic biology","preprint_date":"2019-11-26","published_date":"2020-03-03","preprint_abstract":"Geobacter sulfurreducens pilin-based electrically conductive protein nanowires (e-PNs) are a revolutionary electronic material. They offer novel options for electronic sensing applications and have the remarkable ability to harvest electrical energy from atmospheric humidity. However, technical constraints limit mass cultivation and genetic manipulation of G. sulfurreducens. Therefore, we designed a strain of Escherichia coli to express e-PNs by introducing a plasmid that contained an inducible operon with E. coli genes for type IV pili biogenesis machinery and a synthetic gene designed to yield a peptide monomer that could be assembled into e-PNs. The e-PNs expressed in E. coli, and harvested with a simple filtration method, had the same diameter (3 nm) and conductance as e-PNs expressed in G. sulfurreducens. These results, coupled with the robustness of E. coli for mass cultivation and the extensive E. coli toolbox for genetic manipulation, greatly expands opportunities for large-scale fabrication of novel e-PNs.","preprint_author_corresponding":"Derek R Lovley","preprint_author_corresponding_institution":"University of Massachusetts-Amherst, Amherst, MA, USA"},{"preprint_doi":"10.1101\/2019.12.18.881003","published_doi":"10.1371\/journal.pone.0227316","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"Phenylephrine induces relaxation of longitudinal strips from small arteries of goat legs","preprint_authors":"Marconi, K. P.; Bharathi, B.; Venis, A. M.; Raj, R.; Amirtham, S. M.; Subramani, S.","preprint_category":"physiology","preprint_date":"2019-12-18","published_date":"2020-03-03","preprint_abstract":"Alpha adrenergic stimulation is known to produce vasoconstriction. We have earlier shown that, in spiral strips of small arteries Phenylephrine (PE) caused vasorelaxation under high nitric oxide (NO) environment. However on further experimentation it was realized that the PE-induced vasorelaxant response occurred only with longitudinal strips of small arteries even under normal NO environment while circular strips showed contraction with PE even under high NO environment. Such PE-induced vasorelaxation of longitudinal strips was blocked by Phentolamine, an alpha-adrenergic receptor blocker. On delineation of specific receptor subtype, PE-induced relaxation was found to be mediated through alpha 1D receptor. However, this phenomenon is specific to small artery, as longitudinal smooth muscle of aorta showed only contractile response to adrenergic stimulation. There is no prior report of longitudinal smooth muscle in small artery up to our knowledge. The results of this study and histological examination of vessel sections suggest the presence of longitudinal smooth muscle in small artery and their relaxant response to alpha adrenergic stimulation is a novel phenomenon.","preprint_author_corresponding":"Sathya  Subramani","preprint_author_corresponding_institution":"Christian medical college"},{"preprint_doi":"10.1101\/425306","published_doi":"10.1371\/journal.pone.0230000","published_journal":"PLOS ONE","preprint_platform":"bioRxiv","preprint_title":"Changes in pregnancy-related serum biomarkers early in gestation are associated with later development of preeclampsia","preprint_authors":"Hao, S.; You, J.; Chen, L.; Zhao, H.; Huang, Y.; Zheng, L.; Tian, L.; Maric, I.; Liu, X.; Li, T.; Bianco, Y. K.; Winn, V. D.; AGHAEEPOUR, N.; Gaudilliere, B.; Angst, M. S.; Zhou, X.; Li, Y.-M.; Mo, L.; Wong, R. J.; Shaw, G. M.; Stevenson, D.; Cohen, H. J.; MCELHINNEY, D. B.; Sylvester, K. G.; Ling, X. B.","preprint_category":"molecular biology","preprint_date":"2018-09-26","published_date":"2020-03-03","preprint_abstract":"BackgroundPlacental protein expression plays a crucial biological role during normal and complicated pregnancies. We hypothesized that: (1) circulating pregnancy-associated, placenta-related protein levels throughout gestation reflect the uncomplicated, full-term temporal progression of human gestation, and effectively estimates gestational ages (GAs); (2) pregnancies with underlying placental pathology, such as preeclampsia (PE), are associated with disruptions in this GA estimation in early gestation; (3) malfunctions of this GA estimation can be employed to identify impending PE. In addition, to explore the underlying biology and PE etiology, we set to compare protein gestational patterns of human and mouse, using pregnant heme oxygenase-1 (HO-1) heterozygote (Het) mice, a mouse model reflecting PE-like symptoms.\\n\\nMethodsSerum levels of circulating placenta-related proteins - leptin (LEP), chorionic somatomammotropin hormone like 1 (CSHL1), elabela (ELA), activin A, soluble fms-like tyrosine kinase 1 (sFlt-1), and placental growth factor (PlGF)- were quantified by ELISA in blood serially collected throughout human pregnancies (20 normal subjects with 66 samples, and 20 PE subjects with 61 samples). Linear multivariate analysis of the targeted serological protein levels was performed to estimate the normal GA. Logarithmic transformed mean-squared errors of GA estimations were used to identify impending PE. Then the human gestational protein patterns were compared to those in the pregnant HO-1 mice.\\n\\nResultsAn elastic net (EN)-based gestational dating model was developed (R2 = 0.76) and validated (R2 = 0.61) using the serum levels of the 6 proteins at various GAs from women with normal uncomplicated pregnancies (n = 10 for training and n = 6 for validation). In pregnancies complicated by PE (n = 14), the EN model was not (R2 = -0.17) associated with GA at sampling in PE. Statistically significant deviations from the normal GA EN model estimations were observed in PE-associated pregnancies between GAs of 16-30 weeks (P = 0.01). The EN model developed with 5 proteins (ELA excluded due to the lack of robustness of the mouse ELA essay) performed similarly on normal human (R2 = 0.68) and WT mouse (R2 = 0.85) pregnancies. Disruptions of this model were observed in both human PE-associated (human: R2 = 0.27) and mouse HO-1 Het (mouse: R2 = 0.30) pregnancies. LEP out performed sFlt-1 and PlGF in differentiating impending PE at early human and late mouse gestations.\\n\\nConclusionsAs revealed in both human and mouse GA EN analyses, temporal serological placenta-related protein patterns are tightly regulated throughout normal human pregnancies and can be significantly disrupted in pathologic PE states. LEP changes earlier during gestation than the well-established late GA PE biomarkers (sFlt-1 and PlGF). Our HO-1 Het mouse analysis provides direct evidence of the causative action of HO-1 deficiency in LEP upregulation in a PE-like murine model. Therefore, longitudinal analyses of pregnancy-related protein patterns in sera, may not only help in the exploration of underlying PE pathophysiology but also provide better clinical utility in PE assessment.","preprint_author_corresponding":"Xuefeng B Ling","preprint_author_corresponding_institution":"Stanford University"},{"preprint_doi":"10.1101\/741496","published_doi":"10.1371\/journal.pntd.0007719","published_journal":"PLOS Neglected Tropical Diseases","preprint_platform":"bioRxiv","preprint_title":"Responses of the putative trachoma vector, Musca sorbens, to volatile semiochemicals from human faeces","preprint_authors":"Robinson, A.; Bristow, J.; Holl, M. V.; Makalo, P.; Alemayehu, W.; Bailey, R. L.; McLeod, D.; Birkett, M. A.; Caulfield, J. C.; Sarah, V.; Pickett, J. A.; Dewhirst, S.; Chen-Hussey, V.; Woodcock, C.; D'Alessandro, U.; Burton, M. J.; Last, A.; Lindsay, S. W.; Logan, J. G.","preprint_category":"ecology","preprint_date":"2019-08-20","published_date":"2020-03-03","preprint_abstract":"BackgroundThe putative vector of trachoma, Musca sorbens, prefers to lay its eggs on human faeces on the ground. This study sought to determine whether M. sorbens females were attracted to volatile odours from human faeces in preference to odours from the faeces of other animals, and to determine whether specific volatile semiochemicals mediate selection of the faeces.\\n\\nMethodology\/Principal findingsTraps baited with the faeces of humans and local domestic animals were used to catch flies at two trachoma-endemic locations in The Gambia and one in Ethiopia. At all locations, traps baited with faeces caught more female M. sorbens than control traps baited with soil, and human faeces was the most successful bait compared with soil (mean rate ratios 44.40, 61.40, 10.50 [P<0.001]; 8.17 for child faeces [P=0.004]). Odours from human faeces and some domestic animals were sampled by air entrainment. Extracts of the volatiles from human faeces were tested by coupled gas chromatography-electroantennography with laboratory-reared female M. sorbens. Twelve compounds were electrophysiologically active and tentatively identified by coupled mass spectrometry-gas chromatography, these included cresol, indole, 2-methylpropanoic acid, butanoic acid, pentanoic acid and hexanoic acid.\\n\\nConclusions\/SignificanceIt is possible that some of these volatiles govern the strong attraction of M. sorbens flies to human faeces. If so, a synthetic blend of these chemicals, at the correct ratios, may prove to be a highly attractive lure. This could be used in odour-baited traps for monitoring or control of this species in trachoma-endemic regions.\\n\\nAuthor summaryMusca sorbens, also known as the Bazaar Fly, visits peoples faces to feed on ocular and nasal discharge. While feeding, M. sorbens can transmit Chlamydia trachomatis, the bacterium that causes the infectious eye disease trachoma. Around 1.9 million people worldwide are visually impaired or blind from this disease. Although it is believed that M. sorbens transmits trachoma, very few studies have looked at ways to control this fly. A large-scale trial has shown that control of fly populations with insecticide reduces active trachoma disease prevalence. Odour-baited traps for the suppression of disease vector populations are an attractive option as there is no widespread spraying of insecticide, however, highly attractive baits are critical to their success. Here we demonstrate that the preference of these flies for breeding in human faeces is probably mediated by odour cues, and we isolate chemicals in the odour of human faeces that cause a response in the antennae of M. sorbens. These compounds may play a role in the specific attractiveness of human faeces to these flies, perhaps by being present in greater amounts or at favourable ratios. These may be developed into a chemical lure for odour-baited trapping to suppress M. sorbens populations.","preprint_author_corresponding":"Ailie  Robinson","preprint_author_corresponding_institution":"London School of Hygiene and Tropical Medicine"},{"preprint_doi":"10.1101\/775783","published_doi":"10.1371\/journal.pcbi.1007406","published_journal":"PLOS Computational Biology","preprint_platform":"bioRxiv","preprint_title":"Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila","preprint_authors":"Bernasek, S. M.; Pelaez, N.; Carthew, R.; Bagheri, N.; Amaral, L.","preprint_category":"systems biology","preprint_date":"2019-09-19","published_date":"2020-03-03","preprint_abstract":"Mosaic analysis provides a means to probe developmental processes in situ by generating loss-of-function mutants within otherwise wildtype tissues. Combining these techniques with quantitative microscopy enables researchers to rigorously compare RNA or protein expression across the resultant clones. However, visual inspection of mosaic tissues remains common in the literature because quantification demands considerable labor and computational expertise. Practitioners must segment cell membranes or cell nuclei from a tissue and annotate the clones before their data are suitable for analysis. Here, we introduce Fly-QMA, a computational framework that automates each of these tasks for confocal microscopy images of Drosophila imaginal discs. The framework includes an unsupervised annotation algorithm that incorporates spatial context to inform the genetic identity of each cell. We use a combination of real and synthetic validation data to survey the performance of the annotation algorithm across a broad range of conditions. By contributing our framework to the open-source software ecosystem, we aim to contribute to the current move toward automated quantitative analysis among developmental biologists.\\n\\nAuthor summaryBiologists use mosaic tissues to compare the behavior of genetically distinct cells within an otherwise equivalent context. The ensuing analysis is often limited to qualitative insight. However, it is becoming clear that quantitative models are needed to unravel the complexities of many biological systems. In this manuscript we introduce Fly-QMA, an open-source software framework that automates the quantification of mosaic analysis for Drosophila imaginal discs, a common setting for studies of developmental processes. The software automatically extracts quantitative measurements from confocal images of mosaic tissues, rectifies any cross-talk between fluorescent reporters, and identifies clonally-related subpopulations of cells. Together, these functions allow users to rigorously ascribe changes in gene expression to the presence or absence of particular genes. We validate the performance of our framework using both real and synthetic data. Through its publication, we aim to contribute to the current move toward automated quantitative analysis among biologists.","preprint_author_corresponding":"Sebastian  Michal  Bernasek","preprint_author_corresponding_institution":"Northwestern University"},{"preprint_doi":"10.1101\/849406","published_doi":"10.1111\/jeb.13610","published_journal":"Journal of Evolutionary Biology","preprint_platform":"bioRxiv","preprint_title":"Climate associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps.","preprint_authors":"Capblancq, T.; Morin, X.; Gueguen, M.; Renaud, J.; Lobreaux, S.; Bazin, E.","preprint_category":"evolutionary biology","preprint_date":"2019-11-21","published_date":"2020-03-03","preprint_abstract":"Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming must induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could imped the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a ddRAD-seq approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. An RDA-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings predicted a severe range contraction and a shift towards higher altitudes for F. sylvatica in the Alps and allowed to identify populations at risk, which could be helpful for future management plans.","preprint_author_corresponding":"Thibaut  Capblancq","preprint_author_corresponding_institution":"Univ. Grenoble Alpes, CNRS, LECA UMR 5553, Grenoble, France"}]}