title: T helper 2 transcriptional profile predicts single-cell HIV envelope-specific polyfunctional CD4+ T cells correlated with reduced risk of infection in RV144 trial

abstract:
Despite the critical role antigen-specific T cells play in responding to viral infections, their aggregate frequencies in peripheral blood have not correlated with clinical protection during HIV infection. However, a subset of HIV-specific CD4+ T cells, termed polyfunctional T cells, can produce multiple effector cytokines simultaneously. In the RV144 HIV vaccine trial, polyfunctional T cells correlated with reduced risk of HIV infection. Little is known about what differentiates polyfunctional T cells from other vaccine-elicited T cells. Therefore, we developed a novel live-cell multiplexed cytokine capture assay, to identify and transcriptionally profile vaccine-specific polyfunctional CD4+ T cells. We applied these methods to samples from the HVTN 097 clinical trial of the same vaccine regimen as RV144. We discovered two surface receptors that were enriched among polyfunctional CD4+ T cells and a Th2-biased signature (IL-4, IL-5, and IL-13) that specifically predicted the envelope-specific polyfunctional CD4+ T cells that were correlated with reduced risk of HIV infection in RV144. By linking single-cell transcriptional and functional profiles, we may be able to further define the role of vaccine-elicited polyfunctional T cells in contributing to effective immunity.

Key PointsO_LINovel ex vivo multiplexed cytokine capture assay to enumerate and single-cell sort polyfunctional T cells for downstream analyses
C_LIO_LIPolyfunctional T cells were specifically detected among the HIV envelope-stimulated CD4+ T cells
C_LIO_LISingle-cell RNA sequencing identified novel surface markers enriched among vaccine-specific polyfunctional CD4+ T cells
C_LIO_LITh2 transcriptional signature predicted polyfunctional CD4+ T cell profile that had correlated with reduced risk of HIV infection in the RV144 HIV efficacy trial
C_LI


title: FETCH: A platform for high-throughput quantification of gap junction hemichannel docking

abstract: Gap junctions are membrane spanning channels that connect the cytoplasm of apposed cells, allowing for the passage of small molecules and ions. They are formed by the connexin (Cx) family of proteins which assemble into hexameric hemichannels on each cell and dock to create gap junctional channels between two cells. Despite importance of various Cx isoforms in human physiology and disease, available tools for screening and discriminating their interactions such as hemichannel compatibility, docking and permeability are limited. Here, we developed FETCH (flow enabled tracking of connexosomes in HEK cells), a method which utilizes the generation of annular gap junctions (connexosomes) as downstream indicators of hemichannel compatibility for intercellular docking. First, we show that fluorescent connexosomes create a cellular phenotype that is detectable by flow cytometry analysis. We then show that FETCH identifies homotypic and heterotypic docking of many single isoform connexin hemichannels. Finally, we demonstrate that FETCH captures the impact of disease-relevant connexin protein mutations on gap junction formation. Thus, we establish a new flow cytometry-based method that is amenable to the high-throughput classification of gap junction hemichannel docking.

category: cell biology


title: Multifunctionality of belowground food webs: resource, size and spatial energy channels

abstract: The belowground compartment of terrestrial ecosystems drives nutrient cycling, the decomposition and stabilisation of organic matter, and supports aboveground life. Belowground consumers create complex food webs that regulate functioning, ensure stability and support biodiversity both below and above ground. However, existing soil food-web reconstructions do not match recently accumulated empirical evidence and there is no comprehensive reproducible approach that accounts for the complex resource, size and spatial structure of food webs in soil. Here I build on generic food-web organization principles and use multifunctional classification of soil protists, invertebrates and vertebrates, to reconstruct  multichannel food-web across size classes of soil-associated consumers. This reconstruction is based on overlying feeding preference, prey protection, size spectrum and spatial distribution matrices combined with biomasses of trophic guilds to infer weighted trophic interactions. I then use food-web reconstruction, together with assimilation efficiencies, to calculate energy fluxes assuming a steady-state energetic system. Based on energy fluxes, I describe a number of indicators, related to stability, biodiversity and multiple ecosystem-level functions such as herbivory, top-down control, translocation and transformation of organic matter. I illustrate the approach with an empirical example, comparing it with traditional resource-focused soil food-web reconstruction. The multichannel reconstruction can be used to assess trophic multifunctionality (analogous to ecosystem multifunctionality), i.e. simultaneous support of multiple trophic functions by the food-web, and compare it across communities and ecosystems spanning beyond the soil. With further validation and parametrization, my multichannel reconstruction approach provides an effective tool for understanding and analysing soil food webs. I believe that having this tool will inspire more people to comprehensively describe soil communities and belowground-aboveground interactions. Such studies will provide informative indicators for including consumers as active agents in biogeochemical models, not only locally but also on regional and global scales.

category: ecology


title: Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans

abstract: Post-translational modification of histones, particularly lysine methylation, are thought to play a crucial role in the aging process. Histone 3 lysine 4 (H3K4) methylation, a modification associated with active chromatin, is mediated by a family of SET1 methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work in model organisms with partial or complete deletion of COMPASS subunits has yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan regulation and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans homolog of SET1. We show that animals bearing catalytically inactive SET-2 retain the ability to form COMPASS complexes but have a marked global loss of H3K4 dimethylation and trimethylation. Consistent with previous work, reduced H3K4 methylation was accompanied by loss of fertility; however, in striking contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Furthermore, other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks a non-catalytic SET1/COMPASS component and displays reduced H3K4 methylation. These results challenge previously held views and establish that wild-type H3K4 methylation levels are necessary to achieve a normal lifespan in C. elegans.

category: genetics


title: A comprehensive investigation of m6A regulators prognostic value and associated molecular pathways in breast invasive cancer

abstract: Breast invasive cancer (BIC) is one of the most commonly observed and the deadliest cancer among women. Despite the progress that has been made in improving breast cancer outcomes by the development of advanced treatment options, due to the heterogeneity and complexity of the disease, more studies are required to explore underlying molecular mechanisms of breast cancer which may provide useful insights to overcome the constraints related to current therapeutic options. The goal of this study was to reveal the crucial roles of m6A regulatory proteins in BIC development using various publicly available datasets and databases. We first conducted a comprehensive analysis to depict the mutation frequency and types for m6A regulatory genes in sub-types of BIC for the evaluation of the genetic alterations landscape of breast cancer. Changes in expression levels of m6A regulatory factors were identified as the key genetic alteration in BIC. Implementation of Kaplan-Meier tool to assess the predictive value of m6A pathway components in BIC validated the use of VIRMA, METTL14, RBM15B, EIF3B, YTHDF1, and YTHDF3 as prognostic biomarkers of breast cancer. We then examined the enriched gene ontology (GO) terms and KEGG pathways for the tumor samples with genetic alterations in the m6A pathway. Dysregulation of m6A regulatory factors in BIC was associated with cell division and survival-related pathways such as  nuclear division and  chromosome segregation via the upregulation of the genes functioning in these biological processes and the gained overactivity of these pathways may account for poor prognosis of the disease. The performed analyses highlighted m6A pathway genes as potential regulators of BIC growth and as a valuable set to be utilized as clinical biomarkers in BIC disease.

category: bioinformatics


title: Analysis of microvascular thrombus mechanobiology with a novel particle-based model

abstract:
Platelet accumulation at the site of vascular injury is regulated by soluble platelet agonists, which induce various types of platelet responses, including integrin activation and granule secretion. The interplay between local biochemical cues, mechanical interactions between platelets and macroscopic thrombus dynamics is poorly understood.

Here we describe a novel computational model of microvascular thrombus formation for detailed analysis of thrombus mechanics. Adopting a previously developed two-dimensional particle-based model focused on the thrombus shell formation, we revise it to introduce platelet agonists. Blood flow is simulated via computational fluid dynamics approach. In order to model soluble platelet activators, we apply Langevin dynamics to a large number of non-dimensional virtual particles. Taking advantage of the available data on platelet dense granule secretion kinetics, we model platelet degranulation as a stochastic agonist-dependent process.

The new model qualitatively reproduces enhanced thrombus formation due to granule secretion in line with in vivo findings and provides a mechanism for thrombin confinement at the early stages of aggregate formation. Our calculations also predict that release of dense granules results in additional mechanical stabilization of the inner layers of the thrombus. Distribution of the inter-platelet forces throughout the aggregate reveals multiple weak spots in the outer regions of thrombus, which are expected to result in mechanical disruptions at the later stages of thrombus formation.

category: biophysics


title: E156/G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.167.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape

abstract:
Emerging variants of SARS-CoV-2 with better immune escape mechanisms and higher transmissibility remains a persistent threat across the globe. B.1.617.2 (Delta) variant was first emerged from Maharashtra, India in December, 2020. This variant is classified to be a major cause and concern of the second wave of COVID-19 in India. In the present study, we explored the genomic and structural basis of this variant through computational analysis, protein modelling and molecular dynamics (MD) simulations approach. B.1.617.2 variant carried E156G and Arg158, Phe-157/del mutations in NTD of spike protein. These mutations in N-terminal domain (NTD) of spike protein of B.1.617.2 variant revealed more rigidity and reduced flexibility compared to spike protein of Wuhan isolate. Further, docking and MD simulation study with 4A8 monoclonal antibody which was reported to bind NTD of spike protein suggested reduced binding of B.1.617.2 spike protein compared to that of spike protein of Wuhan isolate. The results of the present study demonstrate the possible case of immune escape and thereby fitness advantage of the new variant and further warrants demonstration through experimental evidence. Our study identified the probable mechanism through which B.1.617.2 variant is more pathogenically evolved with higher transmissibility as compared to the wild-type.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/447321v3_ufig1.gif" ALT="Figure 1">
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category: systems biology


title: E156G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.617.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape


title: DNA damage induces senescent phenotypes in mouse NIT1 beta cells and human islets

abstract:
ObjectiveType 1 Diabetes (T1D) is characterized by progressive loss of insulin-producing pancreatic {beta} cells as a result of autoimmune destruction. In addition to {beta} cell death, recent work has shown that subpopulations of {beta} cells acquire dysfunction during T1D. We previously reported that some {beta} cells adopt a senescent fate involving a DNA damage response (DDR) during the pathogenesis of T1D, however, the question of how senescence develops in {beta} cells has not been investigated.

MethodsHere, we tested the hypothesis that unrepaired DNA damage triggers {beta} cell senescence using culture models including the mouse NIT1 {beta} cell line derived from the T1D-susceptible nonobese diabetic (NOD) strain, human donor islets and EndoC {beta} cells. DNA damage was chemically induced using etoposide or bleomycin and cells or islets were analyzed by a combination of molecular assays for senescence phenotypes including Western blotting, qRT-PCR, Luminex assays, flow cytometry and histochemical staining. RNA-seq was carried out to profile global transcriptomic changes in human islets undergoing DDR and senescence. Insulin ELISAs were used to quantify glucose stimulated insulin secretion from chemically-induced senescent islets and cells in culture.

ResultsSub-lethal DNA damage in NIT1 cells led to several classical hallmarks of senescence including sustained DDR activation, growth arrest, enlarged flattened morphology and a senescence-associated secretory phenotype (SASP) resembling what occurs in primary {beta} cells during T1D in NOD mice. Some of these phenotypes differed between NIT1 cells and the MIN6 {beta} cell line derived from a non-T1D susceptible mouse strain. RNA-seq analysis of human islets undergoing DDR and early senescence revealed a coordinated p53-p21 transcriptional program and upregulation of prosurvival signaling and SASP genes, which were confirmed in independent islet preparations at the protein level. Importantly, chemically induced DNA damage also led to DDR activation and senescence phenotypes in the EndoC-{beta}H5 human {beta} cell line, confirming that this response can occur directly in human {beta} cells. Finally, DNA damage and senescence in both mouse {beta} cell lines and human islets led to decreased insulin content.

ConclusionsTaken together, these findings suggest that some of the phenotypes of {beta} cell senescence during T1D can be modeled by chemically induced DNA damage in mouse {beta} cell lines and human islets and {beta} cells in culture. These culture models will be useful tools to understand some of the mechanisms of {beta} cell senescence in T1D.

HighlightsO_LIDNA damage induces senescent phenotypes in mouse {beta} cell lines
C_LIO_LIDNA damage induces a p53-p21 transcriptional program and senescent phenotypes in human islets and EndoC cells
C_LIO_LIDNA damage and senescence leads to decreased insulin content
C_LIO_LIDNA damage models some aspects of {beta} cell senescence in Type 1 Diabetes
C_LI


title: DNA damage models phenotypes of beta cell senescence in Type 1 Diabetes


title: Ultra fast and highly realistic numerical modelling of the surface EMG

abstract: Modelling the biophysics underlying the generation and recording of electromyographic (EMG) signals has had a fundamental role in our understanding of muscle electrophysiology as well as in the validation of algorithms for information extraction from the EMG. Current EMG models differ for the complexity of the description of the volume conductor. Analytical solutions are computationally efficient for a small number of fibers but limited to simplified geometries. Numerical solutions are based on accurate anatomical descriptions but require long computational time and are therefore impractical for applications requiring a large number of simulations across a broad variety of conditions. Here, we propose a computationally efficient and realistic EMG model. The volume conductor is described from magnetic resonance images (MRI) or tissue surfaces by discretization in a tetrahedral mesh. The numerical solution of the forward model is optimized by reducing the main calculations to the solutions in a minimal number of basis points, from which the general solution can be obtained. This approach allows the lowest computational time than any current EMG models and also provides a scalable solution. New solutions for the same volume conductor can indeed be obtained without recomputing the volume conductor transformation. This property provides almost real-time simulations, without any constraints on the complexity of the volume conductor or of the transmembrane current source. Because of the high computational efficiency, the proposed model can be used as a basis for the solution of the inverse model or as a means to simulate a large number of data for artificial intelligence (AI) based EMG processing.

category: bioengineering


title: Bioelectromagnetic platform for stimulation

abstract: Magnetogenetics is a new field that utilizes electromagnetic fields to remotely control cellular activity. In addition to the development of the biological genetic tools, this approach requires designing hardware with a specific set of demands for the electromagnets used to provide the desired stimulation for electrophysiology and imaging experiments. Here we present a universal stimulus delivery system comprised of four magnet designs compatible with electrophysiology, fluorescence and luminescence imaging, microscopy, and freely behaving animal experiments. The overall system includes a low-cost stimulation controller which enables rapid switching between active and sham stimulation trials as well as precise control of stimulation delivery.


title: An extension of Wang protein design model using Blosum62 substitution matrix

abstract: Humans life depends on the functionality of molecules in the body. One of these essential molecules is the protein that plays a vital role in our life, such that its malfunction can cause severe damages. Such roles make protein structure and its functionality necessary to understand. One of the problems that help us understand the relation between protein structure is the well-known protein design problem which attempts to find an amino acid sequence that can fold into a desired tertiary structure. However, despite having an acceptable accuracy in protein design, this accuracy is an identical percentage of amino acid retrieving. At the same time, it is well-known that amino acids can replace each other in evolution while the function and structure of protein stay the same. Thus the designed sequence does not have the opportunity to be close to the target in the evolutionary aspect. This paper presents an extension to Wangs deep learning model, which uses evolutionary information in the Blosum62 substitution matrix to take amino acid replacement probability into account while designing a sequence.


title: RBPSpot: Learning on Appropriate Contextual Information for RBP Binding Sites Discovery

abstract: Identifying RBP binding sites and mechanistic factors determining the interactions remain a big challenge. Besides the sparse binding motifs across the RNAs, it also requires a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites while using an ultra-fast BWT/FM-indexing coupled inexact k-mer spectrum search for statistically significant seeds. The seed works as an anchor to evaluate the context and binding potential using flanking region information while leveraging from Deep Feed-forward Neural Network (DNN). Contextual features based on pentamers/dinucloetides which also capture shape and structure properties appeared critical. Contextual CG distribution pattern appeared important. The developed models also got support from MD-simulation studies and the implemented software, RBPSpot, scored consistently high for the considered performance metrics including average accuracy of [~]90% across a large number of validated datasets while maintaining consistency. It clearly outperformed some recently developed tools, including some with much complex deep-learning models, during a highly comprehensive bench-marking process involving three different data-sets and more than 50 RBPs. RBPSpot, has been made freely available, covering most of the human RBPs for which sufficient CLIP-seq data is available (131 RBPs). Besides identifying RBP binding spots across RNAs in human system, it can also be used to build new models by user provided data for any species and any RBP, making it a valuable resource in the area of regulatory system studies.


title: Evolutionary velocity with protein language models

abstract: Predicting the order of biological homologs is a fundamental task in evolutionary biology. For protein evolution, this order is often determined by first arranging sequences into a phylogenetic tree, which has limiting assumptions and can suffer from substantial ambiguity. Here, we demonstrate how machine learning algorithms called language models can learn mutational likelihoods that predict the directionality of evolution, thereby enabling phylogenetic analysis that addresses key limitations of existing methods. Our main conceptual advance is to construct a "vector field" of protein evolution through local evolutionary predictions that we refer to as evolutionary velocity (evo-velocity). We show that evo-velocity can successfully predict evolutionary order at vastly different timescales, from viral proteins evolving over years to eukaryotic proteins evolving over geologic eons. Evo-velocity also yields new evolutionary insights, predicting strategies of viral-host immune escape, resolving conflicting theories on the evolution of serpins, and revealing a key role of horizontal gene transfer in the evolution of eukaryotic glycolysis. In doing so, our work suggests that language models can learn sufficient rules of natural protein evolution to enable evolutionary predictability.


title: Alpha and beta rhythms differentially support the effect of symbols on visual object recognition

abstract: Hearing spoken words can enhance visual object recognition, detection and discrimination. Yet, the mechanisms that underpin this facilitation are incompletely understood. On one account, words do not bias early visual processing, but rather affect later semantic or decision-making stages. However, recent proposals suggest that words can alter early visual processes by activating category-specific priors in sensory regions. A prediction of this account is that top-down priors evoke changes in occipital areas in anticipation of visual stimuli. Here, we tested the hypothesis that neural oscillations serve as a mechanism to activate language-generated visual priors. Participants performed a cue-picture matching task where cues were either spoken words, in their native or second language, or natural sounds, while their EEG and reaction times were recorded. Behaviorally, we replicated the previously reported label-advantage effect, with images cued by words being recognized faster than those cued by natural sounds. A time-frequency analysis of cue-target intervals revealed that this behavioral label-advantage was associated with enhanced power in posterior alpha (9-11 Hz) and beta oscillations (17-19 Hz), both of which were larger when the image was preceded by a word compared to a natural sound. Importantly, object recognition performance improved with high alpha power but slowed down with enhancement of beta synchronization. These results suggest that alpha and beta rhythms play distinct functional roles to support language-mediated visual object recognition: alpha might function to amplify sensory priors in posterior regions, while beta may (re)activate the network states elicited by the auditory cue.

category: neuroscience


title: Hippocampal ripples signal contextually-mediated episodic recall

abstract:
High-frequency oscillatory events, termed ripples, represent synchrony of neural activity in the brain. Recent evidence suggests medial temporal lobe (MTL) ripples support memory retrieval. However, it is unclear if ripples signal the reinstatement of episodic memories. Analyzing electrophysiological MTL recordings from 219 neurosurgical participants performing episodic recall tasks, we find that the rate of hippocampal ripples rises just prior to the free recall of recently-formed memories. This pre-recall ripple effect (PRE) is stronger in the CA1 and dentate gyrus (DG) subfields of hippocampus than neighboring MTL regions entorhinal and parahippocampal cortex. The PRE is also stronger prior to the retrieval of temporally and semantically clustered as compared with unclustered recalls, indicating the involvement of ripples in contextual reinstatement, which is a hallmark of episodic memory.

One sentence summaryHigh frequency human hippocampal ripples occur prior to those memories most likely retrieved via episodic mechanisms.


title: Reducing susceptibility distortion related image blurring in diffusion MRI EPI data

abstract: Diffusion magnetic resonance imaging (MRI) is an increasingly popular technique in basic and clinical neuroscience. One promising application is to combine diffusion MRI with myelin maps from complementary MRI techniques such as multi-parameter mapping (MPM) to produce g-ratio maps that represent the relative myelination of axons and predict their conduction velocity. Statistical Parametric Mapping (SPM) can process both diffusion data and MPMs, making SPM the only widely accessible software that contains all the processing steps required to perform group analyses of g-ratio data in a common space. However, limitations have been identified in its method for reducing susceptibility-related distortion in diffusion data. More generally, susceptibility-related image distortion is often corrected by combining reverse phase-encoded images (blip-up and blip-down) using the arithmetic mean (AM), however, this can lead to blurred images. In this study we sought to (1) improve the susceptibility-related distortion correction for diffusion MRI data in SPM; (2) deploy an alternative approach to the AM to reduce image blurring in diffusion MRI data when combining blip-up and blip-down EPI data after susceptibility-related distortion correction; and (3) assess the benefits of these changes for g-ratio mapping. We found that the new processing pipeline, called consecutive Hyperelastic Susceptibility Artefact Correction (HySCO) improved distortion correction when compared to the standard approach in the ACID toolbox for SPM. Moreover, using a weighted average (WA) method to combine the distortion corrected data from each phase-encoding polarity achieved greater overlap of diffusion and more anatomically faithful structural white matter probability maps derived from minimally distorted multi-parameter maps as compared to the AM. Third, we showed that the consecutive HySCO WA performed better than the AM method when combined with multi-parameter maps to perform g-ratio mapping. These improvements mean that researchers can conveniently access a wide range of diffusion-related analysis methods within one framework because they are now available within the open-source ACID toolbox as part of SPM, which can be easily combined with other SPM toolboxes, such as the hMRI toolbox, to facilitate computation of myelin biomarkers that are necessary for g-ratio mapping.


title: PALB2 maintains redox and mitochondrial homeostasis in the brain and cooperates with ATG7 to suppress p53 dependent neurodegeneration

abstract: The PALB2 tumor suppressor plays key roles in DNA repair and has been implicated in redox homeostasis. Autophagy maintains mitochondrial quality, mitigates oxidative stress and suppresses neurodegeneration. Here we show that Palb2 deletion in the mouse brain leads to motor deficits and that co-deletion of Palb2 with the essential autophagy gene Atg7 accelerates and exacerbates neurodegeneration induced by ATG7 loss. Palb2 deletion leads to elevated DNA damage, oxidative stress and mitochondrial markers, especially in Purkinje cells, and co-deletion of Palb2 and Atg7 results in accelerated Purkinje cell loss. Further analyses suggest that the accelerated Purkinje cell loss and severe neurodegeneration in the double deletion mice are due to oxidative stress and mitochondrial dysfunction, rather than DNA damage, and partially dependent on p53 activity. Our studies uncover a role of PALB2 in mitochondrial regulation and a cooperation between PALB2 and ATG7/autophagy in maintaining redox and mitochondrial homeostasis essential for neuronal survival.


title: Myofibroblast differentiation is governed by adhesion mechanics, and inhibition of the stress sensor Talin2 reverses lung fibrosis

abstract:
Fibrosis is involved in 45% of deaths in the United States, and no treatment exists to reverse progression of the disease. In order to find novel targets for fibrosis therapeutics, we developed a model for the differentiation of monocytes to myofibroblasts that allowed us to screen for proteins involved in myofibroblast differentiation. Inhibition of a novel protein target generated by our model, talin2, reduces myofibroblast morphology, -smooth muscle actin content, collagen I content, and lowers the pro-fibrotic secretome of myofibroblasts. We find that knockdown of talin2 de-differentiates myofibroblasts, talin2 knockdown reverses bleomycin-induced lung fibrosis in mice, and Tln2 -/-mice are resistant to unilateral ureteral obstruction-induced kidney fibrosis and are resistant to bleomycin-induced lung fibrosis. Talin2 inhibition is a potential treatment for reversing lung and kidney fibroses.

One Sentence SummarySilencing the stress sensor Talin2 reverses myofibroblast differentiation and existing fibrosis.

category: immunology


title: B.1.1.7 and B.1.351 variants are highly virulent in K18-ACE2 transgenic mice and show different pathogenic patterns from early SARS-CoV-2 strains

abstract: SARS-CoV-2 continues to circulate globally resulting in emergence of several variants of concern (VOC), including B.1.1.7 and B.1.351 that show increased transmissibility and enhanced resistance to antibody neutralization. In a K18-hACE2 transgenic mouse model, we demonstrate that Both B.1.1.7 and B.1.351 are 100 times more lethal than the original SARS-CoV-2 bearing 614D. Mice infected with B.1.1.7 and B.1.351 exhibited more severe lesions in internal organs than those infected with early SARS-CoV-2 strains bearing 614D or 614G. Infection of B.1.1.7 and B.1.351 also results in distinct tissue-specific cytokine signatures, significant D-dimer depositions in vital organs and less pulmonary hypoxia signaling before death as compared to the mice infected with early SARS-CoV-2 strains. However, K18-hACE2 mice with the pre-existing immunity from prior infection or immunization were resistant to the lethal reinfection of B.1.1.7 or B.1.351, despite having reduced neutralization titers against these VOC. Our study reveals distinguishing pathogenic patterns of B.1.1.7 and B.1.351 variants from those early SARS-CoV-2 strains in K18-hACE2 mice, which will help to inform potential medical interventions for combatting COVID-19.


title: The interaction of enteric bacterial effectors with the host engulfment pathway control innate immune responses

abstract:
BackgroundHost engulfment protein ELMO1 generates intestinal inflammation following internalization of enteric bacteria. In Shigella, bacterial effector IpgB1 interacts with ELMO1 and promotes bacterial invasion. IpgB1 belongs to the WxxxE effector family, a motif found in several effector of enteric pathogens. Here, we have studied the role of WxxxE effectors, with emphasis on Salmonella SifA and whether it interacts with ELMO1 to regulate inflammation.

MethodologyIn-silico-analysis of WxxxE effectors was performed using BLAST search and Clustal W program. The interaction of ELMO1 with SifA was assessed by GST pulldown assay and co-immunoprecipitation. ELMO1 knock-out mice, and ELMO1-depleted murine macrophage J774 cell lines were challenged with WT and SifA mutant Salmonella. Bacterial effectors containing the WxxxE motif were transfected in WT and ELMO1-depleted J774 cells to assess the inflammatory cytokines.

ResultsELMO1 generates differential pro-inflammatory cytokines between pathogenic and non-pathogenic bacteria. WxxxE motif is present in pathogens and in the TIR domain of host proteins. The C-terminal part of ELMO1 interacts with SifA where WxxxE motif is important for interaction. ELMO1-SifA interaction affects the bacterial colonization, dissemination, and inflammatory cytokines in vivo. Moreover, ELMO1-SifA interaction increases TNF- and IL-6 production from the macrophage cell line and is associated with enhanced Rac1 activity. ELMO1 also interacts with WxxxE effectors IpgB1, IpgB2, and Map, and induces inflammation after challenge with microbe or microbial ligand.

ConclusionELMO1 generates a differential response through interaction with the WxxxE motif which is absent in commensals. ELMO1-WxxxE interaction plays a role in bacterial pathogenesis and induction of inflammatory response.

HighlightsO_LIELMO1 generates a differential immune response between enteric pathogens and commensals.
C_LIO_LIEnteric bacterial effectors containing WxxxE signature motif interact with ELMO1.
C_LIO_LIThe WxxxE effector of Salmonella SifA interacts with the C-terminal part of ELMO1.
C_LIO_LIELMO1-SifA interaction increases the inflammatory response in vivo and in vitro.
C_LI

category: microbiology


title: Bacterial gasdermins reveal an ancient mechanism of cell death

abstract: Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. Here we discover gasdermin homologs encoded in bacteria that execute prokaryotic cell death. Structures of bacterial gasdermins reveal a conserved pore-forming domain that is stabilized in the inactive state with a buried lipid modification. We demonstrate that bacterial gasdermins are activated by dedicated caspase-like proteases that catalyze site-specific cleavage and removal of an inhibitory C-terminal peptide. Release of autoinhibition induces the assembly of >200 [A] pores that form a mesh-like structure and disrupt membrane integrity. These results demonstrate that caspase-mediated activation of gasdermins is an ancient form of regulated cell death shared between bacteria and animals.


title: The local anaesthetic procaine prodrugs ProcCluster(R) and Procaine-hydrochloride impair SARS-CoV-2 replication in vitro

abstract: The SARS-CoV-2 pandemic has had the world in suspense for more than a year. Even if more and more vaccines are approved there is still an urgent need for efficient antiviral treatment strategies. Here, we present data on the inhibitory effect of the local anaesthetic procaine, especially the prodrugs ProcCluster(R) and Procaine-hydrochloride on SARS-CoV-2 infection in vitro. Remarkably, similar effects could be shown on the replication of influenza A viruses in cell culture systems. Since the active ingredient procaine is well-tolerated and already used in the clinics for anaesthetic purposes, the further investigation of this substance could enable its reuse in antiviral therapy, including SARS-CoV-2.


title: Hot water extract of Arthrospira maxima (AHWE) has broad-spectrum antiviral activity against RNA virus including coronavirus SARS-CoV2, and the antivirus spray application

abstract: The emergence and re-emergence of RNA virus outbreaks highlight the urgent need for the development of broad-spectrum antiviral agents. Arthrospira maxima has be used as a food source for a long time, and the protein or polysaccharide fractions were evidenced to have antiviral activity, therefore we examined the antiviral efficacy of hot water extract from Arthrospira maxima (AHWE), on Enterovirus 71 (EV71), Influenza virus, Herpes simplex virus (HSV), Respiratory syncytial virus (RSV), Ebola virus, and Coronavirus for antiviral spray application. In this study, we demonstrated that the AHWE shown 90 to 100% inhibition rate on the plaque formation of EV71, HSV-1, HSV-2, influenza virus, RSV, 229E and SARS-COV2 at virus attachment stage, and the long-lasting protection study also found while the AHWE was pre-exposed to the open air for more than 4 hours in plaque reduction assay. In addition, AHWE also had inhibitory effect on Ebola virus replication at 500 ug/ml. Finally, AHWE also shown no toxicity and skin sensitivity that imply it could be safe for future clinical use if approved by FDA. In conclusion, this study suggests that AHWE could be developed as a potential broad-spectrum antivirus spray product and therapeutic agent.


title: AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space

abstract: Genomes and metagenomes contain a considerable percentage of genes of unknown function, which are often excluded from downstream analyses limiting our understanding of the studied biological systems. To address this challenge, we developed AGNOSTOS, a combined database-computational workflow resource that unifies the known and unknown coding sequence space of genomes and metagenomes. Here, we present AGNOSTOS-DB, an extensive database of high-quality gene clusters enriched with functional, ecological and phylogenetic information. Moreover, AGNOSTOS allows integrating new data into existing AGNOSTOS-DBs, maximizing the information retrievable for the genes of unknown function. As a proof of concept, we provide a seed database that integrates the predicted genes from marine and human metagenomes, as well as from Bacteria, Archaea, Eukarya and giant viruses environmental and cultivar genomes. The seed database comprises 6,572,081 gene clusters connecting 342 million genes and represents a comprehensive and scalable resource for the inclusion and exploration of the unknown fraction of genomes and metagenomes.


title: Droplets of amyotrophic lateral sclerosis-associated p62/SQSTM1 mutants show slower inner fluidity

abstract: A series of amyotrophic lateral sclerosis (ALS)-related proteins such as FUS, TDP-43 and hnRNPA1 has an ability to be liquid-liquid phase separation, and their disease-related mutations cause the transition of their responsible liquid droplets to aggregates. Missense mutations in SQSTM1/p62, which have been identified throughout the gene, are associated with ALS, frontotemporal degeneration (FTD) and Pagets disease of bone. SQSTM1/p62 protein forms liquid-droplets through the interaction with ubiquitinated proteins, and the droplet serves as a platform of autophagosome formation and anti-oxidative stress response via the LC3-interacting region (LIR) and Keap1-interacting region (KIR), respectively. However, it remains unclear whether ALS/FTD-related p62 mutations in LIR and KIR form aberrant liquid droplets, cause defective autophagy and stress response or both. To evaluate the effects of ALS/FTD-related p62 mutations in LIR and KIR on a major oxidative stress system, the Keap1-Nrf2 pathway and the autophagic turnover, we developed systems that enable to monitor them with high sensitivity. These systems revealed that some mutants but not all have their less abilities on the Nrf2-activation and show the delayed turnover. By contrast, while the sufficient ability to form liquid droplets, all droplets consisting of p62 mutants showed slower inner fluidity. These results indicate that like other ALS-related mutant proteins, a primary defect in ALS/FTD with p62 missense mutations is a qualitative change of p62-liquid droplets.


title: Photoreceptor Compartment-Specific TULP1 Interactomes

abstract: Photoreceptors are highly compartmentalized cells with large amounts of proteins synthesized in the inner segment (IS) and transported to the outer segment (OS) and synaptic terminal. Tulp1 is a photoreceptor-specific protein localized to the IS and synapse. In the absence of Tulp1, several OS-specific proteins are mislocalized and synaptic vesicle recycling is impaired. To better understand the involvement of Tulp1 in protein trafficking, our approach was to physically isolate Tulp1-containing photoreceptor compartments by serial tangential sectioning of retinas and to identify compartment-specific Tulp1 binding partners by immunoprecipitation followed by liquid chromatography tandem mass spectrometry. Our results indicate that Tulp1 has two distinct interactomes. We report the identification of: 1) an IS-specific interaction between Tulp1 and the motor protein Kinesin family member 3a (Kif3a), 2) a synaptic-specific interaction between Tulp1 and the scaffold protein Ribeye, and 3) an interaction between Tulp1 and the cytoskeletal protein Microtubule-associated protein 1B (MAP1B) in both compartments. Immunolocalization studies in the wild-type retina indicate that Tulp1 and its binding partners co-localize to their respective compartments. Our observations are compatible with Tulp1 functioning in protein trafficking in multiple photoreceptor compartments, likely as an adapter molecule linking vesicles to molecular motors and the cytoskeletal scaffold.


title: NanoDam identifies novel temporal transcription factors conserved between the Drosophila central brain and visual system

abstract: Temporal patterning of neural progenitors is an evolutionarily conserved strategy for generating neuronal diversity. Type II neural stem cells in the Drosophila central brain produce transit-amplifying intermediate neural progenitors (INPs) that exhibit temporal patterning. However, the known temporal factors cannot account for the neuronal diversity in the adult brain. To search for new temporal factors, we developed NanoDam, which enables rapid genome-wide profiling of endogenously-tagged proteins in vivo with a single genetic cross. Mapping the targets of known temporal transcription factors with NanoDam identified Homeobrain and Scarecrow (ARX and NKX2.1 orthologues) as novel temporal factors. We show that Homeobrain and Scarecrow define middle-aged and late INP temporal windows and play a role in cellular longevity. Strikingly, Homeobrain and Scarecrow have conserved functions as temporal factors in the developing visual system. NanoDam enables rapid cell type-specific genome-wide profiling with temporal resolution and can be easily adapted for use in higher organisms.

category: developmental biology


title: How host phenology impacts multi-season epidemic cycles

abstract: Parasite-host interactions can result in periodic population dynamics when parasites over-exploit host populations. The timing of host seasonal activity, or host phenology, determines the frequency and demographic impact of parasite-host interactions which may govern if the parasite can sufficiently over-exploit their hosts to drive population cycles. We describe a mathematical model of a monocyclic, obligate-killer parasite system with seasonal host activity to investigate the consequences of host phenology on host-parasite dynamics. The results suggest that parasites can reach the densities necessary to destabilize host dynamics and drive cycling in only some phenological scenarios, such as environments with short seasons and synchronous host emergence. Further, only parasite lineages that are sufficiently adapted to phenological scenarios with short seasons and synchronous host emergence can achieve the densities necessary to over-exploit hosts and produce population cycles. Host-parasite cycles can also generate an eco-evolutionary feedback that slows parasite adaptation to the phenological environment as rare advantageous phenotypes are driven to extinction when introduced in phases of the cycle where host populations are small and parasite populations are large. The results demonstrate that seasonal environments can drive population cycling in a restricted set of phenological patterns and provides further evidence that the rate of adaptive evolution depends on underlying ecological dynamics.


title: Host phenology regulates ecological and eco-evolutionary feedbacks underlying parasite-host demographic cycles


title: Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

abstract:
SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didnt identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2s integration into host genome is lacking.

One-Sentence SummarySARS-CoV-2 does not integrate into host genome through whole genome sequencing.

category: genomics


title: Cannabinoids vs. whole metabolome: relevance of cannabinomics in analyzing Cannabis varieties

abstract: Cannabis sativa has a long history of domestication both for its bioactive compounds and its fibers. This has produced hundreds of varieties, usually characterized in the literature by chemotypes, with {Delta}9-THC and CBD content as the main markers. However, chemotyping could also be done based on minor compounds (phytocannabinoids and others). In this work, a workflow, which we propose to name cannabinomics, combines mass spectrometry of the whole metabolome and statistical analysis to help differentiate C. sativa varieties and deciphering their characteristic markers. By applying this cannabinomics approach to the data obtained from 20 varieties of C. sativa (classically classified as chemotype I, II, or III), we compared the results with those obtained by a targeted quantification of 11 phytocannabinoids. Cannabinomics can be considered as a complementary tool for phenotyping and genotyping, allowing the identification of minor compounds playing a key role as markers of differentiation.

category: biochemistry


title: Strain-Programmable Patch for Diabetic Wound Healing

abstract:
Chronic wounds with impaired healing capability such as diabetic foot ulcers (DFU) are devastating complications in diabetic patients, inflicting rapidly growing clinical and economic burdens in aging societies. Despite recent advances in therapeutic approaches, limited benefits of the existing solutions highlight the critical need for novel therapeutic solutions for diabetic wound healing. Here we propose a strain-programmable patch capable of rapid robust adhesion on and programmable mechanical contraction of wet wounded tissues over days to offer a new therapeutic platform for diabetic wounds. The strain-programmable patch, consisting of a dried bioadhesive layer and a pre-stretched elastomer backing, implements a hydration-based shape-memory mechanism to achieve both uniaxial and biaxial contractions and stress remodeling of wet wounds in a programmable manner. We develop theoretical and numerical models to rationally guide the strain-programming and mechanical modulation of wounds. In vivo rodent and ex vivo human skin culture models validate the programmability and efficacy of the proposed platform and identify mechanisms of action for accelerated diabetic wound healing.

One Sentence SummaryA strain-programmable bioadhesive patch is developed for accelerated closure and healing of wounds in diabetic mice and human skin.


title: Distribution and vulnerability of transcriptional outputs across the genome in Myc-amplified medulloblastoma cells

abstract: Myc plays a central role in tumorigenesis by orchestrating the expression of genes essential to numerous cellular processes1-4. While it is well established that Myc functions by binding to its target genes to regulate their transcription5, the distribution of the transcriptional output across the human genome in Myc-amplified cancer cells, and the susceptibility of such transcriptional outputs to therapeutic interferences remain to be fully elucidated. Here, we analyze the distribution of transcriptional outputs in Myc-amplified medulloblastoma (MB) cells by profiling nascent total RNAs within a temporal context. This profiling reveals that a major portion of transcriptional action in these cells was directed at the genes fundamental to cellular infrastructure, including rRNAs and particularly those in the mitochondrial genome (mtDNA). Notably, even when Myc protein was depleted by as much as 80%, the impact on transcriptional outputs across the genome was limited, with notable reduction mostly only in genes involved in ribosomal biosynthesis, genes residing in mtDNA or encoding mitochondria-localized proteins, and those encoding histones. In contrast to the limited direct impact of Myc depletion, we found that the global transcriptional outputs were highly dependent on the activity of Inosine Monophosphate Dehydrogenases (IMPDHs), rate limiting enzymes for de novo guanine nucleotide synthesis and whose expression in tumor cells was positively correlated with Myc expression. Blockage of IMPDHs attenuated the global transcriptional outputs with a particularly strong inhibitory effect on infrastructure genes, which was accompanied by the abrogation of MB cells proliferation in vitro and in vivo. Together, our findings reveal a real time action of Myc as a transcriptional factor in tumor cells, provide new insight into the pathogenic mechanism underlying Myc-driven tumorigenesis, and support IMPDHs as a therapeutic vulnerability in cancer cells empowered by a high level of Myc oncoprotein.

category: cancer biology


title: B1L regulates lateral root development by exocytic vesicular trafficking-mediated polar auxin transport

abstract: Auxin and auxin-mediated signaling pathways involved in the regulation of lateral root development are well documented. Although exocytic vesicle trafficking plays an important role in auxin efflux carriers PIN recycling, and polar auxin transport during lateral root formation, however, the mechanistic details of these processes are not well understood. Here, we demonstrate that BYPASS1-LIKE (B1L) regulate lateral root development via exocytic vesicular trafficking-mediated polar auxin transport in Arabidopsis. In b1l mutants, the number of lateral roots increased significantly, and the phenotypes were mainly attributed to lateral root primordium initiation but not to the defects in lateral root primordium development. Furthermore, the auxin signal was stronger in the lateral root primordium of the b1l mutant at stage I than those observed in the wild-type (WT). Moreover, exogenous auxin and auxin transport inhibitory treatments indicated that the phenotype of lateral roots in b1l mutants can be attributed to higher auxin levels and that B1L regulates auxin efflux. Consistently, auxin efflux carriers PIN1-GFP and PIN3-GFP were expressed at higher levels in the lateral root primordium of the b1l mutants. Interestingly, we found that B1L interacted with the exocyst and b1l mutant showed a defect in PIN2 exocytosis. Finally, we found that B1L cooperated with EXO70B1 to regulate lateral root formation. Our findings reveal an essential regulatory mechanism of B1L that interacts with the exocyst to regulate PIN-mediated polar auxin transport and lateral root initiation.

category: plant biology


title: Analysis-rcs-data: Open-source toolbox for the ingestion, time-alignment, and visualization of sense and stimulation data from the Medtronic Summit RC+S system

abstract: Closed-loop neurostimulation is a promising therapy being tested and clinically implemented in a growing number of neurological and psychiatric indications. This therapy is enabled by chronically implanted, bidirectional devices including the Medtronic Summit RC+S system. In order to successfully optimize therapy for patients implanted with these devices, analyses must be conducted offline on the recorded neural data, in order to inform optimal sense and stimulation parameters. The file format, volume, and complexity of raw data from these device necessitate conversion, parsing, and time reconstruction ahead of time-frequency analyses and modeling common to standard neuroscientific analyses. Here, we provide an open-source toolbox written in Matlab which takes raw files from the Summit RC+S and transforms these data into a standardized format amenable to conventional analyses. Furthermore, we provide a plotting tool which can aid in the visualization of multiple data streams and sense, stimulation, and therapy settings. Finally, we describe an analysis module which replicates RC+S on-board power computations, functionality which can accelerate biomarker discovery. This toolbox aims to accelerate the research and clinical advances made possible by longitudinal neural recordings and adaptive neurostimulation in people with neurological and psychiatric illnesses.


title: Blocking antibodies against integrin-α3, integrin-αM, and integrin-αMβ2 de-differentiate myofibroblasts and reverse lung and kidney fibroses in a mouse model

abstract:
Fibrosis is involved in 45% of deaths in the United States, and no treatment exists to reverse the progression of the disease. Myofibroblasts are key to the progression and maintenance of fibrosis. We investigated features of cell adhesion necessary for monocytes to differentiate into myofibroblasts, seeking to identify pathways key to myofibroblast differentiation. Blocking antibodies against integrins 3, M, and M{beta}2 de-differentiate myofibroblasts in vitro, lower the pro-fibrotic secretome of myofibroblasts, and reverse lung and kidney fibrosis in vivo. Decorins collagen-binding peptide directs blocking antibodies (against integrins-3, -M, -M{beta}2) to both fibrotic lungs and fibrotic kidneys, reducing the dose of antibody necessary to reverse fibrosis. This targeted immunotherapy blocking key integrins may be an effective therapeutic for the treatment and reversal of fibrosis.

SummaryBlocking antibodies against integrins-3, -M, and -M{beta}2 can be targeted to sites of fibrosis, reverse lung and kidney fibroses, and offer the potential to bring immunotherapy to fibrosis


title: Blocking antibodies against integrin-a3, integrin-aM, and integrin-aMb2 de-differentiate myofibroblasts and reverse lung and kidney fibroses in a mouse model


title: Dual roles of a novel oncolytic viral vector-based SARS-CoV-2 vaccine: preventing COVID-19 and treating tumor progression

abstract:
The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cancer patients are usually immunocompromised and thus are particularly susceptible to SARS-CoV-2 infection resulting in COVID-19. Although many vaccines against COVID-19 are being preclinically or clinically tested or approved, none have yet been specifically developed for cancer patients or reported as having potential dual functions to prevent COVID-19 and treat cancer. Here, we confirmed that COVID-19 patients with cancer have low levels of antibodies against the spike (S) protein, a viral surface protein mediating the entry of SARS-CoV-2 into host cells, compared with COVID-19 patients without cancer. We developed an oncolytic herpes simplex virus-1 vector-based vaccine named oncolytic virus (OV)-spike. OV-spike induced abundant anti-S protein neutralization antibodies in both tumor-free and tumor-bearing mice, which inhibit infection of VSV-SARS-CoV-2 and wild-type (WT) live SARS-CoV-2 as well as the B.1.1.7 variant in vitro. In the tumor-bearing mice, OV-spike also inhibited tumor growth, leading to better survival in multiple preclinical tumor models than the untreated control. Furthermore, OV-spike induced anti-tumor immune response and SARS-CoV-2-specific T cell response without causing serious adverse events. Thus, OV-spike is a promising vaccine candidate for both preventing COVID-19 and enhancing the anti-tumor response.

One Sentence SummaryA herpes oncolytic viral vector-based vaccine is a promising vaccine with dual roles in preventing COVID-19 and treating tumor progression


title: Small Molecule Stabilization of PINK-1/PINK1 Improves Neurodegenerative Disease

abstract: Macroautophagic recycling of dysfunctional mitochondria, known as mitophagy, is essential for mitochondrial homeostasis and cell viability. Accumulation of defective mitochondria and impaired mitophagy have been widely implicated in many neurodegenerative diseases, and loss-of-function mutations of two regulators of mitophagy, PINK1 and Parkin, are amongst the most common causes of recessive Parkinsons disease. Activation of mitophagy via pharmacological treatments may be a feasible approach for combating neurodegeneration. In this effort, we screened [~]45,000 small molecules for the ability to activate mitophagy. A high-throughput, whole-organism, phenotypic screen was conducted by monitoring stabilization of PINK-1/PINK1, a key event in mitophagy activation, in a Caenorhabditis elegans strain carrying a Ppink-1::PINK-1::GFP reporter. We obtained eight hits that induced mitophagy, as evidenced by increased mitochondrial fragmentation and autophagosome formation. Several of the compounds also reduced ATP production, oxygen consumption, mitochondrial mass, and/or mitochondrial membrane potential. Importantly, we found that treatment with two compounds, which we named PS83 and PS106 (more commonly known as sertraline) reduced neurodegenerative disease phenotypes (including delayed paralysis in a C. elegans Alzheimers model) in a PINK-1/PINK1-dependent manner. This report presents a promising step toward the identification of compounds that will stimulate mitochondrial turnover.


title: Acceleration of Evolutionary Processes by Learning and Extended Fisher's Fundamental Theorem

abstract: Natural selection is general and powerful concept not only to explain evolutionary processes of biological organisms but also to design engineering systems such as genetic algorithms and particle filters. There is a surge of interest, both from biology and engineering, in considering natural selection of intellectual agents that can learn individually. Learning by individual agents of better behaviors for survival may accelerate the evolutionary processes by natural selection. We have accumulating pieces of evidence that organisms can transmit its information to the next generation via epigenetic states or memes. Also, such idea is important for engineering applications to improve the genetic algorithms and the particle filter. To accelerate the evolutionary process, an agent should change their strategy so that the population fitness increases the most. Equivalently, an agent should update the strategy towards a gradient (derivative) of the population fitness with respect to the strategy. However, it has not yet been clarified whether and how an agent can estimate the gradient and accelerate the evolutionary process. We also lack methodology to quantify the acceleration to understand and predict the impact of learning. In this paper, we address these problems. We show that an learning agent can accelerate the evolutionary process by proposing ancestral learning, which uses the information transmitted from the ancestor (ancestral information) via epigenetic states or memes. Numerical experiments show that ancestral learning actually accelerates the evolutionary process. We next show that the ancestral information is sufficient to estimate the gradient. In particular, learning can accelerate the evolutionary process without communications between agents. Finally, to quantify the acceleration, we extend the Fishers fundamental theorem (FF-thm) for natural selection to ancestral learning. The conventional FF-thm relates the speed of evolution by natural selection to the variety of the individual fitness in the population. Our extended FF-thm relates the acceleration of the evolutionary process to the variety of individual fitness of the agent. By the theorem, we can quantitatively understand when and why learning is beneficial.

category: evolutionary biology


title: Combinatorial small molecule-mediated activation of CBP/p300 with environmental enrichment in chronic severe experimental spinal cord injury to enable axon regeneration and sprouting for functional recovery

abstract: The interruption of spinal circuitry following spinal cord injury disrupts neural activity and is followed by a failure to mount an effective regenerative gene expression response resulting in permanent neurological disability. Functional recovery requires the enhancement of axonal and synaptic plasticity of spared as well as injured fibres, which need to sprout and/or regenerate to form new connections. Here we will investigate whether the combined epigenetic stimulation of the regenerative gene expression program with neuronal activity-dependent enhancement of neuroplasticity and guidance can overcome the current inability to promote neurological recovery in severe and chronic spinal cord injury. This will be carried out by delivering the small molecule CBP/p300 activator CSP-TTK21 in combination with environmental enrichment. We will deliver the CBP/p300 activator CSP-TTK21 weekly between week twelve and twenty following a severe transection model of spinal cord injury in the mouse. Data analysis will assess modifications in regenerative signalling, in motor and sensory axon sprouting and regeneration, in synaptic plasticity as well as in neurological sensorimotor recovery. This approach will advance our mechanistic understanding of regenerative failure and provide insight of whether combining growth promoting strategies with enhancement of neural activity is an effective therapeutic strategy in chronic spinal cord injury.


title: Bidirectional cooperation between Ubtf1 and SL1 determines RNA Polymerase I promoter recognition in cell and is negatively affected in the UBTF-E210K neuroregression syndrome.

abstract: Transcription of the [~]200 mouse and human ribosomal RNA genes (rDNA) by RNA Polymerase I (RPI/PolR1) accounts for 80% of total cellular RNA, around 35% of all nuclear RNA synthesis, and determines the cytoplasmic ribosome complement. It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15kbp nucleosome free region (NFR). Formation of this NFR is also essential for recruitment of the TBP-TAFI factor SL1 and for preinitiation complex (PIC) formation at the gene and enhancer-associated promoters of the rDNA. However, these promoters show little sequence commonality and neither UBTF nor SL1 display significant DNA sequence binding specificity, making what drives PIC formation a mystery. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. We find that conditional deletion of the Taf1b subunit of SL1 causes a striking depletion UBTF at both rDNA promoters but not elsewhere across the rDNA. We also find that while both UBTF1 and -2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. We suggest the underlying cause of the UBTF-E210K syndrome is therefore a reduction in cooperative UBTF1-SL1 promoter recruitment that may be partially compensated by enhanced rDNA activation.

category: molecular biology


title: Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways

abstract:
The angiotensin-converting enzyme 2 (ACE2) protein has been highly studied as a key catalytic regulator of the renin-angiotensin system (RAS), involved in fluid homeostasis and blood pressure modulation. In addition to its important physiological role as a broadly-expressed membrane-bound protein, ACE2 serves as a cell-surface receptor for some viruses - most notably, coronaviruses such as SARS-CoV and SARS-CoV-2. Differing levels of ACE2 expression may impact viral susceptibility and subsequent changes to expression may be a pathogenic mechanism of disease risk and manifestation. Therefore, an improved understanding of how ACE2 expression is regulated at the genomic and transcriptional level may help us understand not only how the effects of pre-existing conditions (e.g., chronic obstructive pulmonary disease) may manifest with increased COVID-19 incidence, but also the mechanisms that regulate ACE2 levels following viral infection. Here, we initially perform bioinformatic analyses of several datasets to generate hypotheses about ACE2 gene-regulatory mechanisms in the context of immune signaling and chronic oxidative stress. We then identify putative non-coding regulatory elements within ACE2 intronic regions as potential determinants of ACE2 expression activity. We perform functional validation of our computational predictions in vitro via targeted CRISPR-Cas9 deletions of the identified ACE2 cis-regulatory elements in the context of both immunological stimulation and oxidative stress conditions. We demonstrate that intronic ACE2 regulatory elements are responsive to both immune signaling and oxidative-stress pathways, and this contributes to our understanding of how expression of this gene may be modulated at both baseline and during immune challenge. Our work supports the further pursuit of these putative mechanisms in our understanding, prevention, and treatment of infection and disease caused by ACE2-utilizing viruses such as SARS-CoV, SARS-CoV-2, and future emerging SARS-related viruses.

Author SummaryThe recent emergence of the virus SARS-CoV-2 which has caused the COVID-19 pandemic has prompted scientists to intensively study how the virus enters human host cells. This work has revealed a key protein, ACE2, that acts as a receptor permitting the virus to infect cells. Much research has focused on how the virus physically interacts with ACE2, yet little is known on how ACE2 is turned on or off in human cells at the level of the DNA molecule. Understanding this level of regulation may offer additional ways to prevent or lower viral entry into human hosts. Here, we have examined the control of the ACE2 gene, the DNA sequence that instructs ACE2 protein receptor formation, and we have done so in the context of immune stimulation. We have indeed identified a number of DNA on/off switches for ACE2 that appear responsive to immuno-logical and oxidative stress. These switches may fine-tune how ACE2 is turned on or off before, during, and/or after infection by SARS-CoV-2 or other related coronaviruses. Our studies help pave the way for additional functional studies on these switches, and their potential therapeutic targeting in the future.


title: Presynaptic FMRP and local protein synthesis support structural and functional plasticity of glutamatergic axon terminals

abstract:
Learning and memory critically rely on long-lasting, synapse-specific modifications. While postsynaptic forms of plasticity typically require local protein synthesis, whether and how local protein synthesis contributes to presynaptic changes remains unclear. Here, we examined the hippocampal mossy fiber (MF)-CA3 synapse which expresses both structural and functional presynaptic plasticity. We report that MF boutons synthesize protein locally and contain ribosomes. Long-term potentiation of MF-CA3 synaptic transmission (MF-LTP) was associated with translation-dependent enlargement of MF boutons. Moreover, increasing in vitro and in vivo MF activity enhanced protein synthesis in MFs. Remarkably, deletion of presynaptic Fragile X mental retardation protein (FMRP), an RNA-binding protein expressed in MF boutons and previously implicated in local postsynaptic protein synthesis-dependent plasticity, blocked structural and functional MF-LTP, suggesting that FMRP is a critical regulator of presynaptic function. Thus, presynaptic FMRP and protein synthesis dynamically control presynaptic structure and function in the mature brain.

HighlightsO_LIMossy fiber boutons (MFBs) synthesize protein locally and contain ribosomes
C_LIO_LILocal presynaptic translation is increased by in vitro and in vivo GC activity
C_LIO_LIMFB structural plasticity relies on de novo protein synthesis.
C_LIO_LIPresynaptic FMRP is required for MF-CA3 structural and functional plasticity
C_LI

In BriefMonday et al. report that FMRP and protein synthesis in hippocampal mossy fiber boutons mediate functional and structural presynaptic plasticity.


title: Activity in the dorsomedial striatum decreases with improvement in motor coordination

abstract: It has been suggested that the dorsomedial striatum (DMS) facilitates the early stages of motor learning for goal-directed actions, whereas at later stages, control is transferred to the dorsolateral striatum (DLS), which enables the motor actions to become a skill or habit. It is unknown whether these striatal regions are simultaneously active while expertise is acquired during skill learning. To address this question, we developed the "treadmill training task" to track changes in mouse locomotor coordination during practice at running that simultaneously provides a means to measure local neuronal activity using photometry. We analyzed body position and paw movement to evaluate changes in motor coordination over practice sessions on the treadmill using DeepLabCut and custom-built code. By correlating improvements in motor coordination during training with simultaneous neuronal calcium activity in the striatum, we found that DMS direct pathway neurons exhibited decreased activity as the mouse gains proficiency at running. In contrast, direct pathway activity in the DLS was similar throughout training and did not correlate with learned skill proficiency. Pharmacological blockade of D1 dopamine receptors in these subregions during task performance confirmed that dopamine neurotransmission in the DMS direct pathway activity is necessary for efficient motor coordination learning, while dopamine signalling in the DLS is important for both coordination learning and maintenance of the acquired skill. These results provide new tools to measure changes in fine motor skills during simultaneous recordings of brain activity, revealing fundamental features of the neuronal substrates of motor learning.


title: A dopamine-dependent decrease in dorsomedial striatum direct pathway neuronal activity is required for learned motor coordination


title: eIF2B-capturing viral protein NSs suppresses the integrated stress response

abstract: Various stressors such as viral infection lead to the suppression of cap-dependent translation and the activation of the integrated stress response (ISR), since the stress-induced phosphorylated eukaryotic translation initiation factor 2 [eIF2(P)] tightly binds to eIF2B to prevent it from exchanging guanine nucleotides on unphosphorylated eIF2. Sandfly fever Sicilian virus (SFSV) evades this cap-dependent translation suppression through the interaction between its nonstructural protein NSs and host eIF2B. Our cryo-electron microscopy (cryo-EM) analysis revealed that SFSV NSs binds to the -subunit of eIF2B in a competitive manner with eIF2(P). Together with SFSV NSs, eIF2B exhibits normal nucleotide exchange activity even in the presence of eIF2(P). A genome-wide ribosome profiling analysis clarified that SFSV NSs in human cultured cells attenuates the ISR. Furthermore, SFSV NSs exhibited neuroprotective effects against the ISR-inducing stress. Since the ISR inhibition is beneficial in various neurological disease models, SFSV NSs is promising as a therapeutic ISR inhibitor.


title: Constitutive AP2gamma deficiency reduces postnatal hippocampal neurogenesis and induces behavioral deficits in juvenile mice that persist during adulthood

abstract:
The transcription factor activating protein two gamma (AP2{gamma}) is an important regulator of neurogenesis both during embryonic development as well as in the postnatal brain, but its role for neurophysiology and behavior at distinct postnatal periods is still unclear. In this work, we explored the neurogenic, behavioral, and functional impact of a constitutive AP2{gamma} heterozygous deletion in mice from early postnatal development until adulthood. Constitutive AP2{gamma} heterozygous deletion in mice caused a reduction of hippocampal transient amplifying progenitors (TAPs) in the postnatal brain, inducing significant impairments on hippocampal-dependent emotional- and cognitive-behavioral tasks including anxiety-like behavior and cognitive deficits, typically associated with an intact neurogenic activity. Moreover, AP2{gamma} deficiency impairs dorsal hippocampus-to-prefrontal cortex functional connectivity.

We observed a progressive and cumulative impact of constitutive AP2{gamma} deficiency on the hippocampal glutamatergic neurogenic process, as well as alterations on limbic-cortical connectivity, together with impairments on emotional and cognitive behaviors from juvenile to adult periods. Collectively, the results herein presented demonstrate the importance of AP2{gamma} in the generation of glutamatergic neurons in the postnatal brain and its impact on behavioral performance.


title: Variation in Human Herpesvirus 6B telomeric integration, excision and transmission between tissues and individuals

abstract: Human herpesviruses 6A and 6B (HHV-6A/6B) are ubiquitous pathogens that persist lifelong in latent form and can cause severe conditions upon reactivation. They are spread by community-acquired infection of free virus (acqHHV6A/6B) and by germline transmission of inherited chromosomally- integrated HHV-6A/6B (iciHHV-6A/6B) in telomeres. We exploited a hypervariable region of the HHV- 6B genome to investigate the relationship between acquired and inherited virus and revealed predominantly maternal transmission of acqHHV-6B in families. Remarkably, we demonstrate that some copies of acqHHV-6B in saliva from healthy adults gained a telomere, indicative of integration and latency, and that the frequency of viral genome excision from telomeres in iciHHV-6B carriers is surprisingly high and varies between tissues. In addition, newly formed short telomeres generated by partial viral genome release are frequently lengthened, particularly in telomerase-expressing pluripotent cells. Consequently, iciHHV-6B carriers are mosaic for different iciHHV-6B structures, including circular extra-chromosomal forms that have the potential to reactivate. Finally, we show transmission of an HHV-6B strain from an iciHHV-6B mother to her non-iciHHV-6B son. Altogether we demonstrate that iciHHV-6B can readily transition between telomere-integrated and free virus forms.


title: Genome wide association mapping of Pyrenophora teres f. maculata and Pyrenophora teres f. teres resistance loci utilizing natural Turkish wild and landrace barley populations

abstract: Unimproved landraces and wild relatives of crops are sources of genetic diversity that were lost post domestication in modern breeding programs. To tap into this rich resource, genome wide association studies in large plant genomes have enabled the rapid genetic characterization of desired traits from natural landrace and wild populations. Wild barley (Hordeum spontaneum), the progenitor of domesticated barley (H. vulgare), is dispersed across Asia and North Africa, and has co-evolved with the ascomycetous fungal pathogens Pyrenophora teres f. teres and P. teres f. maculata, the casual agents of the diseases net form of net blotch and spot form of net blotch, respectively. Thus, these wild and local adapted barley landraces from the region of origin of both the host and pathogen represent a diverse gene pool to identify new sources of resistance, due to millions of years of co-evolution. The barley - P. teres pathosystem is governed by complex genetic interactions with dominant, recessive, and incomplete resistances and susceptibilities, with many isolate-specific interactions. Here we provide the first genome wide association study of wild and landrace barley from the Fertile Crescent for resistance to both forms of P. teres. A total of 14 loci, four against P. teres f. maculata and ten against Pyrenophora teres f. teres, were identified in both wild and landrace populations, showing that both are genetic reservoirs for novel sources of resistance. We also highlight the importance of using multiple algorithms to both identify and validate additional loci.


title: Development of methods for purification of individual biological active substances obtained from extracts of Hedysarum neglectum

abstract: Hedysarum neglectum is a forage plant. Xanthone glycoside - mangiferin is extracted from this plant and used for medicine "Alpizarin". In addition to substances of xanthone nature (mangiferin and isomangiferin) Hedysarum neglectum contains sugars, vitamins and provitamins, tannins; in the underground part it contains oligomeric catechins, isoflavonoids, butylphenols, alkaloids, tannins, flavonoids, saponins, coumarins, carbohydrates, vitamin C. For selecting optimal schemes of fractionization of substances, it is necessary to resort to multi-stage schemes of group-wide (preliminary) isolation and preparative accumulation. In particular cases, it is necessary to take into account the presence of concomitant substances, as well as the effectiveness and selectivity of the sorption-chromatographic technologies used. According to the results of the studies, the use of silica gel and sefadex LH-20 for the isolation of a complex of flavonoids and gallic acid is the most effective method for the selection of the optimal variant of the preparative isolation of the total amount of BAS in mcg/ml. The results of the research allowed us to identify the target biologically active substances with a degree of extraction of at least 80%: - fractions of xanthones, flavonoids, gallic acid.


title: Study of growth characteristics of callus, suspension and root crops Scutellaria baicalensis

abstract: Scutellaria baicalensis is a popular traditional plant in Chinese medicine. Widely distributed biologically active substances of Scutellaria baicalensis are flavonoids (baicalin, baicalein, vogonin and vogonoside), which are responsible for the antitumor activity. Their antitumor effect is due to the absorption of oxidative radicals, the weakening of the activity of NF-kB (nuclear factor-kB), the suppression of the expression of the COX-2 gene and the regulation of the cell cycle. In addition, baicalein, baicalin, and vogonin showed strong antioxidant activity. The root culture in vitro of the medicinal plant Scutellaria baicalensis is characterized by intensive growth. The growth index at the end of the cultivation cycle was 40. The growth curve has a standard S-shape, with pronounced growth phases. The stationary phase was observed from 5-7 weeks of cultivation. The root culture growth index was 22.


title: Across-animal odor decoding by probabilistic manifold alignment

abstract: Identifying the common structure of neural dynamics across subjects is key for extracting unifying principles of brain computation and for many brain machine interface applications. Here, we propose a novel probabilistic approach for aligning stimulus-evoked responses from multiple animals in a common low dimensional manifold and use hierarchical inference to identify which stimulus drives neural activity in any given trial. Our probabilistic decoder is robust to a range of features of the neural responses and significantly outperforms existing neural alignment procedures. When applied to recordings from the mouse olfactory bulb, our approach reveals low-dimensional population dynamics that are odor specific and have consistent structure across animals. Thus, our decoder can be used for increasing the robustness and scalability of neural-based chemical detection.


title: A Computational Model of Phosphene Appearance for Epiretinal Prostheses

abstract: Retinal neuroprostheses are the only FDA-approved treatment option for blinding degenerative diseases. A major outstanding challenge is to develop a computational model that can accurately predict the elicited visual percepts (phosphenes) across a wide range of electrical stimuli. Here we present a phenomenological model that predicts phosphene appearance as a function of stimulus amplitude, frequency, and pulse duration. The model uses a simulated map of nerve fiber bundles in the retina to produce phosphenes with accurate brightness, size, orientation, and elongation. We validate the model on psychophysical data from two independent studies, showing that it generalizes well to new data, even with different stimuli and on different electrodes. Whereas previous models focused on either spatial or temporal aspects of the elicited phosphenes in isolation, we describe a more comprehensive approach that is able to account for many reported visual effects. The model is designed to be flexible and extensible, and can be fit to data from a specific user. Overall this work is an important first step towards predicting visual outcomes in retinal prosthesis users across a wide range of stimuli.


title: Exploring the Self-Assembly of Encapsulin Protein Nanocages from Different Structural Classes

abstract: Encapsulins, self-assembling icosahedral protein nanocages derived from prokaryotes, represent a versatile set of tools for nanobiotechnology. However, a comprehensive understanding of the mechanisms underlying encapsulin self-assembly, disassembly, and reassembly is lacking. Here, we characterise the disassembly/reassembly properties of three encapsulin nanocages that possess different structural architectures: T = 1 (24 nm), T = 3 (32 nm), and T = 4 (42 nm). Using spectroscopic techniques and electron microscopy, encapsulin architectures were found to exhibit varying sensitivities to the denaturant guanidine hydrochloride (GuHCl), extreme pH, and elevated temperature. While all encapsulins showed the capacity to reassemble following GuHCl-induced disassembly (within 75 min), only the smallest T = 1 nanocage reassembled after disassembly in basic pH (within 15 min). Furthermore, atomic force microscopy revealed that all encapsulins showed a significant loss of structural integrity after undergoing sequential disassembly/reassembly steps. These findings provide insights into encapsulins disassembly/reassembly dynamics, thus informing their future design, modification, and application.


title: A screen of covalent inhibitors in Mycobacterium tuberculosis identifies serine hydrolases involved in lipid metabolism as potential therapeutic targets

abstract: The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat necessitating the development of new antibiotics. Serine hydrolases (SHs) are a promising class of targets because of their importance for the synthesis of the mycobacterial cell envelope. We screened a library of small molecules containing serine-reactive electrophiles and identified narrow spectrum inhibitors of M. tuberculous growth. Using these lead molecules, we performed competitive activity-based protein profiling and identified multiple SH targets, including enzymes with uncharacterized functions. Lipidomic analyses of compound-treated cultures revealed an accumulation of free lipids and a substantial decrease in lipooligosaccharides, linking SH inhibition to defects in cell envelope biogenesis. Mutant analysis revealed a path to resistance via the synthesis of mycocerates, but not through mutations to target enzymes. Our results suggest that simultaneous inhibition of multiple SH enzymes is likely to be an effective therapeutic strategy for the treatment of M. tuberculosis infections.


title: DRUG-seq Provides Unbiased Biological Activity Readouts for Drug Discovery

abstract: Unbiased transcriptomic RNA-seq data has provided deep insights about biological processes. However, its impact in drug discovery has been narrow given high costs and low throughput. Proof-of-concept studies with Digital RNA with pertUrbation of Genes (DRUG)-seq demonstrated the potential to address this gap. We extended the DRUG-seq platform by subjecting it to rigorous testing and by adding an open-source analysis pipeline. The results demonstrate high reproducibility and ability to resolve the mechanism(s) of action for a diverse set of compounds. Overall, the protocol and open-source analysis pipeline are a step towards industrializing RNA-seq for high complexity transcriptomics studies performed at a saturating scale.


title: Foot scales in the Early Cretaceous bird  Gansus yumenensis from China

abstract: Most modern birds have scales covering the foot and feathers elsewhere. Discoveries of fossil feathers attached to the metatarsus in non-avian dinosaurs and basal birds suggests that the avian scales are secondarily derived from feathers. However, our knowledge of early avian scales and their taphonomy is still limited, due to the scarcity of fossil record. Here we employ multiple techniques to characterize the morphological and chemical details preserved and investigate how they are preserved in the skin of IVPP V15077, a referred specimen of the Early Cretaceous Gansus yumenensis. Results show that two types of scales, scutellate and interstitial scales, are preserved in IVPP V15077, which, in combination with previous discovery of scutate and reticulate scales in other Early Cretaceous birds, indicates that all four types of scales present in modern birds have appeared in the Early Cretaceous. SEM observations and Raman analysis suggest that the skin of Gansus yumenensis may be pigmented. Elemental mapping indicates that aluminosilicates and calcium phosphate are involved in the mineralization of the skin.

category: paleontology


title: Assessing student success in a Peer Assisted Learning program using propensity score matching

abstract: The Peer Assisted Learning program at Sacramento State University (PAL) was established in 2012 with one section supporting introductory chemistry. It now serves 17 gatekeeper courses in Biology, Chemistry, Mathematics, Physics, and Statistics, enrolling approximately 1,400 students annually. Adapting the Peer-Led Team Learning model, PAL Facilitators do not teach, tutor, or even confirm answers; they do ask scaffolding questions, provide encouragement, and ensure that all group members participate in problem-solving. Here we assess the efficacy of the program in terms of student success in the parent course. As PAL is an opt-in program, we employ propensity score matching techniques to account for confounding factors. Our analysis of 11 classes shows that PAL provides an average course GPA bump ranging from .23 to .71 grade points (mean .42). Compared to the non-PAL baseline course GPA, this amounts to an increase of 9% to 51% (mean 23%). We consider data from over 25,000 students, and our propensity score analysis uses over 10,000 students (4,519 PAL, 5,814 non-PAL) for whom appropriate matches could be found.

category: scientific communication and education


title: Estimating the absolute number of axons connecting different cortical areas in humans with diffusion MRI

abstract: The tracts between cortical areas are conceived as playing a central role in cortical information processing, but their actual numbers have never been determined in humans. Here we estimate the absolute number of axons linking cortical areas from a whole-cortex diffusion-MRI (dMRI) connectome, calibrated using the histologically-measured callosal fiber density. Median connectivity is estimated as ~6200 axons between cortical areas within-hemisphere and ~1300 axons inter-hemispherically, with axons connecting functionally-related areas surprisingly sparse. For example, we estimate that <5% of the axons in the trunk of the arcuate and superior longitudinal fasciculi connect Wernickes and Brocas areas. These results suggest that detailed information is transmitted between cortical areas either via linkage of the dense local connections or via rare, extraordinarily privileged long-range connections.


title: Human cortical areas are sparsely connected: Combining histology with diffusion MRI to estimate the absolute number of axons


title: An estimation of the absolute number of axons indicates that human cortical areas are sparsely connected


title: The payoffs and tradeoffs of hygienic behavior: A large-scale field study on a local population of honey bees

abstract: Honey bees (Apis mellifera) are exposed to a variety of risk factors, but the ectoparasitic mite Varroa destructor and its associated viruses are considered to be the most significant problem worldwide. It has been widely recognized that honey bee stocks resistant to the mites are an essential part of any sustainable long-term management of Varroa. The aim of this study was to evaluate the efficacy of hygienic behavior in a local population of honey bees in order to reduce Varroa infestation. A bi-directional selection for high and low rates of hygienic behavior was carried out in Israel using either queen artificially inseminated or naturally mated. Colonies were screened for performance: population size, honey production, control of Varroa infestation, and the level of hygienic behavior. Furthermore, we examined the costs and benefits of selection using measurements of colony performance. Either way, selected lines should be tested for trade-offs and benefits to ensure their productivity. The selection process revealed that the trait is heritable. Maternal phenotype has a significant effect on Varroa load, as colonies founded by hygienic daughter queens showed a significantly lower parasite load. No major trade-offs were found between the rate of hygienic behavior, honey yield, and population size. Measuring the direct benefits of hygienic behavior through colony performance suggests that breeding for this trait makes bees more resistant to Varroa destructor. These results are promising for our successful local bee breeding programs in a Mediterranean climate.

category: pathology


title: Cognitive functions and respective parameters of human brain physiology are chronotype-dependent

abstract: Circadian rhythms have natural relative variations among humans known as chronotype. Chronotype or being a morning or evening person, has a specific physiological, behavioural, and also genetic manifestation. Whether and how chronotype modulates human brain physiology and cognition is, however, not well understood. Here we examine how cortical excitability, neuroplasticity, and cognition are associated with chronotype in early and late chronotype individuals. We monitor motor cortical excitability, brain stimulation-induced neuroplasticity, and examine motor learning and cognitive functions at circadian-preferred and non-preferred times of day in 32 individuals. Motor learning and cognitive performance (working memory, and attention) along with their electrophysiological components are significantly enhanced at the circadian-preferred, compared to the non-preferred time. This outperformance is associated with enhanced cortical excitability (prominent cortical facilitation, diminished cortical inhibition), and long-term potentiation/depression-like plasticity. Our data show convergent findings of chronotype can modulate human brain functions from basic physiological mechanisms to behaviour and higher cognitive functions.


title: Cognitive functions and underlying parameters of human brain physiology are associated with chronotype


title: Bayesian mapping of the striatal microcircuit reveals robust asymmetries in the probabilities and distances of connections

abstract: The striatums complex microcircuit is made by connections within and between its D1- and D2-receptor expressing projection neurons and at least five species of interneuron. Precise knowledge of this circuit is likely essential to understanding striatums functional roles and its dysfunction in a wide range of movement and cognitive disorders. We introduce here a Bayesian approach to mapping neuron connectivity using intracellular recording data, which lets us simultaneously evaluate the probability of connection between neuron types, the strength of evidence for it, and its dependence on distance. Using it to synthesise a complete map of the mouse striatum, we find strong evidence for two asymmetries: a selective asymmetry of projection neuron connections, with D2 neurons connecting twice as densely to other projection neurons than do D1 neurons, but neither subtype preferentially connecting to another; and a length-scale asymmetry, with interneuron connection probabilities remaining non-negligible at more than twice the distance of projection neuron connections. We further show our Bayesian approach can evaluate evidence for wiring changes, using data from the developing striatum and a mouse model of Huntingtons disease. By quantifying the uncertainty in our knowledge of the microcircuit, our approach reveals a wide range of potential striatal wiring diagrams consistent with current data.


title: Differential ampicillin/ceftriaxone susceptibility among diverse Enterococcus faecalis from infective endocarditis

abstract: Enterococcus faecalis is a leading cause of infective endocarditis (IE), especially among older patients with comorbidities. Here we investigated the genomic diversity and antimicrobial susceptibility of 33 contemporary E. faecalis isolates from definite or probable IE cases at the University of Pittsburgh Medical Center (UPMC) between 2018 and 2020. Isolates belonging to two multi-locus sequence types (STs), ST6 and ST179, were isolated from nearly 40% of IE patients. Both of these dominant STs carried known beta-lactam resistance-associated mutations affecting the low-affinity penicillin-binding protein 4 (PBP4). We assessed the ability of ampicillin and ceftriaxone (AC) both alone and in combination to inhibit genetically diverse E. faecalis IE isolates in checkerboard synergy assays and an in vitro one-compartment pharmacokinetic-pharmacodynamic (PK-PD) model of AC treatment. ST6 isolates as well as an isolate with a mutation in the PP2C-type protein phosphatase IreP had higher ceftriaxone MICs compared to other isolates, and showed diminished in vitro synergy of AC. Additionally, both ST6 and ST179 isolates exhibited regrowth after 48 hours of humanized exposures to AC. Overall, we found evidence for diminished in vitro AC activity among E. faecalis IE isolates with PBP4 and IreP mutations. This study highlights the need to evaluate alternate antibiotic combinations in clinical practice against diverse contemporary E. faecalis IE isolates.


title: Viral Evasion of the Integrated Stress Response Through Antagonistic eIF2-P Mimicry

abstract: Viral infection triggers activation of the integrated stress response (ISR). In response to viral double-stranded RNA (dsRNA), RNA-activated protein kinase (PKR) phosphorylates the translation initiation factor eIF2, converting it from a translation initiator into a potent translation inhibitor and this restricts the synthesis of viral proteins. Phosphorylated eIF2 (eIF2-P) inhibits translation by binding to eIF2s dedicated, heterodecameric nucleotide exchange factor eIF2B and conformationally inactivating it. We show that the NSs protein of Sandfly Fever Sicilian virus (SFSV) allows the virus to evade the ISR. Mechanistically, NSs tightly binds to eIF2B (KD = 43 nM), blocks eIF2-P binding, and rescues eIF2B GEF activity. Cryo-EM structures demonstrate that SFSV NSs and eIF2-P directly compete, with the primary NSs contacts to eIF2B mediated by five  aromatic fingers. NSs binding preserves eIF2B activity by maintaining eIF2Bs conformation in its active A-State.


title: Super-cells untangle large and complex single-cell transcriptome networks

abstract: The exponential scaling of scRNA-seq data represents an important hurdle for downstream analyses. Here we develop a coarse-graining framework where highly similar cells are merged into metacells. We demonstrate that metacells not only preserve but often improve the results of downstream analyses including visualization, clustering, differential expression, cell type annotation, gene correlation, imputation, RNA velocity and data integration. By capitalizing on the redundancy inherent to scRNA-seq data, metacells significantly facilitate and accelerate the construction and interpretation of single-cell atlases, as demonstrated by the integration of 1.46 million cells from COVID-19 patients in less than two hours on a standard desktop.

category: bioinformatics


title: Metacells untangle large and complex single-cell transcriptome networks