title: Foveal vision predictively sensitizes to defining features of eye movement targets

abstract: Despite the foveas singular importance for active human vision, the impact of large eye movements on foveal processing remains elusive. Building on findings from passive fixation tasks, we hypothesized that during the preparation of rapid eye movements (saccades), foveal processing anticipates soon-to-be fixated visual features. Using a dynamic large-field noise paradigm, we indeed demonstrate that sensitivity for defining features of a saccade target is enhanced in the pre-saccadic center of gaze. Enhancement manifested in higher Hit Rates for foveal probes with target-congruent orientation, and a sensitization to incidental, target-like orientation information in foveally presented noise. Enhancement was spatially confined to the center of gaze and its immediate vicinity. We suggest a crucial contribution of foveal processing to trans-saccadic visual continuity which has previously been overlooked: Foveal processing of saccade targets commences before the movement is executed and thereby enables a seamless transition once the center of gaze reaches the target.


title: Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome

abstract: Copy number variations (CNV) are associated with psychiatric and neurodevelopmental disorders (NDDs), and most, including the recurrent 15q13.3 microdeletion disorder, have unknown disease mechanisms. We used a heterozygous 15q13.3 microdeletion mouse model and patient iPSC-derived neurons to reveal developmental defects in neuronal maturation and network activity. To identify the underlying molecular dysfunction, we developed a neuron-specific proximity-labeling proteomics (BioID2) pipeline, combined with patient mutations, to target the 15q13.3 CNV genetic driver OTUD7A. OTUD7A is an emerging independent NDD risk gene with no known function in the brain, but has putative deubiquitinase (DUB) function. The OTUD7A protein-protein interaction (PPI) network revealed interactions with synaptic, axonal, and cytoskeletal proteins and was enriched for known ASD and epilepsy risk genes. The interactions between OTUD7A and the NDD risk genes Ankyrin-G (Ank3) and Ankyrin-B (Ank2) were disrupted by an epilepsy-associated OTUD7A L233F variant. Further investigation of Ankyrin-G in mouse and human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed protein instability, increased polyubiquitination, and decreased levels in the axon initial segment (AIS), while structured illumination microscopy identified reduced Ankyrin-G nanodomains in dendritic spines. Functional analysis of human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed shared and distinct impairments to axonal growth and intrinsic excitability. Importantly, restoring OTUD7A or Ankyrin-G expression in 15q13.3 microdeletion neurons led to a reversal of abnormalities. These data reveal a critical OTUD7A-Ankyrin pathway in neuronal development, which is impaired in the 15q13.3 microdeletion syndrome, leading to neuronal dysfunction. Further, our study highlights the utility of targeting CNV genes using cell-type specific proteomics to identify shared and unexplored disease mechanisms across NDDs.

category: neuroscience


title: NNeurite: artificial neuronal networks for the unsupervised extraction of axonal and dendritic time-lapse signals

abstract: Fluorescence microscopy of Ca2+ transients in small neurites of the behaving mouse provides an unprecedented view of the micrometer-scale mechanisms supporting neuronal communication and computation, and therefore opens the way to understanding their role in cognition. However, the exploitation of this growing and precious experimental data is impeded by the scarcity of methods dedicated to the analysis of images of neurites activity in vivo. We present NNeurite, a set of mathematical and computational techniques specialized for the analysis of time-lapse microscopy images of neurite activity in small behaving animals. Starting from noisy and unstable microscopy images containing an unknown number of small neurites, NNeurite simultaneously aligns images, denoises signals and extracts the location and the temporal activity of the sources of Ca2+ transients. At the core of NNeurite is a novel artificial neuronal network (NN) which we have specifically designed to solve the non-negative matrix factorization (NMF) problem modeling source separation in fluorescence microscopy images. For the first time, we have embedded non-rigid image alignment in the NMF optimization procedure, hence allowing to stabilize images based on the transient and weak neurite signals. NNeurite processing is free of any human intervention as NN training is unsupervised and the unknown number of Ca2+ sources is automatically obtained by the NN-based computation of a low-dimensional representation of time-lapse images. Importantly, the spatial shapes of the sources of Ca2+ fluorescence are not constrained in NNeurite, which allowed to automatically extract the micrometer-scale details of dendritic and axonal branches, such dendritic spines and synaptic boutons, in the cortex of behaving mice. We provide NNeurite as a free and open-source library to support the efforts of the community in advancing in vivo microscopy of neurite activity.


title: Panoramic visual statistics shape retina-wide organization of receptive fields

abstract: Visual systems have adapted to the structure of natural stimuli. In the retina, center-surround receptive fields (RFs) of retinal ganglion cells (RGCs) appear to efficiently encode natural sensory signals 1-4. Conventionally, it has been assumed that natural scenes are isotropic and homogeneous; thus, the RF properties are expected to be uniform across the visual field. However, natural scene statistics such as luminance and contrast are not uniform and vary significantly across elevation 5,6. Here, by combining theory and novel experimental approaches, we demonstrate that this inhomogeneity is exploited by RGC RFs across the entire retina to increase the coding efficiency. We formulated three predictions derived from the efficient coding theory: (i) optimal RFs should strengthen their surround from the dimmer ground to the brighter sky, (ii) RFs should simultaneously decrease their center size and (iii) RFs centered at the horizon should have a marked surround asymmetry due to a stark contrast drop-off. To test these predictions, we developed a new method to image high-resolution RFs of thousands of RGCs in individual retinas. We found that the RF properties match theoretical predictions, and consistently change their shape from dorsal to the ventral retina, with a distinct shift in the RF surround at the horizon. These effects are observed across RGC subtypes, which were thought to represent visual space homogeneously, indicating that functional retinal streams share common adaptations to visual scenes. Our work shows that RFs of mouse RGCs exploit the non-uniform, panoramic structure of natural scenes at a previously unappreciated scale, to increase coding efficiency.


title: Brain responses in aggression-prone individuals: A systematic review and meta-analysis of functional magnetic resonance imaging (fMRI) studies of anger- and aggression-eliciting tasks

abstract:
BackgroundWhile reactive aggression (in response to a perceived threat or provocation) is part of humans adaptive behavioral repertoire, it can violate social and legal norms. Understanding brain function in individuals with high levels of reactive aggression as they process anger- and aggression-eliciting stimuli is critical for refining interventions. Three neurobiological models of reactive aggression-the limbic hyperactivity, prefrontal hypoactivity, and dysregulated limbic-prefrontal connectivity models-have been proposed. However, these models are based on neuroimaging studies involving mainly healthy individuals, leaving it unclear which model best describes brain function in aggression-prone individuals.

MethodsWe conducted a systematic literature search (PubMed and Psycinfo) and Multilevel Kernel Density meta-analysis (MKDA) of nine functional magnetic resonance imaging (fMRI) studies of brain responses to tasks putatively eliciting anger and aggression in aggression-prone individuals alone, and relative to healthy controls.

ResultsAggression-prone individuals exhibited greater activity during reactive aggression relative to baseline in the superior temporal gyrus and in regions comprising the cognitive control and default mode networks (right posterior cingulate cortex, precentral gyrus, precuneus, right inferior frontal gyrus). Compared to healthy controls, aggression-prone individuals exhibited increased activity in limbic regions (left hippocampus, left amygdala, left parahippocampal gyrus) and temporal regions (superior, middle, inferior temporal gyrus), and reduced activity in occipital regions (left occipital cortex, left calcarine cortex).

ConclusionsThese findings lend support to the limbic hyperactivity model and further indicate altered temporal and occipital activity in anger- and aggression-eliciting situations that involve face and speech processing.


title: Acetazolamide modulates intracranial pressure directly by its action on the cerebrospinal fluid secretion apparatus

abstract: Elevated intracranial pressure (ICP) is observed in many neurological pathologies, e.g. hydrocephalus and stroke. This condition is routinely relieved with neurosurgical approaches, since effective and targeted pharmacological tools are still lacking. The carbonic anhydrase inhibitor, acetazolamide (AZE), may be employed to treat elevated ICP. However, its effectiveness is questioned, its location of action unresolved, and its tolerability low. Here, we employed in vivo and ex vivo approaches to reveal the efficacy and mode of action of AZE in the rat brain. The drug effectively reduced the ICP, irrespective of the mode of drug administration and level of anaesthesia. The effect occurred via a direct action on the choroid plexus and an associated decrease in cerebrospinal fluid secretion, and not indirectly via the systemic action of AZE on renal and vascular processes. Upon a single administration, the reduced ICP endured for approximately 10 h post-AZE delivery with no long-term changes of brain water content or choroidal transporter expression. However, a persistent reduction of ICP was secured with repeated AZE administrations throughout the day. Future specific targeting of choroidal carbonic anhydrases may limit the systemic side effects, and therefore enhance the treatment tolerability and effectiveness in select patient groups experiencing elevated ICP.


title: Cd59 and inflammation orchestrate Schwann cell development

abstract: Efficient neurotransmission is essential for organism survival and is enhanced by myelination. However, the genes that regulate myelin and myelinating glial cell development have not been fully characterized. Data from our lab and others demonstrates that cd59, which encodes for a small GPI-anchored glycoprotein, is highly expressed in developing zebrafish, rodent, and human oligodendrocytes (OLs) and Schwann cells (SCs), and that patients with CD59 dysfunction develop neurological dysfunction during early childhood. Yet, the function of CD59 in the developing nervous system is currently undefined. In this study, we demonstrate that cd59 is expressed in a subset of developing SCs. Using cd59 mutant zebrafish, we show that developing SCs proliferate excessively, which leads to reduced myelin volume, altered myelin ultrastructure, and perturbed node of Ranvier assembly. Finally, we demonstrate that complement activity is elevated in cd59 mutants and that inhibiting inflammation restores SC proliferation, myelin volume, and nodes of Ranvier to wildtype levels. Together, this work identifies Cd59 and developmental inflammation as key players in myelinating glial cell development, highlighting the collaboration between glia and the innate immune system to ensure normal neural development.


title: FTY720 requires vitamin B12-TCN2-CD320 signaling in astrocytes to reduce disease in an animal model of multiple sclerosis

abstract: FTY720 (fingolimod) is a sphingosine 1-phosphate (S1P) receptor modulator and sphingosine analogue approved for multiple sclerosis (MS) therapy, which can functionally antagonize the S1P receptor, S1P1. Vitamin B12 (B12) deficiency produces neurological manifestations resembling MS. Here, we report a new mechanism where FTY720 suppresses neuroinflammation by regulating B12 metabolic pathways. Nuclear RNA-seq of c-Fos-activated astrocytes (called ieAstrocytes) from experimental autoimmune encephalomyelitis (EAE) spinal cords identified up-regulation of CD320, a transcobalamin 2 (TCN2)-B12 receptor, by S1P1 inhibition. CD320 was reduced in MS plaques. Deficiency of CD320 or dietary B12 worsened EAE and eliminated FTY720s efficacy, while concomitantly down-regulating type I interferon signaling. TCN2 functioned as a chaperone for FTY720 and sphingosine, which induced astrocytic CD320 internalization. An accompanying paper identified a requirement for astrocyte sphingosine kinases in FTY720 efficacy and its altered expression in MS brains, molecularly linking MS and B12 deficiency that can be accessed by sphingolipid/fingolimod metabolic pathways.


title: Hebbian activity-dependent plasticity in white matter

abstract: Synaptic plasticity is required for learning and follows Hebbs Rule, the com-putational principle underpinning associative learning. In recent years, a complementary type of brain plasticity has been identified in myelinated axons, which make up the majority of brains white matter. Like synaptic plasticity, myelin plasticity is required for learning, but it is unclear whether it is Hebbian or whether it follows different rules. Here, we provide evidence that white matter plasticity operates following Hebbs Rule in humans. Across two experiments, we find that co-stimulating cortical areas to induce Hebbian plasticity leads to relative increases in cortical excitability and associated increases in a myelin marker within the stimulated fiber bundle. We conclude that Hebbian plasticity extends beyond synaptic changes, and can be observed in human white matter fibers.


title: Corrective feedback control of competing neural network with entire connections

abstract: Continuous persist activity of the competitive network is related to many functions, such as working memory, oculomotor integrator and decision making. Many competition models with mutual inhibition structures achieve activity maintenance via positive feedback, which requires meticulous fine tuning of the network parameters strictly. Negative derivative feedback, according to recent research, might represent a novel mechanism for sustaining neural activity that is more resistant to multiple neural perturbations than positive feedback. Many classic models with only mutual inhibition structure are not capable of providing negative derivative feedback because double-inhibition acts as a positive feedback loop, and lack of negative feedback loop that is indispensable for negative derivative feedback. Here in the proposal, we aim to derive a new competition network with negative derivative feedback. The network is made up of two symmetric pairs of EI populations that the four population are completely connected. We conclude that the negative derivative occurs in two circumstances, in which one the activity of the two sides is synchronous but push-pull-like in the other, as well as the switch of two conditions in mathematical analysis and numerical simulation.


title: Differentiation of a CD4+/CD8αβ+ Double Positive T Cell Population From The CD8 Pool Is Sufficient To Mediate Graft-vs-Host Disease but not Graft-vs-Leukemia Effects

abstract:
Acute graft-vs-host disease (aGVHD) and tumor relapse remain the primary complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT) for malignant blood disorders. While post-transplant cyclophosphamide has reduced the overall prevalence and severity of aGVHD, relapse rates remain a concern. Thus, there remains a need to identify the specific human T cell subsets mediating GVHD pathology versus graft-versus-leukemia (GVL) effects. In xenogeneic transplantation studies using primary human cells from a variety of donors and tissue sources, we observed the development of a mature CD4+/CD8{beta}+ double positive T cell (DPT) population in mice succumbing to lethal aGVHD but not in mice that failed to develop aGVHD. The presence of DPT, irrespective of graft source, was predictive of lethal GVHD as early as one week after xenogeneic transplantation. DPT co-express the master transcription factors of the CD8 and CD4 lineages, RUNX3 and THPOK respectively, and produce both cytotoxic and modulatory cytokines. To identify the origin of DPT, we transplanted isolated human CD4 or CD8 T cells, which in turn revealed that DPT only arise from the CD8 pool. Interestingly, re-transplantation of sorted CD8 T cells from GVHD mice did not reveal a second wave of DPT differentiation. Re-transplantation of flow-sorted DPT, CD8 or CD4 T cells from GVHD mice revealed that DPT are sufficient to mediate GVHD pathology but not GVL effects versus B-cell acute lymphoblastic leukemia. Lastly, we confirmed the presence and correlation of DPT with aGVHD pathology in a small cohort of allo-HSCT patients that developed grade 2-4 aGVHD in our clinic. Further understanding of DPT differentiation and pathology may lead to targeted prophylaxis and/or treatment regimens for aGVHD and potentially other human chronic inflammatory diseases.

Key PointsO_LIHuman DPT cell differentiation is a predictive metric of xenogeneic GVHD lethality
C_LIO_LIThe origin of DPT are CD8 T cells that gain THPOK expression and CD4 lineage effector functions
C_LIO_LIDPT cells are sufficient to mediate GVHD pathology but not GVL effects
C_LI

Visual Abstract

O_FIG O_LINKSMALLFIG WIDTH=120 HEIGHT=200 SRC="FIGDIR/small/475845v1_ufig1.gif" ALT="Figure 1">
View larger version (34K):
org.highwire.dtl.DTLVardef@90200eorg.highwire.dtl.DTLVardef@28aed0org.highwire.dtl.DTLVardef@ed1023org.highwire.dtl.DTLVardef@1be7490_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: immunology


title: In vivo imaging of calcium dynamics in zebrafish hepatocytes

abstract: Hepatocytes were the first cell-type for which oscillations of cytoplasmic calcium levels in response to hormones were described. Since then, investigation of calcium dynamics in liver explants and culture has greatly increased our understanding of calcium signaling. A bottleneck, however, exists in observing calcium dynamics in a non-invasive manner due to the optical inaccessibility of the mammalian liver. Here we take advantage of the transparency of the zebrafish larvae to develop a setup that allows in vivo imaging of calcium flux in zebrafish hepatocytes at cellular resolution. Using this, we provide quantitative assessment of intracellular calcium dynamics during multiple contexts, including growth, feeding, ethanol-induced stress and cell ablation. Specifically, we show that synchronized calcium oscillations are present in vivo, which are lost upon starvation. Feeding recommences calcium waves in the liver, but in a spatially restricted manner. Further, ethanol treatment as well as cell ablation induces calcium flux, but with different dynamics. The former causes asynchronous calcium oscillations, while the latter leads to a single calcium spike. Overall, we demonstrate the presence of oscillations, waves and spikes in vivo. Thus, our study introduces a platform for observing diverse calcium dynamics while maintaining the native environment of the liver, which will help investigations into the dissection of molecular mechanisms supporting the intra- and intercellular calcium signaling in the liver.

category: developmental biology


title: Aedes aegypti and Aedes albopictus abundance, landscape coverage and spectral indices effects in a subtropical city of Argentina

abstract: The presence, abundance and distribution of Aedes (Stegomyia) aegypti (Linnaeus 1762) and Aedes (Stegomyia) albopictus (Skuse 1894) could be conditioned by different data obtained from satellite remote sensors. In this paper, we aim to estimate the effect of landscape coverage and spectral indices on the abundance of Ae. aegypti and Ae. albopictus from the use of satellite remote sensors in Eldorado, Misiones, Argentina. Larvae of Aedes aegypti and Ae. albopictus were collected monthly from June 2016 to April 2018, in four outdoor environments: tire repair shops, cemeteries, family dwellings, and an urban natural park. The proportion of each land cover class was determined by Sentinel-2 image classification. Furthermore spectral indices were calculated. Generalized Linear Mixed Models were developed to analyze the possible effects of landscape coverage and vegetation indices on the abundance of mosquitoes. The models results showed the abundance of Ae. aegypti was better modeled by the minimum values of the NDVI index, the maximum values of the NDBI index and the interaction between both variables. In contrast, the abundance of Ae. albopictus has to be better explained by the model that includes the variables bare soil, low vegetation and the interaction between both variables.

category: ecology


title: Loss of plastid developmental genes coincides with a reversion to monoplastidy in hornworts

abstract: The first plastid evolved from an endosymbiotic cyanobacterium in the common ancestor of the Archaeplastida. The transformative steps from cyanobacterium to organelle included the transfer of control over developmental processes; a necessity for the host to orchestrate, for example, the fission of the organelle. The plastids of almost all embryophytes divide independent from nuclear division, leading to cells housing multiple plastids. Hornworts, however, are monoplastidic (or near-monoplastidic) and their photosynthetic organelles are a curious exception among embryophytes for reasons such as the occasional presence of pyrenoids. Here we screened genomic and transcriptomic data of eleven hornworts for components of plastid developmental pathways. We find intriguing differences among hornworts and specifically highlight that pathway components involved in regulating plastid development and biogenesis were differentially lost in this group of bryophytes. In combination with ancestral state reconstruction, our data suggest that hornworts have reverted back to a monoplastidic phenotype due to the combined loss of two plastid division-associated genes: ARC3 and FtsZ2.

category: evolutionary biology


title: Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

abstract:
Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genome-wide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and contact zones.

Significance StatementUnderstanding how past climatic events, human actions and evolutionary forces contributed to the present distribution of genetic diversity is crucial to predict their reaction to the current climate crisis. Vast distribution shifts induced by past environmental changes, local ecological processes, natural selection and human transfers contributed to the current distribution of Norway spruce across Northern Europe. Genome-wide polymorphisms from thousands of individuals show that Scandinavia was recolonized after the Last Glacial from both south and north. This two-pronged recolonization established a contact zone between two genetic clusters that matches the limit between two major climate zones. The contact zone is shaped and maintained by natural selection on a large number of loci that form blocks of co-adapted loci spread genome-wide.


title: Background selection theory overestimates effective population size for high mutation rates

abstract: Simple models from the neutral theory of molecular evolution are claimed to be flexible enough to incorporate the complex effects of background selection against linked deleterious mutations. Complexities are collapsed into an "effective" population size that specifies neutral genetic diversity. To achieve this, current background selection theory assumes linkage equilibrium among deleterious variants. Data do not support this assumption, nor do theoretical considerations when the genome-wide deleterious mutation is realistically high. We simulate genomes evolving under background selection, allowing the emergence of linkage disequilibria. With realistically high deleterious mutation rates, neutral diversity is much lower than predicted from previous analytical theory.


title: Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae)

abstract: Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that do not reflect the same traits as their adult forms. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. However, whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. Integrating a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, we reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.


title: De novo protein structure prediction by incremental inter-residue geometries prediction and model quality assessment using deep learning

abstract:
MotivationThe successful application of deep learning has promoted progress in protein model quality assessment. How to use model quality assessment to further improve the accuracy of protein structure prediction, especially not reliant on the existing templates, is helpful for unraveling the folding mechanism. Here, we investigate whether model quality assessment can be introduced into structure prediction to form a closed-loop feedback, and iteratively improve the accuracy of de novo protein structure prediction.

ResultsIn this study, we propose a de novo protein structure prediction method called RocketX. In RocketX, a feedback mechanism is constructed through the geometric constraint prediction network GeomNet, the structural simulation module, and the model quality evaluation network EmaNet. In GeomNet, the co-evolutionary features extracted from MSA that search from the sequence databases are sent to an improved residual neural network to predict the inter-residue geometric constraints. The structure model is folded based on the predicted geometric constraints. In EmaNet, the 1D and 2D features are extracted from the folded model and sent to the deep residual neural network to estimate the inter-residue distance deviation and per-residue lDDT of the model, which will be fed back to GeomNet as dynamic features to correct the geometries prediction and progressively improve model accuracy. RocketX is tested on 483 benchmark proteins and 20 FM targets of CASP14. Experimental results show that the closed-loop feedback mechanism significantly contributes to the performance of RocketX, and the prediction accuracy of RocketX outperforms that of the state-of-the-art methods trRosetta (without templates) and RaptorX. In addition, the blind test results on CAMEO show that although no template is used, the prediction accuracy of RocketX on medium and hard targets is comparable to the advanced methods that integrate templates.

AvailabilityThe RocketX web server are freely available at http://zhanglab-bioinf.com/RocketX.

Contactzgj@zjut.edu.cn

category: bioinformatics


title: Transitivity scores to account for triadic edge weight similarity in undirected weighted graphs

abstract: The graph transitivity measures the probability that adjacent vertices in a network are interconnected, thus revealing the existence of tightly connected neighborhoods playing a role in information and pathogen circulation. When the connections vary in strength, focusing on whether connections exist or not can be reductive. I score the weighted transitivity according to the similarity between the weights of the three possible links in each triad. I illustrate the biological relevance of that information with two reanalyses of animal contact networks. In the rhesus macaque Macaca mulatta, a species in which kin relationships strongly predict social relationships, the new metrics revealed striking similarities in the configuration of grooming networks in captive and free-ranging groups, but only as long as the matrilines were preserved. In the barnacle goose Branta leucopsis, in an experiment designed to test the long-term effect of the goslings social environment, the new metrics uncovered an excess of weak triplets closed by strong links in males compared to females, and consistent with the triadic process underlying goose dominance relationships.


title: Weighted transitivity scores that account for triadic edge similarity in undirected graphs


title: High-fructose feeding suppresses cold-stimulated brown adipose tissue glucose uptake in young men independently of changes in thermogenesis and the gut microbiome

abstract: Diets rich in added sugars, especially high in fructose, are associated with metabolic diseases such as insulin resistance, and non-alcoholic fatty liver disease. Studies have shown a link between these pathologies and changes in the microbiome and its metabolites. Given the reported associations in animal models between the microbiome and brown or beige adipose tissue (BAT) function, and the alterations in the microbiome induced by high glucose or high fructose diets, we investigated the potential causal link between high glucose or fructose diets and BAT dysfunction in humans. We show that BAT glucose uptake, but not thermogenesis, is impaired by a high fructose but not high glucose diet, in the absence of changes in body mass, the gastrointestinal microbiome, and faecal short-chain fatty acids. We conclude that BAT metabolic dysfunction occurs independently from changes in gut microbiome composition, and earlier than other pathophysiological abnormalities associated with insulin resistance and dyslipidemia during fructose overconsumption in humans.

category: physiology


title: Sri Lankan Footprint in Global Aquatic Science Research: A Scientometric Analysis

abstract: The present study summarizes the research productivity and international collaboration in aquatic studies conducted by Sri Lankan scholars during 2000-2019. The study was based on the SCOPUS(R) database. R programming language, package bibliometrix and Vosviewer software were employed in the analysis. Results of the present study indicate that increasing growth trend in the annual number of publications. A significant correlation (p<0.05) between the number of articles and per capita GDP (Gross Domestic Production) was also observed. Senior authors dominated in terms of the article count, citation count, h index, and other author productivity indices. Journal of the National Science Foundation of Sri Lanka had the highest article count (n=33). Aquatic studies in Sri Lanka were more locally funded. Sri Lanka had strong research collaborations with Japan, South Korea and Australia. During 2000-2019, the transition of aquatic studies from lacustrine field studies to molecular lab-based studies were observed. The findings of the present study may provide a comprehensive understanding on the current context and future directions of aquatic studies in Sri Lanka.

category: scientific communication and education


title: Optimal protein production by a synthetic microbial consortium: Coexistence, distribution of labor, and syntrophy

abstract: The bacterium E. coli is widely used to produce recombinant proteins such as growth hormone and insulin. One inconvenience with E. coli cultures is the secretion of acetate through overflow metabolism. Acetate inhibits cell growth and represents a carbon diversion, which results in several negative effects on protein production. One way to over-come this problem is the use of a synthetic consortium of two different E. coli strains, one producing recombinant proteins and one reducing the acetate concentration. In this paper, we study a chemostat model of such a synthetic community where both strains are allowed to produce recombinant proteins. We give necessary and sufficient conditions for the existence of a coexistence equilibrium and show that it is unique. Based on this equilibrium, we define a multi-objective optimization problem for the maximization of two important bioprocess performance metrics, process yield and productivity. Solving numerically this problem, we find the best available trade-offs between the metrics. Under optimal operation of the mixed community, both strains must produce the protein of interest, and not only one (distribution instead of division of labor). Moreover, in this regime acetate secretion by one strain is necessary for the survival of the other (syntrophy). The results thus illustrate how complex multi-level dynamics shape the optimal production of recombinant proteins by synthetic microbial consortia.

category: synthetic biology


title: Pathological relevance of post-translationally modified alpha-synuclein (pSer87, pSer129, nTyr39) in idiopathic Parkinson's disease and Multiple System Atrophy.

abstract: Aggregated alpha-synuclein (-synuclein) is the main component of Lewy bodies (LBs), Lewy neurites (LNs), and glial cytoplasmic inclusions (GCIs), which are pathological hallmarks of idiopathic Parkinsons disease (IPD) and multiple system atrophy (MSA), respectively. Initiating factors that culminate in forming LBs/LNs/GCIs remain elusive. Several species of -synuclein exist, including phosphorylated and nitrated forms. It is unclear which -synuclein post-translational modifications (PTMs) appear within aggregates throughout disease pathology. Herein we aimed to establish the predominant -synuclein PTMs in post-mortem IPD and MSA pathology using immunohistochemistry. We examined the patterns of three -synuclein PTMs (pS87, pS129, nY39) simultaneously in pathology-affected regions of 15 PD, 5 MSA, 6 neurologically normal controls. All antibodies recognized LBs, LNs, and GCIs, albeit to a variable extent. pS129 -synuclein antibody was particularly immunopositive for LNs and synaptic dot-like structures followed by nY39 -synuclein antibody. GCIs, neuronal inclusions, and small threads were positive for nY39 -synuclein in MSA. Quantification of the LB scores revealed that pS129 -synuclein was the dominant and earliest -synuclein PTM followed by nY39 -synuclein, while lower amounts of pSer87 -synuclein appeared later in disease progression in PD. These results may have implications for novel biomarker and therapeutic developments.


title: Optimization of an unscented Kalman filter for an embedded platform

abstract:
The unscented Kalman filter (UKF) is finding increased application in biological fields. While realizing a complex UKF system in a low-power embedded platform offers many potential benefits including wearability, it also poses significant design challenges. Here we present a method for optimizing a UKF system for realization in an embedded platform. The method seeks to minimize both computation time and error in UKF state reconstruction and forecasting. As a case study, we applied the method to a model for the rat sleep-wake regulatory system in which 432 variants of the UKF over six different variables are considered. The optimization method is divided into three stages that assess computation time, state forecast error, and state reconstruction error. We apply a cost function to variants that pass all three stages to identify a variant that computes 27 times faster than the reference variant and maintains required levels of state estimation and forecasting accuracy. We draw the following insights: 1) process noise provides leeway for simplifying the model and its integration in ways that speed computation time while maintaining state forecasting accuracy, 2) the assimilation of observed data during the UKF correction step provides leeway for simplifying the UKF structure in ways that speed computation time while maintaining state reconstruction accuracy, and 3) the optimization process can be accelerated by decoupling variables that directly impact the underlying model from variables that impact the UKF structure.

Author summaryPowerful statistical tools can be used to estimate unmeasured information in biological systems and predict the systems future state. Translating these tools from a desktop computer to small, wearable or implantable platforms can unlock many benefits, but presents many design challenges, because tradeoffs between computational simplicity and system accuracy must be balanced. We present an approach to translating one such widely used statistical tool, the unscented Kalman filter, from a desktop computer to a miniature device. We demonstrate the approach with a case study centering on the neural circuits governing the mammalian sleep-wake cycle. By exploiting uncertainty in the biology being estimated and the corrective influence of biological measurements, we arrive at a design that is easily computable on the miniature device and maintains a high level of accuracy. We anticipate that our approach will aid others in designing such miniaturized systems for a broad range of applications.


title: SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction

abstract:
Coronavirus disease-2019 (COVID-19) is primarily a respiratory disease, however, an increasing number of reports indicate that SARS-CoV-2 infection can also cause severe neurological manifestations, including precipitating cases of probable Parkinsons disease. As microglial NLRP3 inflammasome activation is a major driver of neurodegeneration, here we interrogated whether SARS-CoV-2 can promote microglial NLRP3 inflammasome activation utilising a model of human monocyte-derived microglia. We identified that SARS-CoV-2 isolates can bind and enter microglia, triggering inflammasome activation in the absence of viral replication. Mechanistically, microglial NLRP3 could be both primed and activated with SARS-CoV-2 spike glycoprotein in a NF-{kappa}B and ACE2-dependent manner. Notably, virus- and spike protein-mediated inflammasome activation in microglia was significantly enhanced in the presence of -synuclein fibrils, which was entirely ablated by NLRP3-inhibition. These results support a possible mechanism of microglia activation by SARS-CoV-2, which could explain the increased vulnerability to developing neurological symptoms akin to Parkinsons disease in certain COVID-19 infected individuals, and a potential therapeutic avenue for intervention.

SIGNIFICANCE STATEMENTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) principally affects the lungs, however there is evidence that the virus can also reach the brain and lead to chronic neurological symptoms. In this study, we examined the interaction SARS-CoV-2 with brain immune cells, by using an ex-vivo model of human monocyte-derived microglia. We identified robust activation of the innate immune sensor complex, NLRP3 inflammasome, in cells exposed to SARS-CoV-2. This was dependent on spike protein-ACE2 receptor interaction and was potentiated in the presence of -synuclein. We therefore identify a possible mechanism for SARS-CoV-2 and increased vulnerability to developing neurological dysfunction. These findings support a potential therapeutic avenue for treatment of SARS-CoV-2 driven neurological manifestations, through use of NLRP3 inflammasome or ACE2 inhibitors.


title: "Learning in reverse: Dopamine errors drive excitatory and inhibitory components of backward conditioning in an outcome-specific manner".

abstract:
For over two decades, midbrain dopamine was considered synonymous with the prediction error in temporal-difference reinforcement learning. Central to this proposal is the notion that reward-predictive stimuli become endowed with the scalar value of predicted rewards. When these cues are subsequently encountered, their predictive value is compared to the value of the actual reward received allowing for the calculation of prediction errors. Phasic firing of dopamine neurons was proposed to reflect this computation, facilitating the backpropagation of value from the predicted reward to the reward-predictive stimulus, thus reducing future prediction errors. There are two critical assumptions of this proposal: 1) that dopamine errors can only facilitate learning about scalar value and not more complex features of predicted rewards, and 2) that the dopamine signal can only be involved in anticipatory learning in which cues or actions precede rewards. Recent work has challenged the first assumption, demonstrating that phasic dopamine signals across species are involved in learning about more complex features of the predicted outcomes, in a manner that transcends this value computation. Here, we tested the validity of the second assumption. Specifically, we examined whether phasic midbrain dopamine activity would be necessary for backward conditioning--when a neutral cue reliably follows a rewarding outcome. Using a specific Pavlovian-to-Instrumental Transfer (PIT) procedure, we show rats learn both excitatory and inhibitory components of a backward association, and that this association entails knowledge of the specific identity of the reward and cue. We demonstrate that brief optogenetic inhibition of VTADA neurons timed to the transition between the reward and cue, reduces both of these components of backward conditioning. These findings suggest VTADA neurons are capable of facilitating associations between contiguously occurring events, regardless of the content of those events. We conclude that these data are in line with suggestions that the VTADA error acts as a universal teaching signal. This may provide insight into why dopamine function has been implicated in a myriad of psychological disorders that are characterized by very distinct reinforcement-learning deficits.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/475719v1_ufig1.gif" ALT="Figure 1">
View larger version (13K):
org.highwire.dtl.DTLVardef@192012forg.highwire.dtl.DTLVardef@8bdf86org.highwire.dtl.DTLVardef@ffe1faorg.highwire.dtl.DTLVardef@14d0152_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Localized Cardiolipin Synthesis is Required for the Assembly of MreB During the Polarized Cell Division of Chlamydia trachomatis

abstract: Pathogenic Chlamydia species are coccoid bacteria that use the rod-shape determining protein MreB to direct septal peptidoglycan synthesis during their polarized cell division process. How the site of polarized budding is determined in this bacterium, where contextual features like membrane curvature are seemingly identical, is unclear. We hypothesized that the accumulation of the phospholipid, cardiolipin (CL), in specific regions of the cell membrane induces localized membrane changes that trigger the recruitment of MreB to the site where the bud will arise. To test this, we ectopically expressed cardiolipin synthase (Cls) and observed a polar distribution for this enzyme in Chlamydia trachomatis. In early division intermediates, Cls was restricted to the bud site where MreB is localized and peptidoglycan synthesis is initiated. The localization profile of Cls throughout division mimicked the distribution of lipids that stain with NAO, a dye that labels CL. Treatment of Chlamydia with 3,6-dinonylneamine (diNN), an antibiotic targeting CL-containing membrane domains, resulted in redistribution of Cls and NAO-staining phospholipids. In addition, MreB localization was altered by diNN treatment, suggesting an upstream regulatory role for CL-containing membranes in directing the assembly of MreB. This hypothesis is consistent with the observation that the clustered localization of Cls is not dependent upon MreB function or peptidoglycan synthesis. Furthermore, expression of a CL-binding protein at the inner membrane of C. trachomatis dramatically inhibited bacterial growth supporting the importance of CL in the division process. Our findings implicate a critical role for localized CL synthesis in driving MreB assembly at the bud site during the polarized cell division of Chlamydia.

category: microbiology


title: RNA-based therapy for Cryptosporidium parvum infection: proof-of-concept studies

abstract: Cryptosporidium is a leading cause of moderate-to-severe diarrhea in children. Nitazoxanide, the only FDA-approved treatment for cryptosporidiosis, has limited efficacy in those at highest risk for sequelae. RNA-argonaute (Ago) complexes to Cryptosporidium nucleoside diphosphate kinase (cpNDK) decreased the Cryptosporidium parvum mRNA by 95% in infected cells in vitro. Treatment of mice by oral gavage with ssRNA/Ago complexes encapsulated in lipid nanoparticles led to delivery of the complexes into intestinal epithelial cells. Treatment of C. parvum infected mice with ssRNA/Ago complexes targeting cpNDK led to the resolution of oocyst shedding in 4/5 SCID/beige mice. These results confirm the potential use of antisense therapy as an alternative approach to cryptosporidiosis treatment.


title: Evolution of a cis-acting SNP that controls Type VI Secretion in Vibrio cholerae

abstract:
Mutations in regulatory mechanisms that control gene expression contribute to phenotypic diversity and thus facilitate the adaptation of microbes and other organisms to new niches. Comparative genomics can be used to infer rewiring of regulatory architecture based on large effect mutations like loss or acquisition of transcription factors but may be insufficient to identify small changes in non-coding, intergenic DNA sequence of regulatory elements that drive phenotypic divergence. In human-derived Vibrio cholerae, the response to distinct chemical cues triggers production of multiple transcription factors that can regulate the Type VI Secretion System (T6), a broadly distributed weapon for interbacterial competition. However, to date, the signaling network remains poorly understood because no regulatory element has been identified for the major T6 locus. Here we identify a conserved cis-acting single nucleotide polymorphism (SNP) controlling T6 transcription and activity. Sequence alignment of the T6 regulatory region from diverse V. cholerae strains revealed conservation of the SNP that we rewired to interconvert V. cholerae T6 activity between chitin-inducible and constitutive states. This study supports a model of pathogen evolution through a non-coding cis-regulatory mutation and preexisting, active transcription factors that confers a different fitness advantage to tightly regulated strains inside a human host and unfettered strains adapted to environmental niches.

ImportanceOrganisms sense external cues with regulatory circuits that trigger the production of transcription factors, which bind specific DNA sequences at promoters ("cis" regulatory elements) to activate target genes. Mutations of transcription factors or their regulatory elements create phenotypic diversity, allowing exploitation of new niches. Waterborne pathogen Vibrio cholerae encodes the Type VI Secretion System "nanoweapon" to kill competitor cells when activated. Despite identification of several transcription factors, no regulatory element has been identified in the promoter of the major Type VI locus, to date. Combining phenotypic, genetic, and genomic analysis of diverse V. cholerae strains, we discovered a single nucleotide polymorphism in the Type VI promoter that switches its killing activity between a constitutive state beneficial outside hosts and an inducible state for constraint in a host. Our results support a role for non-coding DNA in adaptation of this pathogen.


title: Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India

abstract: We report patho-morphological and virological characterization of SARS-CoV-2 in naturally infected, free ranging Indian Leopard (Panthera pardus fusca). Whole genome sequence analysis confirmed infection of Delta variant of SARS-CoV-2, possibly spill over from humans, but the case was detected when infection level had dropped significantly in human population. This report underlines the need for intensive screening of wild animals for keeping track of the virus evolution and development of carrier status of SARS-CoV-2 among wildlife species.


title: Generation and characterisation of P. falciparum parasites with a G358S mutation in the PfATP4 Na+ pump and clinically relevant levels of resistance to some PfATP4 inhibitors

abstract: Small-molecule inhibitors of PfATP4, a Plasmodium falciparum protein that is believed to pump Na+ out of the parasite while importing H+, are on track to become much-needed new antimalarial drugs. The spiroindolone cipargamin is poised to become the first PfATP4 inhibitor to reach the field, having performed strongly in Phase 1 and 2 clinical trials. Previous attempts to generate cipargamin-resistant parasites in the laboratory have yielded parasites with reduced susceptibility to the drug; however, the highest 50% inhibitory concentration reported to date is 24 nM. Here, we show that P. falciparum parasites can acquire a clinically-significant level of resistance to cipargamin that enables them to withstand micromolar concentrations of the drug. Independent experiments to generate high-level cipargamin resistance using different protocols and strains led to the same change each time - a G358S mutation in PfATP4. Parasites with this mutation showed high-level resistance not only to cipargamin, but also to the dihydroisoquinolone (+)-SJ733. However, for certain other (less clinically advanced) PfATP4-associated compounds the G358S mutation in PfATP4 conferred only moderate resistance or no resistance. The G358S mutation in PfATP4 did not affect parasite susceptibility to antimalarials that do not target PfATP4. The G358S mutation in PfATP4, and the equivalent mutation in the Toxoplasma gondii ATP4 homologue (G419S), decreased the sensitivity of the Na+-ATPase activity of ATP4 to inhibition by cipargamin and (+)-SJ733, and decreased the sensitivity of parasites expressing these ATP4 mutations to disruption of parasite Na+ regulation by cipargamin- and (+)-SJ733. The G358S mutation in PfATP4 reduced the affinity of the protein for Na+ and was associated with an increase in the parasites resting cytosolic Na+ concentration; however, no significant defect in parasite growth rate was observed. Our findings suggest that codon 358 in pfatp4 should be monitored closely in the field as a molecular marker for cipargamin resistance, and that PfATP4 inhibitors in clinical development should be tested for their activity against PfATP4G358S parasites.


title: Vitamin C functions as double-edge sword on cancer progression depending on ERK activation or inhibition mediated by its receptor SVCT2

abstract:
The effect of Vitamin C (Vc) in oncotherapy was controversial for decades. And hyperactivation of extracellular signal-regulated kinase (ERK) drove tumorigenesis. Herein, we demonstrated that Vc activated ERK through sodium-dependent Vc transporter 2 (SVCT2), while high-dose Vc resulted in persistent ERK feedback inhibition following activation. Extracellular Vc binding to SVCT2 initiated ERK activation, then transmembrane transport of Vc induced dimerization of SVCT2. Activated ERK phosphorylated protein tyrosine phosphatase non-receptor type 12 (PTPN12) at Ser434 and inhibited PTPN12 activity, thus enhancing phosphorylation of Janus kinase 2 (JAK2), which phosphorylated growth factor receptor bound protein 2 (GRB2) at Tyr160 to promote GRB2 dimers dissociation and recruitment of GRB2 to SVCT2, leading to further ERK activation. Different cancers have different sensitivities to Vc, the dose effects of Vc on cancer phenotypes depended on that ERK was activated or inhibited. These findings suggest SVCT2 is a Vc receptor mediating the ERK-PTPN12-JAK2-GRB2-ERK positive feedback loop and a potential target for oncotherapy.

Abstract graphic

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/475954v2_ufig1.gif" ALT="Figure 1">
View larger version (72K):
org.highwire.dtl.DTLVardef@9f75e7org.highwire.dtl.DTLVardef@f5bc18org.highwire.dtl.DTLVardef@10fe4c4org.highwire.dtl.DTLVardef@742b7d_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: molecular biology


title: Comparison of double-stranded and single-stranded cfDNA library construction methods for targeted genome and methylation sequencing

abstract: Cell-free DNA (cfDNA) profiling by next generation sequencing (NGS) has wide applications in cancer diagnosis, prognosis, and therapy response monitoring. One key step of cfDNA deep sequencing workflow is NGS library construction, whose efficiency determines effective sequencing depth, sequencing quality, and accuracy. In this study, we compared two different cfDNA library construction methods for the applications of mutation detection and methylation profiling: the conventional method which captures double-stranded DNA (dsDNA) molecules, namely the dsLib workflow, and an alternative method which captures single-stranded DNA (ssDNA), namely the ssLib workflow. Our results suggest that the dsLib method was preferrable for mutation detection while the ssLib method proved more efficient for methylation analysis. Our findings could help researchers choose more appropriate library construction method for corresponding downstream sequencing applications.


title: Epac1 regulates cellular SUMOylation by promoting the formation of SUMO-activating nuclear condensates

abstract: Protein SUMOylation plays an essential role in maintaining cellular homeostasis when cells are under stress. However, precisely how SUMOylation is regulated, and a molecular mechanism linking cellular stress to SUMOylation remains elusive. Herein, we report that cAMP, a major stress-response second messenger, acts through Epac1 as a regulator of cellular SUMOylation. The Epac1-associated proteome is highly enriched with components of the SUMOylation pathway. Activation of Epac1 by intracellular cAMP triggers phase separation and the formation of nuclear condensates containing Epac1 and general components of the SUMOylation machinery to promote cellular SUMOylation. Furthermore, genetic knockout of Epac1 obliterates oxidized low-density lipoprotein induced cellular SUMOylation in macrophages, leading to suppression of foam cell formation. These results provide a direct nexus connecting two major cellular stress responses to define a molecular mechanism in which cAMP regulates the dynamics of cellular condensates to modulate protein SUMOylation.

category: cell biology


title: cdon and boc affect trunk neural crest cell migration through a non-cell autonomous reduction of hedgehog signaling in zebrafish slow-twitch muscle

abstract: The immunoglobin superfamily members cdon and boc are transmembrane proteins implicated in regulating hedgehog signaling during vertebrate development. Recent work showing roles for these genes in axon guidance and neural crest cell migration further suggest that cdon/boc may play additional functions in regulating directed cell movements during development. Here we use novel and existing mutants to investigate a role for cdon and boc in zebrafish neural crest cell migration. We find that single cdon or boc mutant embryos exhibit normal neural crest phenotypes, but that neural crest migration is strikingly disrupted in double cdon/boc mutant embryos. We further show that this neural crest migration phenotype is associated with defects to the differentiation of slow-twitch muscle cells, and that this slow-twitch muscle phenotype is a consequence of reduced hedgehog signaling in mutant fish. While neural crest migratory ability is not affected in double mutant embryos, neural crest directionality is severely affected. These data suggest that neural crest migration defects are likely to be secondary to defects in slow-twitch muscle differentiation. Combined, our data add to a growing literature showing that cdon and boc act synergistically to promote hedgehog signaling during vertebrate development, and provide a foundation for using zebrafish to further study the function of these hedgehog receptor paralogs.


title: Geometric control of Myosin-II orientation during axis elongation

abstract: The actomyosin cytoskeleton is a crucial driver of morphogenesis. Yet how the behavior of large-scale cytoskeletal patterns in deforming tissues emerges from the interplay of geometry, genetics, and mechanics remains incompletely understood. Convergent extension flow in D. melanogaster embryos provides the opportunity to establish a quantitative understanding of the dynamics of anisotropic non-muscle myosin II. Cell-scale analysis of protein localization in fixed embryos suggests that there are complex rules governing how the control of myosin anisotropy is regulated by gene expression patterns. However, technical limitations have impeded quantitative and dynamic studies of this process at the whole embryo level, leaving the role of geometry open. Here we combine in toto live imaging with quantitative analysis of molecular dynamics to characterize the distribution of myosin anisotropy and corresponding genetic patterning. We found pair rule gene expression continuously deformed, flowing with the tissue frame. In contrast, myosin anisotropy orientation remained nearly static, aligned with the stationary dorsal-ventral axis of the embryo. We propose myosin recruitment by a geometrically defined static source, potentially related to the embryo-scale epithelial tension, and account for transient deflections by the interplay of cytoskeletal turnover with junction reorientation by flow. With only one parameter, this model quantitatively accounts for the time course of myosin anisotropy orientation in wild-type, twist, and even-skipped embryos as well as embryos with perturbed egg geometry. Geometric patterning of the cytoskeleton suggests a simple physical strategy to ensure a robust flow and formation of shape.


title: Ablation of SAMD1 in Mice Causes Failure of Angiogenesis, Embryonic Lethality

abstract: Pathological retention of LDL in the intima is involved in atherosclerosis, although the retention mechanisms are not well-understood. Previously, we reported Sterile Alpha Motif Domain Containing 1 (SAMD1), a protein secreted by intimal smooth muscle cells in atherosclerotic lesions, appears to bind LDL in extracellular matrix around intimal cells. Fab-fragment inhibitors of apparently irreversible SAMD1/LDL binding reduced LDL retention in carotid injury models, but did not have a significant effect on early spontaneous lesion development. Our histology of mouse atherosclerosis models revealed extensive SAMD1 expression, possibly related to cell phenotype modulation and antigen presentation. Although the normal function of SAMD1 is unknown, it may have multiple epigenetic roles. For this report, we generated SAMD1-/-, SAMD1-/+, and SAMD1-/+ apoE-/- mice to further explore SAMD1s role in atherosclerosis. SAMD1 was found in tissues throughout the SAMD1+/+ and SAMD1-/+ embryos. Homozygous loss of SAMD1 was embryonic lethal: at embryonic day 14, organs were partially developed and/or degraded; heads and brains were malformed; no blood vessels were observed; red blood cells were scattered and pooled, primarily near the embryo surface; and cell death was occurring. Development appeared normal in heterozygous SAMD1 embryos, but postnatal genotyping showed a reduced ability to thrive. Growth of atherosclerotic lesions in SAMD1-/+ apoE-/- after 35 weeks was not significantly less than in mice SAMD1+/+ apoE-/- mice.


title: Evolution under juvenile malnutrition impacts adult metabolism and fitness

abstract: Juveniles are often first to suffer from nutrient shortage, and juvenile undernutrition is likely an important force of natural selection shaping animal physiology, with consequences potentially extending into adulthood. We combined RNAseq, targeted metabolomics and genomics to study the consequences of experimental evolution under juvenile undernutrition for metabolism of reproductively active adult females of Drosophila melanogaster. Compared to six Control populations maintained on standard diet, six Selected populations evolved for over 230 generations on a nutrient-poor larval diet showed major changes in adult gene expression and metabolite abundance. In particular, Selected flies were relatively deficient in essential amino acids and purine nucleotides, but showed overabundance of several non-essential amino-acids involved in purine synthesis and overexpression of multiple enzymes catalyzing this pathway. Selected flies also accumulated medium-chain acylcarnitines suggestive of congestion in beta-oxidation, possibly linked to deficiency of electron transporters. Some aspects of the metabolic profile of Selected flies resembled that of flies subject to starvation. Furthermore, differences between Selected and Control populations in adult gene expression were in general positively correlated with differences in larval expression, consistent with pleiotropy in gene regulation between the life stages. Finally, Selected flies were less fit in terms of fecundity than Controls even when both were raised under the conditions under which the Selected populations evolved. These results suggest that evolutionary adaptation to juvenile undernutrition has large pleiotropic consequences for adult metabolism, and that they are costly rather than adaptive for adult fitness.


title: Two modes of evolution shape bacterial strain diversity in the gut for thousands of generations

abstract: How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show that gut environments can rapidly generate diversifying selection and ecotype formation.


title: A survey on antimicrobial resistance genes of frequently used bacteria in kefir and yoghurt

abstract: Antimicrobial resistance (AMR) is one of the foremost threats facing the treatment of infectious diseases worldwide. Recent studies have highlighted the potential for antimicrobial resistance genes (ARGs) in fermented foods to contribute to AMR via horizontal gene transfer (HGT). The focus of our study was investigating the ARG content (resistome) and mobility potential of the ARGs (mobilome) of bacterial strains commonly used in probiotic products, namely yoghurt and kefir. We performed metagenomic analyses on freely available data sets (n=584) originating from various kefir and yoghurt strains using next generation sequencing (NGS) in order to gain an insight into the ARG diversity, frequency and mobility. Our study shows that kefir and yoghurt products carry diverse and significant amounts of ARGs and that these genes may often be associated with iMGEs or plasmids, conferring mobility. Certain bacteria species such as Bifidobacterium animalis and Streptococcus thermophilus were found to have higher ARG content. Overall, our results support the hypothesis that ARGs are present in fermented foods, namely yoghurt and kefir, and have the potential to contribute to AMR.

category: genomics


title: A bacterial secretosome for regulated envelope biogenesis and quality control

abstract: As the first line of defence against antibiotics, the Gram-negative bacterial envelope and its biogenesis are of considerable interest to the microbiological and biomedical communities. All bacterial proteins are synthesised in the cytosol, so inner- and outer-membrane proteins, and periplasmic residents have to be transported to their final destinations via specialised protein machinery. The Sec translocon, a ubiquitous integral inner-membrane (IM) complex, is key to this process as the major gateway for protein transit from the cytosol to the cell envelope; this can be achieved during their translation, or afterwards. Proteins need to be directed to the inner-membrane (usually co-translational), otherwise SecA utilises ATP and the proton-motive-force (PMF) to drive proteins across the membrane post-translationally. These proteins are then picked up by chaperones for folding in the periplasm or delivered to the {beta}-barrel assembly machinery (BAM) for incorporation into the outer-membrane. The core heterotrimeric SecYEG-complex forms the hub for an extensive network of interactions that regulate protein delivery and quality control. Here, we conduct a biochemical exploration of this  secretosome - a very large, versatile and inter-changeable assembly with the Sec-translocon at its core; featuring interactions that facilitate secretion (SecDF), inner- and outer-membrane protein insertion (respectively, YidC and BAM), protein folding and quality control (e.g. PpiD, YfgM and FtsH). We propose the dynamic interplay amongst these and other factors act to ensure efficient whole envelope biogenesis, regulated to accommodate the requirements of cell elongation and division. This organisation would be essential for cell wall biogenesis and remodelling and thus its perturbation would be a good strategy for the development of anti-microbials.

category: biochemistry


title: Structural and functional impact by SARS-CoV-2 Omicron spike mutations

abstract: The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), bearing an unusually high number of mutations, has become a dominant strain in many countries within several weeks. We report here structural, functional and antigenic properties of its full-length spike (S) protein with a native sequence in comparison with those of previously prevalent variants. Omicron S requires a substantially higher level of host receptor ACE2 for efficient membrane fusion than other variants, possibly explaining its unexpected cellular tropism. Mutations not only remodel the antigenic structure of the N-terminal domain of the S protein, but also alter the surface of the receptor-binding domain in a way not seen in other variants, consistent with its remarkable resistance to neutralizing antibodies. These results suggest that Omicron S has acquired an extraordinary ability to evade host immunity by excessive mutations, which also compromise its fusogenic capability.


title: Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo

abstract: Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes, but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyzed lysosomes and early endosomes. Based on the identification of 5,376 cross-links, we investigated protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and heterodimeric/- multimeric structures of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2- positive early endosomes, we identified >300 proteins presenting putative cargo, and confirm the latrophilin family of adhesion G protein-coupled receptors as substrates for flotillin-dependent endocytosis.


title: Factor VII activating protease (FSAP) inhibits the outcome of ischemic stroke in mouse models.

abstract: Factor VII activating protease (FSAP) is a circulating serine protease, and individuals with the Marburg I (MI) single nucleotide polymorphism (SNP), which results in an inactive enzyme, have an increased risk of stroke. The outcome of ischemic stroke is more marked in FSAP-deficient mice compared to their wild-type (WT) counterparts. Plasma FSAP levels are raised in patients as well as mice after stroke. In vitro, FSAP promotes fibrinolysis by cleavage of fibrinogen, activates protease-activated receptors and decreases the cellular cytotoxicity of histones. Since these are desirable properties in stroke treatment, we tested the effect of recombinant serine protease domain of FSAP (FSAP-SPD) on ischemic stroke in mice. A combination of tissue plasminogen activator (tPA) and FSAP-SPD enhanced clot lysis, improved microvascular perfusion and neurological outcome and reduced infarct volumes in a mouse model of thromboembolic stroke. In the tail bleeding model FSAP-SPD treatment provoked a faster clotting time indicating that it has a pro-coagulant effect that is described before. FSAP-SPD improved stroke outcome and diminished the negative effects of co-treatment with tPA in the transient middle cerebral artery occlusion model. The inactive MI-isoform of FSAP did not have any effects in either model. In mice with FSAP deficiency there were minor differences in the outcomes of stroke but the treatment with FSAP-SPD was equally effective. Thus, FSAP represents a promising novel therapeutic strategy in the treatment of ischemic stroke that requires further evaluation.


title: The channel activities of the full-length prion and truncated proteins

abstract: Prion disease is a fatal neurodegenerative disorder, in which the cellular prion protein PrPC is converted to a misfolded prion which in turn is hypothesized to permeabilize cellular membranes. The pathways leading to toxicity in prion disease are not yet completely elucidated and whether it also includes formation of membrane pores remains to be answered. Prion protein consists of two domains: a globular domain (GD) and a flexible N-terminus (FT) domain. Although a proximal nine polybasic amino acid (FT(23-31)) sequence of FT is a prerequisite for cellular membrane permeabilization, other functional domain regions may influence FT(23-31) and its permeabilization. By using single-channel electrical recordings, we reveal that FT(23-50) dominates the membrane permeabilization within the full-length mouse PrP (mPrP(23-230)). The other domain of FT(51-110) or C-terminal domain down-regulates the channel activity of FT(23-50) and the full-length mouse PrP (mPrP(23-230)). The addition of prion mimetic antibody, POM1 significantly enhances mPrP(23-230) membrane permeabilization, whereas POM1-Y104A, a POM1 mutant that binds to PrP but cannot elicit toxicity has negligible effect on membrane permeabilization. Additionally, anti-N-terminal antibody POM2 or Cu2+ stabilizes FT domain, thus provoking FT(23-110) channel activity. Furthermore, our setup provides a more direct method without an external fused protein to study the channel activity of truncated PrP in the lipid membranes. We therefore hypothesize that the primary N-terminal residues are essential for membranes permeabilization and other functional segments play a vital role to modulate the pathological effects of PrP-medicated neurotoxicity. This may yield essential insights into molecular mechanisms of prion neurotoxicity to cellular membranes in prion disease.


title: Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances

abstract: Sketching methods offer computational biologists scalable techniques to analyze data sets that continue to grow in size. MinHash is one such technique that has enjoyed recent broad application. However, traditional MinHash has previously been shown to perform poorly when applied to sets of very dissimilar sizes. FracMinHash was recently introduced as a modification of MinHash to compensate for this lack of performance when set sizes differ. While experimental evidence has been encouraging, FracMinHash has not yet been analyzed from a theoretical perspective. In this paper, we perform such an analysis and prove that while FracMinHash is not unbiased, this bias is easily corrected. Next, we detail how a simple mutation model interacts with FracMinHash and are able to derive confidence intervals for evolutionary mutation distances between pairs of sequences as well as hypothesis tests for FracMinHash. We find that FracMinHash estimates the containment of a genome in a large metagenome more accurately and more precisely when compared to traditional MinHash, and the confidence interval performs significantly better in estimating mutation distances. A python-based implementation of the theorems we derive is freely available at https://github.com/KoslickiLab/mutation-rate-ci-calculator. The results presented in this paper can be reproduced using the code at https://github.com/KoslickiLab/ScaledMinHash-reproducibles.


title: Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers

abstract: The identification of reference genomes and taxonomic labels from metagenome data underlies many microbiome studies. Here we describe two algorithms for compositional analysis of metagenome sequencing data. We first investigate the FracMinHash sketching technique, a derivative of modulo hash that supports Jaccard containment estimation between sets of different sizes. We implement FracMinHash in the sourmash software, evaluate its accuracy, and demonstrate large-scale containment searches of metagenomes using 700,000 microbial reference genomes. We next frame shotgun metagenome compositional analysis as the problem of finding a minimum collection of reference genomes that "cover" the known k-mers in a metagenome, a minimum set cover problem. We implement a greedy approximate solution using FracMinHash sketches, and evaluate its accuracy for taxonomic assignment using a CAMI community benchmark. Finally, we show that the minimum metagenome cover can be used to guide the selection of reference genomes for read mapping. sourmash is available as open source software under the BSD 3-Clause license at github.com/dib-lab/sourmash/.


title: Reciprocal epigenetic Sox2 regulation by SMAD1-SMAD3 is critical for anoikis resistance and metastasis in cancer

abstract:
Growth factors in the tumor environment are key regulators of cell survival and metastasis. Here we reveal, dichotomy between TGF-{beta} superfamily growth factors BMP and TGF-{beta}/activin, and their downstream SMAD effectors. Gene expression profiling uncovered Sox2 as a key signaling node regulated in an opposing manner by anoikis-promoting BMP2, 4 and 9, and anoikis-suppressing TGF-{beta} and activin A. We find that Sox2 repression by BMPs robustly inhibits intraperitoneal tumor burden and increases survival in multiple ovarian cancer models. Repression of Sox2 is driven by SMAD1 dependent histone H3K27me3 recruitment and DNA methylation at SOX2s promoter. Conversely, TGF-{beta} and activin A promote Sox2 expression, and anoikis resistance by SMAD3 mediated histone H3K4me3 recruitment. We find that balancing Sox2 levels is critical for anoikis, as transcriptomics reveals regulation of key cell death pathways. Moreover, BMP-driven SMAD1 signaling can override TGF-{beta} and activins effect on Sox2, which has clinical significance due to the high levels of TGF-{beta} we find in ovarian cancer patients. Together, our findings identify Sox2 as a contextual and contrastingly regulated key node, downstream of TGF-{beta} superfamily members controlling anoikis and metastasis in ovarian cancers.

HighlightsO_LISox2 is a key node for anoikis resistance in cancer
C_LIO_LISox2 is differentially regulated by TGF-{beta}/activin and BMPs in broad cancers
C_LIO_LIBMP9 is a robust metastasis suppressor by lowering Sox2
C_LIO_LISox2 regulation is contextual, epigenetic and at the transcriptional level
C_LI

category: cancer biology


title: Skeletal muscle regeneration is altered in the R6/2 mouse model of Huntington's disease

abstract:
Huntingtons disease (HD) is caused by CAG repeat expansion in the huntingtin (HTT) gene. Skeletal muscle wasting alongside central pathology is a well-recognized phenomenon seen in patients with HD and HD mouse models. HD muscle atrophy progresses with disease and affects prognosis and quality of life. Satellite cells, progenitors of mature skeletal muscle fibers, are essential for proliferation, differentiation, and repair of muscle tissue in response to muscle injury or exercise.

In this study, we aim to investigate the effect of mutant HTT on the differentiation and regeneration capacity of HD muscle by employing in vitro mononuclear skeletal muscle cell isolation and in vivo acute muscle damage model in R6/2 mice.

We found that, similar to R6/2 adult mice, neonatal R6/2 mice also exhibit a significant reduction in myofiber width and morphological changes in gastrocnemius and soleus muscles compared to WT mice. Cardiotoxin (CTX)-induced acute muscle damage in R6/2 and WT mice showed that the Pax7+ satellite cell pool was dampened in R6/2 mice at 4 weeks post-injection, and R6/2 mice exhibited an altered inflammatory profile in response to acute damage.

Our results suggest that, in addition to the mutant HTT degenerative effects in mature muscle fibers, expression of mutant HTT in satellite cells might alter developmental and regenerative processes to contribute to the progressive muscle mass loss in HD. Taken together, the results presented here encourage further studies evaluating the underlying mechanisms of satellite cell dysfunction in HD mouse models.

category: pathology


title: Collaborative workflow between pathologists and deep learning for evaluation of tumor cellularity in lung adenocarcinoma

abstract:
Owing to the high demand for molecular testing, the reporting of tumor cellularity in cancer samples has become a mandatory task for pathologists. However, the pathological estimation of tumor cellularity is often inaccurate.

We developed a collaborative workflow between pathologists and artificial intelligence (AI) models to evaluate tumor cellularity in lung cancer samples and prospectively applied it to routine practice. We also developed a quantitative model that we validated and tested on retrospectively analyzed cases and ran the model prospectively in a collaborative workflow where pathologists could access the AI results and apply adjustments (Adjusted-Score). The Adjusted-Scores were validated by comparing them with the ground truth established by manual annotation of hematoxylin-eosin slides with reference to immunostains with thyroid transcription factor-1 and napsin A. For training, validation, retrospective testing, and prospective application of the model, we used 40, 10, 50, and 151 whole slide images, respectively.

The sensitivity and specificity of tumor segmentation were 97% and 87%, and the accuracy of nuclei recognition was 99%. Pathologists altered the initial scores in 87% of the cases after referring to the AI results and found that the scores became more precise after collaborating with AI. For validation of Adjusted-Score, we found the Adjusted-Score was significantly closer to the ground truth than non-AI-aided estimates (p<0.05). Thus, an AI-based model was successfully implemented into the routine practice of pathological investigations. The proposed model for tumor cell counting efficiently supported the pathologists to improve the prediction of tumor cellularity for genetic tests.


title: Potentiation of drug toxicity through virus latency reversal promotes preferential elimination of HIV infected cells

abstract: Eliminating latently infected cells is a highly challenging, indispensable step towards the overall cure for HIV/AIDS. We recognized that the unique HIV protease cut site (Phe-Pro) can be reconstructed using a potent toxin, monomethyl auristatin F (MMAF), which features Phe at its C-terminus. We hypothesized that this presents opportunities to design prodrugs that are specifically activated by the HIV protease. To investigate this, a series of MMAF derivatives was synthesized and evaluated in cell culture using latently HIV-infected cells. Cytotoxicity of compounds was enhanced upon latency reversal by up to 11-fold. In a mixed cell population, nanomolar concentrations of the lead compound depleted predominantly the HIV-infected cells and in doing so markedly enriched the pool with the uninfected cells. Despite expectation, mechanism of action of the synthesized toxins was not as HIV protease-specific prodrugs, but likely through the synergy of toxicities between the toxin and the reactivated virus.

category: pharmacology and toxicology


title: Maternally transferred monoclonal antibodies protect neonatal mice from herpes simplex virus-induced mortality and morbidity

abstract:
Neonatal herpes simplex virus (HSV) infections often result in significant mortality and neurological morbidity despite antiviral drug therapy. Maternally-transferred HSV-specific antibodies reduce the risk of clinically-overt neonatal HSV (nHSV), but this observation has not been translationally applied. Using a neonatal mouse model, we tested the hypothesis that passive transfer of HSV-specific human monoclonal antibodies (mAbs) can prevent mortality and morbidity associated with nHSV. The mAbs were expressed in vivo by vectored immunoprophylaxis, or administered in vivo following recombinant expression in vitro. Through these maternally-derived routes or through direct administration to pups, diverse mAbs to HSV glycoprotein D protected against neonatal HSV-1 and HSV-2 infection. Using in vivo bioluminescent imaging, both pre- and post-exposure mAb treatment significantly reduced viral load. Administration of mAb also reduced nHSV-induced behavioral morbidity, as measured by anxiety-like behavior. Together these studies support the notion that HSV-specific mAb-based therapies may prevent or improve HSV infection outcomes in neonates.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/476098v1_ufig1.gif" ALT="Figure 1">
View larger version (29K):
org.highwire.dtl.DTLVardef@175f6eaorg.highwire.dtl.DTLVardef@1a59e39org.highwire.dtl.DTLVardef@36c484org.highwire.dtl.DTLVardef@19fec96_HPS_FORMAT_FIGEXP  M_FIG C_FIG Different antibody sources were used to maternally-transfer or directly administer HSV-specific mAbs to mouse pups. Neonatal mice were challenged with wild type or bioluminescent virus before or after mAb acquisition. Following infection, pups were assessed for survival, virus-induced bioluminescence and anxiety-like behavior as a measure of neurological morbidity. Efficacy was time and mAb dependent. Notably, all HSV-specific mAbs prevented nHSV-associated mortality.


title: A Longitudinal Study of Dominant E. coli Lineages and Antimicrobial Resistance in the Gut of Children Living in an Upper Middle-income Country

abstract:
The gastrointestinal tract constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem, nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. In this prospective study, a fresh fecal sample was obtained from children longitudinally over one year (30 fecal samples at sampling period 1 and 22 fecal samples at sampling periods 2 and 3). From each stool sample, five E. coli colonies were randomly selected (n = 405 E. coli isolates total) in order to characterize the genotype and phenotypic antimicrobial resistance patterns. We found that all numerically dominant E. coli lineages in childrens intestines were transient colonizers, and antimicrobial resistance phenotypes of these strains varied significantly over time without any apparent selective force. Whole-genome sequencing of 3 isolates belonging to ST131 found in one child during the sampling period I and II indicated that isolates were three different ST 131 clones that carried extended-spectrum {beta}-lactamase (ESBL) genes.

IMPORTANCEThe length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance in a community. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine. We found that E. coli lineages in the children's gut change considerably and rapidly over time. This study suggests that some phenotypic resistance patterns may result from the random distribution of genes in E. coli populations over time and may not be associated with differential exposure to antimicrobials.


title: GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes

abstract:
Carbapenem resistance and other antibiotic resistance genes (ARGs) can be found in plasmids in Acinetobacter, but many plasmid types in this genus have not been well-characterised. Here we describe the distribution, diversity and evolutionary capacity of rep group 13 (GR13) plasmids that are found in Acinetobacter species from diverse environments. Our investigation was prompted by the discovery of two GR13 plasmids in A. baumannii isolated in an intensive care unit (ICU). The plasmids harbour distinct accessory genes: pDETAB5 contains blaNDM-1 and genes that confer resistance to four further antibiotic classes, while pDETAB13 carries putative alcohol tolerance determinants. Both plasmids contain multiple dif modules, which are flanked by pdif sites recognised by XerC/XerD tyrosine recombinases. The ARG-containing dif modules in pDETAB5 are almost identical to those found in pDETAB2, a GR34 plasmid from an unrelated A. baumannii isolated in the same ICU a month prior. Examination of a further 41 complete, publicly available plasmid sequences revealed that the GR13 pangenome consists of just four core but 1086 accessory genes, 123 in the shell and 1063 in the cloud, reflecting substantial capacity for diversification. The GR13 core genome includes genes for replication and partitioning, and for a putative tyrosine recombinase. Accessory segments encode proteins with diverse putative functions, including for metabolism, antibiotic/heavy metal/alcohol tolerance, restriction-modification, an anti-phage system and multiple toxin-antitoxin systems. The movement of dif modules and actions of insertion sequences play an important role in generating diversity in GR13 plasmids. Discrete GR13 plasmid lineages are internationally disseminated and found in multiple Acinetobacter species, which suggests they are important platforms for the accumulation, horizontal transmission and persistence of accessory genes in this genus.

Impact statementAcinetobacter species are particularly well-adapted for persistence in hospital environments where they pose a life-threatening infection risk to the most clinically-vulnerable patients. Plasmids with the potential to transfer multiple antibiotic resistance determinants between Acinetobacter species are therefore concerning, but most are not well-characterised. This work sheds further light on the poorly-understood mobile gene pool associated with Acinetobacter. We show here that GR13 plasmids carry a small set of core genes but have access to a highly diverse set of accessory segments that might provide fitness advantages under certain conditions. The complex evolutionary dynamics of GR13 plasmids appear to be driven by the exchange of dif modules and by the actions of a diverse population of insertion sequences. The novel dif modules characterised here emphasise the broader importance of these elements to the dissemination of accessory genes in Acinetobacter. This study has improved our understanding of the diversity and distribution of dif modules, plasmids that carry them, and how both disseminate in the continuum of Acinetobacter populations that link hospitals and the wider environment.


title: Hemagglutinin stability determines influenza A virus susceptibility to a broad-spectrum fusion inhibitor Arbidol

abstract: Understanding mechanisms of resistance to antiviral inhibitors can reveal nuanced features of targeted viral mechanisms and, in turn, lead to improved strategies for inhibitor design. Arbidol is a broad-spectrum antiviral which binds to and prevents the fusion-associated conformational changes in the trimeric influenza hemagglutinin (HA). The rate-limiting step during HA-mediated membrane fusion is the release of the hydrophobic fusion peptides from a conserved pocket on HA. Here, we investigated how destabilizing or stabilizing mutations in or near the fusion peptide affect viral sensitivity to Arbidol. The degree of sensitivity was proportional to the extent of fusion peptide stability on the pre-fusion HA: stabilized mutants were more sensitive, and destabilized ones resistant to Arbidol. Single-virion membrane fusion experiments for representative Wild Type and mutant viruses demonstrated that resistance is a direct consequence of fusion-peptide destabilization not dependent on reduced Arbidol binding to HA at neutral pH. Our results support the model whereby the probability of individual HAs extending to engage the target membrane is determined by the composite of two critical forces: a  tug on the fusion peptide by the extension of the central coiled-coil on HA, and the key interactions stabilizing fusion peptide in the pre-fusion pocket. Arbidol increases the free-energy penalty for coiled-coil extension, but destabilizing mutations decrease the free-energy cost for fusion peptide release, accounting for the observed resistance. Our findings have broad implications for fusion-inhibitor design, viral mechanisms of resistance, and our basic understanding of HA-mediated membrane fusion.


title: Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species

abstract:
In species with seasonal breeding, male specimens undergo substantial testicular regression during the non-breeding period of the year. However, the molecular mechanisms that control this biological process are largely unknown. Here, we report a transcriptomic analysis on the Iberian mole, Talpa occidentalis, in which the desquamation of live, non-apoptotic germ cells is the major cellular event responsible for testis regression. By comparing testes at different reproductive states (active, regressing and inactive), we demonstrate that the molecular pathways controlling the cell adhesion function in the seminiferous epithelium, such as the MAPK, ERK and TGF-{beta} signalling, are altered during the regression process. In addition, inactive testes display a global upregulation of genes associated with immune response, indicating a selective loss of the "immune privilege" that normally operates in sexually active testes. Interspecies comparative analyses using analogous data from the Mediterranean pine vole, a rodent species where testis regression is controlled by halting meiosis entry, revealed a common gene expression signature in the regressed testes of these two evolutionary distant species. Our study advances in the knowledge of the molecular mechanisms associated to gonadal seasonal breeding, highlighting the existence of a conserved transcriptional program of testis involution across mammalian clades.

Research HighlightsBy comparing the trascriptomes of the testes from males of the iberian mole, Talpa occidentalis (order Eulipotyphla), captured at different stages of the seasonal breeding cycle of this species, we show that two main functions are altered during seasonal testis regression: cell adhesion and immune response. The fact that the same functions alre also altered in the Mediterranean pine vole, Microtus duodecimcostatus (order Rodentia), evidences the existence of a conserved transcriptional program of testis regression across mammalian clades.


title: Myeloid-biased HSC require Semaphorin 4A from the bone marrow niche for self-renewal under stress and life-long persistence

abstract: Tissue stem cells are hierarchically organized. Those that are most primitive serve as key drivers of regenerative response but the signals that selectively preserve their functional integrity are largely unknown. Here, we identify a secreted factor, Semaphorin 4A (Sema4A), as a specific regulator of myeloid-biased hematopoietic stem cells (myHSC), which are positioned at the top of the HSC hierarchy. Lack of Sema4A leads to exaggerated myHSC (but not downstream "balanced" HSC) proliferation after acute inflammatory stress, indicating that Sema4A enforces myHSC quiescence. Strikingly, aged Sema4A knock-out myHSC expand but almost completely lose reconstitution capacity. The effect of Sema4A is non cell-autonomous, since upon transplantation into Sema4A-deficient environment, wild-type myHSC excessively proliferate but fail to engraft long-term. Sema4A constrains inflammatory signaling in myHSC and acts via a surface receptor Plexin-D1. Our data support a model whereby the most primitive tissue stem cells critically rely on a dedicated signal from the niche for self-renewal and life-long persistence.


title: Effect of cannabidiol on apoptosis and cellular interferon and interferon-stimulated gene responses to the SARS-CoV-2 genes ORF8, ORF10 and M protein

abstract:
AimsTo study effects on cellular innate immune responses to novel genes ORF8 and ORF10, and the more conserved Membrane protein (M protein) from the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19, either alone, or in combination with cannabidiol (CBD).

Main MethodsHEK293 cells were transfected with a control plasmid, or plasmids expressing ORF8, ORF10, or M protein, and assayed for cell number and markers of apoptosis at 24 h, and expression of interferon and interferon-stimulated genes at 14 h.

Key findingsA significant reduction in cell number, and increase in early and late apoptosis, was found after 24 h in cells where expression of viral genes was combined with 1-2 M CBD treatment, but not in control-transfected cells treated with CBD, or in cells expressing viral genes but treated only with vehicle. CBD (2 M) augmented expression of IFN{gamma}, IFN{lambda}1 and IFN{lambda}2/3, as well as the 2-5-oligoadenylate synthetase (OAS) family members OAS1, OAS2, OAS3, and OASL, in cells expressing ORF8, ORF10, and M protein. CBD also augmented expression of these genes in control cells not expressing viral genes, without enhancing apoptosis.

SignificanceOur results demonstrate a poor ability of HEK293 cells to respond to SARS-CoV-2 genes alone, but suggest an augmented innate anti-viral response to these genes in the presence of CBD. Furthermore, our results indicate that CBD may prime components of the innate immune system, increasing readiness to respond to viral infection without activating apoptosis, and therefore could be studied for potential in prophylaxis.