title: Spatiotemporal dynamics of molecular expression pattern and intercellular interactions in glial scar responding to spinal cord injury

abstract:
Adult regeneration in spinal cord is poor in mammalian but remarkable in the neonatal mammals and some vertebrates, including fish and salamanders. Increasing evidences basis of this interspecies and ontogeny highlighted the pivotal roles of neuron extrinsic factors-the glial scar, which exert confusing inhibiting or promoting regeneration function, but the spatiotemporal ordering of cellular and molecular events that drive repair processes in scar formation remains poorly understood. Here, we firstly constructed tissue-wide gene expression measurements of mouse spinal cords over the course of scar formation using the spatial transcriptomics (ST) technology in Spinal cord injury (SCI) repair. We analyzed the transcriptomes of nearly 15449 spots from 32 samples and distinguished normal and damage response regions. Compared to histological changes, spatial mapping of differentiation transitions in spinal cord injury site delineated the possible trajectory between subpopulations of fibroblast, glia and immune cell more comprehensively and defined the extent of scar boundary and core more accurately. Locally, we identified gene expression gradients from leading edge to the core of scar areas that allow for re-understanding of the scar microenvironment and found some regulators in special cell types, such as Thbs1 and Col1a2 in macrophage, CD36 and Postn in fibroblast, Plxnb2 and Nxpe3 in microglia, Clu in astrocyte and CD74 in oligodendrocyte. Last, we profiled the bidirectional ligand-receptor interactions at the neighbor cluster boundary, contributing to maintain scar architecture during gliosis and fibrosis, and found GPR37L1_PSAP and GPR37_PSAP were top 2 enriched gene-pairs between microglia and fibroblast or microglia and astrocyte. Together, the establishment of these profiles firstly uncovered scar spatial heterogeneity and lineage trajectory, provide an unbiased view of scar and served as a valuable resource for CNS injury treatment.

HighlightsO_LISpatial illustration of gene expression pattern after T10 right lateral hemisection.
C_LIO_LISpatial atlas of scar formation by 21 cell types around damaged area.
C_LIO_LIThe origin, trajectory reconstruction and functional diversity of cell types in different stages of scar formation.
C_LIO_LINovel insights for glial scar boundary and potential benefits for recovery intervention after SCI.
C_LI


title: Cerebellar GABA change during visuomotor adaptation relates to adaptation performance and cerebellar network connectivity: A Magnetic Resonance Spectroscopic Imaging study.

abstract:
Motor adaptation is crucial for performing accurate movements in a changing environment and relies on the cerebellum. Although cerebellar involvement has been well characterized, the neurochemical changes in the cerebellum underpinning human motor adaptation remain unknown.

We used a novel Magnetic Resonance Spectroscopic Imaging (MRSI) technique to measure changes in the inhibitory neurotransmitter {gamma}-aminobutyric acid (GABA) in the human cerebellum during visuomotor adaptation. Participants used their right hand to adapt to a rotated cursor in the scanner, compared with a control task requiring no adaptation. We spatially resolved adaptation-driven GABA changes at the cerebellar nuclei and cerebellar cortex in the left and the right cerebellar hemisphere independently and found that simple right-hand movements increase GABA in the right cerebellar nuclei and decreases GABA in the left. When isolating adaptation-driven GABA changes, we found an increase in GABA in the left cerebellar nuclei and decrease in GABA in the right cerebellar nuclei. Early adaptation-driven GABA change in the right cerebellar nuclei correlated with adaptation performance: Participants showing greater GABA decrease adapted better, suggesting early GABA change is behaviourally relevant. Early GABA change also correlated with functional connectivity change in a cerebellar network: Participants showing greater decreases in GABA showed greater strength increases in cerebellar network connectivity. Results were specific to GABA, to adaptation and to the cerebellar network.

This study provides first evidence for plastic changes in cerebellar neurochemistry during motor adaptation. Characterising these naturally occurring neurochemical changes may provide a basis for developing therapeutic interventions to facilitate human motor adaptation.

Significance StatementDespite motor adaptation being fundamental to maintaining accurate movements, its neurochemical basis remains poorly understood, perhaps because measuring neurochemicals in the human cerebellum is technically challenging. Using a novel magnetic resonance spectroscopic imaging method, this study provides evidence for GABA changes in the left and right cerebellar nuclei driven by both simple movement and motor adaptation. The adaptation-driven GABA change in the right cerebellar nuclei correlated with adaptation performance, and with functional connectivity change in a cerebellar network. These results show the first evidence for plastic changes in cerebellar neurochemistry during a cerebellar learning task. This provides the basis for developing therapeutic interventions that facilitate these naturally occurring changes to amplify cerebellar-dependent learning.

category: neuroscience


title: Different excitation-inhibition correlations between spontaneous and tone-evoked activity in primary auditory cortex neurons

abstract: Tone-evoked synaptic excitation and inhibition are highly correlated in many neurons with V-shaped tuning curves in the primary auditory cortex of pentobarbital-anesthetized rats. In contrast, there is less correlation between spontaneous excitation and inhibition in visual cortex neurons under the same anesthetic conditions. However, it was not known whether the primary auditory cortex resembles visual cortex in having spontaneous excitation and inhibition that is less correlated than tone-evoked excitation and inhibition. Here we report whole-cell voltage-clamp measurements of spontaneous excitation and inhibition in primary auditory cortex neurons of pentobarbital-anesthetized rats. The larger excursions of both spontaneous excitatory and inhibitory currents appeared to consist of distinct events, with the inhibitory event rate typically lower than the excitatory event rate. We use the ratio of the excitatory event rate to the inhibitory event rate, and the assumption that the excitatory and inhibitory synaptic currents can each be reasonably described as a filtered Poisson process, to estimate the maximum spontaneous excitatory-inhibitory correlation for each neuron. In a subset of neurons, we also measured tone-evoked excitation and inhibition. In neurons with V-shaped tuning curves, although tone-evoked excitation and inhibition were highly correlated, the spontaneous inhibitory event rate was typically sufficiently lower than the spontaneous excitatory event rate to indicate a lower excitatory-inhibitory correlation for spontaneous activity than for tone-evoked responses.


title: In the back of your mind: Cortical mapping of tactile and proprioceptive paraspinal afferent inputs

abstract: Persistent pain alters brain-body representations, highlighting their potential pathological significance. In chronic low back pain (LBP), sparse evidence points towards a shift of the cortical representation of sensory afferents of the back. However, systematic investigations of the cortical representation of tactile and proprioceptive paraspinal afferents along the thoracolumbar axis are lacking. Detailed cortical maps of paraspinal afferent input might be crucial to further explore potential relationships between brain changes and the development and maintenance of chronic LBP. We therefore validated a novel and functional magnetic resonance imaging-(fMRI-)compatible method of mapping cortical representations of tactile and proprioceptive afferents of the back, using pneumatic vibrotactile stimulation ("pneuVID") at varying frequencies and paraspinal locations, in conjunction with high-resolution fMRI. We hypothesised that: (i) high (80 Hz) frequency stimulation would lead to increased postural sway compared to low (20 Hz) stimulation, due to differential evoked mechanoreceptor contributions to postural control (proprioceptive vs tactile); and (ii) that high (80 Hz) versus low (20 Hz) frequency stimulation would be associated with neuronal activity in distinct primary somatosensory (S1) and motor (M1) cortical targets of tactile and proprioceptive afferents (N=15, healthy volunteers). Additionally, we expected neural representations to vary spatially along the thoracolumbar axis. We found significant differences between neural representations of low and high frequency stimulation and between representations of thoracic and lumbar paraspinal locations, in several bilateral sensorimotor cortical regions. Proprioceptive (80 Hz) stimulation preferentially activated sub-regions S1 3a and M1 4p, while tactile (20 Hz) stimulation was more encoded in S1 3b and M1 4a. Moreover, in S1, lower back proprioceptive stimulation activated dorsal-posterior representations, compared to ventral-anterior representations activated by upper back stimulation. As per our hypotheses, we found distinct sensorimotor cortical tactile and proprioceptive representations, with the latter displaying clear topographic differences between the upper and lower back. This thus represents the first behavioural and neurobiological validation of the novel pneuVID method for stimulating muscle spindles and mapping cortical representations of paraspinal afferents. Future investigations of detailed cortical maps will be of major importance in elucidating the role of cortical reorganization in the pathophysiology of chronic LBP.


title: Testing for implicit emotion regulation in childhood

abstract: Although implicit emotion regulation is thought to be critical for psychosocial development and mental wellbeing, few studies have investigated the neural underpinnings of this form of emotion regulation in children. We used a modified emotional Go/NoGo block design fMRI task to explore the neural correlates of implicit emotion regulation and individual differences in a sample of 40 children (50% female, mean age = 8.65 {+/-} 0.77). Conditions included happy, sad, neutral, and scrambled faces as implicit distractors within the actual Go/NoGo targets. We used a relatively standard preprocessing pipeline via fMRIprep, with T-contrasts for response inhibition and emotional effects, and a nonparametric multiple comparisons procedure, with SnPM, for our group-level analysis. There were multiple significant response inhibition effects, including larger NoGo vs Go activation in the IFG, insula, and MCC/ACC. Valence effects showed significantly greater right putamen activity for the Sad NoGo vs Go contrast and greater bilateral putamen and right pallidum activity for the Happy Go vs Sad Go contrast. These results provide preliminary findings of neural substrates, particularly the putamen, that may be associated with implicit emotion regulation in children.


title: A mechanistically interpretable model of the retinal neural code for natural scenes with multiscale adaptive dynamics

abstract: The visual system processes stimuli over a wide range of spatiotemporal scales, with individual neurons receiving input from tens of thousands of neurons whose dynamics range from milliseconds to tens of seconds. This poses a challenge to create models that both accurately capture visual computations and are mechanistically interpretable. Here we present a model of salamander retinal ganglion cell spiking responses recorded with a multielectrode array that captures natural scene responses and slow adaptive dynamics. The model consists of a three-layer convolutional neural network (CNN) modified to include local recurrent synaptic dynamics taken from a linear-nonlinear-kinetic (LNK) model [1]. We presented alternating natural scenes and uniform field white noise stimuli designed to engage slow contrast adaptation. To overcome difficulties fitting slow and fast dynamics together, we first optimized all fast spatiotemporal parameters, then separately optimized recurrent slow synaptic parameters. The resulting full model reproduces a wide range of retinal computations and is mechanistically interpretable, having internal units that correspond to retinal interneurons with biophysically modeled synapses. This model allows us to study the contribution of model units to any retinal computation, and examine how long-term adaptation changes the retinal neural code for natural scenes through selective adaptation of retinal pathways.


title: Prefrontal cortical contributions to working memory loading, maintenance and recall are parsed by hippocampal-prefrontal oscillatory assembly dynamics

abstract: Working memory enables incorporation of recent experience into subsequent decision-making. This processing recruits both prefrontal cortex and hippocampus, where neurons encode task cues, rules and outcomes. However, precisely which information is carried when, and by which neurons, remains unclear. Using population decoding of activity in rat medial prefrontal cortex (mPFC) and dorsal hippocampal CA1, we confirm that mPFC populations lead in maintaining sample information across delays of an operant nonmatch to sample task, despite individual neurons firing only transiently. During sample encoding, distinct mPFC subpopulations joined distributed CA1-mPFC cell assemblies hallmarked by 4-5Hz rhythmic modulation; CA1-mPFC assemblies re-emerged during choice episodes, but were not 4-5Hz modulated. Delay-dependent errors arose when attenuated rhythmic assembly activity heralded collapse of sustained mPFC encoding; pharmacological disruption of CA1-mPFC assembly rhythmicity impaired task performance. Our results map component processes of memory-guided decisions onto heterogeneous CA1-mPFC subpopulations and the dynamics of physiologically distinct, distributed cell assemblies.


title: All-optical imaging and patterned stimulation with a one-photon endoscope

abstract: While in vivo calcium imaging makes it possible to record activity in defined neuronal populations with cellular resolution, optogenetics allows selective manipulation of neural activity. Recently, these two tools have been combined to stimulate and record neural activity at the same time, but current approaches often rely on two-photon microscopes that are difficult to use in freely moving animals, or one-photon fiberscopes with benchtop-based digital micromirror devices that limit system portability. To address these limitations, we have developed a new integrated system combining a one-photon endoscope and a digital micromirror device for simultaneous calcium imaging and precise optogenetic photo-stimulation (Miniscope with All-optical Patterned Stimulation and Imaging, MAPSI). Using this system, we were able to successfully image striatal neurons from either the direct pathway or the indirect pathway while simultaneously activating any neuron of choice within the field of view or synthesizing arbitrary spatio-temporal patterns of photo-stimulation in freely moving mice. We could also select neurons based on their relationship with behavior and recreate the behavior by mimicking the natural neural activity with photo-stimulation. MAPSI thus provides a powerful tool for in vivo interrogation of neural circuit function.


title: Helminth infection modulates number and function of adipose tissue Tregs in high fat diet-induced obesity

abstract:
BackgroundEpidemiological and experimental studies have shown a protective effect of helminth infections in weight gain and against the development of metabolic dysfunctions in the host. However, the mechanisms induced by the parasite that regulate the development of metabolic diseases in the host are unclear. The present study aimed to verify the influence of Heligmosomoides polygyrus infection in early stages of high fat diet-induced obesity.

Principal FindingsThe presence of infection was able to prevent exacerbated weight gain in mice fed with high fat diet when compared to non-infected controls. In addition, infected animals displayed improved insulin sensitivity and decreased fat accumulation in the liver. Obesity-associated inflammation was reduced in the presence of infection, demonstrated by higher levels of IL10 and adiponectin, increased infiltration of Th2 and eosinophils in adipose tissue of infected animals. Of note, the parasite infection was associated with increased Treg frequency in adipose tissue which showed higher expression of cell surface markers of function and activation, like LAP and CD134. The infection could also revert the loss of function in Tregs associated with high fat diet.

ConclusionThese data suggest that H. polygyrus infection can prevent weight gain and metabolic syndrome in animals fed with high fat diet associated with modulations of adipose tissue Treg cells.

Author summaryHelminth infections are known to modulate the immune system being responsible for protecting the host from developing allergic and autoimmune disorders (Hygiene Hypothesis). We hypothesized that the same immunomodulatory effect can have an impact on immunometabolic diseases, such as obesity and its linked diseases such as type 2 diabetes. Weight disorders have reached epidemic levels, nearly tripling since 1975 and being responsible for almost 5 million premature deaths each year. To test our hypothesis C57BL/6 male mice were fed control or high fat diet, for five weeks, in the presence or not of Heligmosomoides polygyrus infection. Weight gain, development of metabolic disorders, inflammation and cellular migration to the adipose tissue were evaluated. In accordance with our hypothesis, we found that the presence of infection prevented the exacerbated weight gain and also improved metabolic parameters in animals fed a high fat diet. This was associated with the infections ability to modulate parameters of a cell responsible for regulatory functions: Tregs. In the light of these findings, helminth infection could be protective against weight gain and metabolic disturbances.

category: immunology


title: GPR55 in B cells limits atherosclerosis development and regulates plasma cell maturation

abstract: Identifying novel pathways regulating the adaptive immune response in chronic inflammatory diseases such as atherosclerosis is of particular interest in view of developing new therapeutic drugs. Here we report that the lipid receptor GPR55 is highly expressed by splenic B cells and inversely correlates with atheroma plaque size in mice. In human carotid endarterectomy specimen, GPR55 transcript levels were significantly lower in unstable compared to stable carotid plaques. To study the impact of GPR55 deficiency in atherosclerosis, we crossed Gpr55 knockout mice with apolipoprotein E (ApoE) knockout mice and subjected the mice to Western diet for 4 to 16 weeks. Compared to ApoE-/- controls, ApoE-/-Gpr55-/- mice developed larger plaques with increased necrotic core size, associated with elevated circulating and aortic leukocyte counts. Flow cytometry, immunofluorescence and RNA-sequencing analysis of splenic B cells in these mice revealed a hyperactivated B cell phenotype with disturbed plasma cell maturation and immunoglobulin (Ig)G antibody overproduction. The specific contribution of B cell GPR55 in atherosclerosis was further studied in mixed Gpr55-/-/{micro}MT bone marrow chimeras on low density receptor deficiency (Ldlr-/-) background, revealing that B-cell specific depletion of Gpr55 was sufficient to promote plaque development. Conversely, adoptive transfer of wildtype B cells into ApoE-/-Gpr55-/- mice blunted the proatherogenic phenotype. In vitro stimulation of splenocytes with the endogenous GPR55 ligand LPI promoted plasma cell proliferation and enhanced B cell activation marker expression, which was inhibited by the GPR55 antagonist CID16020046. Collectively, these discoveries provide new evidence for GPR55 as key modulator of the adaptive immune response in atherosclerosis. Targeting GPR55 could be useful to limit inflammation and plaque progression in patients suffering from atherosclerosis.


title: Engraftment, fate, and function of HoxB8-conditional neutrophil progenitors in the unconditioned murine host

abstract: The development and use of murine myeloid progenitor cell lines that are conditionally immortalized through expression of HoxB8 has provided a valuable tool for studies of neutrophil biology. Recent work has extended the utility of HoxB8-conditional progenitors to the in vivo setting via their transplantation into irradiated mice. Here, we describe the isolation of HoxB8-conditional progenitor cell lines that are unique in their ability to engraft in the naive host in the absence of conditioning of the hematopoietic niche. Our results indicate that HoxB8-conditional progenitors engraft in a {beta}1 integrin-dependent manner and transiently generate donor-derived mature neutrophils. Furthermore, we show that neutrophils derived in vivo from transplanted HoxB8-conditional progenitors are mobilized to the periphery and recruited to sites of inflammation in a manner that depends on the C-X-C chemokine receptor 2 and {beta}2 integrins, the same mechanisms that have been described for recruitment of endogenous primary neutrophils. Together, our studies advance the understanding of HoxB8-conditional neutrophil progenitors and describe an innovative tool that, by virtue of its ability to engraft in the naive host, will facilitate mechanistic in vivo experimentation on neutrophils.


title: Single-cell RNA sequencing reveals micro-evolution of the stickleback immune system

abstract: Pathogenic infection is an important driver of many ecological processes. Furthermore, variability in immune function is an important driver of differential infection outcomes. New evidence would suggest that immune variation extends to broad cellular structure of immune systems. However, variability at such broad levels is traditionally difficult to detect in non-model systems. Here we leverage single cell transcriptomic approaches to document signatures of microevolution of immune system structure in a natural system, the three-spined stickleback (Gasterosteus aculeatus). We sampled nine adult fish from three populations with variability in resistance to a cestode parasite, Schistocephalus solidus, to create the first comprehensive immune cell atlas for G. aculeatus. Eight major immune cell types, corresponding to major vertebrate immune cells, were identified. We were also able to document significant variation in both abundance and expression profiles of the individual immune cell types, among the three populations of fish. This variability may contribute to observed variability in parasite susceptibility. Finally, we demonstrate that identified cell type markers can be used to reinterpret traditional transcriptomic data. Combined our study demonstrates the power of single cell sequencing to not only document evolutionary phenomena (i.e. microevolution of immune cells), but also increase the power of traditional transcriptomic datasets.


title: Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses

abstract: Common variable immunodeficiency (CVID), the most prevalent symptomatic primary immunodeficiency, is characterized by impaired terminal B-cell differentiation and defective antibody responses. Incomplete genetic penetrance and a wide range of phenotypic expressivity in CVID suggest the participation of additional pathogenic mechanisms. Monozygotic (MZ) twins discordant for CVID are uniquely valuable for studying the contribution of epigenetics to the disease. We used single-cell epigenomics and transcriptomics to create a cell census of naive-to-memory B cell differentiation in a pair of CVID-discordant MZ twins. Our analysis identifies DNA methylation, chromatin accessibility and transcriptional defects in memory B cells that mirror defective cell-cell communication defects following activation. These findings were validated in a cohort of CVID patients and healthy donors. Our findings provide a comprehensive multi-omics map of alterations in naive-to-memory B-cell transition in CVID and reveal links between the epigenome and immune cell cross-talk. Our resource, publicly available at the Human Cell Atlas, paves the way for future diagnosis and treatments of CVID patients.


title: A role for CD4 helper cells in HIV control and progression

abstract:
It remains unclear why HIV persists in most untreated individuals, and why a small minority of individuals can control the virus, either spontaneously or after an early treatment. The present work motivated by the striking differences in the functional avidity of CD4 T cells discovered between patient cohorts in a recent study [1] offers an experimentally-testable mathematical model that explains the diverse outcome of infection. The model predicts an arms race between viral dissemination and the proliferation of HIV-specific CD4 helper cells leading to one of two states: a low-viremia state or a high-viremia state. Helper CD4 cells with a higher avidity favor virus control. The parameter segregating spontaneous and post-treatment controllers is the infectivity asymmetry between activated and resting CD4 T cells. The predictions are found to be consistent with the data from [1] and with data on the avidity CD8 T cells [2]. I also analyze the alternative explanation of T cell exhaustion previously proposed to explain the diverse patient cohorts and demonstrate that it does not explain these and some other experimental data.

ImportanceWhy HIV persists in most untreated individuals, and why a minority can control the virus, either spontaneously or after short treatment, remains unknown. The present study offers a mathematical model of the immune response that explains the differences between the patient cohorts as a result of the arms race between viral dissemination and the proliferation of HIV-specific CD4 T cells. It offers testable predictions and personalized adjustment of early ART to a patient.


title: Interleukin-10 knockout mice do not reliably exhibit macroscopic inflammation: a natural history endoscopic surveillance study

abstract:
BackgroundInterleukin (IL)-10 knockout (KO) mice, used as a model for inflammatory bowel disease (IBD), develop chronic enterocolitis. Endoscopy, the gold standard for evaluation of human mucosal health, is not widely available for murine models. We aimed to assess the natural history of left-sided colitis in IL-10 KO mice via serial endoscopies.

MethodsBALB/cJ IL10 KO mice underwent regular endoscopic assessments from 2 up to 8 months of age. Procedures were recorded and blindly evaluated using a 4-component endoscopic score: mucosal wall transparency, intestinal bleeding, focal lesions and perianal lesions (0-3 points each). An endoscopic score [≥]1 point was considered as the presence of colitis/flare.

ResultsIL-10 KO mice (N=40, 9 female) were assessed. Mean age at first endoscopy was 62.5{+/-}2.5 days; average number of procedures per mouse was 6.0{+/-}1.3. A total of 238 endoscopies were conducted every 24.8{+/-}8.3 days, corresponding to 124.1{+/-}45.2 days of surveillance per mouse (13.6 years cumulative surveillance). Thirty-three endoscopies in 24 mice (60%) detected colitis, mean endoscopy score 2.5{+/-}1.3 (range: 1-6.3). Nineteen mice (47.5%) had one episode of colitis and 5 (12.5%) had 2-3 episodes. All exhibited complete spontaneous healing on subsequent endoscopies.

ConclusionsIn this largest endoscopic surveillance study of IL-10 KO mice, 40% of mice did not develop endoscopic left-sided colitis. Furthermore, IL-10 KO mice did not exhibit persistent colitis and universally exhibited complete spontaneous healing without treatment. The natural history of colitis in IL-10 KO mice may not be comparable with that of IBD in humans and requires careful consideration.


title: Time-resolved assessment of single-cell protein secretion by sequencing

abstract: Secreted proteins play critical roles in cellular communication and functional orchestration. Methods enabling concurrent measurement of cellular protein secretion, phenotypes and transcriptomes are still unavailable. Here, we describe time-resolved assessment of protein secretion from single cells by sequencing (TRAPS-seq). Released proteins are trapped onto cell surface via affinity matrices, and the captured analytes together with phenotypic markers can be probed by oligonucleotide-barcoded antibodies and simultaneously sequenced with transcriptomes. We used TRAPS-seq to interrogate secretion dynamics of pleiotropic cytokines (IFN-{gamma}, IL-2 and TNF-) of early activated human T lymphocytes, unraveling limited correlation between cytokine secretion and its transcript abundance with regard to timing and strength. We found that early central memory T cells with CD45RA expression (TCMRA) are the most effective responders in multiple cytokine secretion, and polyfunctionality involves unique yet dynamic combinations of gene signatures over time. TRAPS-seq presents a useful tool for cellular indexing of secretions, phenotypes, and transcriptomes at single-cell resolution.


title: Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma

abstract: Myasthenia gravis (MG) is a neurological disease caused by autoantibodies against neuromuscular-associated proteins. While MG is frequently developed in thymoma patients, the etiologic factors for MG are not well understood. Here, by constructing a comprehensive atlas of thymoma using bulk and single-cell RNA-seq, we identified ectopic expression of neuromuscular molecules in MG-associated thymoma (MG-thymoma). These molecules were originated from a distinct subpopulation of medullary thymic epithelial cells (mTECs), which we named neuromuscular mTECs (nmTECs). MG-thymoma also exhibited microenvironments dedicated to autoantibody production, including ectopic germinal center formation, T follicular helper cell accumulation, and type 2 conventional dendritic cell migration. Cell-cell interaction analysis also predicted the interaction between nmTECs and T/B cells via CXCL12-CXCR4. The enrichment of nmTECs presenting neuromuscular molecules within MG-thymoma was further confirmed by immunohistochemically and by cellular composition estimation from MG-thymoma transcriptome. Altogether, this study suggests that nmTECs play a significant role in MG pathogenesis via ectopic expression of neuromuscular molecules.


title: Long-lasting germinal center responses to a priming immunization with continuous proliferation and somatic mutation

abstract: Germinal centers (GCs) are the engines of antibody evolution. Using HIV Env protein immunogen priming in rhesus monkeys (RM) followed by a long period without further immunization, we demonstrate GC B cells (BGC) lasted at least 6 months (29 weeks), all the while maintaining rapid proliferation. A 186-fold BGC cell increase was present by week 10 compared to a conventional immunization. Single cell transcriptional profiling revealed that both light zone and dark zone GC states were sustained throughout the 6 months. Antibody somatic hypermutation (SHM) of BGC cells continued to accumulate throughout the 29 week priming period, with evidence of selective pressure. Additionally, Env-binding BGC cells were still 49-fold above baseline 29 weeks after immunization, suggesting that they could be active for significantly longer periods of time. High titers of HIV neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing significant immunodominance challenges for B cells, among other difficulties. Memory B cells (BMem) generated under these long priming conditions had higher levels of SHM, and both BMem cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning the >6-month GC period were identified, demonstrating continuous GC activity and selection for at least 191 days, with no additional antigen exposure. A long prime, adjuvanted, slow delivery (12-day) immunization approach holds promise for difficult vaccine targets, and suggests that patience can have great value for tuning GCs to maximize antibody responses.


title: The African swine fever modelling challenge: objectives, model description and synthetic data generation

abstract:
African swine fever (ASF) is an emerging disease currently spreading at the interface between wild boar and pig farms in Europe and Asia. Current disease control regulations, which involve massive culling with significant economic and animal welfare costs, need to be improved. Modelling enables relevant control measures to be explored, but conducting the exercise during an epidemic is extremely difficult. Modelling challenges enhance modellers ability to provide timely advice to policy makers, improve their readiness when facing emerging threats, and promote international collaborations. The ASF-Challenge, which ran between August 2020 and January 2021, was the first modelling challenge in animal health. In this paper, we describe the objectives and rules of the challenge. We then demonstrate the mechanistic multi-host model that was used to mimic as accurately as possible an ASF-like epidemic, provide a detailed explanation of the surveillance and intervention strategies that generated the synthetic data, and describe the different management strategies that were assessed by the competing modelling teams. We then outline the different technical steps of the challenge as well as its environment. Finally, we synthesize the lessons we learnt along the way to guide future modelling challenges in animal health.

HighlightsO_LIThe 1st modelling challenge in animal health mimics ASF spread with synthetic data
C_LIO_LIA mechanistic spatially explicit stochastic model was developed to represent ASF spread and control
C_LIO_LISynthetic data concerned date and location of detected cases in pigs and wild boar
C_LIO_LIThe wildlife-livestock interface is crucial in infectious animal disease spread
C_LI

category: ecology


title: Evolution of Enterococcus faecium to A Combination of Daptomycin and Fosfomycin Reveals Distinct and Diverse Adaptive Strategies

abstract:
Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) are an important public health threat. VREfm have become increasingly resistant to the front-line antibiotic, daptomycin (DAP). As such, the use of DAP combination therapies (like fosfomycin [FOS]), has received increased attention. Antibiotic combinations could extend the efficacy of current available antibiotics and potentially delay the onset of further resistance. We investigated the potential for E. faecium HOU503, a clinical VREfm isolate that is DAP and FOS susceptible, to develop resistance to a DAP-FOS combination. Of particular interest was whether the genetic drivers for DAP-FOS resistance might be epistatic and, thus, potentially decrease the efficacy of a combinatorial approach in either inhibiting VREfm or in delaying the onset of resistance. We show that resistance to DAP-FOS could be achieved by independent mutations to proteins responsible for cell wall synthesis for FOS and in altering membrane dynamics for DAP. However, we did not observe genetic drivers that exhibited substantial cross-drug epistasis that could undermine DAP-FOS combination. Of interest was that FOS resistance in HOU503 was largely mediated by changes in phosphoenolpyruvate (PEP) flux as a result of mutations in pyruvate kinase (pyk). Increasing PEP flux could be a readily accessible mechanism for FOS resistance in many pathogens. Importantly, we show that HOU503 were able to develop DAP resistance through a variety of biochemical mechanisms and were able to employ different adaptive strategies. Finally, we showed that the addition of FOS can prolong the efficacy of DAP, significantly extending the timeline to resistance in vitro.

ImportanceWhile the discovery of antibiotics was one of the greatest health care advances in history, its success is being challenged by the emergence of multidrug-resistant pathogens, including vancomycin-resistant enterococci (VRE). Daptomycin (DAP), a lipopeptide antibiotic that targets cell membrane, is currently prescribed as a frontline drug to treat VRE infections. However, emergence of daptomycin-resistant VRE is concerning. Consequently, DAP-Fosfomycin (FOS) combination (DF) has been proposed as a potential method to maintain DAP efficacy. Here, we provide evidence that DF successfully delayed the emergence of resistance in vitro. Genetic data indicates that resistance was acquired independently, with little evidence of significant cross-drug epistasis that could undermine a combinatorial approach. We also uncovered a novel FOS resistance mechanism, through changes in phosphoenolpyruvate (PEP) flux, that may potentially be shared with other bacterial species. Additionally, we also have evidence showing that E. faecium was able to employ different resistance mechanisms.

category: evolutionary biology


title: Parental provisioning drives brain size in birds

abstract:
Larger brains should be adaptive because they support numerous eco- and socio-cognitive benefits, but these benefits explain only a modest part of the interspecific variation in brain size. Notably underexplored are the high energetic costs of developing brains, and thus the possible role of parental provisioning in the evolution of adult brain size. We explore this idea in birds, which show considerable variation in both socio-ecological traits and the energy transfer from parents to offspring. Comparative analyses of 1,176 bird species show that the combination of adult body mass, mode of development at hatching, relative egg mass, and the time spent provisioning the young in combination strongly predict relative brain size across species. Adding adult eco- and socio-cognitive predictors only marginally adds explanatory value. We therefore conclude that parental provisioning enabled bird species to evolve into skill-intensive niches, reducing interspecific competition and consequently promoting survival prospects and population stability. Critically, parental provisioning also explains why precocial bird species have smaller brains than altricial ones. Finally, these results suggest that the cognitive adaptations that provide the behavioral flexibility to improve reproductive success and survival are intrinsically linked to successful parental provisioning. Our findings also suggest that the traditionally assessed cognitive abilities may not predict relative brain size.

Significance statementSpecies vary substantially in their brain size, and the idea that larger-brained species are those with a complex social life or enhanced technological skills has generated much interest. Here we explore another explanation. Because the cognitive benefits provided by brains materialize after a long delay, and constructing them independently involves a major bootstrapping problem for the young, parental inputs may be critical for a species brain size. Comparative analyses of a large sample of bird species show that parental provisioning strongly predicts relative brain size across species, swamping the effects of previously considered social or technological cognitive abilities. Thus, cognitive adaptations in birds that enable successful parental provisioning also provide the behavioral flexibility to improve survival and reproductive success.


title: Relatedness modulates reproductive competition among queens in ant societies with multiple queens

abstract: Reproductive sharing in animal groups with multiple breeders, insects and vertebrates alike, contains elements of both conflict and cooperation, and depends on both relatedness between co-breeders, as well as their internal and external conditions. We studied how queens of the ant Formica fusca adjust their reproductive efforts in response to experimental manipulations of the kin competition regime in their nest, as well as their own reproductive status. Queens respond to the presence of competitors by increasing their egg laying efforts, but only if the competitors are highly fecund and distantly related. Furthermore, queens only engage in cannibalism of eggs when the risk of erroneously destroying own offspring is absent. We demonstrate that queens of Formica fusca fine-tune their behaviours in response to kinship and fecundity of others as well as their own physiological state in an unusually precise manner.


title: Cellular development and evolution of the mammalian cerebellum

abstract: The expansion of the neocortex, one of the hallmarks of mammalian evolution1,2, was accompanied by an increase in the number of cerebellar neurons3. However, little is known about the evolution of the cellular programs underlying cerebellum development in mammals. In this study, we generated single-nucleus RNA-sequencing data for [~]400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse, and the marsupial opossum. Our cross-species analyses revealed that the cellular composition and differentiation dynamics throughout cerebellum development are largely conserved, except for human Purkinje cells. Global transcriptome profiles, conserved cell state markers, and gene expression trajectories across neuronal differentiation show that the cerebellar cell type-defining programs have been overall preserved for at least 160 million years. However, we also discovered differences. We identified 3,586 genes that either gained or lost expression in cerebellar cells in one of the species, and 541 genes that evolved new expression trajectories during neuronal differentiation. The potential functional relevance of these cross-species differences is highlighted by the diverged expression patterns of several human disease-associated genes. Altogether, our study reveals shared and lineage-specific programs governing the cellular development of the mammalian cerebellum, and expands our understanding of the evolution of mammalian organ development.


title: Transcriptome of the synganglion and characterization of the cys-loop ligand-gated ion channel gene family in the tick Ixodes ricinus.

abstract: Ticks represent a major health issue for humans and domesticated animals. Assessing the expression patterns of the ticks central nervous system, known as the synganglion, is an important step in understanding tick physiology and in managing tick-borne diseases. Neuron-specific genes like the cys-loop ligand-gated ion channels (cys-loop LGICs) are important pharmacological targets of acaricides. Here, we carried out the sequencing of transcriptomes of the I. ricinus synganglion, for adult ticks in different conditions (unfed males, unfed females, and partially-fed females). The de novo assembly of these transcriptomes allowed us to obtain a large collection of cys-loop LGICs sequences. A reference meta-transcriptome based on synganglion and whole body transcriptomes was then produced, showing high completeness and allowing differential expression analyses between synganglion and whole body. Many of the genes upregulated in the synganglion were related to biological processes or functions associated with neurotransmission and located in neurones or the synaptic membrane, including most of the cys-loop LGICs. As a first step of a functional study of cysLGICs, we cloned the predicted sequence of the resistance to dieldrin (RDL) subunit homologue, and functionally reconstituted the first GABA-gated receptor of Ixodes ricinus using a hetrologous expression approach. A phylogenetic study was performed for the nicotinic acetylcholine receptors (nAChRs) and for other cys-loop LGICs respectively, showing tick-specific expansions of some types of receptors (Histamine-gated, GluCls).


title: Revisiting the number of self-incompatibility alleles in finite populations: from old models to new results

abstract: Under gametophytic self-incompatibility (GSI), plants are heterozygous at the self-incompatibility locus (S-locus) and can only be fertilized by pollen with a different allele at that locus. The last century has seen a heated debate about the correct way of modeling the allele diversity in a GSI population that was never formally resolved. Starting from an individual-based model, we derive the deterministic dynamics as proposed by Fisher (1958), and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (1964) is close to our theoretical prediction, in line with earlier numerical confirmation. Additionally, we approximate the invasion probability of a new S-allele, which scales inversely with the number of resident S-alleles. Lastly, we use the stationary allele frequency distribution to estimate the population size of a plant population from an empirically obtained allele frequency spectrum, which complements the existing estimator of the number of S-alleles. Our expression of the stationary distribution resolves the long-standing debate about the correct approximation of the number of S-alleles and paves the way to new statistical developments for the estimation of the plant population size based on S-allele frequencies.


title: Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain.

abstract: The European polecat (Mustela putorius) is a mammalian predator which occurs across much of Europe east to the Ural Mountains. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as  pure polecats. We quantify this introgression and find introgressed genes under selection that may assist in cognitive function and sight.


title: Fine mapping of goat polledness variant in six Chinese native breeds

abstract:
BackgroundThe genetic mechanism of goat polledness has been studied for decades, but identifying causative variants and functional genes remains challenging.

ResultsUsing a genome-wide association study (GWAS), we identified a significant striking locus for polledness in two different goat breeds. To reduce the linkage disequilibrium among variants for localizing causative variants in the finer region, we sequenced 79 goats from six Chinese native breeds (Jining Gray, Matou, Guizhou black, Yunnan black bone, Chaidamu, and Ujumqin) and identified 483.5 kb CNV (150,334,567-150,818,099) translocated into the previously identified 11.7 kb polled intersex syndrome region, which was consistent with previous research using intersex goat populations. Within the 483.5 kb CNV, a ~322 bp horn-specific element, similar to the superfamily of tRNA-derived families of SINEs, located at the first intron of the ERG gene was identified. The results of the GO enrichment analysis showed that the Horn-SINE element-associated genes were involved in both nervous system and head development. Finally, we used RNA sequencing to investigate gene expression profiles in the horn bud and skin tissues of horned and polled goats. We identified 1077 and 1222 differentially expressed genes between the horn bud and skin tissue in polled and horned goats, respectively. We also identified 367 differentially expressed genes in horn buds between polled and horned animals, and found that the two CNV-related genes, ERG and FOXL2, were upregulated in the horn bud of polled goats. Gene functional enrichment analysis demonstrated that the downregulated genes in the horn bud of polled goats were enriched in skeletal system development, whereas the upregulated genes were significantly overexpressed in muscle tissue development.

ConclusionsBroadly, this study describes a novel structural variant responsible for polledness/intersex traits and contributes to the discovery of molecular mechanisms underlying the development and regulation of the polledness trait.

category: genetics


title: Variant-to-gene-mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as novel regulator of sleep

abstract: Sleep is nearly ubiquitous throughout the animal kingdom, with deficiencies in sleep having been linked to a wide range of human disorders and diseases. While genome wide association studies (GWAS) in humans have identified loci robustly associated with several heritable diseases or traits, little is known about the functional roles of the underlying causal variants in regulating sleep duration or quality. We applied an ATAC-seq/promoter focused Capture C strategy in human iPSC-derived neural progenitors to carry out a  variant-to-gene mapping campaign that identified 88 candidate sleep effector genes connected to relevant GWAS signals. To functionally validate the role of the implicated effector genes in sleep regulation, we performed a neuron-specific RNAi screen in the fruit fly, Drosophila melanogaster. This approach identified a number of genes that regulated sleep, including phosphatidylinositol N-acetylglucosaminyltransferase subunit Q (PIG-Q), a gene that encodes an enzyme involved in the first step of glycosylphosphatidylinositol (GPI)- anchor biosynthesis. We show that flies deficient for PIG-Q have longer sleep during both day and night due to an increase in the total number of sleep bouts. Subsequent systematic investigation of other PIG-family genes identified increased sleep in flies for multiple different genes within the PIG pathway. We then mutated the PIG-Q locus in zebrafish and identified similar increases in sleep to those observed in Drosophila, confirming deep homology of PIG-Q mediated sleep regulation. These results provide the first physical variant-to-gene mapping of human sleep genes followed by a model organism-based prioritization, revealing a novel and conserved role for GPI-anchor biosynthesis in sleep regulation.


title: Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients

abstract: Cystic fibrosis (CF) is a severe genetic disorder that can cause multiple comorbidities affecting the lungs, the pancreas, the luminal digestive system and beyond. In our previous genome-wide association studies (GWAS), we genotyped [~]8,000 CF samples using a mixture of different genotyping platforms. More recently, the Cystic Fibrosis Genome Project (CFGP) performed deep ([~]30x) whole genome sequencing (WGS) of 5,095 samples to better understand the genetic mechanisms underlying clinical heterogeneity among CF patients. For mixtures of GWAS array and WGS data, genotype imputation has proven effective in increasing effective sample size. Therefore, we first performed imputation for the [~]8,000 CF samples with GWAS array genotype using the TOPMed freeze 8 reference panel. Our results demonstrate that TOPMed can provide high-quality imputation for CF patients, boosting genomic coverage from [~]0.3 - 4.2 million genotyped markers to [~]11 - 43 million well-imputed markers, and significantly improving Polygenic Risk Score (PRS) prediction accuracy. Furthermore, we built a CF-specific CFGP reference panel based on WGS data of CF patients. We demonstrate that despite having [~]3% the sample size of TOPMed, our CFGP reference panel can still outperform TOPMed when imputing some CF disease-causing variants, likely due to allele and haplotype differences between CF patients and general populations. We anticipate our imputed data for 4,656 samples without WGS data will benefit our subsequent genetic association studies, and the CFGP reference panel built from CF WGS samples will benefit other investigators studying CF.


title: Landscape genetics across the Andes Mountains: Environmental variation drives genetic divergence in the leaf-cutting ant Atta cephalotes

abstract: Disentangling the mechanisms underlying spatial distribution of genetic variation into those due to environment or physical barriers from mere geographic distance is challenging in complex landscapes. The Andean uplift represents one of the most heterogeneous habitats where these questions remain unexplored as multiple mechanisms might interact, confounding their relative roles. We explore this broad question in the leaf-cutting ant Atta cephalotes, a species distributed across the Andes Mountains using nuclear microsatellite markers and mtCOI gene sequences. We investigate spatial genetic divergence across the Western range of Northern Andes in Colombia by testing the relative role of alternative scenarios of population divergence, including geographic distance (IBD), climatic conditions (IBE), and physical barriers due to the Andes Mountains (IBB). Our results reveal substantial genetic differentiation among A. cephalotes populations for both types of markers, but only nuclear divergence followed a hierarchical pattern with multiple models of genetic divergence imposed by the Western range. Model selection showed that IBD, IBE (temperature and precipitation), and IBB (Andes mountains) models, often proposed as individual drivers of genetic divergence, interact, and explain up to 33% of genetic divergence in A. cephalotes. IBE models remained significant after accounting for IBD, suggesting that environmental factors play a more prominent role when compared to IBB. These factors in combination with idiosyncratic dispersal patterns of ants appear to determine hierarchical patterns of gene flow. This study enriches our understanding of the forces shaping population divergence in complex habitat landscapes.


title: Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data

abstract:
The recent increase in openly available ancient human DNA samples allows for new, large-scale meta analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to, since changes in ancestry - unlike cultural changes seen in the archaeological record - necessarily reflect movements of people. Here we present a new algorithm to quantify past human mobility from large ancient genomic datasets. The key idea of the method is for each individual to compare a hypothetical genetic "origin" point with its actual burial point in space. This is achieved by first creating an interpolated ancestry field through space and time based on Multidimensional scaling and Gaussian process regression, and then using this field to map the ancient individuals into space according to their genetic profile. We apply this new algorithm to a dataset of 3191 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 years and derive a diachronic measure of mobility for subregions in Western, Central, Southern and Eastern Europe. For regions and periods with sufficient data coverage, our mobility estimates show general concordance with previous results, but also reveal new signals of movements beyond the well-known key events.

Significance StatementAncient human DNA (aDNA) extracted from archaeological contexts (e.g. burials) allows to reconstruct past population movements. Relevant methods work by calculating proportions of shared ancestry among individuals or groups in order to answer specific, regional research questions. Here, we propose a largescale algorithm to quantify human mobility through time and space using bulk aDNA data. The algorithm has two core components: i) Interpolation of the spatio-temporal distribution of genetic ancestry to obtain a continuous ancestry information field and ii) estimation of the spatial origin of each input sample by projecting its ancestry into this field. We apply this to thousands of published genomic samples in the last 10,000 years to trace diachronic mobility patterns across Western Eurasia.

category: genomics


title: Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan's offshore islands

abstract: The ability to correlate the functional relationship between microbial communities and their environment is critical to understanding microbial ecology. There is emerging knowledge on island biogeography of microbes but how island characteristics influence functions of microbial community remain elusive. Here, we explored soil mycobiomes from nine islands adjacent to Taiwan using ITS2 amplicon sequencing. Geographical distances and island size were positively correlated to dissimilarity in mycobiomes, and we identified 56 zero-radius operational taxonomic units (zOTUs) that were ubiquitously present across all islands, and as few as five Mortierella zOTUs dominate more than half of mycobiomes. Correlation network analyses revealed that seven of the 45 hub species were part of the ubiquitous zOTUs belonging to Mortierella, Trichoderma, Aspergillus, Clonostachys and Staphylotrichum. We sequenced and annotated the genomes of seven Mortierella isolates, and comparative predictions of KEGG orthologues using PICRUSt2 database updated with new genomes increased sequence reads coverage by 62.9% at the genus level. In addition, genes associated with carbohydrate and lipid metabolisms were differentially abundant between islands which remained undetected in the original database. Predicted functional pathways were similar across islands despite their geographical separation, difference in differentially abundant genes and composition. Our approach demonstrated the incorporation of the key taxa genomic data can improve functional gene prediction results and can be readily applied to investigate other niches of interests.


title: Self-confocal NIR-II fluorescence microscopy for in vivo imaging

abstract: Benefiting from low scatter of NIR-II light in biological tissues and high spatial resolution of confocal microscopy, NIR-II fluorescence confocal microscopy has been developed recently and achieve deep imaging in vivo. However, independence of excitation point and detection point makes this system difficult to be adjusted. New, improved, self-confocal NIR-II fluorescence confocal systems are created in this work. Based on a shared pinhole for excitation light and fluorescence, the system is easy and controlled to be adjusted. The fiber-pinhole confocal system is constructed for cerebrovascular and hepatocellular NIR-II fluorescence intensity imaging. The air-pinhole confocal system is constructed for cerebrovascular NIR-II fluorescence intensity imaging, hepatic NIR-II fluorescence lifetime imaging, and hepatic multiphoton imaging.

category: bioengineering


title: Simulated hemiparesis increases optimal spatiotemporal gait asymmetry but not metabolic cost

abstract:
Several neuromuscular impairments, such as weakness (hemiparesis), occur after an individual has a stroke, and these impairments primarily affect one side of the body more than the other. Predictive musculoskeletal modeling presents an opportunity to investigate how a specific impairment affects gait performance post-stroke. Therefore, our aim was to use to predictive simulation to quantify the spatiotemporal asymmetries and changes to metabolic cost that emerge when muscle strength is unilaterally reduced. We also determined how forced spatiotemporal symmetry affects metabolic cost. We modified a 2-D musculoskeletal model by uniformly reducing the peak isometric muscle force in all left-limb muscles. We then solved optimal control simulations of walking across a range of speeds by minimizing the sum of the cubed muscle excitations across all muscles. Lastly, we ran additional optimizations to test if reducing spatiotemporal asymmetry would result in an increase in metabolic cost. Our results showed that the magnitude and direction of effort-optimal spatiotemporal asymmetries depends on both the gait speed and level of weakness. Also, the optimal metabolic cost of transport was 1.25 m/s for the symmetrical and 20% weakness models but slower (1.00 m/s) for the 40% and 60% weakness models, suggesting that hemiparesis can account for a portion of the slower gait speed seen in people post-stroke. Adding spatiotemporal asymmetry to the cost function resulted in small increases (~4%) in metabolic cost. Overall, our results indicate that spatiotemporal asymmetry may be optimal for people post-stroke, who have asymmetrical neuromuscular impairments. Additionally, the effect of speed and level of weakness on spatiotemporal asymmetry may explain the well-known heterogenous distribution of spatiotemporal asymmetries observed in the clinic. Future work could extend our results by testing the effects of other impairments on optimal gait strategies, and therefore build a more comprehensive understanding of the gait patterns in people post-stroke.

Author SummaryA stroke causes damage to the brain. This typically results in several changes to the nervous and muscular (neuromuscular) system that change how people post-stroke tend to walk and perform other tasks. Individuals post-stroke tend to walk with an asymmetrical motion and expend more energy while walking than other age-matched individuals. We still do not understand how each specific change to the neuromuscular system is linked with changes in walking patterns, in part because it is difficult to test one individual change at a time in people. Instead, we can use a mathematical model of the musculoskeletal system that represents the individual changes to the muscular system that occur in people post-stroke. In this study, we modeled how a common change in people post-stroke (muscle weakness) can impact walking patterns. We found that the level of weakness and the walking speed affect the asymmetrical walking patterns of our models, but do not change the total energy cost. Overall, our study is one step towards better understanding how neuromuscular changes in people post-stroke affects walking patterns. This knowledge could be applied to identify rehabilitation strategies that are most likely to improve walking in people post-stroke.


title: Gene regulation network inference using k-nearest neighbor-based mutual information estimation- Revisiting an old DREAM

abstract:
BackgroundA cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an elaborate gene regulatory network (GRN) in every single cell. In the past twenty years, many groups worked on reconstructing the topological structure of GRNs from large-scale gene expression data using a variety of inference algorithms. Insights gained about participating players in GRNs may ultimately lead to therapeutic benefits. Mutual information (MI) is a widely used metric within this inference/reconstruction pipeline as it can detect any correlation (linear and non-linear) between any number of variables (n-dimensions). However, the use of MI with continuous data (for example, normalized fluorescence intensity measurement of gene expression levels) is sensitive to data size, correlation strength and underlying distributions, and often requires laborious and, at times, ad hoc optimization.

ResultsIn this work, we first show that estimating MI of a bi- and tri-variate Gaussian distribution using k-nearest neighbor (kNN) MI estimation results in significant error reduction as compared to commonly used methods based on fixed binning. Second, we demonstrate that implementing the MI-based kNN Kraskov-Stoogbauer-Grassberger (KSG) algorithm leads to a significant improvement in GRN reconstruction for popular inference algorithms, such as Context Likelihood of Relatedness (CLR). Finally, through extensive in-silico benchmarking we show that a new inference algorithm CMIA (Conditional Mutual Information Augmentation), inspired by CLR, in combination with the KSG-MI estimator, outperforms commonly used methods.

ConclusionsUsing three canonical datasets containing 15 synthetic networks, the newly developed method for GRN reconstruction - which combines CMIA, and the KSG-MI estimator - achieves an improvement of 20-35% in precision-recall measures over the current gold standard in the field. This new method will enable researchers to discover new gene interactions or choose gene candidates for experimental validations.

category: bioinformatics


title: Boosting annotation in nutrimetabolomics by Feature-Based Molecular Networking: analytical and computational strategies applied to human urine samples from an untargeted LC-MS/MS based bilberry-blueberry intervention study.

abstract: Urine represents a challenging metabolite mixture to decipher. Yet, it contains valuable information on dietary intake patterns as typically investigated using randomized, single-blinded, intervention studies. This research demonstrates how the use of Feature-Based Molecular Networking in combination with public spectral libraries, further expanded with an "In-house" library of metabolite spectra, improved the non-trivial annotation of metabolites occurring in human urine samples following bilberry and blueberry intake. Following this approach, 65 berry-related and human endogenous metabolites were annotated, increasing the annotation coverage by 72% compared to conventional annotation approaches. Furthermore, the structures of 15 additional metabolites were hypothesized by spectral analysis. Then, by leveraging the MzMine quantitative information, several molecular families of phase II (e.g., glucuronidated phenolics) and phase I (e.g., phenylpropionic acid and hydroxybenzoic acid molecular scaffolds) metabolism were identified by correlation analysis of postprandial kinetics, and the dietary impact of endogenous and exogenous metabolites following bilberry-blueberry intake was estimated.


title: TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses

abstract: When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortments events from viral sequence data, little is known about its role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.


title: The BioImage Archive - home of life-sciences microscopy data

abstract:
Despite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/.

HighlightsO_LIThe BioImage Archive is a new archival data resource at the European Bioinformatics Institute (EMBL-EBI).
C_LIO_LIThe BioImage Archive aims to accept all biological imaging data associated with peer-reviewed publications using approaches that probe biological structure, mechanism and dynamics, as well as other important datasets that can serve as reference examples for particular biological or technical domains.
C_LIO_LIThe BioImage Archive aims to encourage the use of valuable imaging data, to improve reproducibility of published results that rely on image data, and to facilitate extraction of novel biological insights from existing data and development of new image analysis methods.
C_LIO_LIThe BioImage Archive forms the foundation for an ecosystem of related databases, supporting those resources with storage infrastructure and indexing across databases.
C_LIO_LIAcross this ecosystem, the BioImage Archive already stores and provides access to over 1.5 petabytes of image data from many different imaging modalities and biological domains.
C_LIO_LIFuture development of the BioImage Archive will support the fast-emerging next generation file formats (NGFFs) for bioimaging data, providing access mechanisms tailored toward modern visualisation and data exploration tools, as well as unlocking the power of modern AI-based image-analysis approaches.
C_LI


title: The BioImage Archive - building a home for life-sciences microscopy data


title: Transmission dynamics and control of Sporotrichosis in domestic felines

abstract:
Sporotrichosis is a subcutaneous mycosis with a global distribution, also known as "rose gardeners disease". Brazil is experiencing a rapid spread of the zoonotic transmission of of Sporothrix brasiliensis, the main etiological agent of this disease in this country, affecting domestic felines. Cost-effective interventions need to be developed to control this emergent public health problem. To allow for the comparison of alternative control strategies, we propose in this paper, a mathematical model representing the transmission of S. brasiliensis among cats, stratified by age and sex. Analytical properties of the model are derived and simulations show possible strategies for reducing the endemic levels of the disease in the cat population, with a positive impact on human health. The scenarios included mass treatment of infected cats and mass implementation of contact reduction practices, such as neutering. The results indicate that mass treatment can reduce substantially the disease prevalence, and this effect is potentialized when combined with neutering or other contact-reduction interventions. On the other hand, contact-reduction methods alone are not sufficient to reduce prevalence.

Author summarySporotrichosis, as a neglected tropical mycosis, has in domestic cats a very important reservoir for Sporothrix sp., its pathogen. Infected cats can easily transmit the fungus to other cats and also to humans by means of scratching and biting.

Here we propose a mathematical model incorporating all forms of transmission of Sporothrix within a cat population, taking into account age and sex-related behavioral differences which can affect the transmission dynamics.

The model also includes a treated compartment, which facilitates the exploration of pharmacological interventions to reduce the prevalence of the disease. We derive the next-generation matrix for the model, which allows the calculation of the diseases basic reproduction number under different scenarios.

Using the model, we explore different control scenarios involving treatment of the disease, but also the contribution of neutering of cats to the reduction of transmission through changes induced by neutering, of the cats social interactions.


title: The ground truth of the Data-Iceberg: Correct Meta-data

abstract: Short summaryBiological molecular data such as sequence information increase so rapidly that detailed metadata, describing the process and conditions of data collection as well as proper labelling and typing of the data become ever more important to avoid mistakes and erroneous labeling. Starting from a striking example of wrong labelling of patient data recently published in Nature, we advocate measures to improve software metadata and controls in a timely manner to not rapidly loose quality in the ever-growing data flood.


title: Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

abstract:
The increasingly large amount of proteomics data in the public domain enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively.

In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

Author summaryWe have reanalysed 23 baseline mass spectrometry-based public proteomics datasets stored in the PRIDE database. Overall, the aggregated dataset contained 211 samples, coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We analysed the distribution of protein expression across organs in both species. We also studied how protein abundances compared across different datasets and organs for both species. Then we performed gene ontology and pathway enrichment analyses to identify enriched biological processes and pathways across organs. We also carried out a comparative analysis of baseline protein expression across mouse, rat and human tissues, observing a high level of expression correlation among orthologs in all three species, in brain, kidney, heart and liver samples. To disseminate these findings, we have integrated the protein expression results into the resource Expression Atlas.


title: MSRCall: A Multi-scale Deep Neural Network to Basecall Oxford Nanopore Sequences

abstract:
AO_SCPLOWBSTRACTC_SCPLOWMinION, a third-generation sequencer from Oxford Nanopore Technologies, is a portable device that can provide long nucleotide read data in real-time. It primarily aims to deduce the makeup of nucleotide sequences from the ionic current signals generated when passing DNA/RNA fragments through nanopores charged with a voltage difference. To determine the nucleotides from the measured signals, a translation process known as basecalling is required. However, compared to NGS basecallers, the calling accuracy of MinION still needs to be improved.

In this work, a simple but powerful neural network architecture called MSRCall is proposed. MSRCall comprises a multi-scale structure, recurrent layers, a fusion block, and a CTC decoder. To better identify both short-range and long-range dependencies, the recurrent layer is redesigned to capture various time-scale features with a multi-scale structure. The results show that MSRCall outperforms other basecallers in terms of both read and consensus accuracies.


title: HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization

abstract: The role of repetitive DNA in the 3D organization of the interphase nucleus in plant cells is a subject of intensive study. High-throughput chromosome conformation capture (Hi-C) is a sequencing-based method detecting the proximity of DNA segments in nuclei. We combined Hi-C data, plant reference genome data and tools for the characterization of genomic repeats to build a Nextflow pipeline identifying and quantifying the contacts of specific repeats revealing the preferential homotypic interactions of ribosomal DNA, DNA transposons and some LTR retrotransposon families. We provide a novel way to analyze the organization of repetitive elements in the 3D nucleus.


title: A Parameter-free Deep Embedded Clustering Method for Single-cell RNA-seq Data

abstract: Clustering analysis is widely utilized in single-cell RNA-sequencing (scRNA-seq) data to discover cell heterogeneity and cell states. While many clustering methods have been developed for scRNA-seq analysis, most of these methods require to provide the number of clusters. However, it is not easy to know the exact number of cell types in advance, and experienced determination is not always reliable. Here, we have developed ADClust, an automatic deep embedding clustering method for scRNA-seq data, which can accurately cluster cells without requiring a predefined number of clusters. Specifically, ADClust first obtains low-dimensional representation through pre-trained autoencoder, and uses the representations to cluster cells into initial micro-clusters. The clusters are then compared in between by a statistical test, and similar micro-clusters are merged into larger clusters. According to the clustering, cell representations are updated so that each cell will be pulled toward centres of its assigned cluster and similar clusters, while cells are separated to keep distances between clusters. This is accomplished through jointly optimizing the carefully designed clustering and autoencoder loss functions. This merging process continues until convergence. ADClust was tested on eleven real scRNA-seq datasets, and shown to outperform existing methods in terms of both clustering performance and the accuracy on the number of the determined clusters. More importantly, our model provides high speed and scalability for large datasets.


title: Light-induced Patterning of Electroactive Bacterial Biofilms

abstract: Electroactive bacterial biofilms can function as living biomaterials that merge the functionality of living cells with electronic components. However, the development of such advanced living electronics has been challenged by the inability to control the geometry of electroactive biofilms relative to solid-state electrodes. Here, we developed a lithographic strategy to pattern conductive biofilms of Shewanella oneidensis by controlling aggregation protein CdrAB expression with a blue light-induced genetic circuit. This controlled deposition enabled S. oneiensis biofilm patterning on transparent electrode surfaces and measurements demonstrated tunable biofilm conduction dependent on pattern size. Controlling biofilm geometry also enabled us, for the first time, to quantify the intrinsic conductivity of living S. oneidensis biofilms and experimentally confirm predictions based on simulations of a recently proposed collision-exchange electron transport mechanism. Overall, we developed a facile technique for controlling electroactive biofilm formation on electrodes, with implications for both studying and harnessing bioelectronics.

category: biophysics


title: Electrical activity between skin cells regulates melanoma initiation

abstract: Oncogenes can only initiate tumors in certain cellular contexts, which is referred to as oncogenic competence. In melanoma, whether cells in the microenvironment can endow such competence remains unclear. Using a combination of zebrafish transgenesis coupled with human tissues, we demonstrate that GABAergic signaling between keratinocytes and melanocytes promotes melanoma initiation by BRAFV600E. GABA is synthesized in melanoma cells, which then acts on GABA-A receptors on keratinocytes. Electron microscopy demonstrates synapse-like structures between keratinocytes and melanoma cells, and multi-electrode array analysis shows that GABA acts to inhibit electrical activity in melanoma/keratinocyte co-cultures. Genetic and pharmacologic perturbation of GABA synthesis abrogates melanoma initiation in vivo. These data suggest that electrical activity across the skin microenvironment determines the ability of oncogenes to initiate melanoma.

category: cancer biology


title: BESFA: Bioinformatics based Evolutionary, Structural & Functional Analysis of Prostrate, Placenta, Ovary, Testis, and Embryo (POTE) Paralogs

abstract: The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins structure, function, and Adaptive Divergence. Our result discerns that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this studys outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.


title: Urine and Fecal Microbiota in a Canine Model of      Bladder Cancer

abstract:
IntroductionUrothelial carcinoma (UC) is the tenth most diagnosed cancer in humans worldwide. Dogs are a robust model for invasive UC as tumor development and progression is similar in humans and dogs. Recent studies on urine microbiota in humans revealed alterations in microbial diversity and composition in individuals with UC; however, the potential role of microbiota in UC has yet to be elucidated. Dogs could be valuable models for this research, but microbial alterations in dogs with UC have not been evaluated.

ObjectiveThe objective of this this pilot study was to compare the urine and fecal microbiota of dogs with UC (n = 7) and age-, sex-, and breed-matched healthy controls (n = 7).

MethodsDNA was extracted from mid-stream free-catch urine and fecal samples using Qiagen Bacteremia and PowerFecal kits, respectively. 16S rRNA gene sequencing was performed followed by sequence processing and analyses (QIIME 2 and R).

ResultsCanine urine and fecal samples were dominated by taxa similar to those found in humans. Significantly decreased microbial diversity (Kruskal-Wallis: Shannon, p = 0.048) and altered bacterial composition were observed in the urine but not feces of dogs with UC (PERMANOVA: Unweighted UniFrac, p = 0.011). The relative abundances of Fusobacterium was also increased, although not significantly, in the urine and feces of dogs with UC.

ConclusionThis study characterizes urine and fecal microbiota in dogs with UC, and it provides a foundation for future work exploring host-microbe dynamics in UC carcinogenesis, prognosis, and treatment.


title: Single cell RNA sequencing and lineage tracing confirm mesenchyme to epithelial transformation (MET) contributes to repair of the endometrium at menstruation

abstract:
The human endometrium experiences repetitive cycles of tissue wounding characterised by piecemeal shedding of the surface epithelium and rapid restoration of tissue homeostasis. In this study we used a mouse model of endometrial repair and three transgenic lines of mice to investigate whether epithelial cells that become incorporated into the newly formed luminal epithelium have their origins in one or more of the mesenchymal cell types present in the stromal compartment of the endometrium. Using scRNAseq we identified a novel population of PDGFRb+ mesenchymal stromal cells that developed a unique transcriptomic signature in response to endometrial breakdown/repair. These cells expressed genes usually considered specific to epithelial cells and in silico trajectory analysis suggested they were stromal fibroblasts in transition to becoming epithelial cells. To confirm our hypothesis we used a lineage tracing strategy to compare the fate of stromal fibroblasts (PDGFRa+) and stromal perivascular cells (NG2/CSPG4+). We demonstrated that stromal fibroblasts can undergo a mesenchyme to epithelial transformation and become incorporated into the re-epithelialised luminal surface of the repaired tissue. This study is the first to discover a novel population of wound-responsive, plastic endometrial stromal fibroblasts that contribute to the rapid restoration of an intact luminal epithelium during endometrial repair. These findings form a platform for comparisons both to endometrial pathologies which involve a fibrotic response (Ashermans syndrome, endometriosis) as well as other mucosal tissues which have a variable response to wounding.

HighlightsO_LISingle cell RNA sequencing identified a population of PDGFR{beta}+ mesenchymal cells with a unique transcriptomic signature that arises in response to induction of a menses-like wound
C_LIO_LIThe repair-specific mesenchymal cells express genes considered specific to both mesenchymal and epithelial lineages indicative of an intermediate phenotype and a mesenchymal to epithelial transition (MET)
C_LIO_LIin silico trajectory analysis revealed that repair-specific cells originate from the fibroblast cell clusters, were distinct from perivascular cells, and had a predicted trans-differentiation trajectory towards definitive epithelial cells
C_LIO_LIin vivo lineage tracing in adult mice provides definitive evidence that PDGFR+ endometrial fibroblasts, and not NG2+ perivascular cells, undergo MET and can become incorporated into the luminal epithelium of the post repair tissue
C_LI

category: physiology


title: BACE1, but not BACE2, function is critical for metabolic disorders induced by high-fat diets in C57BL/6N mice

abstract:
Aims/hypothesisBeta-site amyloid precursor protein-cleaving enzyme 1 (BACE1) is required for the production of toxic amyloid peptides and is highly expressed in the brain, but also to a lesser extent in major peripheral organs such as muscle and liver. In contrast, BACE2 is mainly expressed in peripheral tissues and is enriched in pancreatic beta cells, where it regulates beta- cell function and mass. Previous reports demonstrated that loss of BACE1 function decreases body weight, protects against diet-induced obesity and enhances insulin sensitivity in mice, whereas mice lacking Bace2 exhibit reduced blood glucose levels, improved intraperitoneal glucose tolerance and increased beta-cell mass. Impaired glucose homeostasis and insulin resistance are hallmarks of type 2 diabetes and have been implicated in Alzheimers disease. Therefore, we tested the contribution of the individual BACE isoforms to those metabolic phenotypes by placing Bace1 knockout (KO), Bace2 KO, Bace1/2 double knockout (dKO) and wild-type (WT) mice on a high-fat high-cholesterol diet (HFD) for 16 weeks.

MethodsBace1 KO (n = 18), Bace2 KO (n = 18), Bace1/2 dKO (n = 18) and WT C57BL/6N mice (n = 54) were fed a HFD for 16 weeks (age 9-25 weeks). Body composition was measured before initiation of the HFD and after 11 weeks of HFD. Oral glucose tolerance and insulin sensitivity tests were performed after 12 and 13 weeks of HFD, respectively, and full blood chemistry was analyzed after 16 weeks of HFD. The effects of subchronic BACE1/2 inhibition were assessed by administration of 10 mg/kg/day of the dual BACE1/2 inhibitor MBi-3 in a HFD fed to C57BL/6N mice for 3 weeks.

ResultsBace1 KO and Bace1/2 dKO mice showed decreased body weight and improved glucose tolerance and insulin resistance vs. WT mice. Conversely, Bace2 KO mice did not show any significant differences in body weight, glucose tolerance or insulin resistance under our experimental conditions. Finally, subchronic MBi-3-mediated BACE1/2 inhibition in mice in conjunction with a HFD resulted in a modest improvement of glucose tolerance.

Conclusions/interpretationOur data indicate that lack of BACE1 - but not BACE2 - function contributes mainly to the metabolic phenotypic changes observed in Bace1/2 dKO mice, suggesting that inhibition of BACE1 has the greater role (vs. BACE2) in any potential improvements in metabolic homeostasis.

HIGHLIGHTSO_LIInsulin resistance may develop in the brains of patients with Alzheimers disease (83/85 characters)
C_LIO_LIBACE1 and BACE2 may play a role in glucose homeostasis and insulin sensitivity (80/85 characters)
C_LIO_LIBody weight in mice decreased with Bace1 KO and Bace1/2 KO but not Bace2 KO alone (83/85 characters)
C_LIO_LIBace1 and Bace1/2, but not Bace2, KO improved glucose tolerance/insulin resistance (84/85 characters)
C_LIO_LIImproved metabolic homeostasis may follow loss of BACE1 rather than BACE 2 activity (85/85 characters)
C_LI


title: A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females

abstract: Mosquito vectors transmit numerous pathogens, but large gaps remain in our understanding of their physiology. To facilitate future explorations of mosquito biology, with specific attention to the major vector Aedes aegypti, we have created Aegypti-Atlas (http://aegyptiatlas.buchonlab.com/), an online resource hosting RNAseq profiles of Ae. Aegypti body parts (head, thorax, abdomen, gut, Malpighian tubules, and ovaries), gut regions (crop, proventriculus, anterior and posterior midgut, and hindgut), and a time course of blood meal digestion in the gut. Using Aegypti-Atlas, we provide new insights into the regionalization of gut function, blood feeding response, and immune defenses. We find that the anterior and posterior regions of the mosquito midgut possess clearly delineated digestive specializations which are preserved in the blood-fed state. Blood feeding initiates the sequential transcriptional induction and repression/depletion of multiple cohorts of peptidases throughout blood meal digestion. With respect to defense, immune signaling components, but not recognition or effector molecules, show enrichment in ovaries. Basal expression of antimicrobial peptides is dominated by two genes, holotricin and gambicin, that are expressed in the carcass and the digestive tissues, respectively, in a near mutually exclusive manner. In the midgut, gambicin and other immune effector genes are almost exclusively expressed in the anterior regions, while the posterior midgut exhibits the hallmarks of immune tolerance. Finally, in a cross-species comparison between the midguts of Ae. aegypti and Anopheles gambiae, we observe that regional digestive and immune specializations are closely conserved, indicating that our data may yield inferences that are broadly relevant to multiple mosquito vector species. We further demonstrate that the expression of orthologous genes is highly correlated, with the exception of a  species signature comprising a small number of highly/disparately expressed genes. With this work, we show the potential of Aegypti-Atlas to unlock a more complete understanding of mosquito biology.


title: ORA47 is a transcriptional regulator of a general stress response hub

abstract:
Transcriptional regulators of general stress response (GSR) reprogram expression of selected genes to transduce informational signals into cellular events, ultimately manifested in plants ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) that binds to the previously established functional GSR motif, coined Rapid Stress Response Element (RSRE). This led to the isolation of ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47), a Methyl jasmonate (MeJA) inducible protein. Subsequently, the ORA47 transcriptional activity was confirmed using RSRE-driven Luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of MeJA led to enhanced levels of ORA47 and CAMTA3 transcripts, and the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity.

Collectively, the report provides a fresh insight into the initial mechanistic features of transducing the informational signals into adaptive responses in part via the complex functional interplay between JA biosynthesis/signaling cascade and the transcriptional reprogramming necessary for potentiation of GSR, while offering a window into the role of intraorganellar communication in the establishment of adaptive responses.

SignificanceThe work unmasks the initial mechanistic features of adaptive responses that include tight cooperativity between JA biosynthesis and signaling cascade and the nuclear transcriptional machinery comprised of two activators (CAMTA3 and ORA47) and a suppressor JAZ1). The work further identifies CAMTA3 as a functional link between JA signaling and activation of a general stress transcriptional hub.

category: plant biology


title: Terminal heterocyst differentiation in the Anabaena patA mutant as a result of post-transcriptional modifications and molecular leakage

abstract:
The Anabaena genus is a model organism of filamentous cyanobacteria whose vegetative cells can differentiate under nitrogen-limited conditions into a type of cell called heterocyst. These heterocysts lose the possibility to divide and are necessary for the colony because they can fix and share environmental nitrogen. In order to distribute the nitrogen efficiently, heterocysts are arranged to form a quasi-regular pattern whose features are maintained as the filament grows. Recent efforts have allowed advances in the understanding of the interactions and genetic mechanisms underlying this dynamic pattern. However, the main role of the patA and hetF genes are yet to be clarified; in particular, the patA mutant forms heterocysts almost exclusively in the terminal cells of the filament. In this work, we investigate the function of these genes and provide a theoretical model that explains how they interact within the broader genetic network, reproducing their knock-out phenotypes in several genetic backgrounds, including a nearly uniform concentration of HetR along the filament for the patA mutant. Our results suggest a role of hetF and patA in a post-transcriptional modification of HetR which is essential for its regulatory function. In addition, the existence of molecular leakage out of the filament in its boundary cells is enough to explain the preferential appearance of terminal heterocysts, without any need for a distinct regulatory pathway.

Author summaryUnderstanding multicellular pattern formation is key for the study of both natural and synthetic developmental processes. Arguably one of the simplest model systems for this is the filamentous cyanobacterium Anabaena, that in conditions of nitrogen deprivation undergoes a dynamical differentiation process that differentiates roughly one in every ten cells into nitrogen-fixing heterocysts, in a quasi-regular pattern that is maintained as the filament keeps growing. One of the most characteristic mutations affecting this process forms heterocysts mostly constrained to the terminal cells of the filament. We have used experimental observations to propose a mathematical model of heterocyst differentiation able to reproduce this striking phenotype. The model extends our understanding of the regulations in this pattern-forming system and makes several predictions on molecular interactions. Importantly, a key aspect is the boundary condition at the filaments ends: inhibitors of differentiation should be able to leak out of the filament, or otherwise the terminal cells would not differentiate. This highlights, in a very clear example, the importance of considering physical constraints in developmental processes.

category: systems biology


title: Endogenous DAF-16 Spatiotemporal Activity Quantitatively Predicts Lifespan Extension Induced by Dietary Restriction

abstract: In many organisms, dietary restriction (DR) leads to lifespan extension through the activation of cell protection and pro-longevity gene expression programs. In the nematode C. elegans, the DAF-16 transcription factor is a key aging regulator that governs the Insulin/IGF-1 signaling pathway and undergoes translocation from the cytoplasm to the nucleus of cells when animals are exposed to food limitation. In this work, we assess the endogenous activity of DAF-16 under various DR regimes by coupling CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image analysis and machine learning. Our results indicate that lifelong DAF-16 endogenous activity is a robust predictor of mean lifespan in C. elegans, and it accounts for 78% of the lifespan variability induced by DR. We found that this lifespan-extending mechanism occurs mainly in the intestine and neurons, and that DR drives DAF-16 activity in unexpected locations such as the germline and intestinal nucleoli.