title: Insulin exposed endometrial epithelial cells cultured in a microfluidic device alters transcripts involved in translation that may contribute to reduced implantation capacity of the endometrium.

abstract: Obesity is a rapidly growing public health issue among women of reproductive age. It is also associated with decreased reproductive function including implantation failure. Implantation failure can result from a myriad of factors including impaired gametes and endometrial dysfunction. The mechanisms of how obesity-related hyperinsulinaemia disrupts endometrial function and implantation are poorly understood. Our study aims to investigate potential mechanisms by which insulin alters endometrial transcript expression, which may affect endometrial receptivity. Ishikawa cells mimicking human endometrial epithelium were seeded into a microfluidics organ-on-chip device to produce an in vitro endometrium. Syringe pump was attached to the microfluidics device to deliver three varying treatments into Ishikawa cells: 1) media control 2) vehicle control (PBS acidified to pH3 with acetic acid) 3) Insulin (2mg/mL) at a constant flow rate of 1uL/min for 24 hours to mimic secretion in vivo. Three biological replicates were obtained. Insulin-induced transcriptomic response of the in vitro endometrium was quantified via RNA sequencing, and subsequently analysed using DAVID and Webgestalt to identify Gene Ontology (GO) terms and signalling pathways. A Total of 29 transcripts showed differential expression levels across two comparison groups (control v vehicle control; vehicle control v insulin). There were nine transcripts significantly differentially expressed in vehicle control v insulin group (p<0.05). Functional annotation analysis of transcripts altered by insulin (n=9) identified three significantly enriched GO terms: SRP-dependent cotranslational protein targeting to membrane, poly(A) binding, and RNA binding (p<0.05). Over-representation analysis found three significantly enriched signalling pathways relating to insulin-induced transcriptomic response: protein export, glutathione metabolism, and ribosome pathways (p<0.05). Insulin-induced dysregulation of biological functions and pathways highlight potential mechanisms by which high insulin concentrations within maternal circulation may perturb endometrial receptivity.


title: Reciprocity between retrograde signal and putative metalloprotease reconfigures plastidial metabolism and structure

abstract: Reconfiguration of the plastidial proteome in response to environmental inputs is central to readjustment of its metabolic and structural states. This is necessary for the functionality of this metabolic hub, and the maintenance of organismal integrity. This report establishes the role of the plastidial retrograde signaling metabolite, MEcPP, in increasing the abundance of the putative plastidial metalloprotease (VIR3), and the ensuing decline of VIR3 target enzymes, ascorbate peroxidase and glyceraldehyde 3-phophate dehydrogenase B. The decreased abundance of these enzymes is linked to increased levels of their substrates: H2O2, an elicitor of salicylic acid production and stromule formation; and G3P the substrate for MEcPP synthesis. High-light treatment of wild type plants recapitulated the VIR3-associated reconfiguration of the plastidial metabolic and structural states. These results identify a previously unrecognized link between the stress-induced plastidial retrograde signaling metabolite and a putative zinc-binding metalloprotease. Moreover, the data reveal that the reciprocity between these two components, results in the reconfiguration of the metabolic and structural states of the plastid, deemed necessary to maintain cellular integrity and to shape adaptive responses.

category: plant biology


title: Differential requirement for the EDS1 catalytic triad in A. thaliana and N. benthamiana

abstract:
O_LIHeterodimeric complexes incorporating the lipase-like proteins EDS1 with PAD4 or SAG101 are central hubs in plant innate immunity. EDS1 functions encompass signal relay from TIR domain-containing intracellular NLR-type immune receptors (TNLs) towards RPW8-type helper NLRs (RNLs) and, in A. thaliana, bolstering of signaling and resistance mediated by cell-surface pattern recognition receptors (PRRs). Biochemical activities underlying these mechanistic frameworks remain unknown.
C_LIO_LIWe used CRISPR/Cas-generated mutant lines and agroinfiltration-based complementation assays to interrogate functions of EDS1 complexes in N. benthamiana.
C_LIO_LIWe do not detect impaired PRR signaling in N. benthamiana lines deficient in EDS1 complexes or RNLs. Intriguingly, mutations within the catalytic triad of Solanaceae EDS1 can abolish or enhance TNL immunity in N. benthamiana. Furthermore, nuclear EDS1 accumulation is sufficient for N. benthamiana TNL (Roq1) immunity.
C_LIO_LIReinforcing PRR signaling in Arabidopsis might be a derived function of the TNL/EDS1 immune sector. Dependency of Solanaceae but not A. thaliana EDS1 on catalytic triad residues raises the possibility that a TNL-derived small molecule binds to the Solanaceae EDS1 lipase-like domain, and that EDS1 lipase-like domain pocket contributions to TNL immune responses vary between lineages. Whether and how nuclear EDS1 activity connects to membrane pore-forming RNLs remains unknown.
C_LI


title: Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

abstract:
The occurrence of horizontal gene transfer (HGT) in Eukarya is increasingly gaining recognition. Nuclear-to-nuclear jump of DNA between plant species at high phylogenetic distance and devoid of intimate association (e.g., parasitism) is still scarcely reported. Within eukaryotes, components of ribosomal DNA (rDNA) multigene family have been found to be horizontally transferred in protists, fungi and grasses. However, in neither case HGT occurred between phylogenetic families, nor the transferred rDNA remained tandemly arrayed and transcriptionally active in the recipient organism. This study aimed to characterize an alien eudicot-type of 45S nuclear rDNA, assumingly transferred horizontally to the genome of monocot European Erythronium (Liliaceae). Genome skimming coupled by PacBio HiFi sequencing of a BAC clone were applied to determine DNA sequence of the alien rDNA. A clear phylogenetic signal traced the origin of the alien rDNA of Erythronium back to the Argentea clade of Potentilla (Rosaceae) and deemed the transfer to have occurred in the common ancestor of E. dens-canis and E. caucasicum. Though being discontinuous, transferred rDNA preserved its general tandemly arrayed feature in the host organism. Southern blotting, molecular cytogenetics, and sequencing of a BAC clone derived from flow-sorted nuclei indicated integration of the alien rDNA into the recipients nuclear genome. Unprecedently, dicot-type alien rDNA was found to be transcribed in the monocot Erythronium albeit much less efficiently than the native counterpart. This study adds a new example to the growing list of naturally transgenic plants while holding the scientific community continually in suspense about the mode of DNA transfer.

Significance StatementRibosomal DNA is an essential component of all cellular genomes. In plants, accidental movement of rDNA via horizontal gene transfer has only been reported in sexually incompatible grasses (monocots) where it involved non-functional rDNA units. In this study, we propose that evolutionary trajectories of eudicots and monocots were bypassed by the jump of rDNA from a Potentilla species (Rosaceae) to a common ancestor of Erythronium dens-canis and E. caucasicum (Liliaceae). The alien eudicot-type rDNA appeared relatively well conserved in the examined host Erythronium genome, being able to be expressed while preserving its general tandemly repeated feature, evidences that have no match in earlier literature.


title: Effect of Light Conditions on In Vitro Adventitious Organogenesis of Cucumber Cultivars

abstract: The response on callus and shoot formation under different light incubation conditions was evaluated in cucumber (Cucumis sativus L.). Four-day-old cotyledon explants from the inbred line  Wisconsin 2843 and the commercial cultivars  Marketer and  Negrito were employed. A four-week culture was conducted on MS-derived shoot induction medium containing 0.5 mg L-1 IAA and 2.5 mg L-1 BAP, under an 8-h dark/ 16-h light regime, or by a one- or two-week dark pre-incubation followed by the same photoperiod. Significant differences were obtained for the regeneration of shoots in all cultivars. The response in both frequency and number of shoots under continuous photoperiod was at least 3-6 fold higher than with dark pre-incubation. The highest genotypes response was obtained by  Negrito and  Marketer with identical values. All explants formed callus, and in two of the three cultivars, the response on callus extension was not significantly affected by incubation conditions. The results clearly show that shoot induction under continuous photoperiod regime was beneficial for adventitious shoot regeneration in cucumber.


title: Period Doubling Bifurcations in a Forced Cell-Free Genetic Oscillator

abstract: Complex non-linear dynamics such as period doubling and chaos have been previously found in computational models of the oscillatory gene networks of biological circadian clocks, but their experimental study is difficult. Here, we present experimental evidence of period doubling in a forced synthetic genetic oscillator operated in a cell-free gene expression system. To this end, an oscillatory negative feedback gene circuit is established in a microfluidic reactor, which allows continuous operation of the system over extended periods of time. We first thoroughly characterize the unperturbed oscillator and find good agreement with a four-species ODE model of the system. Guided by simulations, microfluidics is then used to periodically perturb the system by modulating the concentration of one of the oscillator components with a given amplitude and frequency. When the ratio of the external  zeitgeber period and the intrinisic period is close to 1, we experimentally find period doubling and quadrupling in the oscillator dynamics, whereas for longer zeitgeber periods, we find stable entrainment. Our theoretical model suggests favorable conditions for which the oscillator can be utilized as an externally synchronized clock, but also demonstrates that related systems could, in principle, display chaotic dynamics.

category: synthetic biology


title: The MyLo CRISPR-Cas9 Toolkit: A Markerless Yeast Localization and Overexpression CRISPR-Cas9 Toolkit

abstract: The genetic tractability of the yeast Saccharomyces cerevisiae has made it a key model organism for basic research and a target for metabolic engineering. To streamline the introduction of tagged genes and compartmental markers with powerful CRISPR-Cas9-based genome editing tools we constructed a Markerless Yeast Localization and Overexpression (MyLO) CRISPR-Cas9 toolkit with three components: (i) a set of optimized S. pyogenes Cas9-guide RNA (gRNA) expression vectors with five selectable markers and the option to either pre-clone or co-transform the gRNAs; (ii) vectors for the one-step construction of integration cassettes expressing an untagged or GFP/RFP/HA-tagged gene of interest at one of three levels, supporting localization and overexpression studies; and (iii) integration cassettes containing moderately expressed GFP- or RFP-tagged compartmental markers for colocalization experiments. These components allow rapid, high efficiency genomic integrations and modifications with only transient selection for the Cas9 vector, resulting in markerless transformations. To demonstrate the ease of use, we applied our complete set of compartmental markers to co-label all target subcellular compartments with GFP and RFP. Thus, the MyLO toolkit packages CRISPR-Cas9 technology into a flexible, optimized bundle to simplify yeast research.


title: Intrinsic instability of the dysbiotic microbiome revealed through dynamical systems inference at scale

abstract: Despite the importance of microbial dysbiosis in human disease, the phenomenon remains poorly understood. We provide the first comprehensive and predictive model of dysbiosis at ecosystem-scale, leveraging our new machine learning method for efficiently inferring compact and interpretable dynamical systems models. Coupling this approach with the most densely temporally sampled interventional study of the microbiome to date, using microbiota from healthy and dysbiotic human donors that we transplanted into mice subjected to antibiotic and dietary interventions, we demonstrate superior predictive performance of our method over state-of-the-art techniques. Moreover, we demonstrate that our approach uncovers intrinsic dynamical properties of dysbiosis driven by destabilizing competitive cycles, in contrast to stabilizing interaction chains in the healthy microbiome, which have implications for restoration of the microbiome to treat disease.

category: systems biology


title: Non-random organization of flux control mechanisms in yeast central metabolic pathways

abstract: Metabolic flux can be regulated by a variety of different mechanisms, but the organization of these mechanisms within the metabolic network has remained unknown. Here we test the hypothesis that flux control mechanisms are not distributed randomly in the metabolic network, but rather organized according to pathway. Combining proteomics, phosphoproteomics, and metabolic modeling, we report the largest collection of flux-enzyme-phosphoenzyme relationships to date in Saccharomyces cerevisiae. In support of the hypothesis, we show that (i) amino acid metabolic pathways are predominantly regulated by enzyme abundance stemming from transcriptional regulation; (ii) upper glycolysis and associated pathways, by inactivating enzyme phosphorylation; (iii) lower glycolysis and associated pathways, by activating enzyme phosphorylation; and (iv) glycolipid/glycophospholipid pathways, by a combination of enzyme phosphorylation and metabolic compartmentalization. We delineate the evolutionary history for the observed organization of flux control mechanisms in yeast central metabolic pathways, furthering our understanding of the regulation of metabolism and its evolution.


title: Neural mechanism of experience-dependent sensory gain control in C. elegans

abstract: Animals sensory systems adjust their responsiveness to environmental stimuli that vary greatly in their intensity. Here we report the neural mechanism of experience-dependent sensory adjustment, especially gain control, in the ASH nociceptive neurons in Caenorhabditis elegans. Using calcium imaging under gradual changes in stimulus intensity, we find that the ASH neurons of naive animals respond to concentration increases in a repulsive odor 2-nonanone regardless of the magnitude of the concentration increase. However, after preexposure to the odor, the ASH neurons exhibit significantly weak responses to a small gradual increase in odor concentration while their responses to a large gradual increase remain strong. Thus, preexposure changes the slope of stimulus-response relationships (i.e., gain control). Behavioral analysis suggests that this gain control contributes to the preexposure-dependent enhancement of odor avoidance behavior. Mathematical analysis reveals that the ASH response consists of fast and slow components, and that the fast component is specifically suppressed by preexposure. In addition, genetic analysis suggests that G protein signaling is required for the fast component. Thus, our integrative study demonstrates how prior experience dynamically modulates stimulus-response relationships in sensory neurons, eventually leading to adaptive modulation of behavior.

category: neuroscience


title: Metabolic alterations in a Drosophila model of Parkinson's disease based on DJ-1 deficiency

abstract: Parkinsons disease (PD) is the second most common neurodegenerative disorder whose physiopathology is still unclear. Besides, it is urgent to discover new biomarkers and therapeutic targets to facilitate its diagnosis and treatment. Previous studies performed in PD models and samples from PD patients already demonstrated that metabolic alterations were associated with this disease. In this context, the aim of this study is to give a better understanding of metabolic disturbances underlying PD pathogenesis. To achieve this goal, we used a Drosophila PD model based on inactivation of the DJ-1{beta} gene (ortholog of human DJ-1). Metabolomic analyses were performed in 1-day-old and 15-day-old DJ-1{beta} mutants and control flies using 1H nuclear magnetic resonance spectroscopy, combined with expression and enzymatic activity assays of proteins implicated in altered pathways. Our results showed that PD model flies exhibit protein metabolism alterations, a shift from tricarboxylic acid cycle to glycolytic pathway to obtain ATP, together with an increase in the expression of some urea cycle enzymes. Thus, these metabolic changes could be contributing to PD pathogenesis and might constitute possible therapeutic targets and/or biomarkers for this disease.


title: Leptomeningeal Enhancement in Multiple Sclerosis and Other Neurological Diseases: A Systematic Review and Meta-Analysis

abstract:
BackgroundThe lack of systematic evidence on leptomeningeal enhancement (LME) on MRI in neurological diseases, including multiple sclerosis (MS), hampers its interpretation in clinical routine and research settings.

PurposeTo perform a systematic review and meta-analysis of MRI LME in MS and other neurological diseases.

Materials and MethodsIn a comprehensive literature search in Medline, Scopus, and Embase, out of 2292 publications, 459 records assessing LME in neurological diseases were eligible for qualitative synthesis. Of these, 135 were included in a random-effects model meta-analysis with subgroup analyses for MS.

ResultsOf eligible publications, 161 investigated LME in neoplastic neurological (n=2392), 91 in neuroinfectious (n=1890), and 75 in primary neuroinflammatory diseases (n=4038). The LME-proportions for these disease classes were 0.47 [95%-CI: 0.37-0.57], 0.59 [95%-CI: 0.47-0.69], and 0.26 [95%-CI: 0.20-0.35], respectively. In a subgroup analysis comprising 1605 MS cases, LME proportion was 0.30 [95%-CI 0.21-0.42] with lower proportions in relapsing-remitting (0.19 [95%-CI 0.13-0.27]) compared to progressive MS (0.39 [95%-CI 0.30-0.49], p=0.002) and higher proportions in studies imaging at 7T (0.79 [95%-CI 0.64-0.89]) compared to lower field strengths (0.21 [95%-CI 0.15-0.29], p<0.001). LME in MS was associated with longer disease duration (mean difference 2.2 years [95%-CI 0.2-4.2], p=0.03), higher Expanded Disability Status Scale (mean difference 0.6 points [95%-CI 0.2-1.0], p=0.006), higher T1 (mean difference 1.6ml [95%-CI 0.1-3.0], p=0.04) and T2 lesion load (mean difference 5.9ml [95%-CI 3.2-8.6], p<0.001), and lower cortical volume (mean difference -21.3ml [95%-CI -34.7--7.9], p=0.002).

ConclusionsOur study provides high-grade evidence for the substantial presence of LME in MS and a comprehensive panel of other neurological diseases. Our data could facilitate differential diagnosis of LME in clinical settings. Additionally, our meta-analysis corroborates that LME is associated with key clinical and imaging features of MS.

PROSPERO No: CRD42021235026.

Summary statementOur systematic review and meta-analysis synthesize leptomeningeal enhancement proportions across a comprehensive panel of neurological diseases, including multiple sclerosis, and assesses its prognostic value in multiple sclerosis.

Summary dataO_LILeptomeningeal enhancement (LME) is a nonspecific imaging feature present across many neurological disorders, including neoplasm, infection, and primary neuroinflammation.
C_LIO_LIThe presence of LME is associated with worse clinical and imaging outcomes in multiple sclerosis, justifying its ascertainment in clinical practice.
C_LIO_LINeuroinflammatory animal models can be used to further investigate the pathophysiology of LME, including its pathological tissue signature and/or its association with cortical pathology.
C_LI


title: A mean-field toolbox for spiking neuronal network model analysis

abstract: Mean-field theory of spiking neuronal networks has led to numerous advances in our analytical and intuitive understanding of the dynamics of neuronal network models during the past decades. But, the elaborate nature of many of the developed methods, as well as the difficulty of implementing them, may limit the wider neuroscientific community from taking maximal advantage of these tools. In order to make them more accessible, we implemented an extensible, easy-to-use open-source Python toolbox that collects a variety of mean-field methods for the widely used leaky integrate-and-fire neuron model. The Neuronal Network Mean-field Toolbox (NNMT) in its current state allows for estimating properties of large neuronal networks, such as firing rates, power spectra, and dynamical stability in mean-field and linear response approximation, without running simulations on high performance systems. In this article we describe how the toolbox is implemented, show how it is used to calculate neuronal network properties, and discuss different use-cases, such as extraction of network mechanisms, parameter space exploration, or hybrid modeling approaches. Although the initial version of the toolbox focuses on methods that are close to our own past and present research, its structure is designed to be open and extensible. It aims to provide a platform for collecting analytical methods for neuronal network model analysis and we discuss how interested scientists can share their own methods via this platform.


title: Evolutionary learning in the brain by heterosynaptic plasticity

abstract: How the brain modifies synapses to improve the performance of complicated networks remains one of the biggest mysteries in neuroscience. Existing proposals, which suppose continuous-valued synaptic weights changed according to gradient clues informed by pre- and post-synaptic activities, lack sufficient experimental support. Based on the heterosynaptic plasticity between hippocampal or cortical pyramidal neurons mediated by diffusive nitric oxide and astrocyte calcium wave as well as the flexible dendritic gating of somatostatin interneurons, here we propose that the brain learns by an evolutionary algorithm (EA), which trains biologically plausible binary-weight networks in a gradient-free manner. Our EA provides a framework to re-interpret the biological functions of dopamine, meta-plasticity of dendritic spines, memory replay, and the cooperative plasticity between the synapses within a dendritic neighborhood from a new and coherent aspect. Our EA can train neural networks to exhibit dynamics analogous to brain dynamics in cognitive tasks. Our EA manifests its broad applicability to train spiking or analog neural networks with recurrent or feedforward architecture. Our EA also demonstrates its powerful capability to train deep networks with biologically plausible binary weights in MNIST classification and Atari-game playing tasks up to performance comparable with continuous-weight networks trained by gradient-based methods. Overall, our work leads to a paradigmatically fresh understanding of the brain learning mechanism.


title: Rostral and caudal BLA engage distinct circuits in the prelimbic and infralimbic PFC

abstract: Connections from the basolateral amygdala (BLA) to medial prefrontal cortex (PFC) regulate memory and emotion and become disrupted in neuropsychiatric disorders. We hypothesized that the diverse roles attributed to interactions between the BLA and PFC reflect multiple circuits nested within a wider network. To assess these circuits, we first used anatomy to show that the rostral BLA (rBLA) and caudal BLA (cBLA) differentially project to prelimbic (PL) and infralimbic (IL) subregions of the PFC, respectively. We then combined in vivo silicon probe recordings and optogenetics to show that rBLA primarily engages PL, whereas cBLA mainly influences IL. Using ex vivo whole-cell recordings and optogenetics, we then assessed which neuronal subtypes are targeted, showing that rBLA preferentially drives layer 2 (L2) cortico-amygdalar (CA) neurons in PL, whereas cBLA drives layer 5 (L5) pyramidal tract (PT) cells in IL. Lastly, we used soma-tagged optogenetics to explore the local circuits linking superficial and deep layers of PL, showing how rBLA can also impact L5 PT cells. Together, our findings delineate how subregions of the BLA target distinct networks within the PFC to have different influence on prefrontal output.


title: Pseudomonas aeruginosa utilises host-derived polyamines to facilitate antimicrobial tolerance

abstract: Pseudomonas aeruginosa undergoes diversification during infection of the cystic fibrosis (CF) lung. Understanding these changes requires model systems that capture the complexity of the CF lung environment. We previously identified loss-of-function mutations in the two-component regulatory system sensor kinase gene pmrB, in P. aeruginosa from CF and from experimental infection of mice. Here, we demonstrate that whilst such mutations lower in vitro MICs for multiple antimicrobial classes, this is not reflected in increased antibiotic susceptibility in vivo. Loss of PmrB impairs aminoarabinose modification of lipopolysaccharide, increasing the negative charge of the outer membrane and promoting uptake of cationic antimicrobials. However, in vivo, this can be offset by increased membrane binding of other positively charged molecules present in lungs. The polyamine spermidine readily coats the surface of PmrB-deficient P. aeruginosa, reducing susceptibility to antibiotics that rely on charge differences to bind the outer membrane and increasing biofilm formation. Spermidine is elevated in lungs during P. aeruginosa infection in mice and during episodes of antimicrobial treatment in people with CF. These findings highlight the need to study antimicrobial resistance under clinically relevant environmental conditions. Microbial mutations carrying fitness costs in vitro may be advantageous during infection, where host resources can be utilised.

category: microbiology


title: TRPM4 is required for calcium oscillations downstream from the stretch-activated TRPV4 channel

abstract: Transduction of mechanical information is influenced by physical, chemical and thermal cues but the molecular mechanisms through which transducer activation shapes temporal signaling remain underexplored. In the present study, electrophysiology, histochemistry and functional imaging were combined with gene silencing and heterologous expression to gain insight into calcium signaling downstream from TRPV4 (Transient Receptor Potential Vanilloid 4), a stretch-activated nonselective cation channel. We show that trabecular meshwork (TM) cells, which employ mechanotransduction to actively regulate intraocular pressure, respond to the TRPV4 agonist GSK1016790A with fluctuations in intracellular Ca2+ concentration ([Ca2+]i) and an increase in [Na+]i. ([Ca2+]i oscillations coincided with a monovalent cation current that was suppressed by BAPTA, Ruthenium Red and 9-phenanthrol, an inhibitor of TRPM4 (Transient Receptor Potential Melastatin 4) channels. Accordingly, TM cells expressed TRPM4 mRNA, protein at the expected 130-150 kDa and showed punctate TRPM4 immunoreactivity at the membrane surface. Genetic silencing of TRPM4 antagonized TRPV4-evoked oscillatory signaling whereas TRPV4 and TRPM4 co-expression in HEK-293 cells reconstituted the oscillations. Membrane potential recordings indicated that TRPM4-dependent oscillations required release of Ca2+ from internal stores. 9-phenanthrol did not affect the outflow facility in mouse eyes. Collectively, our results show that TRPV4 activity initiates dynamic calcium signaling in TM cells by stimulating TRPM4 channels and intracellular Ca2+ release. These findings provide insight into the complexity of membrane-cytosolic interactions during TRPV4 signaling and may foster strategies to promote homeostatic regulation and counter pathological remodeling within the conventional outflow pathway of the mammalian eye.

category: cell biology


title: Single-cell resolution unravels spatial alterations in metabolism, transcriptome and epigenome of ageing liver

abstract: Epigenetic ageing clocks have revealed that tissues within an organism can age with different velocity. However, it has not been explored whether cells of one type experience different ageing trajectories within a tissue depending on their location. Here, we employed lipidomics, spatial transcriptomics and single-cell ATAC-seq in conjunction with available single-cell RNA-seq data to address how cells in the murine liver are affected by age-related changes of the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. Particularly periportal hepatocytes were characterized by decreased mitochondrial function and strong alterations in the epigenetic landscape, while pericentral hepatocytes - despite accumulation of large lipid droplets - did not show apparent functional differences. In general, chromatin alterations did not correlate well with transcriptional changes, hinting at post-transcriptional processes that shape gene expression during ageing. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.


title: Spatial effects in parasite induced marine diseases of immobile hosts

abstract: Marine infectious diseases are more prevalent in recent times due to climate change and other anthropogenic pressures, posing a substantial threat to marine ecosystems and the conservation of their biodiversity. An important subset of marine organisms are sessile, for which the most common mechanism for disease transmission is direct contact with waterborne parasites. Only recently, some deterministic compartmental models have been proposed to describe this kind of epidemics, being these models based on non-spatial descriptions where space is homogenised and parasite mobility is not explicitly accounted for. However, in realistic situations, epidemic transmission is conditioned by the spatial distribution of hosts and the parasites mobility patterns. Thus, the interplay between these factors is expected to have a crucial effect in the evolution of the epidemic, so calling for a explicit description of space. In this work we develop a spatially-explicit individual-based model to study disease transmission by waterborne parasites in sessile marine populations. We investigate the impact of spatial disease transmission, performing extensive numerical simulations and analytical approximations. Specifically, the effects of parasite mobility into the epidemic threshold and the temporal evolution of the epidemic are assessed. We show that larger values of pathogen mobility have two main implications: more severe epidemics, as the number of infections increases, and shorter time-scales to extinction. Moreover, an analytical expression for the basic reproduction number of the spatial model, [Formula], is derived as function of the non-spatial counterpart, R0, which characterises a transition between a disease-free and a propagation phase, in which the disease propagates over a large fraction of the system. This allows to determine a phase diagram for the epidemic model as function of the parasite mobility and the basic reproduction number of the non-spatial model.

category: ecology


title: Using Piecewise Regression to Identify Biological Phenomena in Biotelemetry Datasets

abstract: Technological advances in the field of animal tracking have greatly expanded the potential to remotely monitor animals, opening the door to exploring how animals shift their behavior over time or respond to external stimuli. A wide variety of animal-borne sensors can provide information on an animals location, movement characteristics, external environmental conditions, and internal physiological status. Here, we demonstrate how piecewise regression can be used to identify the presence and timing of potential shifts in a variety of biological responses using GPS telemetry and other biologging data streams. Different biological latent states can be inferred by partitioning a time-series into multiple segments based on changes in modeled responses (e.g., their mean, variance, trend, degree of autocorrelation) and specifying a unique model structure for each interval. We provide five example applications highlighting a variety of taxonomic species, data streams, timescales, and biological phenomena. These examples include a short-term behavioral response (flee and return) by a trumpeter swan (Cygnus buccinator) immediately following a GPS collar deployment; remote identification of parturition based on movements by a pregnant moose (Alces alces); a physiological response (spike in heart-rate) in a black bear (Ursus americanus) to a stressful stimulus (presence of a drone); a mortality event of a trumpeter swan signaled by changes in collar temperature and Overall Dynamic Body Acceleration; and an unsupervised method for identifying the onset, return, duration, and staging use of sandhill crane (Antigone canadensis) migration. We implement analyses using the mcp package in R, which provides functionality for specifying and fitting a wide variety of user-defined model structures in a Bayesian framework and methods for assessing and comparing models using information criterion and cross-validation measures. This approach uses simple modeling approaches that are accessible to a wide audience and is a straightforward means of assessing a variety of biologically relevant changes in animal behavior.


title: Exceptions to the rule: Why does resistance evolution not undermine antibiotic therapy in all bacterial infections?

abstract: Antibiotic resistance poses one of the greatest public health challenges of the 21st century. Yet not all pathogens are equally affected by resistance evolution. Why? Here we examine what underlies variation in antibiotic resistance across human bacterial pathogens and the drugs used to treat them. We document the observed prevalence of antibiotic resistance for  pathogen x drug combinations across 57 different human bacterial pathogens and 53 antibiotics from 15 drug classes used to treat them. Using AIC-based model selection we analyze 14 different traits of bacteria and antibiotics that are believed to be important in resistance evolution. Using these data, we identify the traits that best explain observed variation in resistance evolution. Our results show that nosocomial pathogens and indirectly transmitted pathogens are significantly associated with increased prevalence of resistance whereas zoonotic pathogens, specifically those with wild animal reservoirs, are associated with reduced prevalence of resistance. We found partial support for associations between drug resistance and gram classification, human microbiome reservoirs, horizontal gene transfer, and documented human-to human transfer. Global drug use, time since drug discovery, mechanism of drug action, and environmental reservoirs did not emerge as statistically robust predictors of drug resistance in our analyses. To the best of our knowledge this work is the first systematic analysis of resistance across such a wide range of human bacterial pathogens, encompassing the vast majority of common bacterial pathogens. Insights from our study may help guide public health policies and future studies on resistance control.

category: evolutionary biology


title: The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass

abstract:
Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and local adaptation in contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test (Fraser 2020) based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with Quantitative Trait Locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of local adaptation among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seeds traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits.

Impact SummarySeed size and dormancy are key functional traits with important recruitment and fitness consequences. Theory suggests tradeoffs and plasticity in offspring quantity and quality are important in seed evolution. The genetics of seed size and dormancy traits have been studied extensively, but these studies are mostly limited to model system or domesticated crops. We also know very little about the genetic architecture and evolution of seed-based life history traits especially considering adaptation to xeric and mesic habitats. Here, we explored the genetic basis of trade-offs between seed size and dormancy in a C4 perennial grass, Panicum hallii, endemic to North America. We planted seeds of recombinant inbred lines from a cross between a xeric and mesic ecotype of P.hallii and mapped quantitative trait (QTL) loci for seed size, dormancy and seedling vigor traits. We detected a genetic basis of trade-offs between seed size and dormancy, suggesting that natural selection strongly favored specific trait combinations in ecotype formation. We further explored the role of seed size variation on seedling and adult recruitment in contrasting habitats. Our data showed that seed size was under strong selection through recruitment. Overall, our results demonstrate that adaptive differentiation for seed size and early life stages are important factors in adaptation to contrasting habitats.


title: COEVOLUTION WITH SPATIALLY STRUCTURED RICE LANDRACES MAINTAINS MULTIPLE GENERALIST LINEAGES IN THE RICE BLAST PATHOGEN

abstract: Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the eco-evolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Magnaporthe oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life histories. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.


title: Enabling inference for context-dependent models of mutation by bounding the propagation of dependency

abstract: Although the rates at which positions in the genome mutate are known to depend not only on the nucleotide to be mutated, but also on neighboring nucleotides, it remains challenging to do phylogenetic inference using models of context-dependent mutation. In these models, the effects of one mutation may in principle propagate to faraway locations, making it difficult to compute exact likelihoods. This paper shows how to use bounds on the propagation of dependency to compute likelihoods of mutation of a given segment of genome by marginalizing over sufficiently long flanking sequence. This can be used for maximum likelihood or Bayesian inference. Protocols examining residuals and iterative model refinement are also discussed. Tools for efficiently working with these models are provided in an R package, that could be used in other applications. The method is used to examine context dependence of mutations since the common ancestor of humans and chimpanzee.


title: Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species

abstract: Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (A. officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (~1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ~70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.

category: genomics


title: Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies

abstract: The quality and traceability of microbial genomics data in public databases is deteriorating as they rapidly expand and struggle to cope with data curation challenges. While the availability of public genomic data has become essential for modern life sciences research, the curation of the data is a growing area of concern that has significant real-world impacts on public health epidemiology, drug discovery, and environmental biosurveillance research1-6. While public microbial genome databases such as NCBIs RefSeq database leverage the scalability of crowd sourcing for growth, they do not require data provenance to the original biological source materials or accurate descriptions of how the data was produced7. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full data provenance. Over 98% of these ATCC Standard Reference Genomes (ASRGs) are superior to assemblies for comparable strains found in NCBIs RefSeq database. Comparative genomics analysis revealed significant issues in RefSeq bacterial genome assemblies related to genome completeness, mutations, structural differences, metadata errors, and gaps in traceability to the original biological source materials. For example, nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. We suggest there is an intrinsic connection between the quality of genomic metadata, the traceability of the data, and the methods used to produce them with the quality of the resulting genome assemblies themselves. Our results highlight common problems with " reference genomes" and underscore the importance of data provenance for precision science and reproducibility. These gaps in metadata accuracy and data provenance represent an " elephant in the room" for microbial genomics research, but addressing these issues would require raising the level of accountability for data depositors and our own expectations of data quality.


title: Genetic diversity patterns of human ethnic groups as inferred from the 1000 genomes

abstract: Human genetic diversity remains to be better understood. We here analyzed data from the 1000 Genomes Project and defined group specific fixed alleles (GSFAs) as those that are likely fixed in one ethnic group but non-fixed in at least one other group. The fraction of derived alleles in GSFAs indicates relative distance to apes because such alleles are absent in apes. Our results show that different groups differed in GSFA numbers consistent with known genetic diversity patterns, but also differed in the fraction of derived alleles in GSFAs throughout the entire genome, with East Asians having the largest fraction, followed by South Asians, Europeans, Native Americans, and Africans. Fast evolving sites such as intergenic regions were enriched with derived alleles and showed greater differences in GSFA numbers between East Asians and Africans. Furthermore, GSFAs in East Asians are mostly not fixed in other groups especially Africans, which was particularly more pronounced for fast evolving noncoding variants, while GSFAs in Africans are mostly also fixed in East Asians. Finally, variants that are likely non-neutral such as those leading to stop codon gain/loss and splice donor/acceptor gain/loss showed patterns similar to those of fast-evolving noncoding variants. These results can be accounted for by the maximum genetic diversity theory but not by the neutral theory or its inference that Eurasians suffered bottlenecks, and have implications for better management of group specific genetic diseases.


title: Automated identification of chicken distress vocalisations using deep learning models

abstract: The annual global production of chickens exceeds 25 billion birds, and they are often housed in very large groups, numbering thousands. Distress calling triggered by various sources of stress has been suggested as an "iceberg indicator" of chicken welfare. However, to date, the identification of distress calls largely relies on manual annotations, which is very labour-intensive and time-consuming. Thus, a novel light-VGG11 was developed to automatically identify chicken distress calls using recordings (3,363 distress calls and 1,973 natural barn sounds) collected on intensive chicken farms. The light-VGG11 was modified from VGG11 with a significantly smaller size in parameters (9.3 million vs 128 million) and 55.88% faster detection speed while displaying comparable performance, i.e., precision (94.58%), recall (94.89%), F1-score (94.73%), and accuracy (95.07%), therefore more useful for model deployment in practice. To further improve the light-VGG11s performance, we investigated the impacts of different data augmentation techniques (i.e., time masking, frequency masking, mixed spectrograms of the same class, and Gaussian noise) and found that they could improve distress calls detection by up to 1.52%. In terms of precision livestock farming, our research opens new opportunities for developing technologies used to monitor the output of distress calls in large, commercial chicken flocks.

category: animal behavior and cognition


title: Timescale of degradation-driven protein level fluctuation in the yeast Saccharomyces cerevisiae

abstract: Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable control of physiological outcomes in biotechnology applications. Previous studies have shown that controlling RNA transcription achieves perturbations in protein levels over a timescale of several hours. Here, we demonstrate the potential for harnessing the protein degradation machinery to achieve robust, rapid control of a specific protein level in the yeast Saccharomyces cerevisiae. Using a light-driven protein degradation machinery and red fluorescent proteins as reporters, we show that under constant transcriptional induction, repeated triangular fluctuations in protein levels can be generated by controlling the protein degradation rate. Consistent with previous results using transcriptional control, we observed a continuous decrease in the magnitude of fluctuations as the modulation frequency increased, indicating low-pass filtering of input perturbation. However, compared to hour-scale fluctuations observed using transcriptional control, modulating the protein degradation rate enabled five to ten minute-scale fluctuations. Our study demonstrates the potential for repeated control of protein levels by controlling protein degradation rate, at timescales much shorter than that achieved by transcriptional control.

category: bioengineering


title: Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

abstract:
O_LIThe availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection, and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists.
C_LIO_LIWe implemented polymorphism-aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome-wide data. Simultaneously, PoMos can estimate mutation and selection biases.
C_LIO_LIWe have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well-supported species tree, we found a mutation bias favoring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC-biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation.
C_LIO_LIPoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes -- e.g., relaxed clock and divergence time estimation -- offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification.
C_LI

category: bioinformatics


title: Short senolytic or senostatic interventions rescue progression of radiation-induced frailty and premature ageing in mice

abstract:
Cancer survivors suffer from progressive frailty, multimorbidity and premature morbidity. We hypothesize that therapy-induced senescence and senescence progression via bystander effects is a significant cause of this premature ageing phenotype. Accordingly, the study addresses the question whether a short anti-senescence intervention is able to block progression of radiation-induced frailty and disability in a pre-clinical setting.

Male mice were sub-lethally irradiated at 5 months of age and treated (or not) with either a senolytic drug (Navitoclax or dasatinib + quercetin) for 10 days or with the senostatic metformin for 10 weeks. Follow up was for one year. Treatments commencing within a month after irradiation effectively reduced frailty progression (p<0.05) and improved muscle (p<0.01) and liver (p<0.05) function as well as short-term memory (p<0.05) until advanced age with no need for repeated interventions. Senolytic interventions that started late, after radiation-induced premature frailty was manifest, still had beneficial effects on frailty (p<0.05) and short-term memory (p<0.05). Metformin was similarly effective as senolytics. At therapeutically achievable concentrations metformin acted as a senostatic neither via inhibition of mitochondrial complex I, nor via improvement of mitophagy or mitochondrial function, but by reducing non-mitochondrial ROS production via NOX4 inhibition in senescent cells.

Our study suggests that the progression of adverse long-term health and quality-of-life effects of radiation exposure, as experienced by cancer survivors, might be rescued by short-term adjuvant anti-senescence interventions.

category: cancer biology


title: A simple and direct method to define clonal selection in somatic mosaicism

abstract:
Dividing somatic stem cells acquire DNA changes marking different clones. With time, clones can become large, either stochastically through neutral drift, or increased fitness and consequent selection. We present a simple, direct, and general approach that distinguishes between these two processes in normal somatic tissue in individuals. The method relies on single time point whole genome sequencing to study somatic mosaicism as tissues age. Using this method, we show that in human clonal hemopoiesis (CH), clones with CH driver mutations, that comprise a median of 24% of hematopoiesis originate decades before they are detected. They expand, through selection by a median of 26% per year. Overall, there is a 3-fold increased rate of stem cell division and an 8.6-fold increase in active long-term stem cells.

One sentence summaryWe present an approach to distinguish genetic drift from selection, as subclones arise in somatic tissues, in individuals.


title: A mixture of innate cryoprotectants is key for cryopreservation of a drosophilid fly larva.

abstract:
Insects that naturally tolerate internal freezing produce complex mixtures of multiple cryoprotectants (CPs). Better knowledge on composition of these mixtures, and on mechanisms of how the individual CPs interact, could inspire development of laboratory CP formulations optimized for cryopreservation of cells and other biological material. Here we identify and quantify (using high resolution mass spectrometry) a range of putative CPs in larval tissues of a subarctic fly, Chymomyza costata that survives long-term cryopreservation in liquid nitrogen. The CPs (proline, trehalose, glutamine, asparagine, glycine betaine, glycerophosphoethanolamine, glycerophosphocholine, and sarcosine) accumulate in hemolymph in a ratio of 313:108:55:26:6:4:3:0.5 mmol.L-1. Using calorimetry, we show that the artificial mixtures, mimicking the concentrations of major CPs in hemolymph of freeze-tolerant larvae, suppress the melting point of water and significantly reduce the ice fraction. We demonstrate in a bioassay that mixtures of CPs administered through the diet act synergistically rather than additively to enable cryopreservation of otherwise freeze-sensitive larvae. Using MALDI-MSI, we show that during slow extracellular freezing trehalose becomes concentrated in partially dehydrated hemolymph where it stimulates transition to the amorphous glass phase. In contrast, proline moves to the boundary between extracellular ice and dehydrated hemolymph and tissues where it likely forms a layer of dense viscoelastic liquid. We propose that amorphous glass and viscoelastic liquids may protect macromolecules and cells from thermomechanical shocks associated with freezing and transfer into and out of liquid nitrogen.

Summary statementThe composition of natural cryoprotectant mixture of the extremely freeze-tolerant insect is revealed. Components of the mixture work in synergy and behave differently during organismal freezing and cryopreservation.

category: physiology


title: A mixture of innate cryoprotectants is key for freeze tolerance and cryopreservation of a drosophilid fly larva.


title: Loss of Activity-Induced Mitochondrial ATP Production Underlies the Synaptic Defects in a Drosophila model of ALS

abstract:
Mutations in the gene encoding VAPB (vesicle-associated membrane protein B) cause a familial form of Amyotrophic Lateral Sclerosis (ALS). Expression of an ALS-related variant of vapb (vapbP58S) in Drosophila motor neurons results in morphological changes at the larval neuromuscular junction (NMJ) characterized by the appearance of fewer, but larger, presynaptic boutons. Although diminished microtubule stability is known to underlie these morphological changes, a mechanism for the loss of presynaptic microtubules has been lacking. Here, we demonstrate the suppression of vapbP58S- induced changes in NMJ morphology by either the loss of ER Ca2+ release channels or the inhibition Ca2+/calmodulin (CaM)-activated kinase II (CaMKII). These data suggest a model in which decreased stability of presynaptic microtubules at vapbP58S NMJs result from hyperactivation of CaMKII due to elevated cytosolic [Ca2+]. We attribute the Ca2+ dyshomeostasis to delayed extrusion of cytosolic Ca2+ stemming from a paucity of activity-induced mitochondrial ATP production coupled with elevated rates of ATP consumption. Taken together, our data point to bioenergetic dysfunction as the root cause for the synaptic defects in vapbP58S-expressing Drosophila motor neurons.

Significance StatementRates of ATP production and consumption are tightly synchronized in healthy neurons. Whether this synchrony is lost in models of neurodegenerative diseases remains poorly understood. Here, we find that expression of a gene encoding an ALS-causing variant of an ER membrane protein, VAPB, decouples mitochondrial ATP production from neuronal activity. Due to a combination of diminished ATP production and elevated ATP consumption -- established outcomes in ALS neurons -- the levels of ATP in vapbP58S neurons are unable to keep up with the bioenergetic burden of depolarization. The resulting paucity of ATP and attendant decrease in the activity of Ca2+ ATPases results in diminished extrusion of cytosolic Ca2+ in vapbP58S-expressing motor neurons. The accumulation of residual Ca2+ in vapbP58S-expressing neurons underlies paired-pulse facilitation of synaptic vesicle release, and the changes in bouton development at the NMJ. In summary, our findings point to bioenergetic dysfunction due to the loss of activity-induced ATP production as being the cause of the synaptic defects observed in a Drosophila model of ALS.


title: Three simple steps to improve the interpretability of EEG-SVM studies

abstract: Research in machine-learning classification of electroencephalography (EEG) data offers important perspectives for the diagnosis and prognosis of a wide variety of neurological and psychiatric conditions, but the clinical adoption of such systems remains low. We propose here that much of the difficulties translating EEG-machine learning research to the clinic result from consistent inaccuracies in their technical reporting, which severely impair the interpretability of their often-high claims of performance. Taking example from a major class of machine-learning algorithms used in EEG research, the support-vector machine (SVM), we highlight three important aspects of model development (normalization, hyperparameter optimization and cross-validation) and show that, while these 3 aspects can make or break the performance of the system, they are left entirely undocumented in a shockingly vast majority of the research literature. Providing a more systematic description of these aspects of model development constitute three simple steps to improve the interpretability of EEG-SVM research and, in fine, its clinical adoption.


title: De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

abstract: Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

category: molecular biology


title: Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice

abstract:
Inflammatory and immune responses are essential and dynamic biological processes that protect the body against acute and chronic adverse stimuli. While conventional protein markers have been used to evaluate systemic inflammatory response, the immunological response to stimulation is complex and involves modulation of a large set of genes and interacting signaling pathways of innate and adaptive immune systems. Therefore, there is a need for a non-invasive tool that can comprehensively evaluate and monitor molecular dysregulations associated with inflammatory and immune responses. Here we utilized cell-free messenger RNA (cf-mRNA) RNA-Seq whole transcriptome profiling to assess lipopolysaccharide (LPS) induced and JAK inhibitor modulated inflammatory and immune responses in mouse plasma samples. Considering that, both organspecific recruitment of immune cells and organ resident bespoke immune cells contributes to restoration of organ homeostasis, we also examined LPS-induced gene-expression dysregulation of multiple organs to shed light on organ crosstalk. Cf-mRNA profiling displayed a pattern of systemic immune responses elicited by LPS and dysregulation of associated pathways. Moreover, attenuation of several inflammatory pathways, including STAT and interferon pathways, were observed following the treatment of JAK inhibitor. Lastly, we identified the dysregulation of liverspecific transcripts in cf-mRNA which reflected changes in the gene-expression pattern in this biological compartment. Collectively, using a preclinical model, we demonstrated the potential of plasma cf-mRNA profiling for systemic and organ-specific characterization of drug-induced molecular alterations that are associated with inflammatory and immune responses.

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title: Non-invasive Chromatin Deformation and Measurement of Differential Mechanical Properties in the Nucleus

abstract:
The nucleus is highly organized to facilitate coordinated gene transcription. Measuring the rheological properties of the nucleus and its sub-compartments will be crucial to understand the principles underlying nuclear organization. Here, we show that strongly localized temperature gradients (approaching 1{degrees}C /m) can lead to substantial intra-nuclear chromatin displacements (>1 m), while nuclear area and lamina shape remain unaffected. Using particle image velocimetry (PIV), intra-nuclear displacement fields can be calculated and converted into spatio-temporally resolved maps of various strain components. Using this approach, we show that chromatin displacements are highly reversible, indicating that elastic contributions are dominant in maintaining nuclear organization on the time scale of seconds. In genetically inverted nuclei, centrally compacted heterochromatin displays high resistance to deformation, giving a rigid, solid-like appearance. Correlating spatially resolved strain maps with fluorescent reporters in conventional interphase nuclei reveals that various nuclear compartments possess distinct mechanical identities. Surprisingly, both densely and loosely packed chromatin showed high resistance to deformation, compared to medium dense chromatin. Equally, nucleoli display particularly high rigidity and strong local anchoring to heterochromatin. Our results establish how localized temperature gradients can be used to drive nuclear compartments out of mechanical equilibrium to obtain spatial maps of their material responses.

Main FindingsO_LINovel non-invasive active micro-rheology method to probe spatial intranuclear material responses, unhindered by the nuclear lamina, using strongly localized temperature gradients
C_LIO_LIChromatin shows both elastic and viscous properties at the mesoscale with a retardation time of {tau} [~] 1s
C_LIO_LICompacted heterochromatin in a model of nuclear inversion shows high resistance to deformation, suggesting dominantly solid-like behavior
C_LIO_LIThe nucleus displays spatially distinct material properties for different compartments
C_LIO_LIThe nucleolus shows high resistance to deformation on the time scale of seconds
C_LIO_LIImmobile nucleoli appear solidly anchored to and retain the deformation of surrounding chromatin
C_LI


title: The dual role of N6-methyladenosine on mouse maternal RNAs and 2-cell specific RNAs revealed by ULI-MeRIP sequencing

abstract:
N6-methyladenosine (m6A) and its regulatory components play critical roles in various developmental processes in mammals(1-5). However, the landscape and function of m6A in the maternal-to-zygotic transition (MZT) remain unclear due to limited materials. Here, by developing an ultralow-input MeRIP-seq method, we revealed the dynamics of the m6A RNA methylome during the MZT process in mice. We found that more than 1/3 maternal decay and 2/3 zygotic mRNAs were modified by m6A. Moreover, m6As are highly enriched in the RNA of transposable elements MTA and MERVL, which are highly expressed in oocytes and 2-cell embryos, respectively. Notably, maternal depletion of Kiaa1429, a component of the m6A methyltransferase complex, leads to a reduced abundance of m6A-marked maternal RNAs, including both genes and MTA, in GV oocytes, indicating m6A-dependent regulation of RNA stability in oocytes. Interestingly, when the writers were depleted, some m6A-marked 2-cell specific RNAs, including Zscan4 and MERVL, appeared normal at the 2-cell stage but failed to be decayed at later stages, suggesting that m6A regulates the clearance of these transcripts. Together, our study uncovered that m6As function in context-specific manners during MZT, which ensures the transcriptome stability of oocytes and regulates the stage specificity of zygotic transcripts after fertilization.

One Sentence Summarym6A RNA methylation stabilizes the maternal RNAs in mouse oocytes and degrades the 2-cell specific RNAs in the cleavage-stage embryos.

category: developmental biology


title: From Diversity to Complexity: Microbial Networks in Soils

abstract: Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.


title: Seed sourcing for climate-resilient grasslands: the role of seed source diversity during early restoration establishment

abstract: Restoration often advocates for the use of local seed in restoration, however increasingly new strategies have been proposed to incorporate diverse sources to maintain evolutionary potential within seed mixes. Increasing seed sources per species within a seed mix should increase genetic variation, however, few empirical studies have evaluated how seed source diversity impacts plant community composition following restoration. Thus, the goal of this research was to compare the use of single or multi-source seed mix treatments to plant community diversity following restoration. Using 14 species commonly applied in grassland restoration, we examined plant community diversity following restoration comparing seed mixes with either one or five sources per species across two restoration sites in Minnesota and South Dakota, United States. Following seeding, species establishment and abundance were recorded to calculate plant diversity for each seed mix treatment. There were no major effects of seed mix treatment on community emergence and diversity observed, with the majority of plant establishment reflecting non-seeded species. However, site-specific differences were observed. Heterogeneous land-use history associated with the Minnesota site likely contributed to differences across the restoration treatments. In contrast, community diversity at the South Dakota site was homogeneous across seed mix treatments with changes in plant community influenced solely by early season species establishment. This suggests land-use history irrespective of seed mix treatment influences establishment and persistence, particularly in the first year following restoration. Future monitoring across seasons will be needed to evaluate if community diversity changes in response to seed mix treatment.


title: Nest aggregations of wild bees and apoid wasps in urban pavements: a street life to be promoted in urban planning

abstract: In the last 10 years, knowledges of wild bees and apoid wasps community dynamics have gained interest in urban ecology focusing on the availability of floral resources in cities. Although understudied, the urban environment impacts the conditions of their nesting sites. Recent observations in the Brussels-Capital Region (Belgium) showed that urban pavements can be a novel nesting opportunity for Hymenoptera ground-nesting species such as wild bees and apoid wasps. Here, using citizen science, we investigated the richness of ground-nesting species living under urban pavements, the preferences of the sidewalk joint size related to ground-nesting species size and for sidewalk type or for soils texture under the pavements on the nesting site selection. A total of 22 species belonging to 10 Hymenoptera families of wild bees and digger wasps with their associated kleptoparasites were identified on 89 sites in Brussels. Sandstone setts or concrete slabs with an unbound joint size around 1 cm were found to be best suitable urban pavements for the ground-nesting species. The soil texture under the pavement was highly sandy among our samples. Finally, we also suggest engineering management guidelines to support bee and wasp species nesting under urban pavement in highly urbanized areas. Such observations pave the way for much research in the field of urban ecology to conceive multifunctional pavement promoting biodiversity.


title: Selection on early survival does not explain germination rate clines in Mimulus cardinalis (Phrymaceae)

abstract:
PremiseMany traits covary with environmental gradients to form phenotypic clines. While local adaptation to the environment can generate phenotypic clines, other nonadaptive processes may also. If local adaptation causes phenotypic clines, then the direction of genotypic selection on traits should shift from one end of the cline to the other. Traditionally genotypic selection on non-Gaussian traits like germination rate have been hampered because it is challenging to measure their genetic variance.

MethodsHere we used quantitative genetics and reciprocal transplants to test whether a previously discovered cline in germination rate showed additional signatures of adaptation in the scarlet monkeyflower (Mimulus cardinalis). We measured genotypic and population level covariation between germination rate and early survival, a component of fitness. We developed a novel discrete log-normal model to estimate genetic variance in germination rate.

ResultsContrary to our adaptive hypothesis, we found no evidence that genetic variation in germination rate contributed to variation in early survival. Across populations, southern populations in both gardens germinated earlier and survived more.

ConclusionsSouthern populations have higher early survival but this is not caused by faster germination. This pattern is consistent with nonadaptive forces driving the phenotypic cline in germination rate, but future work will need to assess whether there is selection at other life stages. The statistical framework should help expand quantitative genetic analyses for other waiting-time traits.


title: An unexpected role for the conserved ADAM-family metalloprotease ADM-2 in Caenorhabditis elegans molting

abstract:
Molting is a widespread developmental process in which the external extracellular matrix (ECM), the cuticle, is remodeled to allow for organismal growth and environmental adaptation. Studies in the nematode Caenorhabditis elegans have identified a diverse set of molting-associated factors including signaling molecules, intracellular trafficking regulators, ECM components, and ECM-modifying enzymes such as matrix metalloproteases. C. elegans NEKL-2 and NEKL-3, two conserved members of the NEK family of protein kinases, are essential for molting and promote the endocytosis of environmental steroid-hormone precursors by the epidermis. Steroids in turn drive the cyclic induction of many genes required for molting. Here we report a novel role for the sole C. elegans ADAM-meltrin metalloprotease family member, ADM-2, as a negative regulator of molting. Whereas loss of adm-2 led to strong suppression of molting defects in partial loss-of-function nekl mutants, overexpression of ADM-2 induced molting defects in wild-type animals. CRISPR genome editing implicated the Zn-binding motif within the metalloprotease domain as critical for mediating the effects of ADM-2 on molting. ADM-2 is expressed in the epidermis, and its trafficking through the endo-lysosomal network was disrupted after NEKL depletion. We also identified the epidermally expressed low-density lipoprotein receptor-related protein, LRP-1, as a candidate target of ADM-2 regulation. Whereas loss of ADM-2 activity led to the upregulation of LRP-1, ADM-2 overexpression caused a reduction in LRP-1 abundance, suggesting that ADM-2 may function as a sheddase for LRP-1. We propose that loss of adm-2 suppresses molting defects in nekl mutants by eliminating a negative regulator of LRP-1, thereby compensating for defects in the efficiency of LRP-1 and sterol uptake. Our findings emphasize the importance of endocytic trafficking for both the internalization of factors that promote molting and the removal of proteins that would otherwise be deleterious to the molting process.

Author SummaryThe molecular and cellular features of molting in nematodes share many similarities with cellular and developmental processes that occur in mammals. This includes the degradation and reorganization of extracellular matrix materials that surround cells, as well as the intracellular machineries that allow cells to communicate and sample their environments. In the current study, we found an unexpected function for a conserved protein that degrades proteins on the external surface of cells. Rather than promoting molting through extracellular matrix reorganization, the ADM-2 protease can inhibit the molting process. This observation can be explained by data showing that ADM-2 negatively regulates LRP-1, a membrane protein that promotes molting by facilitating the uptake of molecular building blocks at the cell surface that are needed for molting-related signaling. Our data provide insights into the mechanisms controlling molting and link several conserved proteins to show how they function together during development.

category: genetics


title: Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis

abstract: Most human genes are co-expressed with a nearby gene. Yet, previous studies only reported this extensive local gene co-expression using bulk RNA-seq. Here, we leverage single cell datasets in >85 individuals to identify gene co-expression across cells, unbiased by cell type heterogeneity and benefiting from the co-occurrence of transcription events in single cells. We discover thousands of co-expressed genes in two cell types and (i) compare single cell to bulk RNA-seq in identifying local gene co-expression, (ii) show that many co-expressed genes - but not the majority - are composed of functionally-related genes and (iii) provide evidence that these genes are transcribed synchronously and their co-expression is maintained up to the protein level. Finally, we identify gene-enhancer associations using multimodal single cell data, which reveal that >95% of co-expressed gene pairs share regulatory elements. Our in-depth view of local gene co-expression and regulatory element co-activity advances our understanding of the shared regulatory architecture between genes.


title: Differing Associations between Optic Nerve Head Strains and Visual Field Loss in Normal- and High-Tension Glaucoma Subjects

abstract:
PurposeTo study the associations between optic nerve head (ONH) strains under intraocular pressure (IOP) elevation with retinal sensitivity in glaucoma subjects.

DesignClinic based cross-sectional study.

Participants229 subjects with primary open angle glaucoma (subdivided into 115 high tension glaucoma (HTG) subjects and 114 normal tension glaucoma (NTG) subjects).

MethodsFor one eye of each subject, we imaged the ONH using spectral-domain optical coherence tomography (OCT) under the following conditions: (1) primary gaze and (2) primary gaze with acute IOP elevation (to approximately 33 mmHg) achieved through ophthalmodynamometry. A 3-dimensional (3D) strain-mapping algorithm was applied to quantify IOP-induced ONH tissue strain (i.e. deformation) in each ONH. Strains in the pre-lamina tissue (PLT)and the retina, the choroid, the sclera and the lamina cribrosa (LC) were associated (using linear regression) with measures of retinal sensitivity from the 24-2 Humphrey visual field test (Carl Zeiss Meditec, Dublin, CA, USA). This was done globally, then locally according to the regionalization scheme of Garway-Heath et al.

Main Outcome MeasuresAssociations between ONH strains and values of retinal sensitivity from visual field testing.

ResultsFor HTG subjects, we found that (1) there were significant negative linear associations between ONH strains and retinal sensitivity (p<0.001) (on average, a 1% increase in ONH strains corresponded to a decrease in retinal sensitivity of 1.1 dB), (2) high strain regions co-localized with anatomically-mapped regions of high visual field loss, (3) the strongest negative associations were observed in the superior region and in the PLT. In contrast, for NTG subjects, no significant associations between strains and retinal sensitivity were observed except in the supero-temporal region of the LC.

ConclusionWe found significant negative associations between IOP-induced ONH strains and retinal sensitivity in a relatively large glaucoma cohort. Specifically, HTG subjects who experienced higher ONH strains were more likely to exhibit lower retinal sensitivities. Interestingly, this trend was in general less pronounced in NTG subjects, which could suggest a distinct pathophysiology between the two glaucoma subtypes.


title: Identifying C. elegans Lifespan Mutants by Screening for Early-Onset Protein Aggregation

abstract: Genetic screens have been widely used to identify genetic pathways that control specific biological functions. In C. elegans, forward genetic screens rely on the isolation of reproductively active mutants that can self-propagate clonal populations. Since aged individuals are unable to generate clonal populations, screens that target post-reproductive phenotypes, such as longevity, are challenging. In this work, we developed an approach that combines microfluidic technologies and image processing to perform a high-throughput, automated screen for mutants with shortened lifespan using protein aggregation as a marker for aging. We take advantage of microfluidics for maintaining a reproductively-active adult mutagenized population and for performing serial high-throughput analysis and sorting of animals with increased protein aggregation, using fluorescently labeled PAB-1 as a readout. We identified five mutants with increased aggregation levels, of which two exhibited a reduced lifespan. We demonstrate that lifespan mutants can be identified by screening for accelerated protein aggregation through quantitative analysis of fluorescently-labeled aggregates in populations that do not require conditional sterilization or manual separation of parental and progeny populations. We further analyzed the morphology of protein aggregates and reveal that patterns of aggregation in naturally-aging animals differ from mutants with increased aggregation, suggesting aggregate growth is time-dependent. This screening approach can be customized to other non-developmental phenotypes that appear during adulthood, as well as to other aging markers to identify additional longevity-regulating genetic pathways.


title: Effective drug release from safe ultrasound-triggered nanocarriers

abstract: Selective delivery of medication into specified tissue targets would realize the promise of personalized medicine with minimal side effects. Focused ultrasound provides noninvasive and practical means to release drugs from nanocarriers selectively at its target. However, which nanocarrier formulations provide safe and effective release and under which ultrasound parameters has been unclear. To expedite regulatory approval, we tested release effectiveness from nanocarriers containing perfluorocarbon cores of relatively high boiling points (up to 142{degrees}C) which show excellent stability compared with those used previously. We confirmed the safety of these nanocarriers and characterized their clearance kinetics and organ biodegradation in non-human primates. Crucially, we found that these safe, high-boiling-point nanocarriers can be used for effective release so long as they are activated by low-frequency ultrasound (300 kHz). This study informs the formulation and release parameters for safe and effective drug delivery in specific parts of the body or brain regions.


title: Physiochemically distinct SU-8 surfaces tailor Xylella fastidiosa cell-surface holdfast and colonization

abstract: SU-8 polymer is an excellent platform for diverse applications due to its high aspect ratio of micro/nanostructures fabrication and exceptional optical, chemical, and biocompatible properties. Although SU-8 has been often investigated for a variety of biological applications, how its surface properties influence both the interaction of bacterial cells with the substrate and its colonization is poorly understood. In this work, we tailor SU-8 nanoscale surface properties to investigate single cell motility, adhesion and successive colonization of a phytopathogenic bacteria, Xylella fastidiosa. Different surface properties of SU-8 thin films have been prepared using photolithography processing and oxygen plasma treatment. We found a significant difference in bacterial cell behavior and subsequent colonization on SU-8 as surface property changes. A larger density of carboxyl groups in hydrophilic plasma-treated SU-8 surfaces promotes faster cell motility in the earlier stage of the growth. The hydrophobic nature of pristine SU-8 surfaces has no trackable bacterial motility with 5 to 10 times more single cells adhered to surface than its plasma-treated counterpart. In fact, plasma-treated SU-8 samples suppressed bacterial adhesion, with surfaces showing less than 5% coverage. These results not only showcase that SU-8 surface properties can impact the bacterial behavior in a spatiotemporal manner, but also provide insights on the prominent ability of pathogens to evolve and adapt to different surface properties.


title: Namco: A microbiome explorer

abstract:
Background16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows for studying microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have been developed for the analysis of 16S rRNA gene data, only few platforms offer a user-friendly interface and none comprehensively cover the whole analysis pipeline from raw data processing down to complex analysis.

ResultsWe introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namcos capabilities by studying the association between rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention.

ConclusionNamco provides a broad range of features from raw data processing and basic statistics down to machine learning and network analysis, thus covering complex data analysis tasks that are not comprehensively covered elsewhere. Namco is freely available at https://exbio.wzw.tum.de/namco/.


title: mslp: a comprehensive pipeline in predicting cancer mutations specific synthetic lethal partners

abstract:
BackgroundMutation specific synthetic lethal partners (SLPs) offer significant insights in identifying novel targets and designing personalized treatments in cancer studies. Large scale genetic screens in cell lines and model organisms provide crucial resources for mining SLPs, yet those experiments are expensive and might be difficult to set up. Various computational methods have been proposed to predict the potential SLPs from different perspectives. However, those efforts are hampered by the low signal-to-noise ratio in simple correlation based approaches, or incomplete reliable training sets in supervised approaches.

ResultsHere we present mslp, a comprehensive pipeline to identify potential SLPs via integrating genomic and transcriptomic datasets from both patient tumours and cancer cell lines. Leveraging cuttingedges algorithms, we identify a broad spectrum of primary SLPs for mutations presented in patient tumours. Further, for mutations detected in cell lines, we develop the idea of consensus SLPs which are also identified as screen hits, and show consistency impact on cell viability. Applied in real datasets, we successfully identified known synthetic lethal gene pairs. Remarkably, genetic screen results suggested that consensus SLPs have a significant impact on cell viability compared to common hits.

ConclusionsMslp is a powerful and flexible pipeline to identify potential SLPs in a cancer context-specific manner, which might aid in drug developments and precise medicines in cancer treatments. The pipeline is implemented in R and freely available in github.


title: Self-consistent migration puts tight constraintson the spatio-temporal organization ofspecies-rich metacommunities

abstract: Biodiversity is often attributed to a dynamic equilibrium between immigration of species and competition-driven extinction. This equilibrium forms a common basis for studying ecosystem assembly from a static reservoir of migrants-the mainland. Yet, natural ecosystems often consist of many coupled communities (i.e. metacommunities) and migration occurs between these communities. The pool of migrants then depends on what is sustained in the ecosystem, which in turn depends on the dynamic migrant pool. This chicken-and-egg problem of survival and migration is poorly understood in communities of many competing species, except for the neutral case - the "unified neutral theory of biodiversity". Employing spatio-temporal simulations and mean-field analyses, we show that self-consistent migration puts rather tight constraints on the dynamic migration-extinction equilibrium. When the number of species is large, even weak competitions push species to the edge of their global extinction, such that the overall diversity is highly sensitive to perturbations in demographic parameters, including growth and dispersal rates. When migration is short-range, the resulting spatiotemporal abundance patterns follow broad scale-free distributions that correspond to a directed percolation phase transition. The qualitative agreement of our results for short-range and long-range migration suggests that this self-organization process is a general property of species-rich metacommunities. Our study shows that self-sustaining metacommunities are highly sensitive to environmental change and provides insights into how biodiversity can be rescued and maintained.

category: biophysics


title: Inhibition of the sodium-dependent HCO3 -transporter SLC4A4, produces a cystic fibrosis-like airway disease phenotype.

abstract: Bicarbonate secretion is a fundamental process involved in maintaining acid-base homeostasis. Disruption of bicarbonate entry into airway lumen, as has been observed in cystic fibrosis, produces several defects in lung function due to thick mucus accumulation. Bicarbonate is critical for correct mucin deployment and there is increasing interest in understanding its role in airway physiology, particularly in the initiation of lung disease in children affected by cystic fibrosis, in the absence of detectable bacterial infection. The current model of anion secretion in mammalian airways consists of CFTR and TMEM16A as apical anion exit channels, with limited capacity for bicarbonate transport compared to chloride. However, both channels can couple to SLC26A4 anion exchanger to maximise bicarbonate secretion. Nevertheless, current models lack any details about the identity of the basolateral protein(s) responsible for bicarbonate uptake into airway epithelial cells. We report herein that the electrogenic, sodium-dependent, bicarbonate cotransporter, SLC4A4, is expressed in the basolateral membrane of human and mouse airways, and that its pharmacological inhibition or genetic silencing reduces bicarbonate secretion. In fully differentiated primary human airway cells, SLC4A4 inhibition induced an acidification of the airways surface liquid and markedly reduced the capacity of cells to recover from an acid load. Studies in the Slc4a4-null mice revealed a previously unreported lung phenotype, characterized by mucus accumulation and reduced mucociliary clearance. Collectively, our results demonstrate that the reduction of SLC4A4 function induced a CF-like phenotype, even when chloride secretion remained intact, highlighting the important role SLC4A4 plays in bicarbonate secretion and mammalian airway function.


title: Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-players game

abstract: During infection, plant pathogenic fungi secrete a set of molecules collectively known as effectors, involved in overcoming the host immune system and in disease establishment. Effector genes are concertedly expressed as waves all along plant pathogenic fungi lifecycle. However, little is known about how coordinated expression of effector genes is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in the regulation of effector expression was recently investigated. In Leptosphaeria maculans, causing stem canker of oilseed rape, we established that the repressive histone modification H3K9me3 (trimethylation of Lysine 9 of Histone H3), deposited by the histone methyltransferase KMT1, was involved in the regulation of expression of genes highly expressed during infection, including effectors. Nevertheless, inactivation of KMT1 did not induce expression of these genes at the same level as observed during infection of oilseed rape, suggesting that a second regulator, such as a transcription factor (TF), might be involved. Pf2, a TF belonging to the Zn2Cys6 fungal specific TF family, was described in several Dothideomycete species as essential for pathogenicity and effector gene expression. We identified the orthologue of Pf2 in L. maculans, LmPf2, and investigated the role of LmPf2 together with KMT1, by inactivating and over-expressing LmPf2 in a wild type (WT) strain and a{Delta} kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis. Transcriptomic analyses during axenic growth showed that LmPf2 is involved in the control of effector gene expression. We observed an enhanced effect of the over-expression of LmPf2 on effector gene expression in a{Delta} kmt1 background, suggesting an antagonist role between KMT1 and LmPf2.

category: plant biology


title: Ethyl-Iophenoxic acid as a serum marker for oral baiting of carnivorous marsupials

abstract:
ContextEthyl-Iophenoxic acid (Et-IPA) has been widely used as a bait biomarker to determine oral bait consumption by vertebrate wildlife species. Oral bait vaccines have been delivered to numerous wildlife species to protect them from disease. The Tasmanian devil (Sarcophilis harrisii), the largest extant carnivorous marsupial species, is threatened by the transmissible cancers known as devil facial tumour disease (DFTD). Development of a protective DFTD vaccine is underway, and an oral bait has been proposed to deliver the vaccine in the wild. The bait delivery system requires a biomarker that can be detected for several months post-consumption in Tasmanian devils.

AimTo determine the suitability of Et-IPA as a bait biomarker in the Tasmanian devil.

MethodTwo Tasmanian devils were fed 50 mg Et-IPA (4.5 to 7.1 mg Et-IPA/kg bodyweight). Liquid chromatography with tandem mass spectrometry (LC-MS/-MS) was used to directly measure Et-IPA in baseline serum samples and samples collected on days 1, 14, 26 and 56 post-baiting.

Key resultBoth devils retained serum Et-IPA concentrations at two orders of magnitude above negative control sera when this study concluded.

ConclusionsEt-IPA is a useful bait biomarker for Tasmanian devils and can be included in future DFTD bait vaccine field trials to determine bait vaccine uptake.

category: zoology