title: Fighting cancer with oncolytic viral therapy: identifying threshold parameters for success

abstract:
We model interactions between cancer cells and free virus during oncolytic viral therapy. One of our main goals is to identify parameter regions that yield treatment failure or success. We show that the tumor size under therapy at a particular time is less than the size without therapy. Our analysis shows there are two thresholds for the horizontal transmission rate: a "Control threshold", the threshold above which treatment is efficient, and an "optimum threshold", the threshold beyond which infection prevalence reaches 100% and the tumor shrinks to its smallest size. Moreover, we explain how changes in the virulence level of the free virus alter the optimum threshold and the minimum tumor size. We identify a threshold for the virulence level of the virus and show how this threshold depends on the timescale of virus dynamics. Our results suggest that when the timescale of virus dynamics is fast, the administration of a more virulent virus leads to more tumor reduction. Conversely, when the viral timescale is slow, a higher virulence will have drawbacks on the results, such as high amplitude oscillations. Furthermore, our numerical observation depicts fast and slow dynamics. Our numerical simulations indicate there exists a two-dimensional globally attracting surface that includes the unstable manifold of the interior equilibrium. All solutions with positive initial conditions rapidly approach this two-dimensional attracting surface. In contrast, the trajectories on the attracting surface slowly tend to the periodic solution.

HighlightsO_LIThe assumption that the viral load is in a quasi-steady state is relaxed, and infected cells are assumed to be mitotic.
C_LIO_LIOur model strongly suggests that the tumor size is always reduced by therapy.
C_LIO_LIWe identify minimum tumor size, control threshold, and optimum threshold of the therapy.
C_LIO_LIOur analysis shows optimal virulence level of oncolytic virus depends on the time scale of virus dynamics.
C_LIO_LIWhen virus dynamic is slow, highly virulent virus causes long remission before relapse.
C_LI

category: cancer biology


title: Tissue-Specific Biochemical Differences Between Chronic Wasting Disease Prions Isolated From Free Ranging, White-Tailed Deer (Odocoileus virginianus)

abstract: Chronic wasting disease (CWD) is an invariably fatal prion disease affecting cervid species world-wide. Prions can manifest as distinct strains that can influence disease pathology and transmission. CWD is profoundly lymphotropic and most infected cervids likely shed peripheral prions replicated in lymphoid organs. However, CWD is a neurodegenerative disease and most research on prion strains has focused on neurogenic prions. Thus, a knowledge gap exists comparing prions in the brain to prions in the lymph node. In this study we compared prions from the obex and lymph node of naturally exposed white-tailed deer to identify potential biochemical strain differences. Here, we report biochemical evidence of strain differences between the brain and lymph node from these animals. Future work should examine the biological and zoonotic impact of these biochemical differences and examine more cervids from multiple locations to see if these differences are conserved across species and locations.

category: pathology


title: Profiling of human neural crest chemoattractant activity as replacement of fetal bovine serum for in vitro chemotaxis assays

abstract: Fetal bovine serum (FBS) is the only known stimulus for migration of human neural crest cells (NCCs). Non-animal chemoattractants are desirable for the optimization of chemotaxis assays to be incorporated in a test battery for reproductive and developmental toxicity. We confirmed here in an optimized transwell assay that FBS triggers directed migration along a concentration gradient. The responsible factor was found to be a protein in the 30-100 kDa size range. In a targeted approach, we tested a large panel of serum constituents known to be chemotactic for NCCs in animal models (e.g. VEGF, PDGF, FGF, SDF-1/CXCL12, ephrins, endothelin, Wnt, BMPs). None of the corresponding human proteins showed any effect in our chemotaxis assays based on human NCCs. We then examined, whether human cells would produce any factor able to trigger NCC migration in a broad screening approach. We found that HepG2 hepatoma cells produced chemotaxis-triggering activity (CTA). Using chromatographic methods and by employing the NCC chemotaxis test as bioassay, the responsible protein was enriched by up to 5000-fold. We also explored human serum and platelets as direct source, independent of any cell culture manipulations. A CTA was enriched from platelet lysates several thousand-fold. Its temperature and protease- sensitivity suggested also a protein component. The capacity of this factor to trigger chemotaxis was confirmed by single-cell video-tracking analysis of migrating NCCs. The human CTA characterized here may be employed in the future for the setup of assays testing for the disturbance of directed NCC migration by toxicants.

category: pharmacology and toxicology


title: A New Proposal of an Index for Regional Cerebral Perfusion Pressure - A Theoretical Approach with Fluid Dynamics

abstract:
Cerebral blood flow (CBF) / cerebral blood volume (CBV) ratio derived by [15O] H2O/ CO2 and CO positron emission tomography (PET) examination has been used empirically as an index for cerebral perfusion pressure (CPP). However, this equation lacks a theoretical basis and furthermore, has not been confirmed to be proportionate to CPP, as direct measurement of local CPP is not practical.

We have developed a new index for CPP using the Poiseuille equation based on a simple model. Our model suggests that CBF/CBV2 is proportionate to CPP and that it is mathematically a more accurate index than CBF/CBV.

category: physiology


title: A Novel Proposal for an Index for Regional Cerebral Perfusion Pressure - A Theoretical Approach Using Fluid Dynamics


title: Energetics but not development is impacted in coral embryos exposed to ocean acidification

abstract:
In light of the chronic stress and mass mortality reef-building corals face under climate change, it is critical to understand the processes essential to reef persistence and replenishment, including coral reproduction and development. Here we quantify gene expression and size sensitivity to ocean acidification across a set of developmental stages in the rice coral, Montipora capitata. Embryos and swimming larvae were exposed to pH treatments 7.8 (Ambient), 7.6 (Low) and 7.3 (Xlow) from fertilization to 9 days post-fertilization. Embryo and larval volume, and stage-specific gene expression were compared between treatments to determine the effects of acidified seawater on early development. While there was no measurable size differentiation between fertilized eggs and prawn chips exposed to pH 7.8, 7.6, and 7.3, early gastrula and planula raised in reduced pH treatments were significantly smaller than those raised in ambient seawater, suggesting an energetic cost to developing under low pH. However, no differentially expressed genes emerged until 9 days post-fertilization. Notably, gene expression patterns of larvae developing at pH 7.8 and pH 7.3 were more similar than those developing at pH 7.6. Larvae from pH 7.6 showed upregulation of genes involved in cell division, regulation of transcription, lipid metabolism, and oxidative stress in comparison to the other two treatments. While low pH appears to increase energetic demands and trigger oxidative stress, the developmental process is robust to this at a molecular level, with swimming larval stage reached in all pH treatments.

Summary statementThis developmental time series tracks the physiological and transcriptomic outcomes of early coral development under ambient pH (pH 7.8), and two low pH conditions (pH 7.6 and 7.3).


title: Identification of green lineage osmotic stress pathways

abstract: Maintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the green alga Chlamydomonas reinhardtii to establish a foundational understanding of evolutionarily conserved osmotic-stress signaling pathways in the green lineage through transcriptomics, phosphoproteomics, and functional genomics approaches. Five genes acting across diverse cellular pathways were found to be essential for osmotic-stress tolerance in Chlamydomonas including cytoskeletal organization, potassium transport, vesicle trafficking, mitogen-activated protein kinase and chloroplast signaling. We show that homologs of these genes in the multicellular land plant Arabidopsis thaliana have conserved functional roles in stress tolerance and reveal a novel PROFILIN-dependent actin remodeling stage of acclimation that ensures cell survival and tissue integrity upon osmotic stress. This study highlights the conservation of the stress response in algae and land plants and establishes Chlamydomonas as a unicellular plant model system to dissect the osmotic stress signaling pathway.

category: plant biology


title: Bayesian optimisation for yield in high-dimensional trait-space identifies crop ideotypes in Oil Seed Rape

abstract:
The improvement of crop yield has long been a major breeding target and is increasingly becoming a goal in many areas of plant research. Yield has been shown to be a complex trait, depending on multiple genes, plant architecture and plant-environment interactions. This complexity is frequently reduced by focussing on contributing factors to yield (yield traits). However, a quantitative understanding of the interplay between yield traits, and the effect of these relationships on yield is largely unexplored. Consequently, the extent to which crop varieties achieve their optimal morphology in a given environment and how this impacts on seed yield is unknown.

Here we use causal inference to model the hierarchically structured effects of 27 macro and micro yield traits on each other over the course of plant development, and on seed yield in Spring and Winter oilseed rape plants. We perform Bayesian optimisation on the modelled yield potential, identifying the morphology of ideotype plants which are expected to be higher yielding than the existing varieties in the studied panels. We find that existing Spring varieties occupy the optimal regions of trait-space, but that potentially high yielding strategies are unexplored in extant Winter varieties.

In addition to concrete recommendations for varietal improvement in oilseed rape, this work provides a novel, general methodological framework for the study of crop breeding as an optimisation problem.


title: CHOmpact: a reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability

abstract: Metabolic modelling has emerged as a key tool for the characterisation of biopharmaceutical cell culture processes. Metabolic models have also been instrumental in identifying genetic engineering targets and developing feeding strategies that optimise the growth and productivity of Chinese hamster ovary (CHO) cells. Despite their success, metabolic models of CHO cells still present considerable challenges. Genome scale metabolic models (GeMs) of CHO cells are very large (>6000 reactions) and are, therefore, difficult to constrain to yield physiologically consistent flux distributions. The large scale of GeMs also makes interpretation of their outputs difficult. To address these challenges, we have developed CHOmpact, a reduced metabolic network that encompasses 101 metabolites linked through 144 reactions. Our compact reaction network allows us to deploy multi-objective optimisation and ensure that the computed flux distributions are physiologically consistent. Furthermore, our CHOmpact model delivers enhanced interpretability of simulation results and has allowed us to identify the mechanisms governing shifts in the anaplerotic consumption of asparagine and glutamate as well as an important mechanism of ammonia detoxification within mitochondria. CHOmpact, thus, addresses key challenges of large-scale metabolic models and, with further development, will serve as a platform to develop dynamic metabolic models for the control and optimisation of biopharmaceutical cell culture processes.

category: systems biology


title: As potential biomarkers, kinetic network features may be more predictive than molecule abundances

abstract:
The identification of prognostic biomarkers fuels personalized medicine. Here we tested two underlying, but often overlooked assumptions: 1) measurements at the steady state are sufficient for predicting the response to drug action, and 2) specifically, measurements of molecule abundances are sufficient. It is not clear that these are justified, as 1) the response results from non-linear molecular relationships, and 2) the steady state is defined by both abundance and orthogonal flux information. An experimentally validated mathematical model of the cellular response to the anti-cancer agent TRAIL was our test case. We developed a mathematical representation in which abundances and fluxes (static and kinetic network features) are largely independent, and simulated heterogeneous drug responses. Machine learning revealed predictive power, but that kinetic, not static network features were most informative. Analytical treatment of the underlying network motif identified kinetic buffering as the relevant circuit design principle. Our work suggests that network topology considerations ought to guide biomarker discovery efforts.

Graphic abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/452900v1_ufig1.gif" ALT="Figure 1">
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- Our method allows separate consideration of heterogeneous abundances and fluxes
- For the TRAIL cell death network machine learning reveals fluxes as more predictive
- Network motif analyses could render biomarker discovery efforts more productive

eTOC blurbPrecision medicine relies on discovering which measurements of the steady state predict therapeutic outcome. Loriaux et al show - using a new analytical approach - that depending on the underlying molecular network, synthesis and degradation fluxes of regulatory molecules may be more predictive than their abundances. This finding reveals a flaw in an implicit but hitherto untested assumption of biomarker discovery efforts and suggests that dynamical systems modeling is useful for directing future clinical studies in precision medicine.


title: Hyperspectral characterisation of natural illumination in woodland and forest environments

abstract: Light in nature is complex and dynamic, and varies along spectrum, space, direction, and time. While both spectrally resolved measurements and spatially resolved measurements are widely available, spectrally and spatially resolved measurements are technologically more challenging. Here, we present a portable imaging system using off-the-shelf components to capture the full spherical light environment in a spectrally and spatially resolved fashion. The method relies on imaging the 4{pi}-steradian light field reflected from a mirrored chrome sphere using a commercial hyperspectral camera (400-1000 nm) from multiple directions and an image-processing pipeline for extraction of the mirror sphere, removal of saturated pixels, correction of specular reflectance of the sphere, promotion to a high dynamic range, correction of misalignment of images, correction of intensity compression, erasure of the imaging system, unwrapping of the spherical images, filling-in blank regions, and stitching images collected from different angles. We applied our method to Wytham Woods, an ancient semi-natural woodland near Oxford, UK. We acquired a total of 168 images in two sites with low and high abundance of ash, leading to differences in canopy, leading to a total 14 hyperspectral light probes. Our image-processing pipeline corrected small (<3 {degrees}) field-based misalignment adequately. Our novel hyperspectral imaging method is adapted for field conditions and opens up novel opportunities for capturing the complex and dynamic nature of the light environment.


title: Global distribution and diversity of alien Ponto-Caspian amphipods

abstract: The Ponto-Caspian region is an important donor of aquatic alien species throughout the Northern Hemisphere, many of which are amphipod crustaceans. Despite decades of ongoing spread and negative effects on native biota, a complete picture of the global diversity and distribution of these amphipods has yet to emerge, hampering efficient monitoring and predictions of future invasions. Herein, we provide a comprehensive summary of alien species taxonomic and ecomorphological diversity, as well as high-resolution distribution maps and biogeographical patterns based on >8000 global records. We find that up to 39 species in 19 genera and five families, belonging to all four currently recognized ecomorphs, are potentially alien, their diversity gradually decreasing with distance from the native region. Most species (62%) have limited distributions, 15% are widespread, and 23% exhibit intermediate ranges. We also find that regions adjacent to the native areal are comparatively less well-sampled than more distant regions. Biogeographical clustering revealed three faunal provinces that largely correspond with the Southern, Central and Northern invasion corridors. We conclude that 1) alien amphipods are a representative subsample of the native Ponto-Caspian phylogenetic and ecomorphological diversity, and 2) that their biogeographical patterns are driven by anthropogenic factors acting on distinct native regional species pools.

category: zoology


title: Losartan shifts social reward motivation and punishment feedback sensitivity via modulating midbrain-striato-frontal circuits

abstract: Social deficits and dysregulations in dopaminergic midbrain-striato-frontal circuits represent transdiagnostic symptoms across psychiatric disorders. Animal models suggest that modulating interactions between the dopamine and renin-angiotensin system with the angiotensin receptor antagonist Losartan (LT) can modulate learning and reward-related processes. We have therefore determined the behavioral and neural effects of LT on social reward and punishment processing in humans. A pre-registered randomized double-blind placebo-controlled between-subject pharmacological design was combined with a social incentive delay fMRI paradigm during which subjects could avoid social punishment or gain social reward. Healthy volunteers received a single-dose of LT (50mg, n=43) or placebo (n=44). Reaction times and emotional ratings served as behavioral outcomes, on the neural level activation, connectivity and social feedback prediction errors were modelled. Relative to placebo, LT switched reaction times and arousal away from prioritizing punishment towards social reward. On the neural level the LT-enhanced motivational salience of social rewards was accompanied by stronger ventral striatum-prefrontal connectivity during reward anticipation and attenuated activity in the ventral tegmental area (VTA) and associated connectivity with the bilateral insula in response to punishment during the outcome phase. Computational modelling further revealed an LT-enhanced social reward prediction error signal in VTA and dorsal striatum. LT shifted motivational and emotional salience away from social punishment towards social reward via modulating distinct core nodes of the midbrain-striato-frontal circuits. The findings document a modulatory role of the renin-angiotensin system in these circuits and associated social processes, suggesting a promising treatment target to alleviate social dysregulations.

category: neuroscience


title: The angiotensin antagonist Losartan shifts social reward motivation and punishment feedback sensitivity via modulating midbrain-striato-frontal circuits


title: Residual dynamics resolves recurrent contributions to neural computation

abstract: Relating neural activity to behavior requires an understanding of how neural computations arise from the coordinated dynamics of distributed, recurrently connected neural populations. However, inferring the nature of recurrent dynamics from partial recordings of a neural circuit presents significant challenges. Here, we show that some of these challenges can be overcome by a fine-grained analysis of the dynamics of neural residuals, i.e. trial-by-trial variability around the mean neural population trajectory for a given task condition. Residual dynamics in macaque pre-frontal cortex (PFC) in a saccade-based perceptual decision-making task reveals recurrent dynamics that is time-dependent, but consistently stable, and implies that pronounced rotational structure in PFC trajectories during saccades are driven by inputs from upstream areas. The properties of residual dynamics restrict the possible contributions of PFC to decision-making and saccade generation, and suggest a path towards fully characterizing distributed neural computations with large-scale neural recordings and targeted causal perturbations.


title: Specialized neurons in the right habenula mediate response to aversive olfactory cues

abstract: Hemispheric specializations are well studied at the functional level but less is known about the underlying neural mechanisms. We identified a small cluster of cholinergic neurons in the right dorsal habenula (dHb) of zebrafish, defined by their expression of the lecithin retinol acyltransferase domain containing 2a (lratd2a) gene and their efferent connections with a subregion of the ventral interpeduncular nucleus (vIPN). The unilateral lratd2a-expressing neurons are innervated by a subset of mitral cells from both the left and right olfactory bulb and are activated upon exposure of adult zebrafish to the aversive odorant cadaverine that provokes avoidance behavior. Using an intersectional strategy to drive expression of the botulinum neurotoxin specifically in these neurons, we find that adults no longer show protracted avoidance to cadaverine. Mutants with left-isomerized dHb that lack these neurons are less repelled by cadaverine and their behavioral response to alarm substance, a potent aversive cue, is diminished. However mutants in which both dHb have right identity appear more reactive to alarm substance. The results implicate an asymmetric dHb-vIPN neural circuit in processing of aversive olfactory cues and modulating resultant behavioral responses.


title: Connectivity and dynamics in the olfactory bulb

abstract:
Dendrodendritic interactions between excitatory mitral cells and inhibitory granule cells in the olfactory bulb create a dense interaction network, reorganizing sensory representations of odors and, consequently, perception. Large-scale computational models are needed for revealing how the collective behavior of this network emerges from its global architecture. We propose an approach where we summarize anatomical information through dendritic geometry and density distributions which we use to calculate the probability of synapse between mitral and granule cells, while capturing activity patterns of each cell type in the neural dynamical systems theory of Izhikevich. In this way, we generate an efficient, anatomically and physiologically realistic large-scale model of the olfactory bulb network. Our model reproduces known connectivity between sister vs. non-sister mitral cells; measured patterns of lateral inhibition; and theta, beta, and gamma oscillations. It in turn predicts testable relations between network structure, lateral inhibition, and odor pattern decorrelation; between the density of granule cell activity and LFP oscillation frequency; how cortical feedback to granule cells affects mitral cell activity; and how cortical feedback to mitral cells is modulated by the network embedding. Additionally, the methodology we describe here provides a tractable tool for other researchers.

Author summaryThe function of the olfactory bulb (OB) critically depends on connectivity patterns between its excitatory and inhibitory cells. Here, we develop an anatomically grounded algorithm for efficiently determining the probability of synapses between mitral cells and granule cells in the OB. We use this algorithm to generate a large-scale network model of the OB with characteristic connectivity distributions between cell types, as well as between sister mitral cells. We simulate the network using the dynamical systems approach of Izhikevich for describing neurons, and show how network structure affects GC-mediated processes, including LFP oscillation frequency, lateral inhibition, odor decorrelation, and cortical feedback. Our results suggest how alterations to the OB network through processes like neurogenesis, or via injury or disease, can have significant effects on function.


title: Distinct but cooperating brain networks supporting semantic cognition

abstract: Semantic cognition is a complex brain function involving multiple processes from sensory systems, semantic systems, to domain-general cognitive systems, reflecting its multifaceted nature. However, it remain unclear how these systems cooperate with each other to achieve effective semantic cognition. Here, we investigated the neural networks involved in semantic cognition using independent component analysis (ICA). We used a semantic judgement task and a pattern matching task as a control task with two levels of difficulty to disentangle task-specific networks from domain-general networks and to delineate task-specific involvement of these networks. ICA revealed that semantic processing recruited two task-specific networks (semantic network [SN] and extended semantic network [ESN]) as well as domain general networks including the frontoparietal network (FPN) and default mode network (DMN). Specifically, two distinct semantic networks were differently modulated by task difficulty. The SN was coupled with the extended semantic network and FPN but decoupled with the DMN, whereas the ESN was synchronised with the FPN and DMN. Furthermore, the degree of decoupling between the SN and DMN was associated with semantic performance. Our findings suggest that human higher cognition is achieved by the neural dynamics of brain networks, serving distinct and shared cognitive functions depending on task demands.


title: Differential stimulation of pluripotent stem cell-derived human microglia leads to exosomal proteomic changes affecting neurons

abstract:
Microglial exosomes are an emerging communication pathway, implicated in fulfilling homeostatic microglial functions and transmitting neurodegenerative signals. Gene variants of the triggering receptor expressed myeloid cells-2 (TREM2) are associated with an increased risk of developing dementia. We investigated the influence of the TREM2 Alzheimers disease risk variant, R47Hhet, on the microglial exosomal proteome consisting of 3019 proteins secreted from human iPS-derived microglia (iPS-Mg). Exosomal protein content changed according to how iPS-Mg were stimulated. Thus lipopolysaccharide (LPS) induced microglial exosomes to contain more inflammatory signals, whilst stimulation with the TREM2 ligand phosphatidylserine (PS+) increased metabolic signals within the microglial exosomes. We tested the effect of these exosomes on neurons and found that the exosomal protein changes were functionally relevant and influenced downstream functions in both neurons and microglia. Exosomes from R47Hhet iPS-Mg contained disease-associated microglial (DAM) signature proteins, and were less able to promote outgrowth of neuronal processes and increase mitochondrial metabolism in neurons compared with exosomes from TREM2 common variant iPS-Mg. Taken together these data highlight the importance of microglial exosomes in fulfilling microglial functions. Additionally, variations in the exosomal proteome influenced by the R47Hhet TREM2 variant may underlie the increased risk of Alzheimers disease associated with this variant.

Graphical Abstract

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title: Prenatal androgen treatment does not alter the firing activity of hypothalamic arcuate kisspeptin neurons in female mice

abstract:
Neuroendocrine control of reproduction is disrupted in many individuals with polycystic ovary syndrome, who present with increased luteinizing hormone (LH), and presumably gonadotropin-releasing hormone (GnRH), release frequency, and high androgen levels. Prenatal androgenization (PNA) recapitulates these phenotypes in primates and rodents. Female offspring of mice injected with dihydrotestosterone (DHT) on gestational D16-18 exhibit disrupted estrous cyclicity, increased LH and testosterone, and increased GnRH neuron firing rate as adults. PNA also alters the developmental trajectory of GnRH neuron firing rates, markedly blunting the prepubertal peak in firing that occurs in 3wk-old controls. GnRH neurons do not express detectable androgen receptors and are thus probably not the direct target of DHT. Rather, PNA likely alters GnRH neuronal activity by modulating upstream neurons, such as hypothalamic arcuate neurons co-expressing kisspeptin, neurokinin B (gene Tac2), and dynorphin, aka KNDy neurons. We hypothesized PNA treatment changes firing rates of KNDy neurons in a similar age-dependent manner as GnRH neurons. We conducted targeted extracellular recordings (0.5-2h) of Tac2-identified KNDy neurons from control and PNA mice at 3wks of age and in adulthood. About half of neurons were quiescent (<0.005Hz). Long-term firing rates of active cells varied, suggestive of episodic activity, but were not different among groups. Short-term burst firing was also similar. We thus reject the hypothesis that PNA alters the firing rate of KNDy neurons. This does not preclude altered neurosecretory output of KNDy neurons, involvement of other neuronal populations, or in-vivo networks as critical drivers of altered GnRH firing rates in PNA mice.

Significance statementPrenatal androgenization (PNA) recapitulates key aspects of the common reproductive disorder polycystic ovary syndrome. It is postulated that disruptions in the episodic pattern of gonadotropin-releasing hormone (GnRH) secretion in part underly this disorder, yet GnRH neurons do not express androgen receptor to respond directly to elevated androgens. A population of kisspeptin, neurokinin B, and dynorphin-expressing (KNDy) neurons in the hypothalamic arcuate nucleus are thought to regulate pulsatile GnRH release and some express androgen receptor. We did not find evidence, however, that PNA altered spontaneous activity of KNDy neurons before puberty at 3wks of age or in adulthood. This suggests that PNA likely acts through other components of the broader hypothalamic network to change the patterns of GnRH release.


title: Plasticity of the dopaminergic phenotype and of locomotion in larval zebrafish induced by changes in brain excitability during the embryonic period.

abstract:
During the embryonic period, neuronal communication starts before the establishment of the synapses with forms of neuronal excitability, called here Embryonic Neuronal Excitability (ENE). ENE has been shown to modulate the correct unfolding of development transcriptional programs but the global consequences for the developing organisms are not all understood. Here we monitored calcium transients in zebrafish embryos as a proxy for ENE to assess the efficacy of transient pharmacological treatments able to either increase or decrease ENE. Increasing or decreasing ENE for 24 hour at 2 days post fertilization (dpf) promoted respectively an increase or decrease in the post-mitotic differentiation of the dopamine (DA) neurons in the telencephalon and in the olfactory bulb of zebrafish larvae at 6 dpf. This plasticity of dopaminergic specification occurs within a stable population of vMAT2 immuno-reactive cells, hence identifying an unanticipated biological marker for this pool of reserve cells, that can be recruited through ENE.

Modulating ENE also affected locomotion several days after the end of the treatments. In particular, the increase of ENE from 2 to 3 dpf promoted an hyperlocomotion in 6 dpf zebrafish larvae, reminiscent of endophenotypes reported for Attention Deficit with Hyperactivity Disorders and schizophrenia in zebrafish. These results provide a convenient framework to identify environmental factors that could disturb ENE as well as to study the molecular mechanisms linking ENE to the neurotransmitters specification, with clinical relevance for the pathogenesis of neurodevelopmental disorders.

Significance StatementO_LISpontaneous calcium spikes, used as a proxy for Embryonic Neuronal Excitability (ENE), are detected in the forebrain of embryonic zebrafish.
C_LIO_LITransients pharmacological treatments applied by balneation could be used to increase or decrease ENE.
C_LIO_LIThe post-mitotic differentiation of the dopaminergic phenotype is modulated by ENE in the zebrafish forebrain.
C_LIO_LIThe plasticity of the dopaminergic specification occurs within a reserve pool of vMAT2 immuno-reactive cells.
C_LIO_LITransient increase of ENE at the end of the embryonic period induces a hyperlocomotion, a phenotype associated with ADHD and schizophrenia in this model.
C_LIO_LIOur results open clinically relevant perspectives to study the pathogenesis of neurodevelopmental disorders in zebrafish.
C_LI


title: Plasticity of the dopaminergic phenotype and of locomotion in larval zebrafish induced by changes in brain excitability during the embryonic period


title: Ecotoxicological effects of silver nanoparticles in marine mussels

abstract:
In the marine bioindicator species M. galloprovincialis Lam we predicted toxicity and bioaccumulation of 5 nm alkane-coated and 50 nm uncoated silver nanoparticles (AgNPs) along with Ag+, as a function of the actual dose level. We generated a time persistence model of silver concentration in seawater and used the Area Under the Curve (AUC) as independent variable in hazard assessment. This approach allowed us to evaluate unbiased ecotoxicological endpoints for acute (survival) and chronic toxicity (byssal adhesion). Logistic regression analysis rendered LC5096h values of 0.68 {+/-} 0.08; 1.00 {+/-} 0.20; 1.00 {+/-} 0.42 mg h L-1 respectively for Ag+, 5 nm and 50 nm AgNP posing no evidence the silver form is a necessary variable to predict the survival outcome. By contrast, for byssal adhesion regression analysis revealed a much higher toxicological potential of Ag+ vs AgNPs, 0.0021 {+/-} 0.0009; 0.053 {+/-} 0.016; 0.021 (no computable error for 50 nm AgNP) mg h L-1, and undoubtedly confirmed a role of the silver form.

Bioaccumulation was higher for Ag+ > 5 nm AgNP > 50 nm AgNP reflecting a parallel with the preferential uptake route / target organ.

We, eventually, provided a full range of toxicological endpoints to derive risk quotients.

category: ecology


title: Paninvasion severity assessment of a US grape pest to disrupt the global wine market

abstract: Economic impacts from plant pests are often felt at the regional scale, yet some impacts expand to the global scale through the alignment of a pests invasion potentials. Such globally invasive species (i.e., paninvasives) are like the human pathogens that cause pandemics; and like pandemics, assessing paninvasion risk for an emerging regional pest is key for stakeholders to take early actions that avoid market disruption. Here, we develop the paninvasion severity assessment framework and use it to assess a rapidly spreading regional US grape pest, the spotted lanternfly planthopper (Lycorma delicatula; SLF), to spread and disrupt the global wine market. We found that SLF invasion potentials are aligned globally because important viticultural regions with suitable environments for SLF establishment also heavily trade with invaded US states. If the US acts as an invasive bridgehead, Italy, France, Spain, and other important wine exporters are likely to experience the next SLF introductions. Risk to the global wine market is high unless stakeholders work to reduce SLF invasion potentials in the US and globally.


title: Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics across a river catchment

abstract: Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food-webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups; local richness showed seasonally dependent and statistically significant increases and decreases towards downstream positions within the catchment for fish and bacteria respectively, while invertebrate richness remained unchanged with increased downstream position. The local food-webs, formed by these taxonomic groups, also showed a variation in their structure, such as link density and nestedness, to both space and time, yet these patterns did not necessarily mirror those of biodiversity and functional feeding characteristics. In order to conserve species diversity as well as their functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied, as our results suggest that they are not directly scalable to each other even at the same spatial and temporal scales.


title: Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA


title: The genetic basis of cooperation and conflict in natural populations of a model symbiont

abstract: Given the need to predict the outcomes of evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We conducted genome-wide association studies (GWAS) to examined naturally-occurring genetic variation in 191 strains of the model microbial symbiont, Ensifer meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments. Using this data, we determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring microbes. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes potentially acts to maintain, rather than erode, genetic diversity, thus, explaining why variation in mutualism traits persists in nature.

category: evolutionary biology


title: The genetic basis of interspecies cooperation and conflict in naturally-occurring isolates of a model plant symbiont


title: Evolutionary Sparse Learning for phylogenomics

abstract: AO_SCPLOWBSTRACTC_SCPLOWWe introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci--such as genes, proteins, genomic segments, and positions--as parameters. Using the Least Absolute Shrinkage and Selection Operator (LASSO), ESL selects only the most important genomic loci to explain a given phylogenetic hypothesis or presence/absence of a trait. ESL does not directly model conventional parameters such as rates of substitutions between nucleotides, rate variation among positions, and phylogeny branch lengths. Instead, ESL directly employs the concordance of variation across sequences in an alignment with the evolutionary hypothesis of interest. ESL provides a natural way to combine different molecular and non-molecular data types and incorporate biological and functional annotations of genomic loci directly in model building. We propose positional, gene, function, and hypothesis sparsity scores, illustrate their use through an example and suggest several applications of ESL. The ESL framework has the potential to drive the development of a new class of computational methods that will complement traditional approaches in evolutionary genomics. ESLs fast computational times and small memory footprint will also help democratize big data analytics and improve scientific rigor in phylogenomics.


title: Reticulate evolution in a neutral model: speciation, extinctions, and hybridizations

abstract: Evolution is usually pictured as a tree where ancient species branch into new ones and eventually disappear. In this simplified view, the balance between speciation and extinction fully determines the diversity of life. Hybridization, how-ever, introduces another level of complexity, allowing neighboring branches of the tree to interact, mixing their genetic content. This generates further diversity leading to reticulated phylogenetic trees. In this paper we study processes of speciation, extinction and hybridization using a genetically and spatially explicit neutral model of diversification. Speciation, extinction and hybridization events are tracked throughout the evolutionary process leading to complete and exact phylogenetic trees. We found that genome size played a key role in these processes, increasing the extinction rate and decreasing the hybridization rate. In our simulations, hybridization after one speciation event occurred throughout the evolutionary process but hybridization after two speciation events was only observed during the initial radiation. Most hybridization occurred between relatively abundant species, discarding lack of sexual partners or small population sizes as potential causes. We found that hybridization occurred mostly because of opportunity (genetic similarity and spatial proximity) between recently branched species, when the number of accumulated mutations is not yet too large.


title: An improved auxin-inducible degron system for fission yeast

abstract: Conditional degron technologies, which allow a protein of interest to be degraded in an inducible manner, are important tools for biological research, and are especially useful for creating conditional loss-of-function mutants of essential genes. The auxin-inducible degron (AID) technology, which utilizes plant auxin signaling components to control protein degradation in non-plant species, is a widely used small-molecular-controlled degradation method in yeasts and animals. However, the currently available AID systems still have room for further optimization. Here, we have improved the AID system for the fission yeast Schizosaccharomyces pombe by optimizing all three components: the AID degron, the small-molecule inducer, and the inducer-responsive F-box protein. We chose a 36-amino-acid sequence of the Arabidopsis IAA17 protein as the degron and employed three tandem copies of it to enhance efficiency. To minimize undesirable side effects of the inducer, we adopted a bulky analog of auxin, 5-adamantyl-IAA, and paired it with the F-box protein OsTIR1 that harbors a mutation (F74A) at the auxin-binding pocket. 5-adamantyl-IAA, when utilized with OsTIR1-F74A, is effective at concentrations thousands of times lower than auxin used in combination with wild-type OsTIR1. We tested our improved AID system on 10 essential genes and achieved inducible lethality for all of them, including ones that could not be effectively inactivated using a previously published AID system. Our improved AID system should facilitate the construction of conditional loss-of-function mutants in fission yeast.

category: genetics


title: A Bayesian model selection approach for mediation analysis

abstract: Mediation analysis is a powerful tool for discovery of causal relationships. We describe a Bayesian model selection approach to mediation analysis that is implemented in our bmediatR software. Using simulations, we show that bmediatR performs as well or better than established methods including the Sobel test, while allowing greater flexibility in both model specification and in the types of inference that are possible. We applied bmediatR to genetic data from mice and human cell lines to demonstrate its ability to derive biologically meaningful findings. The Bayesian model selection framework is extensible to support a wide variety of mediation models.


title: A Bayesian model selection approach to mediation analysis


title: An ancient polymorphic regulatory region within the BDNF gene associated with obesity modulates anxiety-like behaviour in mice and humans.

abstract: Obesity and anxiety are morbidities notable for their increased impact on society during the recent COVID-19 pandemic. Understanding the mechanisms governing susceptibility to these conditions will increase quality of life and our resilience to future pandemics. In the current study we explored the function of a highly conserved regulatory region (BE5.1) within the BDNF gene that harbours a polymorphism strongly associated with obesity (rs10767664; p=4.69x10-26). Analysis in primary cells suggested that the major T-allele of BE5.1 was an enhancer whereas the obesity associated A-allele was not. However, CRISPR/CAS9 deletion of BE5.1 from the mouse genome (BE5.1KO) produced no significant effect on the expression of BDNF transcripts in the hypothalamus, no change in weight gain after 28 days and only a marginally significant increase in food intake. Nevertheless, transcripts were significantly increased in the amygdala of female mice and elevated zero maze and marble burying tests demonstrated a significant increase in anxiety-like behaviour that could be reversed by diazepam. Consistent with these observations, human GWAS cohort analysis demonstrated a significant association between rs10767664 and anxiousness in human populations. Intriguingly, interrogation of the human GTEx eQTL database demonstrated no effect on BDNF mRNA levels associated with rs10767664 but a highly significant effect on BDNF-antisense (BDNF-AS) gene expression and splicing suggesting a possible mechanism. We discuss our findings within the context of the known function and regulation of BDNF in obesity and anxiety whilst exploring the validity of interrogating GWAS data using comparative genomics and functional analysis using CRISPR genome editing in mice.


title: Genetic basis of enhanced stress resistance in long-lived mutants highlights key role of innate immunity in determining longevity

abstract:
Mutations that extend lifespan are associated with enhanced resistance to stress. To better understand the molecular mechanisms underlying this relationship, we studied nine long-lived C. elegans mutants representative of different pathways of lifespan extension. We directly compared the magnitude of their lifespan extension and their ability to resist various external stressors (heat, oxidative stress, bacterial pathogens, osmotic stress, and anoxia). Furthermore, we analysed gene expression in each of these mutants to identify genes and pathways responsible for the enhanced resistance to stress. All of the examined long-lived mutants have increased resistance to one or more type of stress. Resistance to each of the examined types of stress had a significant, positive correlation with lifespan, with bacterial pathogen resistance showing the strongest relationship. All of the examined long-lived mutants have significant upregulation of multiple stress response pathways but differ in which stress response pathway has the greatest enrichment of genes. We used RNA sequencing data to identify which genes are most highly correlated with each type of stress resistance. There was a highly significant overlap between genes highly correlated with stress resistance, and genes highly correlated with longevity, suggesting that the same genetic pathways drive both phenotypes. This was especially true for genes correlated with bacterial pathogen resistance, which showed an 84% overlap with genes correlated with lifespan. Overall, our results demonstrate a strong correlation between stress resistance and longevity that results from the high degree of overlap in genes contributing to each phenotype.

SIGNIFICANCE STATEMENTWhile increased resistance to stress has been correlated with longevity, the genetic basis for this relationship is incompletely understood. To advance our understanding of the relationship between stress resistance and lifespan, we measured lifespan, stress resistance and gene expression in a panel of nine long-lived mutants in C. elegans. All of the long-lived mutants exhibit enhanced resistance to at least one external stressor resulting from significant upregulation of multiple stress response pathways. Importantly, our data indicates that the same genetic pathways control stress resistance and lifespan, thereby accounting for the strong correlation between these two phenotypes. This work demonstrates the importance of innate immune signaling and other stress response pathways in determining longevity.


title: CUT&Tag-BS: an efficient and low-cost method for simultaneous profiling of histone modification and DNA methylation

abstract: It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic localization of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS shows similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further reveals that H3K4me1-marked regions are mostly CpG-poor, lack methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenarios with precious biological samples.

category: genomics


title: CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

abstract:
BackgroundUsing long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the best workflow is a complex task.

ResultsTo tackle this challenge, we developed CulebrONT, an open-source, scalable, modular and traceable Snakemake pipeline for assembling long reads data. CulebrONT enables to perform tests on multiple samples and multiple long reads assemblers in parallel, and can optionally perform, downstream circularization and polishing. It further provides a range of assembly quality metrics summarized in a final user-friendly report.

ConclusionsCulebrONT alleviates the difficulties of assembly pipelines development, and allow users to identify the best assembly options.

category: bioinformatics


title: Diisopropylfluorophosphate (DFP) volatizes and cross-contaminates wells in a common 96-well plate zebrafish larvae exposure method

abstract: Diisopropylfluorophosphate (DFP) is an organophosphate (OP) that is commonly used to study the neurotoxic effects of acutely intoxicating OP exposure. In preliminary studies, we discovered abnormal deaths in DMSO-only exposed larvae housed in the same plate as DFP-exposed larvae, and hypothesized that DFP volatilizes and cross-contaminates wells when using a 96-well plate exposure method for exposing zebrafish larvae. Survivability and acetylcholinesterase activity assays confirmed DFP presence in the tissues of zebrafish ostensibly exposed to DMSO only. These findings indicate DFP cross-contamination, which raises concerns for the experimental design of studies evaluating the toxicity of volatile and semi-volatile substances.


title: Cardiac-generated sympathetic stress alters heart-brain communication, reduces EEG-theta activity, and increases locomotor behavior

abstract: Brain modulation of myocardial activity via the autonomic nervous system is increasingly well characterized. Conversely, how primary alterations in cardiac function, such as an intrinsic increase in heart rate or contractility, reverberate on brain signaling/adaptive behaviors - in a bottom-up modality - remains largely unclear. Mice with cardiac-selective overexpression of adenylyl cyclase type 8 (TGAC8) display increased heart rate and reduced heart rhythm complexity associated with a nearly abolished response to external sympathetic inputs. Here, we tested whether chronically elevated intrinsic cardiac performance alters the heart-brain informational flow, affecting brain signaling and, thus, behavior. To this end, we employed dual lead telemetry for simultaneous recording of EEG and EKG time series in awake, freely behaving TGAC8 mice and wild-type (WT) littermates. We recorded EEG and EKG signals, while monitoring mouse behavior with established tests. Using heart rate variability (HRV) in vivo and isolated atria response to sympathomimetic agents, we first confirmed that the TGAC8 murine heart evades autonomic control. The EEG analysis revealed a substantial drop in theta-2 (4-7 Hz) activity in these transgenic mice. Next, we traced the informational flow between EKG and EEG in the theta-2 frequency band via the Granger causality statistical approach and we found a substantial decrement in the extent of heart/brain bidirectional communication. Finally, TGAC8 mice displayed heightened locomotor activity in terms of behavior, with higher total time mobile, distance traveled, and movement speed while freezing behavior was reduced. Increased locomotion correlated negatively with theta-2 waves count and amplitude. Our study shows that cardiac-born persistent sympathetic stress disrupts the information flow between the heart and brain while influencing central physiological patterns, such as theta activity that controls locomotion. Thus, cardiac-initiated disorders, such as persistently elevated cardiac performance that escapes autonomic control, are penetrant enough to alter brain functions and, thus, primary adaptive behavioral responses.


title: Typical and disrupted brain circuitry for conscious awareness in full-term and preterm infants

abstract: One of the great frontiers of consciousness science is understanding how early consciousness arises in the development of the human infant. The reciprocal relationship between the default mode network (DMN) and frontoparietal networks -- the dorsal attention network (DAN) and executive control network (ECN) -- is thought to facilitate integration of information across the brain and its availability for conscious access to a wide set of mental operations. It remains unknown whether the brain mechanism of conscious awareness is instated in infants from birth. To address this gap, we asked what the impact of prematurity and neonate age is on the development the default mode and fronto-parietal networks, and of their reciprocal relationship. To address these questions, we used the Developing Human Connectome Project (dHCP), a unique Open Science project which provides a large sample of neonatal functional Magnetic Resonance Imaging (fMRI) data with high temporal and spatial resolution. Resting state fMRI data for full-term neonates (N = 282, age 41.2 w {+/-} 12 d), and preterm neonates scanned at term-equivalent age (TEA) (N = 73, 40.9 w {+/-} 14.5 d), or before TEA (N = 73, 34.6 w {+/-} 13.4 d) were obtained from the dHCP, and for a reference adult group (N = 176, 22 - 36 years), from the Human Connectome Project. For the first time, we show that the reciprocal relationship between the DMN and DAN was present at full-term birth or TEA. Although different from the adult networks, the DMN, DAN and ECN were present as distinct networks at full-term birth or TEA, but premature birth disrupted network development. By contrast, neonates before TEA showed dramatic underdevelopment of high-order networks. Only the DAN was present as a distinct network and the reciprocal network relationship was not yet formed. Our results suggest that, at full-term birth or by term-equivalent age, infants possess key features of the neural circuitry that enables integration of information across diverse sensory and high-order functional modules, giving rise to conscious access. Conversely, they suggest that this brain infrastructure is not present before infants reach term-equivalent age. These findings improve understanding of the ontogeny of high-order network dynamics that support conscious awareness, and of their disruption by premature birth.


title: Emergence and fragmentation of the alpha-band driven by neuronal network dynamics

abstract:
Rhythmic neuronal network activity underlies brain oscillations. To investigate how connected neuronal networks contribute to the emergence of the -band and the regulation of Up and Down states, we study a model based on synaptic short-term depression-facilitation with afterhyperpolarization (AHP). We found that the -band is generated by the network behavior near the attractor of the Up-state. Coupling inhibitory and excitatory networks by reciprocal connections leads to the emergence of a stable -band during the Up states, as reflected in the spectrogram. To better characterize the emergence and stability of thalamocortical oscillations containing  and{delta} rhythms during anesthesia, we model the interaction of two excitatory with one inhibitory networks, showing that this minimal network topology leads to a persistent -band in the neuronal voltage characterized by dominant Up over Down states. Finally, we show that the emergence of the -band appears when external inputs are suppressed, while the fragmentation occurs at small synaptic noise or with increasing inhibitory inputs. To conclude, interaction between excitatory neuronal networks with and without AHP seems to be a general principle underlying changes in network oscillations that could apply to other rhythms.

Author summaryBrain oscillations recorded from electroencephalograms characterize behaviors such as sleep, wakefulness, brain evoked responses, coma or anesthesia. The underlying rhythms for these oscillations are associated at a neuronal population level to fluctuations of the membrane potential between Up (depolarized) and Down (hyperpolarized) states. During anesthesia with propofol, a dominant alpha-band (8-12Hz) can emerge or disappear, but the underlying mechanisms remain unclear. Using modeling, we report that the alpha-band appears during Up states in neuronal populations driven by short-term synaptic plasticity and noise. Moreover, we show that three connected networks representing the thalamocortical loop reproduce the dynamics of the alpha-band, which emerges following the arrest of excitatory stimulations, but can disappear by increasing inhibitory inputs. To conclude, short-term plasticity in well connected neuronal networks can explain the emergence and fragmentation of the alpha-band.


title: Diet modifies allele-specific phenotypes in Drosophila carrying epilepsy-associated PNPO variants

abstract: Pyridox(am)ine 5-phosphate oxidase (PNPO) catalyzes the rate-limiting step in the synthesis of pyridoxal 5-phosphate (PLP), the active form of vitamin B6 required for the synthesis of neurotransmitters GABA and monoamines. Pathogenic variants in PNPO have been repeatedly identified in patients with neonatal epileptic encephalopathy and early-onset epilepsy. These patients often exhibit different types of seizures and variable comorbidities, including developmental impairment and intellectual disability. It is unclear how seizure types and associated comorbidities are linked to specific PNPO alleles and to what degree diet can modify their expression. Furthermore, the molecular characteristics of PNPO variants have not been examined in model systems. Using CRISPR/Cas9, we generated four knock-in Drosophila alleles, hWT, hR116Q, hD33V, and hR95H, in which the endogenous Drosophila PNPO (sugarlethal) was replaced by wild-type human PNPO cDNA and epilepsy-associated variants corresponding to R116Q, D33V, and R95H, respectively. We examined these knock-in flies at the molecular, circuitry, and behavioral levels. Collectively, we found a wide range of phenotypes in an allele- and diet-dependent manner. Specifically, the D33V mutation reduces the mRNA level, R95H reduces the protein stability, and R116Q alters the protein localization of PNPO in the brain. D33V and R95H mutations lead to partial and complete lethality during development, respectively and R116Q and D33V mutations shorten lifespan. At the behavioral level, hD33V/hR95H trans-heterozygous flies are hypoactive on all tested diets whereas hR116Q flies show diet-dependent locomotor activities. At the circuitry level, hD33V homozygotes show rhythmic burst firing and hD33V/hR95H trans-heterozygotes exhibit spontaneous seizure discharges. In hR95H homozygotes rescued with PLP supplementation, we uncovered that PLP deficiency abolishes development and causes extreme seizures in adults. Lastly, genetic and electrophysiological analyses demonstrate that hWT/hR95H heterozygous flies are prone to seizures due to a dominant-negative effect of hR95H on hWT, highlighting the possibility that human R95H carriers may also be susceptible to epilepsy. Together, this study demonstrates that human PNPO variants interact with diet to contribute to phenotypic variations; and that the knock-in Drosophila model offers a powerful approach to systematically examine clinical manifestations and the underlying mechanisms of human PNPO deficiency.


title: Postsynaptic neuroligin-1 mediates presynaptic endocytosis during neuronal activity

abstract: Fast, high-fidelity neurotransmission and synaptic efficacy requires tightly regulated coordination of pre- and postsynaptic compartments and alignment of presynaptic release sites with postsynaptic receptor nanodomains. Neuroligin-1 (Nlgn-1) is a postsynaptic cell-adhesion protein exclusively localised to excitatory synapses that is crucial for coordinating the transsynaptic alignment of presynaptic release sites with postsynaptic AMPA receptors as well as postsynaptic transmission and plasticity. However, little is understood about whether the postsynaptic machinery can mediate the molecular architecture and activity of the presynaptic nerve terminal, and thus it remains unclear whether there are presynaptic contributions to Nlgn1-dependent control of signalling and plasticity. Here, we employed a presynaptic reporter of neurotransmitter release and synaptic vesicle dynamics, synaptophysin-pHluorin (sypHy), to directly assess the presynaptic impact of loss of Nlgn1. We show that lack of Nlgn1 had no effect on the size of the readily releasable or entire recycling pool of synaptic vesicles, nor did it impact exocytosis. However, we observed significant changes in the retrieval of synaptic vesicles by compensatory endocytosis, specifically during activity. Our data extends growing evidence that synaptic adhesion molecules critical for forming transsynaptic scaffolds are also important for regulating activity-induced endocytosis at the presynapse.


title: Effects of four antibiotics on the diversity of the intestinal microbiota

abstract: Oral antibiotics remain the therapy of choice for severe bacterial infections; however, antibiotic use disrupts the intestinal microbiota, which increases the risk of colonization with intestinal pathogens. Currently, our understanding of antibiotic-mediated disturbances of the microbiota remains at the level of bacterial families or specific species, and little is known about the effect of antibiotics on potentially beneficial and potentially pathogenic bacteria under conditions of gut microbiota dysbiosis. Additionally, it is controversial whether the effects of antibiotics on the gut microbiota are temporary or permanent. In this study, we used 16S rRNA gene sequencing to evaluate the short-term and long-term effects of ampicillin, vancomycin, metronidazole, and neomycin on the murine intestinal microbiota by analyzing changes in the relative numbers of potentially beneficial and potentially pathogenic bacteria. We found that the changes in the intestinal microbiota reflected the antibiotics mechanisms of action and that dysbiosis of the intestinal microbiota led to competition between the different bacterial communities. Thus, destruction of bacteria with beneficial potential increased the abundance of bacteria with pathogenic potential. In addition, we found that these oral antibiotics had long-term negative effects on the intestinal microbiota and promoted the development of antibiotic-resistant bacterial strains. These results indicate that ampicillin, vancomycin, metronidazole, and neomycin have long-term negative effects and can cause irreversible changes in the diversity of the intestinal microbiota and the relative proportions of bacteria with beneficial potential and bacteria with pathogenic potential, thereby increasing the risk of host disease.

category: microbiology


title: The effect of climate change on the distribution of Canidae

abstract: Land use by humans and climate change have been seriously affecting the distribution of species resulting in a quarter of all known mammals currently threatened with extinction. Here, we modeled the present and future potential distributions of all 36 extant Canidae species to evaluate their response to future climate scenarios. In addition, we tested if canids were likely to experience evolutionary rescue, which could allow some species to adapt to climate change. Our results suggest that global warming will cause most species to lose or maintain their ranges, while a few will have the potential to benefit from future conditions and considerably expand their geographic distributions. Some canids have the potential to experience evolutionary rescue, but Atelocynus microtis and Chrysocyon brachyurus are two concerning cases that do not show this capacity to adapt given the current pace of climate change. We also reveal that most Canidae hotspot regions are outside protected areas, which may be useful for the identification of key areas for conservation.


title: Megasatellite formation and evolution in vertebrates

abstract: Since the formation of the first proto-eukaryotes, more than 1.5 billion years ago, eukaryotic gene repertoire as well as genome complexity has significantly increased. Among genetic elements that are responsible for this increase in genome coding capacity and plasticity are tandem repeats such as microsatellites, minisatellites and their bigger brothers, megasatellites. Although microsatellites have been thoroughly studied in many organisms for the last 20 years, little is known about the distribution and evolution of mini- and megasatellites. Here, we describe the first genome-wide analysis of megasatellites in 58 vertebrate genomes, belonging to 12 monophyletic groups. We show that two bursts of megasatellite formation occurred, one after the radiation between agnatha et gnathostomata fishes and the second one later, in therian mammals. Megasatellites are frequently encoded in genes involved in transcription regulation (zinc-finger proteins) and intracellular trafficking, but also in cell membrane metabolism, reminiscent of what was observed in fungi genomes. The presence of many introns within young megasatellites suggests a model in which an exon-intron DNA segment is first duplicated and amplified before the accumulation of mutations in intronic parts partially erase the tandem repeat in such a way that it becomes detectable only in exonic regions. In addition, evidence for the genetic transfer of megasatellites between unrelated genes suggests that megasatellite formation and evolution is a very dynamic and still ongoing process in vertebrate genomes.


title: The joint evolution of movement and competition strategies

abstract: Competition typically takes place in a spatial context, but eco-evolutionary models rarely address the joint evolution of movement and competition strategies. Here we investigate a spatially explicit producer-scrounger model where consumers can either forage on a heterogeneous resource landscape or steal resource items from conspecifics (kleptoparasitism). We consider three scenarios: (1) a population of foragers in the absence of kleptoparasites; (2) a population of consumers that are either specialized on foraging or on kleptoparasitism; and (3) a population of individuals that can fine-tune their behavior by switching between foraging and kleptoparasitism depending on local conditions. By means of individual-based simulations, we study the joint evolution of movement and competition strategies, and we investigate the implications on the resource landscape and the distribution of consumers over this landscape. In all scenarios and for all parameters considered, movement and competition strategies evolved rapidly and consistently across replicate simulations. The evolved movement and resource exploitation patterns differ considerably across the three scenarios. For example, foragers are attracted by conspecifics in scenario (1), while they are repelled by conspecifics in scenario (2). Generally the movement strategies of kleptoparasites differ markedly from those of foragers, but even within each class of consumers polymorphisms emerge, corresponding to pronounced differences in movement patterns. In all scenarios, the distribution of consumers over resources differs substantially from  ideal free predictions. We show that this is related to the intrinsic difficulty of moving effectively on a depleted landscape with few reliable cues for movement. Our study emphasises the advantages of a mechanistic approach when studying competition in a spatial context, and suggests how evolutionary modelling can be integrated with current work in animal movement ecology.


title: The joint evolution of animal movement and competition strategies


title: Spontaneous emergence of multicellular heritability

abstract: The Major Transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. A change in the means by which genetic information is utilized and transmitted has been presumed necessary. Using analytical models, synthetic biology, and biologicallyinformed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Contrary to existing theory, we show that no additional layer of genetic regulation is necessary for traits of nascent multicellular organisms to become heritable; rather, heritability and the capacity to respond to natural selection on multicellular-level traits can arise "for free." In fact, we find that a key emergent multicellular trait, organism size at reproduction, is usually more heritable than the underlying cell-level trait upon which it is based, given reasonable assumptions.


title: Inference of polyploid origin and inheritance mode from population genomic data

abstract: Summary/AbstractWhole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, here we describe two bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data. The first approach is based on distributions of allelic read depth at the heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.


title: Customization of a dada2-based pipeline for fungal Internal Transcribed Spacer 1 (ITS 1) amplicon datasets

abstract: Identification and analysis of fungal communities commonly rely on internal transcribed spacer (ITS)-based amplicon sequencing. Currently, there is no gold standard to infer and classify fungal constituents, in part since methodologies have been adapted from analyses of bacterial communities. To achieve high resolution inference of fungi in clinical samples, we customized a DADA2-based pipeline using a mock community of eleven medically relevant fungi. While DADA2 allowed the discrimination of ITS1 sequences differing by a single nucleotide, quality filtering, sequencing bias, and database selection were identified as key variables determining the accuracy of sample inference. By fine-tuning quality filtering, we decreased the number of wrongly discarded sequences attributed to Aspergillus species, Saccharomyces cerevisiae, and Candida glabrata reads. We confirmed this effect in patient samples. By adapting a wobble nucleotide in the ITS1 forward primer region, we further increased the yield of S. saccharomyces and C. glabrata sequences. Finally, we showed that a BLAST-based algorithm based on the UNITE+INSD or the NCBI NT database achieved a higher reliability in species-level taxonomic annotation than the naive Bayesian classifier implemented in DADA2. These steps optimized a robust fungal ITS1 sequencing pipeline that, in most instances, enables species level-assignment of community members.


title: Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells

abstract:
BackgroundSAMHD1 mediates resistance to anti-cancer nucleoside analogues, including cytarabine, decitabine, and nelarabine that are commonly used for the treatment of leukaemia, through cleavage of their triphosphorylated forms. Hence, SAMHD1 inhibitors are promising candidates for the sensitisation of leukaemia cells to nucleoside analogue-based therapy. Here, we investigated the effects of the cytosine analogue CNDAC, which has been proposed to be a SAMHD1 substrate, in the context of SAMHD1.

MethodsCNDAC was tested in 13 acute myeloid leukaemia (AML cell lines), in 26 acute lymphoblastic leukaemia cell lines, ten AML sublines adapted to various antileukaemic drugs, 24 single cell-derived clonal AML sublines, and primary leukaemic blasts from 24 AML patients. Moreover, 24 CNDAC-resistant sublines of the AML cell lines HL-60 and PL-21 were established. The SAMHD1 gene was disrupted using CRISPR/Cas9 and SAMHD1 depleted using RNAi, and the viral Vpx protein. Forced DCK expression was achieved by lentiviral transduction. SAMHD1 promoter methylation was determined by PCR after treatment of genomic DNA with the methylation-sensitive HpaII endonuclease. Nucleoside (analogue) triphosphate levels were determined by LC-MS/MS. CNDAC interaction with SAMHD1 was analysed by an enzymatic assay and by crystallisation.

ResultsAlthough the cytosine analogue CNDAC was anticipated to inhibit SAMHD1, SAMHD1 mediated intrinsic CNDAC resistance in leukaemia cells. Accordingly, SAMHD1 depletion increased CNDAC triphosphate (CNDAC-TP) levels and CNDAC toxicity. Enzymatic assays and crystallisation studies confirmed CNDAC-TP to be a SAMHD1 substrate. In 24 CNDAC-adapted acute myeloid leukaemia (AML) sublines, resistance was driven by DCK (catalyses initial nucleoside phosphorylation) loss. CNDAC-adapted sublines displayed cross-resistance only to other DCK substrates (e.g. cytarabine, decitabine). Cell lines adapted to drugs not affected by DCK or SAMHD1 remained CNDAC sensitive. In cytarabine-adapted AML cells, increased SAMHD1 and reduced DCK levels contributed to cytarabine and CNDAC resistance.

ConclusionIntrinsic and acquired resistance to CNDAC and related nucleoside analogues are driven by different mechanisms. The lack of cross-resistance between SAMHD1/ DCK substrates and non-substrates provides scope for next-line therapies after treatment failure.


title: Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae

abstract:
BackgroundCorynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking.

MethodsWe combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST genes diversity among 602 isolates from sporadic clinical cases, small clusters or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages.

ResultsThe cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold, and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed short timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500 cgMLST mismatches threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible at https://bigsdb.pasteur.fr/diphtheria.

ConclusionsStandardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae. The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies into the ecology, evolution and virulence heterogeneity among C. diphtheriae sublineages.


title: Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

abstract:
Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods.

ImportanceEnvironmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made towards containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) [1], a large-scale environmental monitoring effort in elementary school and child care settings, has processed > 13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT - qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.


title: Rapid visual CRISPR assay: a naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and convolutional neural network

abstract: Rapid diagnosis based on naked-eye colorimetric detection remains challenging, but it could build new capacities for molecular point-of-care testing (POCT). In this study, we evaluated the performance of 16 types of single-stranded DNA-fluorophore-quencher (ssDNA-FQ) reporters for use with CRISPR/Cas12a based visual colorimetric assays. Among them, 9 ssDNA-FQ reporters were found to be suitable for direct visual colorimetric detection, with especially very strong performance using ROX-labeled reporters. We optimized the reaction concentrations of these ssDNA-FQ reporters for naked-eye read-out of assay results (no transducing component required for visualization). Subsequently, we developed a convolutional neural network algorithm standardize and to automate the analytical colorimetric assessment of images and integrated this into the MagicEye mobile phone software. A field-deployable assay platform named RApid VIsual CRISPR (RAVI-CRISPR) based on a ROX-labeled reporter with isothermal amplification and CRISPR/Cas12a targeting was established. We deployed RAVI-CRISPR in a single tube towards an instrument-less colorimetric POCT format that requires only a portable rechargeable hand warmer for incubation. The RAVI-CRISPR was successfully used for the single-copy detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and African swine fever virus (ASFV). Our study demonstrates this novel RAVI-CRISPR system for distinguishing different pathogenic nucleic acid targets with high specificity and sensitivity as the simplest-to-date platform for rapid pen-side testing.

category: molecular biology


title: Intrabody induced cell death by targeting the T. brucei cytoskeletal protein TbBILBO1

abstract: Trypanosoma brucei belongs to a genus of protists that cause life-threatening and economically important diseases of human and animal populations in Sub-Saharan Africa. T. brucei cells are covered in surface glycoproteins some of which are used to escape the host immune system. Exo-/endocytotic trafficking of these and other molecules occurs via a single copy organelle called the flagellar pocket (FP). The FP is maintained and enclosed around the flagellum by the flagellar pocket collar (FPC). To date, the most important cytoskeletal component of the FPC is an essential, calcium-binding, polymer-forming protein called TbBILBO1. In searching for novel immune-tools to study this protein, we raised nanobodies against TbBILBO1. Nanobodies (Nb) that were selected according to their binding properties to TbBILBO1, were tested as immunofluorescence tools, and expressed as intrabodies (INb). One of them, Nb48, proved to be the most robust nanobody and intrabody. We further demonstrate that inducible, cytoplasmic expression of INb48 was lethal to these parasites, producing abnormal phenotypes resembling those of TbBILBO1 RNAi knockdown. Our results validate the feasibility of generating functional single-domain antibody derived intrabodies to target trypanosome cytoskeleton proteins.

category: cell biology


title: Intramembrane protease SPP defines a cholesterol-regulated switch of the mevalonate pathway

abstract: Intramembrane proteolysis regulates important processes such as signaling and transcriptional and posttranslational abundance control of proteins with key functions in metabolic pathways. This includes transcriptional control of mevalonate pathway genes, thereby ensuring balanced biosynthesis of cholesterol and other isoprenoids. Our work shows that, at high cholesterol levels, signal peptide peptidase (SPP) cleaves squalene synthase (SQS), an enzyme that defines the branching point for allocation of isoprenoids to the sterol and non-sterol arms of the mevalonate pathway. This intramembrane cleavage releases SQS from the membrane and targets it for proteasomal degradation. Regulation of this mechanism is achieved by the E3 ubiquitin ligase TRC8 that, in addition to ubiquitinating SQS in response to cholesterol levels, acts as an allosteric activator of SPP-catalyzed intramembrane cleavage of SQS and other substrates. Hence, SPP-TRC8 mediated abundance control of SQS acts as a metabolic switch within the mevalonate pathway.


title: A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development

abstract: A  histone code defines system-level crosstalk between histone post-translational modifications (PTMs) to induce specific biological outcomes. Proteome-scale information of co-existing PTM across the entire chromatin landscape of the malaria parasite, Plasmodium falciparum, was lacking. Here, we used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 72 PTMs on H3 and H3.3, of which 30 are novel to the parasite. Co-existing PTMs with unique stage distinction was identified, indicating a dynamic and complex histone code with increased connectivity of novel PTMs seen in gametocytes. Chromatin proteomics of a gametocyte-specific combination, H3R17me2K18acK23ac, identified a SAGA-like effector complex (including the transcription factor AP2-G2) tied to this combination to regulate gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with co-existing partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher order gene regulation for distinct proliferation and differentiation processes.

category: biochemistry


title: The diversity of quinoa morphological traits and seed metabolic composition

abstract:
Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.

O_TBL View this table:
org.highwire.dtl.DTLVardef@160e784org.highwire.dtl.DTLVardef@ff8bd1org.highwire.dtl.DTLVardef@13446daorg.highwire.dtl.DTLVardef@11796eeorg.highwire.dtl.DTLVardef@1b607b8_HPS_FORMAT_FIGEXP  M_TBL C_TBL


title: Sex differences in tissue gene regulation -- contributions of three classes of sex-biasing factors

abstract: Sex differences in physiology and disease in mammals result from the effects of three classes of factors that are inherently unequal in males and females: reversible (activational) effects of gonadal hormones, permanent (organizational) effects of gonadal hormones, and cell-autonomous effects of sex chromosomes, as well as genes driven by these classes of factors. Often, these factors act together to cause sex differences in specific phenotypes, but the relative contribution of each and the interactions among them remain unclear. Here, we used the Four Core Genotypes (FCG) mouse model with or without hormone replacement to distinguish the effects of each class of sex-biasing factors on transcriptome regulation in liver and adipose tissues. We found that the activational hormone levels have the strongest influence on gene expression, followed by the organizational gonadal sex effect and, lastly, sex chromosomal effect, along with interactions among the three factors. Tissue specificity was prominent, with a major impact of estradiol on adipose tissue gene regulation, and of testosterone on the liver transcriptome. The networks affected by the three sex-biasing factors include development, immunity and metabolism, and tissue-specific regulators were identified for these networks. Furthermore, the genes affected by individual sex-biasing factors and interactions among factors are associated with human disease traits such as coronary artery disease, diabetes, and inflammatory bowel disease. Our study offers a tissue-specific account of the individual and interactive contributions of major sex-biasing factors to gene regulation that have broad impact on systemic metabolic, endocrine, and immune functions.


title: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation


title: Dendrite regeneration in C. elegans is controlled by the RAC GTPase CED-10 and the RhoGEF TIAM-1

abstract: Neurons are vulnerable to physical insults which compromise the integrity of both dendrites and axons. Although several molecular pathways of axon regeneration are identified, our knowledge of dendrite regeneration is limited. To understand the mechanisms of dendrite regeneration, we used PVD neurons in C. elegans having stereotyped branched dendrites. Using femtosecond laser, we severed the primary dendrites and axon of this neuron. After severing the primary dendrites near the cell body, we observed sprouting of new branches from the proximal site within 6 hours, which regrew further with timein an unstereotyped manner.This was accompanied by reconnection between the proximal and distal dendrites as well as the fusion among the higher-order branches as reported before. We quantified the regeneration pattern in threeaspects -territory length, number of branchesand fusion phenomena.Axonal injury causes a retraction of the severed end followed by a Dual leucine zipper kinase-1 (DLK-1) dependent regrowth from the severed end.We tested the roles of the major axon regenerationsignaling hubs such as DLK-1-RPM-1, cAMP elevation, let-7 miRNA, AKT-1, Phosphatidyl serine exposure/PS in dendrite regeneration. We found that neither regrowth nor fusionis affected by the axon injury pathway molecules. Surprisingly, we found that the RAC GTPase CED-10and its upstream GEF TIAM-1 play a cell-autonomous role in dendrite regeneration. Additionally, function of CED-10 in epidermal cell is critical for post-dendrotomy fusion phenomena. This work describes a novel regulatory mechanism of dendrite regeneration andprovides a framework for understanding the cellular mechanism of dendrite regeneration using PVD neuron as a model system.


title: Fast grip force adaptation to friction relies on localized fingerpad strains

abstract: AO_SCPLOWBSTRACTC_SCPLOWHumans can quickly adjust their grip force to a change in friction at the object-skin interface during dexterous manipulation in a precision grip. To perform this adjustment, they rely on the feedback of the mechanoreceptive afferents innervating the fingertip skin. Because these tactile afferents encode information related to skin deformation, the nature of the feedback signaling a change in friction must somehow originate from a difference in the way the skin deforms when manipulating objects of different frictions. To better characterize the origin of the underlying sensory events, we asked human participants to perform a grip-lifting task with a manipulandum equipped with an optical imaging system. This system enabled to monitor fingertip skin strains through transparent plates of glass that had different levels of friction. We observed that, following an unexpected change in friction, participants adapted their grip force within 370ms after contact with the surface. By comparing the deformation patterns when unexpectedly switching from a high to a low friction condition, we found a significant increase in skin deformation inside the contact area arising over 100ms before the motor response, during the loading phase, suggesting that local and partial deformation patterns prior to lift-off are used in the nervous system to adjust the grip force as a function of the frictional condition.


title: Don't think, feel: basal ganglia-cortical connectivity underlies self-regulation of brain oscillations in humans

abstract: Brain-computer interfaces (BCIs) provide an artificial link by which the brain can directly interact with the environment. To achieve fine BCI control, participants must modulate the patterns of the cortical oscillations generated from the motor and somatosensory cortices. However, it remains unclear how humans regulate cortical oscillations, the controllability of which substantially varies across individuals. Here, we performed simultaneous electroencephalography (to assess BCI control) and functional magnetic resonance imaging (to measure brain activity) in healthy participants. Self-regulation of cortical oscillations induced activity in the basal ganglia-cortical network (BgCN) and the neurofeedback control network (NfCN). Successful self-regulation correlated with striatal activity in the BgCN, through which patterns of cortical oscillations were likely modulated. Moreover, BgCN and NfCN connectivity correlated with strong and weak self-regulation, respectively. The findings indicate that the BgCN is important for self-regulation, the understanding of which should help advance BCI technology.


title: Mcc1229, an Stx2a-amplifying microcin, is produced in vivo and requires CirA for activity

abstract: Enterohemorrhagic E. coli (EHEC) strains, including the foodborne pathogen E. coli O157:H7, are responsible for thousands of hospitalizations each year. Various environmental triggers can modulate pathogenicity in EHEC by inducing expression of Shiga toxin (Stx), which is encoded on a lambdoid prophage and transcribed together with phage late genes. Cell-free supernatants of the sequence type (ST) 73 E. coli strain 0.1229 are potent inducers of Stx2a production in EHEC, suggesting that 0.1229 secretes a factor that activates the SOS response and leads to phage lysis. We previously demonstrated that this factor, designated microcin (Mcc) 1229, was proteinaceous and plasmid-encoded. To further characterize Mcc1229 and support its classification as a microcin, we investigated its regulation, determined its receptor, and identified loci providing immunity. Production of Mcc1229 was increased upon iron limitation, as determined by ELISA, lacZ fusions, and qRT-PCR. Spontaneous Mcc1229-resistant mutants and targeted gene deletion revealed that CirA was the Mcc1229 receptor. TonB, which interacts with CirA in the periplasm, was also essential for Mcc1229 import. Subcloning of the Mcc1229 plasmid indicated that Mcc activity was neutralized by two ORFs, each predicted to encode a domain of unknown function (DUF)-containing protein. In a germfree mouse model of infection, colonization with 0.1229 suppressed subsequent colonization of EHEC. Although Mcc1229 was produced in vivo, it was dispensable for colonization suppression. The regulation, import, and immunity determinants identified here are consistent with features of other Mccs, suggesting that Mcc1229 be included in this class of small molecules.