A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes, bioRxiv, 2019-12-06
ABSTRACTAn imbalance of normal bacterial groups such as Bacteroidales within the human gut is correlated with diseases like obesity. A current grand challenge in the microbiome field is to identify factors produced by normal microbiome bacteria that cause these observed health and disease correlations. While identifying factors like a bacterial injection system could provide a missing explanation for why Bacteroidales correlates with host health, no such factor has been identified to date. The lack of knowledge about these factors is a significant barrier to improving therapies like fecal transplants that promote a healthy microbiome. Here we show that a previously ill-defined Contractile Injection System is carried in the gut microbiome of 99% of individuals from the United States and Europe. This type of Contractile Injection System, we name here Bacteroidales Injection System (BIS), is related to the contractile tails of bacteriophage (viruses of bacteria) and have been described to mediate interactions between bacteria and diverse eukaryotes like amoeba, insects and tubeworms. Our findings that BIS are ubiquitous within adult human microbiomes suggest that they shape host health by mediating interactions between Bacteroidales bacteria and the human host or its microbiome.
biorxiv microbiology 0-100-users 2019Data structures based on k-mers for querying large collections of sequencing datasets, bioRxiv, 2019-12-06
High-throughput sequencing datasets are usually deposited in public repositories, e.g. the European Nucleotide Archive, to ensure reproducibility. As the amount of data has reached petabyte scale, repositories do not allow to perform online sequence searches; yet such a feature would be highly useful to investigators. Towards this goal, in the last few years several computational approaches have been introduced to index and query large collections of datasets. Here we propose an accessible survey of these approaches, which are generally based on representing datasets as sets of k-mers. We review their properties, introduce a classification, and present their general intuition. We summarize their performance and highlight their current strengths and limitations.
biorxiv bioinformatics 100-200-users 2019Dopamine modulates the size of striatal projection neuron ensembles, bioRxiv, 2019-12-06
SUMMARYDopamine (DA) is a critical modulator of brain circuits that control voluntary movements, but our understanding of its influence on the activity of target neurons in vivo remains limited. Here, we use two-photon Ca2+ imaging to simultaneously monitor the activity of direct and indirect-pathway spiny projection neurons (SPNs) in the striatum of behaving mice during acute and prolonged manipulations of DA signaling. We find that, contrary to prevailing models, DA does not modulate activity rates in either pathway strongly or differentially. Instead, DA exerts a prominent influence on the overall number of direct and indirect pathway SPNs recruited during behavior. Chronic loss of midbrain DA neurons in a model of Parkinson’s disease selectively impacts direct pathway ensembles and profoundly alters how they respond to DA elevation. Our results indicate that DA regulates striatal output by dynamically reconfiguring its sparse ensemble code and provide novel insights into the pathophysiology of Parkinson’s disease.
biorxiv neuroscience 100-200-users 2019Early replacement of West Eurasian male Y chromosomes from the east, bioRxiv, 2019-12-06
AbstractThe genomes of humans outside Africa originated almost entirely from a single migration out ∼50,000-60,000 years ago1,2, followed closely by mixture with Neanderthals contributing ∼2% to all non-Africans3,4. However, the details of this initial migration remain poorly-understood because no ancient DNA analyses are available from this key time period, and present-day autosomal data are uninformative due to subsequent population movementsreshaping5. One locus, however, does retain extensive information from this early period the Y-chromosome, where a detailed calibrated phylogeny has been constructed6. Three present-day Y lineages were carried by the initial migration the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations6,7. We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to EastSouth-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model8,9, and thus informing and constraining models of the initial expansion.
biorxiv genetics 100-200-users 2019Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing, bioRxiv, 2019-12-06
AbstractDespite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotic cells has been hindered by their low levels of mRNA, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline that overcomes these obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. We have demonstrated that PETRI-seq effectively captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and little bias. Although bacteria express only thousands of mRNAs per cell, captured mRNA levels were sufficient to distinguish between the transcriptional states of single cells within isogenic populations. In E. coli, we were able to identify single cells in either stationary or exponential phase and define consensus transcriptomes for these sub-populations. In wild type S. aureus, we detected a rare population of cells undergoing prophage induction. We anticipate that PETRI-seq will be widely useful for studying transcriptional heterogeneity in microbial communities.
biorxiv systems-biology 100-200-users 2019The nucleus measures shape deformation for cellular proprioception and regulates adaptive morphodynamics, bioRxiv, 2019-12-05
AbstractThe physical microenvironment regulates cell behavior during tissue development and homeostasis. How single cells decode information about their geometrical shape under mechanical stress and physical space constraints within their local environment remains largely unknown. Here we show that the nucleus, the biggest cellular organelle, functions as a non-dissipative cellular shape deformation gauge that enables cells to continuously measure shape variations on the time scale of seconds. Inner nuclear membrane unfolding together with the relative spatial intracellular positioning of the nucleus provides physical information on the amplitude and type of cellular shape deformation. This adaptively activates a calcium-dependent mechano-transduction pathway, controlling the level of actomyosin contractility and migration plasticity. Our data support that the nucleus establishes a functional module for cellular proprioception that enables cells to sense shape variations for adapting cellular behaviour to their microenvironment.One Sentence SummaryThe nucleus functions as an active deformation sensor that enables cells to adapt their behavior to the tissue microenvironment.
biorxiv cell-biology 100-200-users 2019