Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4+ T cells, bioRxiv, 2019-06-19
AbstractCD4+ T cells are repositories of immune memory, conferring enhanced immunity to many infectious agents. Studies of acute viral and bacterial infection suggest that memory CD4+ T cells develop directly from effectors. However, delineating these dynamic developmental pathways has been challenging. Here, we used high-resolution single-cell RNA-seq and temporal mixture modelling to examine the fate of Th1 and Tfh effector cells during non-lethal Plasmodium infection in mice. We observed linear Th1 and Tfh pathways towards memory, characterized by progressive halving in the numbers of genes expressed, and partial transcriptomic coalescence. Low-level persisting infection diverted but did not block these pathways. We observed in the Th1-pathway a linear transition from Th1 through a Tr1 state to TEM cells, which were then poised for Th1 re-call. The Tfh-pathway exhibited a modest Th1-signature throughout, with little evidence of Tr1 development, and co-expression of TCM and memory Tfh markers. Thus, we present a high-resolution atlas of transcriptome dynamics for naïve to memory transitions in CD4+ T cells. We also defined a subset of memory-associated genes, including transcription factors Id2 and Maf, whose expression increased progressively against the background of transcriptomic quiescence. Single-cell ATAC-seq revealed substantial heterogeneity in chromatin accessibility in single effectors, which was extensively, though incompletely reset and homogenized in memory. Our data reveal that linear transitions from effector to memory occur in a progressive manner over several weeks, suggesting opportunities for manipulating CD4+ T cell memory after primary infection.Highlights<jatslist list-type=bullet><jatslist-item>scRNA-seq reveals progressive transition from effector to memory in CD4+ T cells.<jatslist-item><jatslist-item>Transcriptome dynamics suggest linear not branching models for memory development.<jatslist-item><jatslist-item>A subset of genes associates with gradual onset of CD4+ T cell memory.<jatslist-item><jatslist-item>Th1Tfh predisposition varies among clonotypes with identical antigen-specificity.<jatslist-item><jatslist-item>scATAC-seq uncovers non-coding “memory” elements in the genome.<jatslist-item>
biorxiv immunology 0-100-users 2019Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology, bioRxiv, 2019-06-18
AbstractHigh-throughput 16S rRNA gene amplicon sequencing is an indispensable method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases, and by the lack of a systematic and comprehensive taxonomic classification for most environmental bacteria. Here we combine high-quality and high-throughput full-length 16S rRNA gene sequencing with a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) to create robust, near-complete 16S rRNA gene databases for complex environmental ecosystems. To demonstrate the benefit of the approach, we created an ecosystem-specific database for wastewater treatment systems and anaerobic digesters. The novel approach allows consistent species-level classification of 16S rRNA amplicons sequence variants (ASVs) and the design of highly specific oligonucleotide probes for fluorescence in situ hybridization, which can reveal in situ properties of microbes at unprecedented taxonomic resolution.
biorxiv microbiology 100-200-users 2019Modular and efficient pre-processing of single-cell RNA-seq, bioRxiv, 2019-06-17
AbstractAnalysis of single-cell RNA-seq data begins with the pre-processing of reads to generate count matrices. We investigate algorithm choices for the challenges of pre-processing, and describe a workflow that balances efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is near-optimal in speed and memory. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses.
biorxiv bioinformatics 200-500-users 2019Probabilistic Models of Larval Zebrafish Behavior Structure on Many Scales, bioRxiv, 2019-06-15
AbstractNervous systems have evolved to combine environmental information with internal state to select and generate adaptive behavioral sequences. To better understand these computations and their implementation in neural circuits, natural behavior must be carefully measured and quantified. Here, we collect high spatial resolution video of single zebrafish larvae swimming in a naturalistic environment and develop models of their action selection across exploration and hunting. Zebrafish larvae swim in punctuated bouts separated by longer periods of rest called interbout intervals. We take advantage of this structure by categorizing bouts into discrete types and representing their behavior as labeled sequences of bout-types emitted over time. We then construct probabilistic models – specifically, marked renewal processes – to evaluate how bout-types and interbout intervals are selected by the fish as a function of its internal hunger state, behavioral history, and the locations and properties of nearby prey. Finally, we evaluate the models by their predictive likelihood and their ability to generate realistic trajectories of virtual fish swimming through simulated environments. Our simulations capture multiple timescales of structure in larval zebrafish behavior and expose many ways in which hunger state influences their action selection to promote food seeking during hunger and safety during satiety.
biorxiv animal-behavior-and-cognition 0-100-users 2019Immune, Autonomic, and Endocrine Dysregulation in Autism and Ehlers-Danlos SyndromeHypermobility Spectrum Disorders Versus Unaffected Controls, bioRxiv, 2019-06-14
ABSTRACTBackgroundA growing body of literature suggests etiological overlap between Ehlers-Danlos syndrome (EDS)hypermobility spectrum disorders (HSD) and some cases of autism, although this relationship is poorly delineated. In addition, immune, autonomic, and endocrine dysregulation are reported in both conditions and may be relevant to their respective etiologies.AimsTo study symptom overlap in these two comorbid spectrum conditions.Methods and ProceduresWe surveyed 702 adults aged 25+ years on a variety of EDSHSD-related health topics, comparing individuals with EDSHSD, autism, and unaffected controls.Outcomes and ResultsThe autism group reported similar though less severe symptomology as the EDSHSD group, especially in areas of immuneautonomicendocrine dysregulation, connective tissue abnormalities (i.e., skin, bruisingbleeding), and chronic pain. EDSHSD mothers with autistic children reported more immune symptoms than EDSHSD mothers without, suggesting the maternal immune system could play a heritable role in these conditions (p = 0.0119).Conclusions and ImplicationsThese data suggest that EDSHSD and autism share aspects of immuneautonomicendocrine dysregulation, pain, and some tissue fragility, which is typically more severe in the former. This overlap, as well as documented comorbidity, suggests some forms of autism may be hereditary connective tissue disorders (HCTD).
biorxiv neuroscience 100-200-users 2019Two distinct feedback codes in V1 for ‘real’ and ‘imaginary’ internal experiences, bioRxiv, 2019-06-14
AbstractVisual illusions and visual imagery are conscious sensory events that lack a corresponding physical input. But while everyday mental imagery feels distinct from incoming stimulus input, visual illusions, like hallucinations, are under limited volitional control and appear indistinguishable from physical reality. Illusions are thought to arise from lower-level processes within sensory cortices. In contrast, imagery involves a wide network of brain areas that recruit early visual cortices for the sensory representation of the imagined stimulus. Here, we combine laminar fMRI brain imaging with psychophysical methods and multivariate pattern analysis to investigate in human participants how seemingly ‘real’ and imaginary non-physical experiences are processed in primary visual cortex (V1). We find that the content of mental imagery is only decodable in deep layers, whereas illusory content is only decodable at superficial depths. This suggests that feedback to the different layers may serve distinct functions low-level feedback to superficial layers might be responsible for shaping perception-like experiences, while deep-layer feedback might serve the formation of a more malleable ‘inner’ world, separate from ongoing perception.
biorxiv neuroscience 0-100-users 2019