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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

DivNet: Estimating diversity in networked communities

Diversity is a marker of ecosystem health in ecology, microbiology and immunology, with implications for disease diagnosis and infection resistance. However, accurately comparing diversity across environmental gradients is challenging, especially when number of different taxonomic groups in the community is large. Furthermore, existing approaches to estimating diversity do not perform well when the taxonomic groups in the community interact via an ecological network, such as by competing within their niche, or with mutualistic relationships. To address this, we propose DivNet, a method for estimating within- and between-community diversity in ecosystems where taxa interact via an ecological network. In particular, accounting for network structure permits more accurate estimates of alpha- and beta-diversity, even in settings with a large number of taxa and a small number of samples. DivNet is fast, accurate, precise, performs well with large numbers of taxa, and is robust to both weakly and strongly networked communities. We show that the advantages of incorporating taxon interactions into diversity estimation are especially clear in analyzing microbiomes and other high-diversity, strongly networked ecosystems. Therefore, to illustrate the method, we analyze the microbiome of seafloor basalts based on a 16S amplicon sequencing dataset with 1490 taxa and 13 samples.

bioinformatics↗

bioRxiv2018

Co-evolution networks of HIV/HCV are modular with direct association to structure and function

Mutational correlation patterns found in population-level sequence data for the Human Immunodeficiency Virus (HIV) and the Hepatitis C Virus (HCV) have been demonstrated to be informative of viral fitness. Such patterns can be seen as footprints of the intrinsic functional constraints placed on viral evolution under diverse selective pressures. Here, considering multiple HIV and HCV proteins, we demonstrate that these mutational correlations encode a modular co-evolutionary structure that is tightly linked to the structural and functional properties of the respective proteins. Specifically, by introducing a robust statistical method based on sparse principal component analysis, we identify near-disjoint sets of collectively-correlated residues (sectors) having mostly a one-to-one association to largely distinct structural or functional domains. This suggests that the distinct phenotypic properties of HIV/HCV proteins often give rise to quasi-independent modes of evolution, with each mode involving a sparse and localized network of mutational interactions. Moreover, individual inferred sectors of HIV are shown to carry immunological significance, providing insight for guiding targeted vaccine strategies.\n\nAuthor summaryHIV and HCV cause devastating infectious diseases for which no functional vaccine exists. A key problem is that while immune cells may induce individual mutations that compromise viral fitness, this is typically restored through other \"compensatory\" mutations, leading to immune escape. These compensatory pathways are complicated and remain poorly understood. They do, however, leave co-evolutionary markers which may be inferred from measured sequence data. Here, by introducing a new robust statistical method, we demonstrated that the compensatory networks employed by both viruses exhibit a remarkably simple decomposition involving small and near-distinct groups of protein residues, with most groups having a clear association to biological function or structure. This provides insights that can be harnessed for the purpose of vaccine design.

bioinformatics↗

bioRxiv2018

A Real Time PCR Assay for Quantification of Parasite Burden in Murine Models of Leishmaniasis

Eukaryotic parasites in the genus Leishmania place approximately 350 million people per year at risk of disease. In addition to their global health significance, Leishmania spp. have served as an important model for delineating basic concepts in immunology such as T-helper cell polarization. There have been many qPCR based assays reported for measuring parasite burden in humans and animals. However, these are largely optimized for use in clinical diagnosis and not specifically for animal models. This has led several of these assays to have suboptimal characteristics for use in animal models. For example, multi-copy number genes have been frequently used to increase sensitivity, but are subject to greater plasticity within the genome and thus may confound effects of experimental manipulations in animal models. In this study, we develop a sybr-green based quantitative touchdown PCR assay for a highly conserved and single copy, putative RNA binding protein, DRBD3. With primers nearly perfectly conserved across all Leishmania spp., this assay rivals the sensitivity of previously reported qPCR based methods of parasite quantitation and successfully detected L. major from mouse infection. Use of this protocol in the future will lead to improved accuracy in animal based models and help to tease apart differences in biology of host-parasite interactions.

microbiology↗

bioRxiv2018

A Composition-Dependent Molecular Clutch Between T Cell Signaling Clusters and Actin

Biomolecular condensates play important roles in eukaryotic cells by concentrating molecules into foci without a surrounding membrane. During T cell activation, biomolecular condensates form at the immunological synapse (IS) through multivalency-driven phase separation of the adaptor protein LAT and its binding partners Grb2, Sos1, SLP-76, Nck and WASP. These condensates move radially at the IS, traversing a radially-oriented and then a concentric actin network. To understand the persistent radial movement, we biochemically reconstituted LAT condensates with mobile actomyosin filaments. We found that basic regions of Nck and N-WASP promote strong association and co-movement of LAT condensates with actin. Condensates lacking these components were instead propelled by steric interactions. In cells, LAT condensates lost Nck while traversing the boundary between the two actin networks, and condensates engineered to constitutively bind actin moved aberrantly. We propose that Nck and WASP form a clutch between LAT condensates and actin, and changes in composition enable condensate movement by distinct actin networks in different regions of the IS.

cell biology↗

bioRxiv2018

ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data

Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) data remains a challenge due to the low depth. Furthermore, there is no method to identify the sequences of unknown HLA types not registered in HLA databases. We developed a Bayesian model, called ALPHLARD, that collects reads potentially generated from HLA genes and accurately determines a pair of HLA types for each of HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes at 6-digit resolution. Furthermore, ALPHLARD can detect rare germline variants not stored in HLA databases and call somatic mutations from paired normal and tumor sequence data. We illustrate the capability of ALPHLARD using 253 WES data and 25 WGS data from Illumina platforms. By comparing the results of HLA genotyping from SBT and amplicon sequencing methods, ALPHLARD achieved 98.8% for WES data and 98.5% for WGS data at 4-digit resolution. We also detected three somatic point mutations and one case of loss of heterozygosity in the HLA genes from the WGS data. ALPHLARD showed good performance for HLA genotyping even from low-coverage data. It also has a potential to detect rare germline variants and somatic mutations in HLA genes. It would help to fill in the current gaps in HLA reference databases and unveil the immunological significance of somatic mutations identified in HLA genes.

bioinformatics↗

bioRxiv2018

Age-specific differences in the dynamics of protective immunity to influenza

Influenza A viruses evolve rapidly to escape host immunity, such that individuals can be infected multiple times with the same subtype. The form and duration of protective immunity after each influenza infection are poorly understood. Here, we quantify the dynamics of protective immunity against influenza A virus infections by fitting individual-level mechanistic models to longitudinal serology from children and adults in a household cohort study. We find that most protection in children is explained by antibody titers measured by the hemagglutination inhibition (HI) assay. In contrast, in adults, HI antibody titers explain a smaller fraction of protection. Protection against circulating strains wanes to approximately 50% of peak levels 3.5-7 years after infection in both age groups, and wanes faster against influenza A(H3N2) than A(H1N1)pdm09. Protection against H3N2 lasts longer in adults than in children. Our results suggest that the focus of influenza antibody responses changes over time from the highly mutable hemagglutinin head to other epitopes, consistent with the immunological theory of original antigenic sin, and that this change of focus might affect protection. Additionally, we estimate that imprinting, or primary infection with a subtype of one phylogenetic group, has little to no effect on the risk of non-medically attended influenza infections in adults. We also find no evidence of long-term cross-protection between subtypes. This work underscores the need for longitudinal data on multiple components of the immune response to better understand the development of immunity and differences in susceptibility within populations.

epidemiology↗

bioRxiv2018

Prolonged culture of primary human keratinocytes isolated from suction blisters

Keratinocytes are the most abundant cell type in the epidermis. They prevent desiccation and provide immunological and barrier defense against potential pathogens such as Staphylococcus aureus and Candida albicans. The study of this first line of immune defense is hindered by invasive isolation methods and insufficient techniques for long-term passage of primary keratinocytes in vitro. Primary keratinocytes have been successfully isolated from blister roofs induced by negative pressure, which separates the epidermis from the dermis in vivo in human subjects. This method allows collection of pure epidermal cells without dermal contamination in a minimally invasive manner. However, the isolated keratinocytes differentiate and senesce when cultured in vitro beyond five passages. Here, we present evidence that the Rho kinase (ROCK) inhibitor Y-27632 can be used to effectively increase the proliferative capabilities of keratinocytes isolated using the suction blister method, similar to what has been previously reported for primary keratinocytes isolated using alternative methods. We show that the increase in passage number is directly correlated to delayed differentiation, and that cells passaged long term with the inhibitor retain their ability to stratify in organotypic raft cultures and respond to cytokine treatment; additionally, the late passage cells have a heterogeneous mix of differentiated and non-differentiated cells which may be predicted by a ratio of select differentiation markers. The described method presents a minimally invasive procedure for keratinocyte isolation and prolonged culture that allows analysis of keratinocyte function in both healthy volunteers and patients with dermatologic diseases.

cell biology↗

bioRxiv2018

cytometree: a binary tree algorithm for automatic gating in cytometry analysis

MotivationFlow cytometry is a powerful technology that allows the high-throughput quantification of dozens of surface and intracellular proteins at the single-cell level. It has become the most widely used technology for immunophenotyping of cells over the past three decades. Due to the increasing complexity of cytometry experiments (more cells and more markers), traditional manual flow cytometry data analysis has become untenable due to its subjectivity and time-consuming nature.\n\nResultsWe present a new unsupervised algorithm called \"cytometree\" to perform automated population discovery (aka gating) in flow cytometry. cytometree is based on the construction of a binary tree, the nodes of which are subpopulations of cells. At each node, the marker distributions are modeled by mixtures of normal distribution. Node splitting is done according to a normalized difference of Akaike information criteria (AIC) between the two models. Post-processing of the tree structure and derived populations allows us to complete the annotation of the derived populations. The algorithm is shown to perform better than the state-of-the-art unsupervised algorithms previously proposed on panels introduced by the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP I) project. The algorithm is also applied to a T-cell panel proposed by the Human Immunology Project Consortium (HIPC) program; it also outperforms the best unsupervised open-source available algorithm while requiring the shortest computation time.\n\nAvailabilityAn R package named \"cytometree\" is available on the CRAN repository.\n\nContactdaniel.commenges@u-bordeaux.fr; rodolphe.thiebaut@u-bordeaux.fr\n\nSupplementary informationSupplementary data are available.

bioinformatics↗

bioRxiv2018

Life history trade-offs in ectotherms impart a pseudo-hormetic response, not hormesis.

All organisms are faced with survival and fitness challenges. However, differences in how ectotherms and endotherms deal with these challenges causes confusion when theoretical explanations are proposed. Herein, an immunochallenged, immature ectothermic vertebrate increased growth in the face of immunochallenge, reminiscent of up-regulated physiological efficiency termed hormesis. The immunochallenged subjects increased food intake relative to control animals, a largely ignored possibility in previous studies. This likely led to an energy surplus that fueled additional growth. Although there was increased resource demand from the immune response that exceeded internal stores, the acceptably sized food items contained more resources than immunologically-driven demand required. We theorize that because ectotherms lack significant internally-stored resources compared to endotherms, they must feed to fuel increased physiological demand. This can lead to excess resource intake because the minimum acceptably sized prey contains more available resources than upregulation required. This creates a pseudo-hormetic hormetic response, fueled by excess food intake rather than significant improved physiological efficiency. Further, we speculate that lifespan and/or maturity may interact with resource management ectotherms, though our data are inconclusive on this matter. Ultimately, our data suggest additional growth when ectotherms face stressors is a pseudo-hormetic response stemming from increased food intake instead of upregulated physiological efficiency.

evolutionary biology↗

bioRxiv2018

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis.

A central tenet of reproducible research is that scientific results are published along with the underlying data and software code necessary to reproduce and verify the findings. A host of tools and software have been released that facilitate such work-flows and scientific journals have increasingly demanded that code and primary data be made available with publications. There has been little practical advice on implementing reproducible research work-flows for large omics or systems biology data sets used by teams of analysts working in collaboration. In such instances it is important to ensure all analysts use the same version of a data set for their analyses. Yet, instantiating relational databases and standard operating procedures can be unwieldy, with high \"startup\" costs and poor adherence to procedures when they deviate substantially from an analysts usual work-flow. Ideally a reproducible research work-flow should fit naturally into an individuals existing work-flow, with minimal disruption. Here, we provide an overview of how we have leveraged popular open source tools, including Bioconductor, Rmarkdown, git version control, R, and specifically Rs package system combined with a new tool DataPackageR, to implement a lightweight reproducible research work-flow for preprocessing large data sets, suitable for sharing among small-to-medium sized teams of computational scientists. Our primary contribution is the DataPackageR tool, which decouples time-consuming data processing from data analysis while leaving a traceable record of how raw data is processed into analysis-ready data sets. The software ensures packaged data objects are properly documented and performs checksum verification of these along with basic package version management, and importantly, leaves a record of data processing code in the form of package vignettes. Our group has implemented this work-flow to manage, analyze and report on pre-clinical immunological trial data from multi-center, multi-assay studies for the past three years.

bioinformatics↗

bioRxiv2018

A novel green approach for treatment of immature Schistosomiasis Mansoni infection in mice; Arabic gum (Acacia Senegal) antischistosomal properties

Schistosomiasis is one of the most socioeconomically exhausting parasitic infection in tropical and subtropical areas. Praziquantel (PZQ), the only common schistosocidal drug in use, is not efficient enough for treatment of immature infection. Arabic gum (AG) is a complex polysaccharide acts as anti-oxidant which modulates the inflammatory and/or immunological processes. This study explores for the first time, the antischistosomal properties of AG in mice infected with the immature stage of Schistosoma mansoni. Mice were divided into four groups: control group (infected non-treated), AG treated group, PZQ treated group, and AG+PZQ treated group. Oral administration of AG in a dose of 1gm/kg body weight, daily for 3 consecutive weeks post-infection (p.i.) resulted in a statistically significant lower worm burden in both AG group and AG+PZQ group compared to PZQ and control groups. AG+PZQ group always showed the best performance when compared with other groups regarding tissue egg load and oogram pattern. AG, both alone and in combination with PZQ, decreased the number, diameter; increased the cellularity and the number of degenerated Schistosoma eggs inside granulomas. Results obtained by this work elucidated a promising AG bioactivity against S. mansoni immature stages and provided a platform for subsequent experimental studies to illuminate the academia more about this novel and \"green\" antischistosomal agent.\n\nAuthor summarySchistosomiasis is a major public health threat in many parts of the world, it affects more than 240 million people in more than 70 countries and almost 800 million people are at risk of acquiring this disease. Serious consequences and disabilities might result from untreated schistosomiasis such as hepatosplenic fibrosis with portal hypertension, gastrointestinal hemorrhage and death.\n\nSchistosomiasis control is focused on periodic treatment with praziquantel (PZQ). However, PZQ has only moderate action against young developing stages of schistosomula. Recently, resistance has emerged to PZQ. Therefore, chemotherapy alone is unlikely to reduce infection levels of schistosomiasis. Several practical approaches have been suggested to augment treatment programs. Of course, the development of a complementary treatment would contribute enormously to the reduction of schistosomiasis. Recently, natural products have been popular and attracted most of the attention as it could offer new effective therapy against schistosomiasis. Arabic gum (AG) is an edible, dried sticky exudate from Acacia Senegal, which is used in this study to assess the AG antischistosomal properties. Our study revealed that AG has an excellent statistically significant effect against immature murine schistosomiasis, both alone and in combination with PZQ. This approach may point to novel targets for treatment of schistosomiasis.

microbiology↗

bioRxiv2018

Cancer stemness, intratumoral heterogeneity, and immune response across cancers

Regulatory programs that control the function of stem cells are active in cancer and confer properties that promote progression and therapy resistance. However, the impact of a stem cell-like tumor phenotype (\"sternness\") on the immunological properties of cancer has not been systematically explored. Using gene expression-based metrics, we evaluate the association of stemness with immune cell infiltration and genomic, transcriptomic, and clinical parameters across 21 solid cancers. We find pervasive negative associations between cancer stemness and anticancer immunity. This occurs despite high stemness cancers exhibiting increased mutation load, cancer-testis antigen expression, and intratumoral heterogeneity. Stemness was also strongly associated with cell-intrinsic suppression of endogenous retroviral expression and type I interferon signaling and increased expression of several therapeutically accessible signaling pathways. Thus, stemness is not only a fundamental process in cancer progression but may represent a unifying mechanism linking antigenicity, intratumoral heterogeneity, and immune suppression across cancers.

cancer biology↗

bioRxiv2018

Functional genomics and programmed genome editing of omega-1 of the blood fluke Schistosoma mansoni

CRISPR/Cas9 based genome editing has yet been reported in parasitic or indeed any species of the phylum Platyhelminthes. We tested this approach by targeting omega-1 ({omega}1) of Schistosoma mansoni as a proof of principle. This secreted ribonuclease is crucial for Th2 priming and granuloma formation, providing informative immuno-pathological readouts for programmed genome editing. Schistosome eggs were either exposed to Cas9 complexed with a synthetic guide RNA (sgRNA) complementary to exon 6 of {omega}1 by electroporation or transduced with pseudotyped lentivirus encoding Cas9 and the sgRNA. Some eggs were also transduced with a single stranded oligodeoxynucleotide donor transgene that encoded six stop codons, flanked by 50 nt-long 5-and 3-microhomology arms matching the predicted Cas9-catalyzed double stranded break (DSB) within {omega}1. CRISPResso analysis of amplicons spanning the DSB revealed [~]4.5% of the reads were mutated by insertions, deletions and/or substitutions, with an efficiency for homology directed repair of 0.19% insertion of the donor transgene. Transcripts encoding {omega}1 were reduced >80% and lysates of {omega}1-edited eggs displayed diminished ribonuclease activity indicative that programmed editing mutated the {omega}1 gene. Whereas lysates of wild type eggs polarized Th2 cytokine responses including IL-4 and IL-5 in human macrophage/T cell co-cultures, diminished levels of the cytokines followed the exposure to lysates of {omega}1-mutated schistosome eggs. Following injection of schistosome eggs into the tail vein of mice, the volume of pulmonary granulomas surrounding {omega}1-mutated eggs was 18-fold smaller than wild type eggs. Programmed genome editing was active in schistosomes, Cas9-catalyzed chromosomal breakage was repaired by homology directed repair and/or non-homologous end joining, and mutation of {omega}1 impeded the capacity of schistosome eggs both to drive Th2 polarization and to provoke formation of pulmonary circumoval granulomas. Knock-out of {omega}1 and the impaired immunological phenotype showcase the novel application of programmed gene editing in and functional genomics for schistosomes.

molecular biology↗

bioRxiv2018

Transcriptomic analysis of fetal membranes reveals pathways involved in preterm birth

Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results of the interaction of both genetic and environmental components and constitutes a complex multifactorial syndrome. Transcriptome analysis of PTB has proved challenging because of the multiple causes of PTB and the numerous maternal and fetal gestational tissues that must interact to facilitate parturition. A common pathway of labor and PTB may be the activation of fetal membranes. In this work, chorioamnion membranes from severe preterm and term fetus were analyzed using RNA sequencing. A total of 270 genes were differentially expressed (DE): 252 were up-regulated and 18 were down-regulated in the severe preterm compared to the term births. We found great gene expression homogeneity in the control samples, and not in severe preterm samples. In this work, we identified up-regulated pathways that were previously suggested as leading to PTB like immunological and inflammatory paths. New pathways that were not identified in preterm like the hemopoietic path appeared up-regulated in preterm membranes. A group of 18 down-regulated genes discriminates between term and severe preterm cases. These genes potentially characterize a severe preterm transcriptome pattern and therefore are candidate genes for understanding the syndrome. Some of the down-regulated genes are involved in the nervous system, morphogenesis (WNT-1, DLX5, PAPPA2) and ion channel complexes (KCNJ16, KCNB1), making them good candidates as biomarkers of PTB.\n\nThe identification of this DE gene pattern may help to develop a multi-gene disease classifier. These markers were generated in an admixtured South American population where PTB has a high incidence. Since genetic background may impact differentially in different populations it is mandatory to include populations like South American and African ones that are usually excluded from high throughput approaches. These classifiers should be compared to those in other populations to get a global landscape of PTB.

genetics↗

bioRxiv2018

Dominance rank-associated immune gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons

In humans and other hierarchical species, social status is tightly linked to variation in health and fitness-related traits. Experimental manipulations of social status in female rhesus macaques suggest that this relationship is partially explained by status effects on immune gene regulation. However, social hierarchies are established and maintained in different ways across species: while some are based on kin-directed nepotism, others emerge from direct physical competition. We investigated how this variation influences the relationship between social status and immune gene regulation in wild baboons, where hierarchies in males are based on fighting ability but female hierarchies are nepotistic. We measured rank-related variation in gene expression levels in adult baboons of both sexes at baseline and in response to ex vivo stimulation with the bacterial endotoxin lipopolysaccharide (LPS). We identified >2000 rank- associated genes in males, an order of magnitude more than in females. In males, high status predicted increased expression of genes involved in innate immunity and preferential activation of the NFkB-mediated pro-inflammatory pathway, a pattern previously associated with low status in female rhesus macaques. Using Mendelian randomization, we reconcile these observations by demonstrating that high status-associated gene expression patterns are precursors, not consequences, of high social status in males, in support of the idea that physiological condition determines who attains high rank. Together, our work provides the first test of the relationship between social status and immune gene regulation in wild primates. It also emphasizes the importance of social context in shaping the relationship between social status and immune function.\n\nSIGNIFICANCESocial status predicts fitness outcomes in social animals, motivating efforts to understand its physiological causes and consequences. We investigated the relationship between social status and immune gene expression in wild baboons, where female status is determined by kinship but male status is determined by fighting ability. We uncover pervasive status-gene expression associations in males, but not females. High status males exhibit high levels of pro-inflammatory gene expression, in contrast to previous findings in hierarchies that are not competitively determined. Using Mendelian randomization, we show that this status-associated variation precedes dominance rank attainment: males who compete successfully for high status are already immunologically distinct. The nature of social hierarchies thus fundamentally shapes the relationship between social status and immune function.

evolutionary biology↗

bioRxiv2018

The respiratory microbiome and susceptibility to influenza virus infection

Influenza is a major cause of morbidity and mortality worldwide. However, vaccine effectiveness has been low to moderate in recent years and vaccine coverage remains low, especially in low- and middle-income countries. Supplementary methods of prevention should be explored to reduce the high burden of influenza.\n\nA potential target is the respiratory tract microbiome, complex microbial communities which envelop the respiratory epithelium and play an important role in shaping host immunity. Using a household transmission study, we examined whether the nose/throat microbiota was associated with influenza susceptibility among participants exposed to influenza virus in the household. Further, we characterized changes in the nose/throat microbiota to explore whether community stability was influenced by influenza virus infection.\n\nUsing a generalized linear mixed effects model, we found a bacterial community type associated with decreased susceptibility to influenza. The community type was rare and transitory among young children but a prevalent and stable community type among adults. Using boosting and linear mixed effects models, we found associations between the nose/throat microbiota and influenza also existed at the taxa level, specifically with the relative abundance of Alloprevotella, Prevotella, and Bacteroides oligotypes.\n\nWe found high rates of change in the bacterial community among both secondary cases and household contacts who were not infected during follow up. Preliminary results suggest short-term changes in the bacterial community structure may differ between the two groups, but further work is needed to validate our observations.\n\nLastly, age was strongly associated with susceptibility to influenza and the nose/throat bacterial community structure. Although additional studies are needed to determine causality, our results suggest the nose/throat microbiome may be a potential target for reducing the burden of influenza.\n\nAuthor summaryMicrobiome research has transformed our understanding of microbes and human health. Resident bacteria can protect the host from pathogens by shaping immunological responses. These new insights suggest the microbiome could be a target for preventing influenza virus infection, a major cause of illness and death worldwide. In this study, we explored the relationship between the nose/throat microbiota and influenza virus in Nicaraguan households.\n\nHousehold members were enrolled immediately after one member was diagnosed with influenza virus infection. This study design allowed us to identify associations between the microbiota and influenza susceptibility. We also explored whether influenza virus infection altered the bacterial community structure and found short-term changes were common among both secondary cases and household members who remained influenza negative during follow up. Lastly, we found age played major roles in both influenza susceptibility and in short-terms changes in the microbiota. Although much work is needed to determine causal relationships, our findings suggest strategies that appropriately modify the microbiome might be useful in preventing influenza virus infections.

epidemiology↗

bioRxiv2018

Identification and characterization of yeast and human glycosphingolipid flippases

Lipid transport is an essential process with manifest importance to human health and disease. Phospholipid flippases (P4-ATPases) transport lipids across the membrane bilayer, and are involved in signal transduction, cell division, and vesicular transport. Mutations in flippase genes cause or contribute to a host of diseases such as cholestasis, neurological deficits, immunological dysfunction, and metabolic disease. Genome-wide association studies have shown that ATP10A and ATP10D variants are associated with an increased risk of diabetes, obesity, myocardial infarction, and atherosclerosis; and ATP10D SNPs are associated with elevated levels of glucosylceramide (GlcCer) in plasma from diverse European populations. Although sphingolipids are strong contributors to metabolic disease, little is known about how GlcCer is transported across cell membranes. We have identified an evolutionarily conserved clade of P4-ATPases from Saccharomyces cerevisiae (Dnf1, Dnf2), Schizosaccharomyces pombe (Dnf2), and Homo sapiens (ATP10A, ATP10D) that transport GlcCer. Further, we establish the structural determinants necessary for the specific recognition of this sphingolipid substrate. Our molecular observations clarify the relationship between these flippases and human disease, and have fundamental implications for membrane organization and sphingolipid homeostasis.

biochemistry↗

bioRxiv2018

Three-dimensional nanostructure of an intact microglia cell

Microglia are non-neuronal cells of the myeloid lineage that invade and take up long-term residence in the brain during development (Ginhoux et al. 2010) and are increasingly implicated in neuronal maturation, homeostasis, and pathology (Bessis et al. 2007; Paolicelli et al. 2011; Li et al. 2012; Aguzzi et al. 2013, Cunningham 2013, Cunningham et al. 2013). Since the early twentieth century several methods for staining and visualizing microglia have been developed. Scientists in Ramon y Cajals group (Achucarro 1913, Rio-Hortega 1919) pioneered these methods and their work led to the christening of microglia as the third element of the nervous system, distinct from astrocytes and neurons. More recently, a combination of imaging, genetic, and immunological tools has been used to visualize microglia in living brain (Davalos et al. 2005; Nimmerjahn et al. 2005). It was found that microglia are highly motile under resting conditions and rapidly respond to injuries (Kettenmann et al. 2011) suggesting a role for microglia in both brain homeostasis and pathology. Transmission Electron microscopy (TEM) has provided crucial complementary information on microglia morphology and physiology but until recently EM analyses have been limited to single or limited serial section studies (Tremblay et al. 2010; Paolicelli et al. 2011; Schafer et al. 2012; Tremblay et al. 2012; Sipe et al. 2016). TEM studies were successful in defining a set of morphological criteria for microglia: a polygonal nucleus with peripheral condensed chromatin, a relatively small cytoplasm with abundant presence of rough endoplasmic reticulum (RER), and a large volume of lysosomes and inclusions in the perikaryon. Recent advances in volumetric electron microscopy techniques allow for 3D reconstruction of large samples at nanometer-resolution, thus opening up new avenues for the understanding of cell biology and architecture in intact tissues. At the same time, correlative light and electron microscopy (CLEM) techniques have been extended to 3D brain samples to help navigate and identify critical molecular landmarks within large EM volumes (Briggman and Denk 2006; Maco et al. 2013; Blazquez-Llorca et al. 2015, Bosch et al. 2015). Here we present the first volumetric ultrastructural reconstruction of an entire mouse hippocampal microglia using serial block face scanning electron microscopy (SBEM). Using CLEM we have ensured the inclusion of both large, small, and filopodial microglia processes. Segmentation of the dataset allowed us to carry out a comprehensive inventory of microglia cell structures, including vesicles, organelles, membrane protrusions, and processes. This study provides a reference that can serve as a data mining resource for investigating microglia cell biology.

neuroscience↗