title: Xtrapol8: automatic elucidation of low-occupancy intermediate-states in crystallographic studies

abstract: Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, hindering structure determination by conventional methods. To automatically extract such structures, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of hitherto unavailable methods; (iii) calculates various types of extrapolated structure factors while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures.


title: Exploitation of neighbouring subsoil for nutrient acquisition under annual-perennial strip intercropping systems

abstract: Little is known of how the deep root systems of perennial crops contribute to deeper and better resource use when intercropped with annuals in arable fields. Therefore, we aimed at measuring the capacity of perennial deep roots, alfalfa (Medicago sativa L.) and curly dock (Rumex crispus L.) to access the nutrient source located under the neighboring annuals at 1.0 and 2.5 m of soil depth. Alfalfa and curly dock were able to access the tracer-labelled source placed at a distance under the annual crop strips. As a result, the reliance on deeper soil layer for nutrient uptake under intercroppings became greater compared with sole-croppings. Combination of an annual cereal (winter rye) and a perennial legume (alfalfa) with contrasting root systems exhibited higher resource complementarity compared with intercroppings having similar root systems or absence of legumes. Our results demonstrated that the deep-rooted perennials when intercropped with annuals can induce vertical niche complementarity, especially at deeper soil layers. This was assumed to be due to the vertically stratified root activity between the crop components, however, the magnitude of the effects depended on choice of crop combinations, and on types of tracers. Future studies should include estimates such as relative yield total and land equivalent ratio to quantitatively determine the effects of resource acquisition under annual-perennial intercropping in arable fields.

category: plant biology


title: Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP

abstract: Maturation of eukaryotic pre-mRNAs via splicing, 3 end cleavage and polyadenylation is modulated across cell types and conditions by a variety of RNA-binding proteins (RBPs). Although over 1500 proteins are associated with RNAs in human cells, their binding motifs, targets and functions still remain to be elucidated, especially in the complex environment of human tissues and in the context of diseases. To overcome the lack of methods for systematic and automated detection of sequence motif-guided changes in pre-mRNA processing based on RNA sequencing (RNA-seq) data we have developed MAPP (Motif Activity on Pre-mRNA Processing). We demonstrate MAPPs functionality by applying it to RNA-seq data from 284 RBP knock-down experiments in the ENCODE project, from which MAPP not only infers position-dependent impact profiles of known regulators, but also reveals RBPs that modulate both the inclusion of cassette exons and the poly(A) site choice. Among these, the Polypyrimidine Tract Binding Protein 1 (PTBP1) has a similar activity in glioblastoma samples. This highlights the ability of MAPP to unveil global regulators of mRNA processing under physiological and pathological conditions.

category: systems biology


title: Localized Synaptic Potentiation is Necessary and Sufficient for Context Fear Memory

abstract: The nature and distribution of the synaptic changes that underlie memory are not well understood. We examined the synaptic plasticity behind context fear learning and found that conditioning produced potentiation of excitatory synapses specifically onto the basolateral amygdala neurons activated during learning. This synaptic potentiation lasted at least 7 days, and its disruption impaired memory recall. High frequency optogenetic stimulation of the CS and US-activated ensembles or biochemical induction of synaptic potentiation in US-responsive neurons alone was sufficient to produce a context fear association without prior associative training. These results suggest that plasticity of CS inputs onto US-responsive amygdala neurons is a necessary and sufficient step in forming context fear associations, and that context discrimination is determined by the CS-specific amygdala inputs activated during retrieval.

category: neuroscience


title: Estradiol mediates stress-susceptibility in the male brain

abstract: In susceptible populations, stress is a major risk factor for the development of mental disorders, including depression. Estradiol, often considered a female hormone, is distributed in the male brain via aromatization of testosterone. The role of estrogen receptors (ERs) in male stress susceptibility and depression is not well understood. We found that absence of ER{beta} is associated with susceptibility to stress in male mice and that activity of ER{beta}-projecting neurons from the basolateral amygdala to nucleus accumbens is reduced in hypogonadal mice subjected to stress, while activation of this circuit reverses stress-induced maladaptive behaviors. We identified that absence of estradiol, but not testosterone per se, underlies stress susceptibility and that brain-selective delivery of estradiol prevents the development of depression-related behaviors. Our findings provide evidence for an estrogen-based mechanism underlying stress susceptibility and offer an unexpected therapeutic strategy for treating depression in males.


title: Patterns of Saliency and Semantic Features Distinguish Gaze of Expert and Novice Viewers of Surveillance Footage

abstract:
When viewing the actions of others, we not only see patterns of body movements, but we also "see" the intentions and social relations of people, enabling us to understand the surrounding social environment. Previous research has shown that experienced forensic examiners--Closed Circuit Television (CCTV) operators--convey superior performance in identifying and predicting hostile intentions from surveillance footages than novices. However, it remains largely unknown what visual content CCTV operators actively attend to when viewing surveillance footage, and whether CCTV operators develop different strategies for active information seeking from what novices do. In this study, we conducted computational analysis for the gaze-centered stimuli captured by experienced CCTV operators and novices eye movements when they viewed the same surveillance footage. These analyses examined how low-level visual features and object-level semantic features contribute to attentive gaze patterns associated with the two groups of participants. Low-level image features were extracted by a visual saliency model, whereas object-level semantic features were extracted by a deep convolutional neural network (DCNN), AlexNet, from gaze-centered regions. We found that visual regions attended by CCTV operators versus by novices can be reliably classified by patterns of saliency features and DCNN features. Additionally, CCTV operators showed greater inter-subject correlation in attending to saliency features and DCNN features than did novices. These results suggest that the looking behavior of CCTV operators differs from novices by actively attending to different patterns of saliency and semantic features in both low-level and high-level visual processing. Expertise in selectively attending to informative features at different levels of visual hierarchy may play an important role in facilitating the efficient detection of social relationships between agents and the prediction of harmful intentions.

Author SummaryImagine seeing a person walking toward another person menacingly on the street, we may instantly feel that some physical confrontation will happen in the next second. However, it remains unclear how we efficiently infer social intentions and outcomes from the observed dynamic visual input. To answer this question, CCTV experts, who have years of experience on observing social scenes and making online predictions of the action outcomes, provide a unique perspective. Here, we collected experts and novices eye movements when observing different action sequences and compared the attended visual information between groups. A saliency model was used to compare low-level visual features such as luminance and color, and a deep convolutional neural network was used to extract object-level semantic visual features. Our findings showed that experts obtained different patterns of low-level and semantic-level features in visual processing compared to novices. Thus, the expertise in selectively attending to informative features at different levels of visual hierarchy may play an important role in facilitating the efficient detection of social relationships between agents and the prediction of harmful intentions.


title: Experimenter sex modulates mouse biobehavioural and pharmacological responses

abstract: Differential rodent responses to the sex of human experimenters could have far reaching consequences in preclinical studies. Here, we show that the sex of human experimenters affects mouse behaviours and responses to the rapid-acting antidepressant ketamine and its bioactive metabolite (2R,6R)-hydroxynorketamine. We found that mice manifest aversion to human male odours, preference to female odours, and increased susceptibility to stress when handled by male experimenters. This male induced aversion and stress susceptibility is mediated by the activation of brain corticotropin-releasing factor (CRF) neurons projecting from the entorhinal cortrex to hippocampal area CA1. We further establish that exposure to male scent prior to ketamine administration activates CRF neurons projecting from the entorhinal cortex to hippocampus, and that CRF is necessary and sufficient for ketamines in vivo and in vitro actions. Further understanding of the specific and quantitative contributions of the sex of human experimenters to different experimental outcomes in rodents may lead not only to reduced heterogeneity between studies, but also increased capability to uncover novel biological mechanisms.


title: Two subsets of circulating Ly6Clo monocytes distinguished by CD138 (syndecan-1) expression and Nr4a1 dependence in pristane-treated mice

abstract: Chronic peritoneal inflammation following pristane injection induces lupus with diffuse alveolar hemorrhage (DAH) and pulmonary capillaritis in C57BL/6 mice. The pathogenesis involves pristane-induced microvascular lung injury. BALB/c mice are resistant to endothelial injury and DAH. Lung disease in C57BL/6 mice is abolished by depleting monocytes/macrophages. The objective of this study was to define the role of myeloid subsets in DAH. Hemorrhage and vasculitis were abolished in Ccr2-/- mice, indicating involvement of bone marrow-derived monocytes/macrophages. Along with Ly6Chi monocytes, we found two subsets of circulating Ly6Clo monocytes: one CD138- and a novel CD138+ subset. Nr4a1-dependent patrolling Ly6Clo monocytes maintain vascular integrity after endothelial injury. Circulating Ly6CloCD138+ monocytes were associated with DAH and were absent in mice without DAH. They also were absent in Nr4a1-/- mice, whereas Ly6CloCD138- monocytes were unaffected. However, Nr4a1-/- mice were susceptible to pristane-induced DAH and lung vasculitis, suggesting that disease onset does not require Ly6CloCD138- monocytes. Peritoneal Ly6CloCD138+ M{phi} were unchanged in Nr4a1-/- mice, indicating that they are not derived from Ly6CloCD138+ monocytes. We conclude that pristane-induced lung microvascular lung injury stimulates a wave of Nr4h1-dependent Ly6CloCD138+ patrolling monocytes in an ineffectual effort to maintain vascular integrity in the face of ongoing endothelial damage.

category: immunology


title: Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing

abstract: Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine intestine, including SELLhi{gamma}{delta} T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular CD4 {beta} T cells, and cycling T/ILCs were enriched in ileum with Peyers patches, while non-cycling{gamma}{delta} T, CD8 {beta} T, and group 1 ILCs were enriched in ileum without Peyers patches. scRNA-seq findings were leveraged to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral porcine ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.


title: Patterns of Structural Variation Define Prostate Cancer Across Disease States

abstract: The complex genomic landscape of prostate cancer evolves across disease states under therapeutic pressure directed toward inhibiting androgen receptor (AR) signaling. While significantly altered genes in prostate cancer have been extensively defined, there have been fewer systematic analyses of how structural variation reflects the genomic landscape of this disease. We comprehensively characterized structural alterations across 278 localized and 143 metastatic prostate cancers profiled by whole genome and transcriptome sequencing. We observed distinct significantly recurrent breakpoints in localized and metastatic castration-resistant prostate cancers (mCRPC), with pervasive alterations in noncoding regions flanking the AR, MYC, FOXA1, and LSAMP genes in mCRPC. We defined nine subclasses of mCRPC based on signatures of structural variation, each associated with distinct genetic features and clinical outcomes. Our results comprehensively define patterns of structural variation in prostate cancer and identify clinically actionable subgroups based on whole genome profiling.

category: genomics


title: Multi-cancer classification; an analysis of neural network complexity

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSCancer identification is generally framed as binary classification, normally discrimination of a control group from a single cancer group. However, such models lack any cancer-specific information, as they are only trained on one cancer type. The models fail to account for competing cancer risks. For example, an ostensibly healthy individual may have any number of different cancer types, and a tumor may originate from one of several primary sites. Pan-cancer evaluation requires a model trained on multiple cancer types, and controls, simultaneously, so that a physician can be directed to the correct area of the body for further testing.

MethodsWe introduce novel neural network models to address multi-cancer classification problems across several data types commonly applied in cancer prediction, including circulating miRNA expression, protein, and mRNA. In particular, we present an analysis of neural network depth and complexity, and investigate how this relates to classification performance. Comparisons of our models with state-of-the-art neural networks from the literature are also presented.

ResultsOur analysis evidences that shallow, feed-forward neural net architectures offer greater performance when compared to more complex deep feed-forward, Convolutional Neural Network (CNN), and Graph CNN (GCNN) architectures considered in the literature.

ConclusionThe results show that multiple cancers and controls can be classified accurately using the proposed models, across a range of expression technologies in cancer prediction.

ImpactThis study addresses the important problem of pan-cancer classification, which is often overlooked in the literature. The promising results highlight the urgency for further research.

category: bioinformatics


title: Collagen XVIII promotes breast cancer through EGFR/ErbB signaling and its ablation improves the efficacy of ErbB-targeting inhibitors

abstract:
The tumor extracellular matrix (ECM) is a critical regulator of cancer progression and metastasis, significantly affecting the treatment response. Expression of collagen XVIII (ColXVIII), a ubiquitous component of basement membranes, is induced in many solid tumors, but its involvement in tumorigenesis has remained elusive. We show here that ColXVIII is markedly upregulated in human breast cancer (BC) cells and is closely associated with a poor prognosis in high-grade BC, especially in human epidermal growth factor receptor 2 (HER2)-positive and basal/triple-negative cases. We identified a novel mechanism of action for ColXVIII as a modulator of epidermal growth factor receptor (EGFR/ErbB) signaling and show that it forms a complex with EGFR, HER2 and 6 integrin to promote cancer cell proliferation in a pathway involving its N-terminal portion and the MAPK/ERK1/2 and PI3K/Akt cascades. In vivo studies with Col18a1 mouse models crossed with the MMTV-PyMT mammary carcinogenesis model showed that the short ColXVIII isoform promotes BC growth and metastasis in a tumor cell-autonomous manner. Moreover, the number of mammary cancer stem cells was significantly reduced in both mouse and human cell models upon ColXVIII inhibition. Finally, ablation of ColXVIII in human BC cells and the MMTV-PyMT model substantially improved the efficacy of certain EGFR/ERbB-targeting therapies, even abolishing resistance to EGFR/ErbB inhibitors in some cell lines. In summary, a new function is revealed for ColXVIII in sustaining the stemness properties of BC cells, and tumor progression and metastasis through EGFR/ErbB signaling, suggesting that targeting ColXVIII in the tumor milieu may have significant therapeutic potential.

One Sentence SummaryCollagen XVIII is upregulated in breast cancer and promotes mammary carcinogenesis through EGFR/ErbB signaling and by sustaining cancer stem cells, so that its targeting improves the efficacy of ErbB-targeted therapies.

category: cancer biology


title: Microstructural Impairments in a Topologically Distinct Prefrontal-Habenular Connection in Cocaine Addiction

abstract: Drug addiction is characterized by neuroadaptations in mesocorticolimbic networks regulating reward and inhibitory control. The habenula (Hb) is central to adaptive reward and aversion-driven behaviors, serving as a hub connecting emotion/cognitive processing regions including the prefrontal cortex (PFC). However, its role in human drug addiction has not been fully explored. Using diffusion tractography, we detailed PFC structural connectivity with three regions, namely the Hb, ventral tegmental area (VTA), and anterior thalamus (AT), and quantified the tract-specific microstructural integrity using diffusion tensor imaging within the anterior limb of the internal capsule (ALIC) in healthy and cocaine-addicted individuals. White matter microstructure in cocaine-addicted individuals was uniquely impaired in PFC-Hb projections in the ALIC, distinguishable from adjacent PFC-VTA and PFC-AT projections, with more pronounced abnormalities in short-term abstinence. These findings extend preclinical evidence of PFC-Hb circuit impairments in addiction and contextualize the plausible existence of a similar PFC-Hb connection in the human brain.


title: Accurate sex classification from neural responses to sexual stimuli

abstract: Sex differences in brain activity evoked by sexual stimuli remain elusive despite robust evidence for stronger enjoyment of and interest towards sexual stimuli in men than in women. To test whether visual sexual stimuli evoke different brain activity patterns in men and women, we measured haemodynamic brain activity induced by visual sexual stimuli in two experiments in 91 subjects (46 males). In one experiment, the subjects viewed sexual and non-sexual film clips and dynamic annotations for nudity in the clips was used to predict their hemodynamic activity. In the second experiment, the subjects viewed sexual and non-sexual pictures in an event-related design. Males showed stronger activation than females in the visual and prefrontal cortices and dorsal attention network in both experiments. Furthermore, using multivariate pattern classification we could accurately predict the sex of the subject on the basis of the brain activity elicited by the sexual stimuli. The classification generalized across the experiments indicating that the sex differences were consistent. Eye tracking data obtained from an independent sample of subjects (N = 110) showed that men looked longer than women at the chest area of the nude female actors in the film clips. These results indicate that visual sexual stimuli evoke discernible brain activity patterns in men and women which may reflect stronger attentional engagement with sexual stimuli in men than women.


title: Short periods of bipolar anodal TDCS induce no instantaneous dose-dependent increase in cerebral blood flow in the targeted human motor cortex

abstract:
BackgroundAnodal transcranial direct current stimulation (aTDCS) of primary motor hand area (M1-HAND) can enhance corticomotor excitability. Yet, it is still unknown which current intensity produces the strongest effect on regional neural activity. Magnetic resonance imaging (MRI) combined with pseudo-continuous Arterial Spin Labeling (pc-ASL MRI) can map regional cortical blood flow (rCBF) and may thus be useful to probe the relationship between current intensity and neural response at the individual level.

ObjectiveHere we employed pc-ASL MRI to map acute rCBF changes during short-duration aTDCS of left M1-HAND. Using the rCBF response as a proxy for regional neuronal activity, we investigated if short-duration aTDCS produces an instantaneous dose-dependent rCBF increase in the targeted M1-HAND that may be useful for individual dosing.

MethodsNine healthy right-handed participants received 30 seconds of aTDCS at 0.5, 1.0, 1.5, and 2.0 mA with the anode placed over left M1-HAND and cathode over the right supraorbital region. Concurrent pc-ASL MRI at 3 T probed TDCS-related rCBF changes in the targeted M1-HAND. Movement-induced rCBF changes were also assessed.

ResultsApart from a subtle increase in rCBF at 0.5 mA, short-duration aTDCS did not modulate rCBF in the M1-HAND relative to no-stimulation periods. None of the participants showed a dose-dependent increase in rCBF during aTDCS, even after accounting for individual differences in TDCS-induced electrical field strength. In contrast, finger movements led to robust activation of left M1-HAND before and after aTDCS.

ConclusionShort-duration bipolar aTDCS does not produce instantaneous dose-dependent rCBF increases in the targeted M1-HAND at conventional intensity ranges.

Therefore, the regional hemodynamic response profile to short-duration aTDCS may not be suited to inform individual dosing of TDCS intensity.

HighlightsO_LIArterial spin labeling (ASL) MRI probed regional cerebral blood flow (rCBF) during anodal TDCS.
C_LIO_LIShort-duration anodal TDCS was applied to left motor hand area (M1-HAND) at 0.5, 1.0, 1.5 and 2.0 mA.
C_LIO_LIAnodal TDCS produced no instantaneous dose-dependent rCBF increase in left M1-HAND.
C_LIO_LIApart from a subtle increase at 0.5 mA, rCBF was not modified in M1-HAND during anodal TDCS.
C_LI


title: Enhancement of central norepinephrinergic neurotransmission contributes to inhibition of seizure-induced respiratory arrest by targeting the beta-1 adrenergic receptor (β1-AR) locating in the cardiomyocytes in the DBA/1 mouse SUDEP model

abstract: Sudden unexpected death of epilepsy (SUDEP) is the leading cause of of death in patients with epilepsy. Due to the complicated pathogenesis of SUDEP, however, the exact mechanism of SUDEP remains elusive. Currently, although it is recognized that the seizure-induced respiratory arrest (S-IRA) may be a main cause for SUDEP, other factors resulting in SUDEP cant be excluded e.g arrhythmias. Our previous findings indicated that the incidence of S-IRA and SUDEP evoked by acoustic stimulation or pentetrazol (PTZ) injection was significantly reduced by atomoxetine, a norepinephrine reuptake inhibitor (NRI), suggesting that noradrenergic neurotransmission modulates S-IRA and SUDEP. Given that norepinephrine acts on the target to modulate respiratory and circulation function by targeting adrenergic receptor  and beta (a-AR and {beta}-AR) and the arrhythmias can be contributed to SUDEP. Meanwhile, to further test whether cardiac factors are implicated in S-IRA and SUDEP, we choose esmolol hydrochloride, a selective antagonist of beta-1 adrenergic receptor ({beta}1-AR) to test it in our models. Our findings demonstrated that the lower incidence of S-IRA and SUDEP evoked by acoustic stimulation or PTZ injection in DBA/1 mice by administration with atomoxetine was significantly reversed by intraperitoneal (IP) of esmolol hydrochloride. Whats more, the data of electrocardiogram (ECG) showed that the cardiac arrhythmia including the ventricular tachycardia, ventricular premature beat and atrioventricular block can be evoked by acoustic stimulation or PTZ injection in our model. Administration of atomoxetine significantly reduced these arrhythmias and the incidence of S-IRA and SUDEP in our models. However, administration of esmolol hydrochloride with the dose without affecting ECG and mortality changing of DBA/1 significantly blocking the protective effects of atomoxetine on S-IRA and SUDEP in our models. Thus, the dysfunction of respiratory and circulation may be implicated in the pathogenesis of S-IRA and SUDEP. Enhancing the central norepinephrinergic neurotransmission in the brain contributes to inhibition of seizure-induced respiratory arrest by targeting {beta}1-AR locating in the cardiomyocytes. Our findings will show a new light on decoding the pathogenesis of SUDEP.


title: A striatal plasticity that supports the long-term preservation of motor function in Parkinsonian mice.

abstract: Motor deficits of Parkinsons disease (PD) such as rigidity, bradykinesia and akinesia result from a progressive loss of nigrostriatal dopamine neurons. No therapies exist that slow their degeneration and the most effective treatments for the motor symptoms: L-dopa -the precursor to dopamine, and deep brain stimulation can produce dyskinesias and are highly invasive, respectively. Hence, alternative strategies targeted to slow the progression or delay the onset of motor symptoms are still highly sought. Here we report the identification of a long-term striatal plasticity mechanism that delays for several months, the onset of motor deficits in a mouse PD model. Specifically, we show that a one-week transient daily elevation of midbrain dopamine neuron activity during depletion preserves the connectivity of direct but not indirect pathway projection neurons. The findings are consistent with the balance theory of striatal output pathways and suggest a novel approach for treating the motor symptoms of PD.


title: Prenatal stress programs behavioral pattern separation in adult mice

abstract: Stress is an unavoidable condition in human life. Stressful events experienced during development, including in utero, have been suggested as one major pathophysiological mechanism for developing vulnerability towards neuropsychiatric and neurodevelopmental disorders in adulthood. One cardinal feature of such disorders is impaired cognitive ability, which may in part rely on abnormal structure and function of the hippocampus. In the hippocampus, the dentate gyrus is a site of continuous neurogenesis, a process that has been recently implicated in spatial pattern separation, a cognitive phenomenon that serves to reduce the degree of overlap in the incoming information to facilitate its storage with minimal interference. We previously reported that adult neurogenesis is altered by prenatal stress allowing us to hypothesize that prenatal stress may possibly lead to impairment in pattern separation. To test this hypothesis, both control (C) and prenatally stressed (PS) adult mice were tested for metric and contextual discrimination abilities. We report for the first time that prenatal stress impairs pattern separation process, a deficit that may underlie their cognitive alterations and that may result in defective behaviors reminiscent of psychiatric illness such as post-traumatic stress disorder.


title: Noise source importance in linear stochastic models of biological systems that grow, shrink, wander, or persist

abstract:
While noise is an important factor in biology, biological processes often involve multiple noise sources, whose relative importance can be unclear. Here we develop tools that quantify the importance of noise sources in a network based on their contributions to variability in a quantity of interest. We generalize the edge importance measures proposed by Schmidt and Thomas [1] for first-order reaction networks whose steady-state variance is a linear combination of variance produced by each directed edge. We show that the same additive property extends to a general family of stochastic processes subject to a set of linearity assumptions, whether in discrete or continuous state or time. Our analysis applies to both expanding and contracting populations, as well as populations obeying a martingale ("wandering") at long times. We show that the original Schmidt-Thomas edge importance measure is a special case of our more general measure, and is recovered when the model satisfies a conservation constraint ("persists"). In the growing and wandering cases we show that the choice of observables (measurements) used to monitor the process does not influence which noise sources are important at long times. In contrast, in the shrinking or persisting case, which noise sources are important depends on what is measured. We also generalize our measures to admit models with affine moment update equations, which admit additional limiting scenarios, and arise naturally after linearization. We illustrate our results using examples from cell biology and ecology: (i) a model for the dynamics of the inositol trisphospate receptor, (ii) a model for an endangered population of white-tailed eagles, and (iii) a model for wood frog dispersal.

Author summaryBiological processes are frequently subject to an ensemble of independent noise sources. Noise sources produce fluctuations that propagate through the system, driving fluctuations in quantities of interest such as population size or ion channel configuration. We introduce a measure that quantifies how much variability each noise source contributes to any given quantity of interest. Using these methods, we identify which binding events contribute significantly to fluctuations in the state of a molecular signalling channel, which life history events contribute the most variability to an eagle population before and after a successful conservation effort rescued the population from the brink of extinction, and which dispersal events, at what times, matter most to variability in the recolonization of a series of ponds by wood frogs after a drought.

category: ecology


title: Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms

abstract: Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.


title: Maternal transmission as a symbiont sieve, and the absence of lactation in male mammals

abstract: Gut microbiomes of humans carry a complex symbiotic assemblage of microorganisms. As in all mammals, the special mode of feeding newborn infants through milk from the mammary gland enhances the opportunity for vertical transmission of elements of this microbiome. This has potential benefits, but it also brings with it some hazards for the host. We point out here that vertical transmission from both parents would allow host populations to be invaded by elements that are deleterious. In contrast, vertical transmission, when restricted to one parent, acts as a sieve preventing the spread of such elements. Because some transmission from mother to infant is unavoidable in placental mammals, uniparental transmission of symbionts, if it were to be selected, would require some separation of the father from the newborn infant. This paper therefore puts forward the hypothesis that the asymmetry in roles of mother and father, together with the hazards that come with biparental transmission, generate a selection pressure against male lactation in humans, and in mammals in general.

category: evolutionary biology


title: The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years

abstract: Long-term genetic studies of wild populations are very scarce but are essential for connecting ecological and population genetics models, and are also necessary for understanding how climate change can affect biodiversity. We present a study of the wild ancestor of modern wheat, carried out over a 36-year period during which atmospheric CO2 increased by 70 ppm and temperature by 1.5{degrees}C. We genotyped 832 individuals that had been collected along the same transects during the course of the experiment. To our surprise, very little changed. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was stable over the 36 generations of the study. Simulations indicate that neutral processes alone are unlikely to fully explain this stability, suggesting a role for fine-scale local adaptation. Our results provide a rare insight into the dynamics of a wild population at the scale of individuals.


title: Stability of the genetic structure of a wild wheat population across microhabitats over 36 years


title: Optimization of capture protocols across species targeting up to 32000 genes and their extension to pooled DNA

abstract:
PremiseIn-solution based capture is becoming a method of choice for sequencing targeted sequence.

Methods and resultsWe assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences.

ConclusionAltogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.


title: The megabase-scale crossover landscape is independent of sequence divergence

abstract: Meiotic recombination frequency varies along chromosomes and strongly correlates with sequence divergence. However, the causality underlying this correlation is unclear. To untangle the relationship between recombination landscapes and polymorphisms, we characterized the genome-wide recombination landscape in the absence of polymorphisms, using Arabidopsis thaliana homozygous inbred lines in which a few hundred genetic markers were introduced through mutagenesis. We found that megabase-scale recombination landscapes in inbred lines are strikingly similar to the recombination landscapes in hybrids, with the sole exception of heterozygous large rearrangements where recombination is prevented locally. In addition, we found that the megabase-scale recombination landscape can be accurately predicted by chromatin features. Our results show that polymorphisms are not causal for the shape of the megabase-scale recombination landscape, rather, favor alternative models in which recombination and chromatin shape sequence divergence across the genome.

category: genetics


title: Evaluation of methods incorporating biological function and GWAS summary statistics to accelerate discovery

abstract: Where sufficiently large genome-wide association study (GWAS) samples are not currently available or feasible, methods that leverage increasing knowledge of the biological function of variants may illuminate discoveries without increasing sample size. We comprehensively evaluated 18 functional weighting methods for identifying novel associations. We assessed the performance of these methods using published results from multiple GWAS waves across each of five complex traits. Although no method achieved both high sensitivity and positive predictive value (PPV) for any trait, a subset of methods utilizing pleiotropy and expression quantitative trait loci nominated variants with high PPV (>75%) for multiple traits. Application of functionally weighting methods to enhance GWAS power for locus discovery is unlikely to circumvent the need for larger sample sizes in truly underpowered GWAS, but these results suggest that applying functional weighting to GWAS can accurately nominate additional novel loci from available samples for follow-up studies.


title: Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission

abstract:
BackgroundInfectious disease spread in populations is controlled by individuals susceptibility (propensity to acquire infection), infectivity (propensity to pass on infection to others) and recoverability (propensity to recover/die). Estimating the effects of genetic risk factors on these host epidemiological traits can help reduce disease spread through genetic control strategies. However, the effects of previously identified  disease resistance SNPs on these epidemiological traits are usually unknown. Recent advances in computational statistics make it now possible to estimate the effects of single nucleotide polymorphisms (SNPs) on these traits from longitudinal epidemic data (e.g. infection and/or recovery times of individuals or diagnostic test results). However, little is known how to optimally design disease transmission experiments or field studies to maximise the precision at which pleiotropic SNP effects estimates for susceptibility, infectivity and recoverability can be estimated.

ResultsWe develop and validate analytical expressions for the precision of SNP effects estimates on the three host traits assuming a disease transmission experiment with one or more non-interacting contact groups. Maximising these leads to three distinct  experimental designs, each specifying a different set of ideal SNP genotype compositions across groups: a) appropriate for a single contact-group, b) a multi-group design termed "pure", and c) a multi-group design termed "mixed", where  pure and  mixed refer to contact groups consisting of individuals with the same or different SNP genotypes, respectively. Precision estimates for susceptibility and recoverability were found to be less sensitive to the experimental design than infectivity. Data from multiple groups were found more informative about infectivity effects than from a single group containing the same number of individuals. Whilst the analytical expressions suggest that the multi-group pure and mixed designs estimate SNP effects with similar precision, the mixed design is preferable because it uses information from naturally occurring infections rather than those artificially induced. The same optimal design principles apply to estimating other categorical fixed effects, such as vaccinations status, helping to more effectively quantify their epidemiological impact.

An online software tool SIRE-PC has been developed which calculates the precision of estimated substitution and dominance effects of a single SNP (or vaccine status) associated with all three traits depending on experimental design parameters.

ConclusionsThe developed methodology and software tool can be used to aid the design of disease transmission experiments for estimating the effect of individual SNPs and other categorical variables underlying host susceptibility, infectivity and recoverability.


title: Sensitive protein detection using site-specifically oligonucleotide-conjugated nanobodies

abstract: High-quality affinity probes are critical for sensitive and specific protein detection, in particular to detect protein biomarkers at early phases of disease development. Clonal affinity reagents can offer advantages over the commonly used polyclonal antibodies (pAbs) in terms of reproducibility and standardization of such assays. In particular, clonal reagents offer opportunities for site-directed attachment of exactly one modification per affinity reagent at a site designed not to interfere with target binding to help standardize assays. The proximity extension assays (PEA) is a widely used protein assay where pairs of protein-binding reagents are modified with oligonucleotides (oligos), so that their proximal binding to a target protein generates a reporter DNA strand for DNA-assisted readout. The assays have been used for high-throughput multiplexed protein detection of up to a few thousand different proteins in one or a few microliters of plasma. Here we explore nanobodies (Nb) as an alternative to polyclonal antibodies pAbs as affinity reagents for PEA. We describe an efficient site-specific approach for preparing high-quality oligo-conjugated Nb probes via Sortase A (SrtA) enzyme coupling. The procedure allows convenient removal of unconjugated affinity reagents after conjugation. The purified high-grade Nb probes were used in PEA and the reactions provided an efficient means to select optimal pairs of binding reagents from a group of affinity reagents. We demonstrate that Nb-based PEA for interleukin-6 (IL6) detection can augment assay performance, compared to the use of pAb probes. We identify and validate Nb combinations capable of binding in pairs without competition for IL6 antigen detection by PEA.

category: bioengineering


title: Model-based hearing-restoration strategies for cochlear synaptopathy pathologies

abstract: It is well known that ageing and noise exposure are important causes of sensorineural hearing loss, and can result in damage of the outer hair cells or other structures of the inner ear, including synaptic damage to the auditory nerve (AN), i.e., cochlear synaptopathy (CS). Despite the suspected high prevalence of CS among people with self-reported hearing difficulties but seemingly normal hearing, conventional hearing-aid algorithms do not compensate for the functional deficits associated with CS. Here, we present and evaluate a number of auditory signal-processing strategies designed to maximally restore AN coding for listeners with CS pathologies. We evaluated our algorithms in subjects with and without suspected age-related CS to assess whether physiological and behavioural markers associated with CS can be improved. Our data show that after applying our algorithms, envelope-following responses and perceptual amplitude-modulation sensitivity were consistently enhanced in both young and older listeners. Speech intelligibility showed small improvements across participants, with the young group benefitting the most from processed speech. Our proposed hearing-restoration algorithms can be rapidly executed and can thus extend the application range of current hearing aids and hearables, while leaving sound amplification unaffected.


title: FunOrder 2.0 - a fully automated method for the identification of co-evolved genes

abstract:
Coevolution is an important biological process that shapes interacting species or even proteins - may it be physically interacting proteins or consecutive enzymes in a metabolic pathway. The detection of co-evolved proteins will contribute to a better understanding of biological systems. Previously, we developed a semi-automated method, termed FunOrder, for the detection of co-evolved genes from an input gene or protein set. We demonstrated the usability and applicability of FunOrder by identifying essential genes in biosynthetic gene clusters from different ascomycetes. A major drawback of this original method was the need for a manual assessment, which may create a user bias and prevents a high-throughput application. Here we present a fully automated version of this method termed FunOrder 2.0. To fully automatize the method, we used several mathematical indices to determine the optimal number of clusters in the FunOrder output, and a subsequent k-means clustering based on the first three principal components of a principal component analysis of the FunOrder output. Further, we replaced the BLAST with the DIAMOND tool, which enhanced speed and allows the future integration of larger proteome databases. The introduced changes slightly decreased the sensitivity of this method, which is outweighed by enhanced overall speed and specificity. Additionally, the changes lay the foundation for future high-throughput applications of FunOrder 2.0 in different phyla to solve different biological problems.

AUTHOR SUMMARYCoevolution is a process which arises between different species or even different proteins that interact with each other. Any change occurring in one partner must be met by a corresponding change in the other partner to maintain the interaction throughout evolution. These interactions may occur in symbiotic relationships or between rivaling species. Within an organism, consecutive enzymes of metabolic pathways are also subjected to coevolution. We developed a fully automated method, FunOrder 2.0, for the detection of co-evolved proteins, which will contribute to a better understanding of protein interactions within an organism. We demonstrate that this method can be used to identify essential genes of the secondary metabolism of fungi, but FunOrder 2.0 may also be used to detect pathogenicity factors or remains of horizontal gene transfer next to many other biological systems that were shaped by coevolution.


title: Control of Leaf Width by the APC/CTAD1-WL1-NAL1 Pathway in Rice

abstract: Leaf morphology is one of the most important features of the ideal plant architecture. However, the genetic and molecular mechanisms controlling leaf morphology in crops remain largely unknown, despite their central importance. Here we demonstrate that the APC/CTAD1-WL1-NAL1 pathway regulates leaf width in rice, and mutation of WL1 leads to width leaf variation. WL1 interacts with TAD1 and is degraded by APC/CTAD1, with the loss of TAD1 function resulting in narrow leaves. The WL1 protein directly binds to the regulatory region of NAL1 and recruits the corepressor TOPLESS-RELATED PROTEIN to inhibit NAL1 expression by down-regulating the level of histone acetylation of chromatin. Furthermore, biochemical and genetic analyses revealed that TAD1, WL1, and NAL1 function in a common pathway to control leaf width. Our study establishes an important framework for the APC/CTAD1-WL1-NAL1 pathway-mediated control of leaf width in rice and introduces novel perspectives for using this regulatory pathway for improving crop plant architecture.


title: Establishment of a hypoxia ischemia reperfusion brain damagemodel in neonatal rats

abstract:
ObjectiveRice-Vannucci model has been widely used as HIE (Hypoxic ischemic encephalopathy) animal model in the past forty years, but it does not mimic reperfusion injury that occurs during HIE. The aim of the present study was to establish a new neonatal rat model by simulating hypoxia ischemia reperfusion brain damage (HIRBD) through "common carotid artery (CCA) muscle bridge".

MethodsSixty 7-day-old male Sprague-Dawley rats were randomly assigned to group A (HIRBD groups, n=36), group B (Rice-Vannucci group, n=12), and group C (sham-operated group, n=12). Rats in group A were assigned to 3 subgroups (A1-A3, 12 animals/subgroup). Dynamic changes in cerebral blood flow (CBF) were evaluated by the laser speckle imaging system. The status of the CCA was observed under a stereomicroscope. Changes in body weight, gross morphology as well as pathological sections of brain tissue were examined to evaluate the feasibility of the model.

ResultsThe results indicated that CCA muscle bridge successfully blocked the CBF. CBF was restored after removal of the CCA muscle bridge in HIRBD groups. The CCA was in good condition after removing the muscle bridge, and blood supply was not affected. Changes in body weight, gross morphology and pathological sections of brain tissue indicated that ischemia reperfusion induced by the CCA muscle bridge method caused varying degrees of brain damage.

ConclusionCCA muscle bridge method is effective for establishing a reliable, stable, and reproducible neonatal rat model for study of HIRBD.


title: A theory of cortical map formation in the visual brain

abstract: The cerebral cortex receives multiple afferents from the thalamus that segregate by stimulus modality forming cortical maps for each sense. In vision, the primary visual cortex maps the multiple dimensions of the visual stimulus in patterns that vary across species for reasons unknown. Here we introduce a general theory of cortical map formation, which proposes that map diversity emerges from species variations in the thalamic afferent density sampling sensory space. In the theory, increasing afferent sampling density enlarges the cortical domains representing the same visual point, allowing the segregation of afferents and cortical targets by multiple stimulus dimensions. We illustrate the theory with an afferent-density model that accurately replicates the maps of different species through afferent segregation followed by thalamocortical convergence pruned by visual experience. Because thalamocortical pathways use similar mechanisms for axon segregation and pruning, the theory may extend to other sensory areas of the mammalian brain.


title: Atlasing white matter and grey matter joint contributions to resting-state networks in the human brain

abstract: Over the past two decades, the study of resting-state functional magnetic resonance imaging (fMRI) has revealed the existence of multiple brain areas displaying synchronous functional blood oxygen level-dependent signals (BOLD) -- resting-state networks (RSNs). The variation in functional connectivity between the different areas of a resting-state network or between multiple networks, have been extensively studied and linked to cognitive states and pathologies. However, the white matter connections supporting each network remain only partially described. In this work, we developed a data-driven method to systematically map the white and grey matter contributing to resting-state networks. Using the Human Connectome Project, we generated an atlas of 30 resting-state networks, each with two maps: white matter and grey matter. By integrating structural and functional neuroimaging data, this method builds an atlas that unlocks the joint anatomical exploration of white and grey matter to resting-state networks. The method also allows highlighting the overlap between networks, which revealed that most (89%) of the brains white matter is shared amongst multiple networks, with 16% shared by at least 7 resting-state networks. These overlaps, especially the existence of regions shared by numerous networks, suggest that white matter lesions in these areas might strongly impact the correlations and the communication within resting-state networks. We provide an open-source software to explore the joint contribution of white and grey matter to RSNs and facilitate the study of the impact of white matter damage on RSNs.


title: Local interactions between steady-state visually evoked potentials at nearby flickering frequencies

abstract: Steady-state visually evoked potentials (SSVEP) are widely used to index top-down cognitive processing in human electroencephalogram (EEG) studies. Typically, two stimuli flickering at different temporal frequencies (TFs) are presented, each producing a distinct response in the EEG at its flicker frequency. However, how SSVEP responses in EEG are modulated in the presence of a competing flickering stimulus just due to sensory interactions is not well understood. We have previously shown in local field potentials (LFP) recorded from awake monkeys that when two overlapping full screen gratings are counter-phased at different TFs, there is an asymmetric SSVEP response suppression, with greater suppression from lower TFs, which further depends on the relative orientations of the gratings (stronger suppression and asymmetry for parallel compared to orthogonal gratings). Here, we first confirmed these effects in both male and female human EEG recordings. Then, we mapped the response suppression of one stimulus (target) by a competing stimulus (mask) over a much wider range than the previous study. Surprisingly, we found that the suppression was not stronger at low frequencies in general, but systematically varied depending on the target TF, indicating local interactions between the two competing stimuli. These results were confirmed in both human EEG and monkey LFP and electrocorticogram (ECoG) data. Our results show that sensory interactions between multiple SSVEPs are more complex than shown previously and are influenced by both local and global factors, underscoring the need to cautiously interpret the results of studies involving SSVEP paradigms.


title: Humanized CYP2C19 transgenic mouse as an animal model of cerebellar ataxia

abstract:
BackgroundAnimal models are essential for understanding etiology and pathophysiology of movement disorders. Previously, we have found that mice transgenic for the human CYP2C19 gene, expressed in the liver and developing brain, exhibit altered neurodevelopment associated with impairments of their motor function and emotionality.

ObjectivesTo characterize motoric phenotype of the CYP2C19 transgenic mice and validate its usefulness as an animal model of ataxia.

MethodsThe rotarod and beam-walking tests were utilized to quantify the functional alterations induced by motoric phenotype. Dopaminergic system was assessed by tyrosine hydroxylase immunohistochemistry and by chromatographic quantification of the whole-brain dopamine levels. Beam-walking test was also repeated after the treatment with the dopamine receptor antagonists, ecopipam and raclopride. The volumes of 20 brain regions in the CYP2C19 transgenic mice and controls were quantified by 9.4T gadolinium-enhanced postmortem structural neuroimaging.

ResultsCYP2C19 transgenic mice were found to exhibit abnormal, unilateral ataxia-like gait, clasping reflex and 5.6-fold more paw-slips using the beam-walking test (p<0.0001, n=89); the phenotype was more pronounced in younger animals. Hyperdopaminergism was observed in the CYP2C19 mice; however, the motoric impairment was not ameliorated by dopamine receptor antagonists and there was also no midbrain dopamine neuron loss in CYP2C19 mice. However, in these mice, cerebellar volume was drastically decreased (11.8% [95%CI: -14.7, -9.0], q<0.0001, n=59), whereas a moderate decrease in hippocampal volume was observed (-4.2% [95%CI: -6.4%, -1.9%], q=0.015, n=59).

ConclusionsHumanized CYP2C19 transgenic mice exhibit altered motoric function and functional motoric impairments; this phenotype is likely caused by an aberrant cerebellar development.


title: Intracellular flow cytometry staining of antibody-secreting cells using phycoerythrin-conjugated antibodies: pitfalls and solutions

abstract: Antibody-secreting cells are terminally differentiated B cells that play a critical role in humoral immunity through immunoglobulin secretion along with possessing the potential to be long-lived. It is now appreciated that antibody-secreting cells regulate multiple aspects of biology through the secretion of various cytokines. In this regard, intracellular flow cytometry is a key tool used to assess the presence of intracellular proteins such as cytokines and transcription factors. Here, we showed that the use of phycoerythrin-containing antibody conjugates led to a false interpretation of antibody-secreting cell intracellular protein expression compared to other cell types. This was mainly due to the inappropriate retention of these antibodies specifically within antibody-secreting cells. Furthermore, we demonstrated how to reduce this retention which allowed for a more accurate comparison of intracellular protein expression between antibody-secreting cells and other cell types such as B lymphocytes. Using this methodology, our data revealed that spleen antibody-secreting cells expressed Toll-like receptor 7 as well as the pro-form of the inflammatory cytokine interleukin-1{beta}.


title: Efficient inactivation of African swine fever virus by a highly complexed iodine combined with compound organic acids

abstract:
African swine fever (ASF) is a highly contagious disease with high morbidity and mortality caused by African swine fever virus (ASFV). Cleaning and disinfection remain one of the most effective biosecurity measures to prevent and control the spread of ASFV. In this study, we evaluated the inactivation effects of highly complexed iodine (HPCI) combined with compound organic acids (COAs) against ASFV under different conditions. The results showed that the inactivation rates of the disinfectants on the reporter ASFV increased in dose- and time-dependent manners, the best inactivation effects were obtained when the compatibility ratio of HPCI and COAs was 5:1 at 25{degrees}C. Furthermore, there were no significant differences by comparing the efficacy of HPCI combined with COAs (HPCI+COAs) in inactivating wild-type ASFV and the reporter ASFV (P > 0.05). ASFV of 104.0 TCID50/mL was completely inactivated by 0.13% HPCI (0.0065% effective iodine), 0.06% COAs or 0.13% HPCI+COAs (approximately 0.0054% effective iodine), respectively, while 106.0 TCID50/mL ASFV was completely inactivated by 1.00% HPCI (0.05% effective iodine), 0.50% COAs or 1.00% HPCI+COAs (0.042% effective iodine), respectively. Therefore, HPCI+COAs had synergistic effects to inactivate ASFV. This study demonstrated that HPCI+COAs could rapidly and efficiently inactivate ASFV and represent an effective compound disinfectant for the control of ASF.

IMPORTANCEAfrican swine fever (ASF) is a highly contagious disease with high morbidity and mortality caused by African swine fever virus (ASFV). Due to the lack of commercial vaccines and treatment available for ASF, effective disinfectants and the proper use of them are extremely essential to inactivate ASFV. The significance of this research is in searching for an ideal disinfectant that not only has the advantages of low toxicity and non-pollution but also can inactivate ASFV rapidly and efficiently. In this study, we proved that HPCI+COAs not only exhibited low cytotoxicity, but also could completely inactivate ASFV within 5 min at 4{degrees}C, 25{degrees}C and 37{degrees}C. In addition, HPCI+COAs had synergistic effects on inactivated ASFV. Thus, HPCI +COAs could be used as an effective disinfectant for the control of ASF.

category: microbiology


title: The dgc2 gene encoding di-guanylate cyclase suppresses both motility and biofilm formation in the filamentous cyanobacterium Leptolyngbya boryana.

abstract:
Colony pattern formations of bacteria with motility manifest complicated morphological self-organization phenomena. Leptolyngbya boryana is the filamentous cyanobacterial species, which has been used as a genetic model organism for studying metabolism including photosynthesis and nitrogen-fixation. Although a widely used type strain (wild type) of this species has not been reported to show any motile activity, we isolated a spontaneous mutant strain which shows active motility (gliding activity) to give rise to complicated colony patters, including comet-like wandering clusters and disk-like rotating vortices on solid media. Whole-genome resequencing identified multiple mutations on the genome in the mutant strain. We confirmed that inactivation of a candidate gene, dgc2 (LBDG_02920), in the wild type background was sufficient to give rise to motility and the morphological colony patterns. This gene encodes a protein, containing the GGDEF motif, which is conserved at the catalytic domain of diguanylate cyclase (DGC). Although DGC has been reported to be involved in biofilm formation, the mutant strain lacking dgc2 significantly facilitated biofilm formation, suggesting a role of DGC for suppressing both gliding motility and biofilm formation. Thus, L. boryana provides an excellent genetic model to study dynamic colony pattern formation, and novel insight on a role of c-di-GMP for biofilm formation.

ImportanceSelf-propelled bacteria often show complicated collective behaviors, such as the formation of dense moving clusters, which is exemplified by wandering comet-like and rotating disk-like colonies, while molecular details of forming such structures remain limited. We found that a strain deficient in the diguanylate cyclase gene dgc2 in the filamentous cyanobacterium L. boryana induces motility, complex and dynamic colony pattern formation including the comet-like and disk-like clusters. While c-di-GMP has been reported to activate biofilm formation in some bacterial species, disruption of the dgc2 gene unexpectedly enhanced it, providing a novel role for c-di-GMP regulatory system in both colony pattern formation and biofilm formation.


title: Hydrogen production in an aerobic environment by Escherichia coli K-12

abstract: Escherichia coli is a facultative anaerobe that can grow in a variety of environmental conditions. In the complete absence of O2, E. coli can perform a mixed-acid fermentation that contains within it an elaborate metabolism of formic acid. In this study, we use cavity-enhanced Raman spectroscopy (CERS), FTIR, liquid Raman spectroscopy, isotopic labelling, and molecular genetics to make advances in the understanding of bacterial formate and H2 metabolism. It is shown that, under anaerobic (anoxic) conditions, formic acid is generated endogenously, excreted briefly from the cell, and then taken up again to be disproportionated to H2 and CO2 by formate hydrogenlyase (FHL-1). However, exogenously added D-labelled formate behaves quite differently from the endogenous formate and is taken up immediately, independently, and possibly by a different mechanism, by the cell and converted to H2 and CO2. Our data support an anion-proton symport model for formic acid transport. In addition, when E. coli was grown in a micro-aerobic (micro-oxic) environment it was possible to analyse aspects of formate and O2 respiration occurring alongside anaerobic metabolism. While cells growing under micro-aerobic conditions generated endogenous formic acid, no H2 was produced. However, addition of exogenous formate at the outset of cell growth did induce FHL-1 biosynthesis and resulted in formate-dependent H2 production in the presence of O2.


title: Hydrogen production in the presence of oxygen by Escherichia coli K-12


title: Adeno-associated Virus Receptor-binding: Flexible Domains and Alternative Conformations through cryo-Electron Tomography of AAV2 and AAV5 complexes

abstract:
Recombinant forms of adeno-associated virus (rAAV) are vectors of choice in the development of treatments for a number of genetic dispositions. Greater understanding of AAVs molecular virology is needed to underpin needed improvements in efficiency and specificity. Recent advances have included identification of a near universal entry receptor, AAVR, and structures by cryo-electron microscopy (EM) single particle analysis (SPA) that revealed, at high resolution, only the domains of AAVR most tightly bound to AAV. Here, cryogenic electron tomography (cryo-ET) is applied to reveal the neighboring domains of the flexible receptor. For AAV5, where the PKD1 domain is bound strongly, PKD2 is seen in three configurations extending away from the virus. AAV2 binds tightly to the PKD2 domain at a distinct site, and cryo-ET now reveals four configurations of PKD1, all different from that seen in AAV5. The AAV2 receptor complex also shows unmodeled features on the inner surface that appear to be an equilibrium alternate configuration. Other AAV structures start near the 5-fold axis, but now {beta}-strand A is the minor conformer and, for the major conformer, partially ordered N-termini near the 2-fold axis join the canonical capsid jellyroll fold at the {beta}A-{beta}B turn. The addition of cryo-ET is revealing unappreciated complexity that is likely relevant to viral entry and to the development of improved gene therapy vectors.

IMPORTANCEWith 150 clinical trials for 30 diseases underway, AAV is a leading gene therapy vector. Immunotoxicity at high doses used to overcome inefficient transduction, has occasionally proven fatal and highlighted gaps in fundamental virology. AAV enters cells, interacting through distinct sites with different domains of the AAVR receptor, according to AAV clade. Single domains are resolved in structures by cryogenic electron microscopy. Here, the adjoining domains are revealed by cryo-electron tomography of AAV2 and AAV5 complexes. They are in flexible configurations interacting minimally with AAV, despite measurable dependence of AAV2 transduction on both domains.


title: EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

abstract: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCCs ability to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.


title: A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis

abstract: Pathogenic spirochetes can alter their morphologies and behaviors to infect and survive within their hosts. Previous reports demonstrate that the formation of so-called  round bodies and biofilms, and chemotaxis are involved in spirochete pathogenesis. Here, in the spirochete Treponema denticola, we report a direct link between these cellular states that involves a new class of protein sensor (CheWS) with hitherto unclear function. Using cryo-EM methods, protein modeling, bioinformatics, genetics methods, and behavioral assays we demonstrate that spirochetes regulate these behaviors in response to the small molecule s-adenosylmethionine (SAM) via a SAM sensor that is anchored to chemotaxis arrays. CheWS influences chemotaxis, biofilm and round body formation under nonstressed conditions by a novel sporulation-like mechanism. Taken together, we establish an improved model for round body formation, we discovered a direct link between this SAM sensor and changes in cellular states, as well as characterized a new sensor class involved in chemotaxis.


title: Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity

abstract: In idiopathic pulmonary fibrosis (IPF) myofibroblasts are key effectors of fibrosis and architectural distortion by excessive deposition of extracellular matrix and their acquired contractile capacity. Single-cell RNA-sequencing has precisely defined the IPF myofibroblast transcriptome, but identifying critical transcription factor activity by this approach is imprecise. We performed and integrated snATAC-seq and scRNA-seq from human IPF and donor control explants to identify differentially accessible chromatin regions and enriched transcription factor motifs within lung cell populations. TWIST1 and other E-box transcription factor motifs were significantly enriched in IPF myofibroblasts compared to both IPF non-myogenic and control fibroblasts. TWIST1 expression was also selectively upregulated in IPF myofibroblasts. Overexpression of Twist1 in lung COL1A2-expressing fibroblasts in bleomycin-injured mice was associated with increased collagen synthesis. Our studies utilizing human multiomic single-cell analyses combined with in vivo murine disease models confirm a critical regulatory function for TWIST1 in IPF myofibroblast activity in the fibrotic lung. Understanding the global process of opening TWIST1 and other E-box TF motifs that govern myofibroblast differentiation may identify new therapeutic interventions for fibrotic pulmonary diseases.

category: molecular biology


title: The RNA-Binding Protein SAM68 regulates cardiomyocyte differentiation by enhancing Gata4 translation

abstract: The signal transduction and activation of RNA (STAR) family is composed of RNA-binding proteins (RBPs) that play a central role in mammalian development. Nonetheless, the functions and modes of action that STAR proteins have in lineage specification are still poorly understood. Here, we characterized the role of STAR proteins SAM68 and QUAKING (QKI) in pluripotency and differentiation by performing their depletion through CRISPR-Cas9 in mouse embryonic stem cells (mESCs). Combining RNA-sequencing, ribosome profiling and advanced computational predictions, we found that both SAM68 and QKI regulate the mESCs self-renewal and are indispensable for cardiomyocyte differentiation. At the molecular level, we discovered that SAM68 and QKI antagonistically control the expression of cardiogenic factors. Our calculations indicated that SAM68, unlike QKI, binds the cardiogenic-specific transcription factor Gata4 in a region spanning nucleotides 500 to 1000 of the mRNA corresponding to part of the 5 untranslated region and the first exon. We validated the predictions by electrophoretic mobility shift assay and RNA immunoprecipitation showing that SAM68 controls the translation of Gata4 during mESCs differentiation towards the cardiomyocyte lineage.


title: Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes

abstract: Reduced representation library approaches are still a valuable tool for breeding and population and ecological genomics, even with impressive increases in sequencing capacity in recent years. Unfortunately, current approaches only allow for multiplexing up to 384 samples. To take advantage of increased sequencing capacity, we present Multi-GBS, a massively multiplexable extension to Genotyping-by-Sequencing that is also optimized for large conifer genomes. In Norway Spruce, a highly repetitive 20Gbp diploid genome with high population genetic variation, we call over a million variants in 32 genotypes from three populations, two natural forest in the Alps and Bohemian Alps, and a managed population from southeastern Austria using the existing TASSEL GBSv2 pipeline. Metric MDS analysis of replicated genotypes shows that technical bias in resulting genotype calling is minimal and that populations cluster in biologically meaningful ways.


title: Membrane-active Polymers: NCMNP13-x, NCMNP21-x and NCMNP21b-x for Membrane Protein Structural Biology

abstract:
Membrane proteins are a ubiquitous group of bio-macromolecules responsible for many crucial biological processes and serve as drug targets for a wide range of modern drugs. Detergent-free technologies such as styrene-maleic acid lipid particles (SMALP), diisobutylene-maleic acid lipid particles (DIBMALP), and native cell membrane nanoparticles (NCMN) systems have recently emerged as revolutionary alternatives to the traditional detergent-based approaches for membrane protein research. NCMN systems aim to create a membrane-active polymer library suitable for high-resolution structure determination. Herein, we report our design, synthesis, characterization and comparative application analyses of three novel classes of NCMN polymers, NCMNP13-x, NCMNP21-x and NCMNP21b-x. Although each NCMN polymer can solubilize various model membrane proteins and conserve native lipids into NCMN particles, only the NCMNP21b-x series reveals lipid-protein particles with good buffer compatibility and high homogeneity suitable for single-particle cryo-EM analysis. Consequently, the NCMNP21b-x polymers that bring out high-quality NCMN particles are particularly attractive for membrane protein structural biology.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/475744v1_ufig1.gif" ALT="Figure 1">
View larger version (33K):
org.highwire.dtl.DTLVardef@dbc1f3org.highwire.dtl.DTLVardef@19a5ff0org.highwire.dtl.DTLVardef@10beceorg.highwire.dtl.DTLVardef@15ec66a_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIDemonstrate straightforward strategies for tailoring styrene-maleic co-polymer (SMA) that revealed novel buffer compatible polymers, NCMNP13-50, NCMNP21-20 and NCMNP21b-x.
C_LIO_LIElucidate how modification factors alter the membrane-active properties of these polymers, i.e., membrane protein extraction efficiency, morphology, etc.
C_LIO_LIProvide valuable insights into the rational design of membrane-active polymers for membrane protein structural biology.
C_LIO_LINCMNP21b-x polymers are highly compatible with high-resolution structure determination using an emerging technique, cryo-EM.
C_LI

category: biochemistry


title: H2A.Z deposition by SWR1C involves multiple ATP-dependent steps

abstract: The histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial, priming step that occurs after ATP addition that likely involves transient DNA unwrapping from the nucleosome. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, the rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate the timely and accurate deposition of H2A.Z at key genomic locations.


title: A Niclosamide-releasing hot-melt extruded catheter prevents Staphylococcus aureus experimental biomaterial-associated infection

abstract: Biomaterial-associated infections are a major healthcare challenge as they are responsible for high disease burden in critically ill patients. In this study, we have developed drug-eluting antibacterial catheters to prevent catheter-related infections. Niclosamide (NIC), originally a well-studied antiparasitic drug, was incorporated into the polymeric matrix of thermoplastic polyurethane (TPU) via solvent casting, and catheters were fabricated using hot-melt extrusion technology. The mechanical and physicochemical properties of TPU polymers loaded with NIC were studied. NIC was released in a sustained manner from the catheters and exhibited antibacterial activity against Staphylococcus aureus and Staphylococcus epidermidis in different in vitro models. Moreover, the antibacterial efficacy of NIC-loaded catheters was validated in an in vivo biomaterial-associated infection mouse model using a methicillin-susceptible and methicillin-resistant strain of S. aureus. The released NIC from the produced catheters reduced bacterial colonization of the catheter as well as of the surrounding tissue. A sustained in vivo release of NIC from the catheters for at least 14 days was observed. In summary, the NIC-releasing hot-melt extruded catheters prevented implant colonization and reduced the bacterial colonization of peri-catheter tissue by methicillin sensitive as well as resistant S. aureus in a biomaterial-associated infection mouse model and has good prospects for preclinical development.


title: Optimized cell culture conditions promote ex-vivo manipulation and expansion of primitive hematopoietic stem cells for therapeutic gene editing.

abstract: During the last few years, gene editing has emerged as a powerful tool for the therapeutic correction of monogenic diseases. CRISPR/Cas9 applied to hematopoietic stem and progenitor cells (HSPCs) has shown great promise in proof-of-principle preclinical studies to treat haematological disorders, and clinical trials using these tools are now underway. Nonetheless, there remain important challenges that need to be addressed, such as the efficiency of targeting primitive, long-term repopulating HSPCs and expand them in vitro for clinical purposes. Here we have tested the effect exerted by different culture media compositions on the ability of HSPCs to proliferate and undergo homology directed repair-mediated knock-in of a reporter gene, while preserving their stemness features during ex-vivo culture. We tested different combinations of compounds and demonstrated that by supplementing the culture media with inhibitors of histone deacetylases, and/or by fine-tuning its cytokine composition it is possible to achieve high levels of gene targeting in long-term repopulating HSPCs both in vitro and in vivo, with a beneficial balance between preservation of stemness and cell expansion, thus allowing to obtain a significant amount of edited, primitive HSPCs compared to established, state-of-the-art culture conditions. Overall, the implantation of this optimized ex vivo HSPC culture protocol will improve the efficacy, feasibility and applicability of gene editing and will likely provide one step further to unlock the full therapeutic potential of such powerful technology.


title: A single-cell atlas reveals shared and distinct immune responses and metabolism during SARS-CoV-2 and HIV-1 infections

abstract:
SARS-CoV-2 and HIV-1 are RNA viruses that have killed millions of people worldwide. Understanding the similarities and differences between these two infections is critical for understanding disease progression and for developing effective vaccines and therapies, particularly for 38 million HIV-1+ individuals who are vulnerable to SARS-CoV-2 co-infection. Here, we utilized single-cell transcriptomics to perform a systematic comparison of 94,442 PBMCs from 7 COVID-19 and 9 HIV-1+ patients in an integrated immune atlas, in which 27 different cell types were identified using an accurate consensus single-cell annotation method. While immune cells in both cohorts show shared inflammation and disrupted mitochondrial function, COVID-19 patients exhibit stronger humoral immunity, broader IFN-I signaling, elevated Rho GTPase and mTOR pathway activities, and downregulated mitophagy. Our results elucidate transcriptional signatures associated with COVID-19 and HIV-1 that may reveal insights into fundamental disease biology and potential therapeutic targets to treat these viral infections.

HighlightsO_LICOVID-19 and HIV-1+ patients show disease-specific inflammatory immune signatures
C_LIO_LICOVID-19 patients show more productive humoral responses than HIV-1+ patients
C_LIO_LISARS-CoV-2 elicits more enriched IFN-I signaling relative to HIV-I
C_LIO_LIDivergent, impaired metabolic programs distinguish SARS-CoV-2 and HIV-1 infections
C_LI


title: Using syncmers improves long-read mapping

abstract:
MotivationSequencing long reads presents novel challenges to mapping. One such challenge is low sequence similarity between the reads and the reference, due to high sequencing error and mutation rates. This occurs, e.g., in a cancer tumor, or due to differences between strains of viruses or bacteria. A key idea in mapping algorithms is to sketch sequences with their minimizers. Recently, syncmers were introduced as an alternative sketching method that is more robust to mutations and sequencing errors.

ResultsWe introduce parameterized syncmer schemes, a generalization of syncmers, and provide a theoretical analysis for multi-parameter schemes. By combining these schemes with downsampling or minimizers we can achieve any desired compression and window guarantee. We implemented the use of parameterized syncmer schemes in the popular minimap2 and Winnowmap2 mappers. In tests on simulated and real long read data from a variety of genomes, the syncmer-based algorithms, with scheme parameters selected on the basis of the theoretical analysis, reduced unmapped reads by 20-60% at high compression while usually using less memory. The advantage was more pronounced at low sequence identity. At sequence identity of 75% and medium compression, syncmer-minimap had only 37% as many unmapped reads, and 8% fewer of the reads that did map were incorrectly mapped. Even at lower compression and error rates, parameterized syncmer based mapping mapped more reads than the original minimizer-based mappers as well as mappers using the original syncmer schemes. We conclude that using parameterized syncmer schemes can improve mapping of long reads in a wide range of settings.

Availabilityhttps://github.com/Shamir-Lab/syncmer_mapping

Supplementary informationSupplementary data are available at https://github.com/Shamir-Lab/syncmer_mapping.

Author summaryPopular long read mappers use minimizers, the minimal hashed k-mers from overlapping windows, as alignment seeds. Recent work showed that syncmers, which select a fixed set of k-mers as seeds, are more likely to be conserved under errors or mutations than minimizers, making them potentially useful for mapping error-prone long reads. We introduce a framework for creating syncmers, that we call parameterized syncmer schemes, which generalize those introduced so far, and provide a theoretical analysis of their properties. We implemented parameterized syncmer schemes in the minimap2 and Winnowmap2 long read mappers. Using parameters selected on the basis of our theoretical analysis we demonstrate improved mapping performance, with fewer unmapped and incorrectly mapped reads on a variety of simulated and real datasets. The improvements are consistent across a broad range of compression rates and sequence identities, with the most significant improvements for lower sequence identity (high error or mutation rates) and high compression.


title: Parameterized syncmer schemes improve long-read mapping


title: Alignment of spatial genomics and histology data using deep Gaussian processes

abstract: Spatially-resolved genomic technologies have allowed us to study the physical organization of cells and tissues, and promise an understanding of the local interactions between cells. However, it remains difficult to precisely align spatial observations across slices, samples, scales, individuals, and technologies. Here, we propose a probabilistic model that aligns a set of spatially-resolved genomics and histology slices onto a known or unknown common coordinate system into which the samples are aligned both spatially and in terms of the phenotypic readouts (e.g., gene or protein expression levels, cell density, open chromatin regions). Our method consists of a two-layer Gaussian process: the first layer maps the observed samples spatial locations into a common coordinate system, and the second layer maps from the common coordinate system to the observed readouts. Our approach also allows for slices to be mapped to a known template coordinate space if one exists. We show that our registration approach enables complex downstream spatially-aware analyses of spatial genomics data at multiple resolutions that are impossible or inaccurate with unaligned data, including an analysis of variance, differential expression across the z-axis, and association tests across multiple data modalities.


title: Pervasive conditional selection of driver mutations and modular epistasis networks in cancer

abstract: Cancer driver mutations often display mutual exclusion or co-occurrence, underscoring the key role of epistasis in carcinogenesis. However, estimating the magnitude of epistasis and quantifying its effect on tumor evolution remains a challenge. We developed a method to quantify COnditional SELection on the Excess of Nonsynonymous Substitutions (Coselens) in cancer genes. Coselens infers the number of drivers per gene in different partitions of a cancer genomics dataset using covariance-based mutation models and determines whether coding mutations in a gene affect selection for drivers in any other gene. Using Coselens, we identified 296 conditionally selected gene pairs across 16 cancer types in the TCGA dataset. Conditional selection affects 25-50% of driver substitutions in tumors with >2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario, where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.


title: Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains

abstract: Salmonella enterica Typhimurium is a serious pathogen that is involved in human nontyphoidal infections. Tackling Typhimurium infections is difficult due to the species dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN). While traditional biomolecular methods provide characterizations of specific regulators, it is laborious to construct the global TRN structure from this bottom-up approach. Here, we used a machine learning technique to understand the transcriptional signatures of S. enterica Typhimurium from the top down, as a whole and in individual strains. Furthermore, we conducted cross-strain comparison of 6 strains in serovar Typhimurium to investigate similarities and differences in their TRNs with pan-genomic analysis. By decomposing all the publicly available RNA-Seq data of Typhimurium with independent component analysis (ICA), we obtained over 400 independently modulated sets of genes, called iModulons. Through analysis of these iModulons, we 1) discover three transport iModulons linked to antibiotic resistance, 2) describe concerted responses to cationic antimicrobial peptides (CAMPs), 3) uncover evidence towards new regulons, and 4) identify two iModulons linked to bile responses in strain ST4/74. We extend this analysis across the pan-genome to show that strain-specific iModulons 5) reveal different genetic signatures in pathogenicity islands that explain phenotypes and 6) capture the activity of different phages in the studied strains. Using all high-quality publicly-available RNA-Seq data to date, we present a comprehensive, data-driven Typhimurium TRN. It is conceivable that with more high-quality datasets from more strains, the approach used in this study will continue to guide our investigation in understanding the pan-transcriptome of Typhimurium. Interactive dashboards for all gene modules in this project are available at https://imodulondb.org/ under the "Salmonella Typhimurium" page to enable browsing for interested researchers.


title: Efficient coding of natural scenes improves neural system identification

abstract: Neural system identification aims at learning the response function of neurons to arbitrary stimuli using experimentally recorded data, but typically does not leverage normative principles such as efficient coding of natural environments. Visual systems, however, have evolved to efficiently process input from the natural environment. Here, we present a normative network regularization for system identification models by incorporating, as a regularizer, the efficient coding hypothesis, which states that neural response properties of sensory representations are strongly shaped by the need to preserve most of the stimulus information with limited resources. Using this approach, we explored if a system identification model can be improved by sharing its convolutional filters with those of an autoencoder which aims to efficiently encode natural stimuli. To this end, we built a hybrid model to predict the responses of retinal neurons to noise stimuli. This approach did not only yield a higher performance than the "stand-alone" system identification model, it also produced more biologically-plausible filters. We found these results to be consistent for retinal responses to different stimuli and across model architectures. Moreover, our normatively regularized model performed particularly well in predicting responses of direction-of-motion sensitive retinal neurons. In summary, our results support the hypothesis that efficiently encoding environmental inputs can improve system identification models of early visual processing.


title: Altered retinal structure and function in Spinocerebellar ataxia type 3

abstract:
Spinocerebellar ataxia type 3 is an autosomal dominant neurodegenerative disorder caused by expansion of a polyglutamine (polyQ)-encoding CAG repeat in the ATXN3 gene. Because the ATXN3 protein regulates photoreceptor ciliogenesis and phagocytosis, we aimed to explore whether expanded polyQ ATXN3 impacts retinal function and integrity in SCA3 patients and transgenic mice.

We evaluated the retinal structure and function in five patients with Spinocerebellar ataxia type 3 and in a transgenic mouse model of this disease (YACMJD84.2, Q84) using, respectively, optical coherence tomography (OCT) and electroretinogram (ERG). We further determined in the transgenic mice: a) the retinal expression pattern of ATXN3 and assessed the distribution of cones and rods by immunofluorescence (IF); and b) the retinal ultrastructure by transmission electron microscopy (TEM).

Some patients with Spinocerebellar ataxia type 3 in our cohort revealed: i) reduced central macular thickness indirectly correlated with disease duration; ii) decreased thickness of the macula and the ganglion cell layer, and reduced macula volume inversely correlated with disease severity (SARA score); and iii) electrophysiological dysfunction of cones, rods, and inner retinal cells. Transgenic mice replicated the human OCT and ERG findings with aged homozygous Q84/Q84 mice showing a stronger phenotype accompanied by further thinning of the outer nuclear layer and photoreceptor layer and highly reduced cone and rod activities, thus supporting severe retinal dysfunction in these mice. In addition, Q84 mice showed progressive accumulation of ATXN3-positive aggregates throughout several retinal layers and depletion of cones alongside the disease course. TEM analysis of aged Q84/Q84 mouse retinas supported the IF ATXN3 aggregation findings by revealing the presence of high number of negative electron dense puncta in ganglion cells, inner plexiform and inner nuclear layers, and further showed thinning of the outer plexiform layer, thickening of the retinal pigment epithelium and elongation of apical microvilli.

Our results indicate that retinal alterations detected by non-invasive eye examination using OCT and ERG could represent a biological marker of disease progression and severity in patients with Spinocerebellar ataxia type 3.


title: SARS-CoV-2 triggers complement activation through interactions with heparan sulfate

abstract: The complement system has been heavily implicated in severe COVID-19 with clinical studies revealing widespread gene induction, deposition, and activation. However, the mechanism by which complement is activated in this disease remains incompletely understood. Herein we examined the relationship between SARS-CoV-2 and complement by inoculating the virus in lepirudin-anticoagulated human blood. This caused progressive C5a production after 30 minutes and 24 hours, which was blocked entirely by inhibitors for factor B, C3, C5, and heparan sulfate. However, this phenomenon could not be replicated in cell-free plasma, highlighting the requirement for cell surface deposition of complement and interactions with heparan sulfate. Additional functional analysis revealed that complement-dependent granulocyte and monocyte activation was delayed. Indeed, C5aR1 internalisation and CD11b upregulation on these cells only occurred after 24 hours. Thus, SARS-CoV-2 is a non-canonical complement activator that triggers the alternative pathway through interactions with heparan sulfate.