title: Selective Vulnerability of Tripartite Synapses in Amyotrophic Lateral Sclerosis.

abstract: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder. Separate lines of evidence suggest that synapses and astrocytes play a role in the pathological mechanisms underlying ALS. Given that astrocytes make specialised contacts with some synapses, called tripartite synapses, we hypothesise that tripartite synapses could act as the fulcrum of disease in ALS. To test this hypothesis, we have performed an extensive microscopy-based investigation of synapses and tripartite synapses in the spinal cord of ALS model mice and post-mortem human tissue from ALS cases. We reveal widescale synaptic changes at the early symptomatic stages of the SOD1G93a mouse model. Super-resolution microscopy reveals that large complex postsynaptic structures are lost in ALS mice. Most surprisingly, tripartite synapses are selectively lost while non-tripartite synapses remain in equal number to healthy controls. Finally, we also observe a similar selective loss of tripartite synapses in human post-mortem ALS spinal cords. From these data we conclude that tripartite synaptopathy is a key hallmark of ALS.


title: Mecp2 deletion results in profound alterations of developmental and adult functional connectivity

abstract: As a regressive neurodevelopmental disorder with a well-established genetic cause, Rett Syndrome and its Mecp2 loss-of-function mouse model provide an excellent opportunity to define potentially translatable functional signatures of disease progression, as well as offer insight into Mecp2s role in functional circuit development. Thus, we applied optical fluorescence imaging to assess mesoscale calcium functional connectivity (FC) in the Mecp2 cortex prior to symptom onset as well as during decline. We found that FC was profoundly disrupted in Mecp2 males both in juvenile development and early adulthood. Female Mecp2 mice displayed a subtle homotopic contralateral increase in motor cortex as juveniles but not in adulthood, where instead parietal regions were implicated. Additionally, conditional rescue studies indicated FC phenotypes are driven by excitatory neurons. Altogether, the female results identify subtle candidate translatable biomarkers of disease progression, while the male results indicate MeCP2 protein is needed in a circuit-specific manner for FC.

category: neuroscience


title: In Vivo MRI of Endogenous Remyelination in a Nonhuman Primate Model of Multiple Sclerosis

abstract: Remyelination is crucial for recovery from inflammatory demyelination in multiple sclerosis (MS). Investigating remyelination in vivo using magnetic resonance imaging (MRI) is difficult in MS, where collecting serial short-interval scans is challenging. Using experimental autoimmune encephalomyelitis (EAE) in common marmosets, a model of MS that recapitulates focal cerebral MS lesions, we investigated whether remyelination can be detected and characterized noninvasively. In 6 animals followed with multisequence 7-tesla MRI, 36 focal lesions, classified as demyelinated or remyelinated based on signal intensity on proton density-weighted images, were subsequently assessed with histopathology. Remyelination occurred in 5 of 6 marmosets and 51% of lesions. Radiological-pathological comparison showed high sensitivity (88%) and specificity (90%) for detecting remyelination by in vivo MRI. This study demonstrates the prevalence of spontaneous remyelination in marmoset EAE and the ability of in vivo MRI to detect it, with implications for preclinical testing of pro-remyelinating agents and translation to clinical practice.


title: Single-nuclei RNA sequencing uncovers non-cell autonomous changes in cerebellar astrocytes and oligodendrocytes that may contribute to Spinocerebellar Ataxia Type 1 (SCA1) pathogenesis

abstract: Glial cells, including astrocytes and oligodendrocytes are important for normal brain function. In many neurodegenerative diseases glial cells undergo significant morphological, functional and gene expression changes termed reactive gliosis. The cause, identity and neuroprotective or neurotoxic nature of these changes remains incompletely understood. This knowledge in needed to develop a framework of how individual pathological changes in glial cells contribute to progressive dysfunction and selective neuronal vulnerability in neurodegenerative diseases. This is particularly relevant during the early disease stages that allow for the effective therapies and reversal or slowing of disease phenotypes. Spinocerebellar ataxia type 1 (SCA1) is a progressive neurodegenerative disease caused by an abnormal expansion of CAG repeats in the gene Ataxin1 (ATXN1). While mutant ATXN1 is expressed broadly throughout the brain, SCA1 is characterized by severe degeneration of cerebellar Purkinje cells (PCs). Despite major advances in dissecting the effects of mutant ATXN1 on Purkinje cells, much less is understood how cerebellar astrocytes and oligodendrocytes respond to and contribute to Purkinje cell dysfunction in SCA1. To address this question we performed cerebellar single nuclei RNA sequencing (snRNA seq) of early disease stage Pcp2-ATXN1[82Q] mice, a transgenic SCA1 mouse model expressing mutant ATXN1 only in Purkinje cells. We found no changes in cell numbers in the SCA1 cerebellum. We validated previously indicated pathway and gene expression changes in the Purkinje cells, and identified novel DEG and pathways in Purkinje cells, including Ralyl that may provide compensatory roles and maintain PC function. Importantly we identified profound non-cell autonomous and potentially neuroprotective gene expression and pathway alterations in Bergman glia, velate astrocytes and oligodendrocytes that may contribute to disease pathogenesis.


title: In-depth immunophenotyping with mass cytometry during TB treatment reveals non-canonical T-cell subsets associated with sputum culture conversion.

abstract:
Tuberculosis (TB) is a difficult-to-treat infection because of multidrug regimen requirements based on drug susceptibility profiles and treatment observance issues. TB cure is defined by mycobacterial sterilization, technically complex to systematically assess. We hypothesized that microbiological outcome was associated with stage-specific immune changes in peripheral whole blood during TB treatment. The T-cell phenotypes of treated TB patients were prospectively characterized in a blinded fashion using mass cytometry after Mycobacterium tuberculosis (Mtb) antigen stimulation, and then correlated to sputum culture status. At two months of treatment, cytotoxic and terminally differentiated CD8+ T-cells were under-represented and naive CD4+ T-cells were over-represented in positive-versus negative-sputum culture patients, regardless of Mtb drug susceptibility. At treatment completion, an antigen-driven T-cell immune shift towards differentiated subpopulations was associated with TB cure. Overall, we identified specific T-cell profiles associated with slow sputum converters, which brings new insights in TB prognostic biomarker research designed for clinical application.

SummaryIn patients treated for pulmonary TB, high-dimensional immune profiling with mass cytometry revealed that Mycobacterium tuberculosis culture conversion is associated with newly characterized peripheral CD8+ T-cell phenotypes. This paves the way for new immune biomarkers associated with mycobacterial sterilization.

category: immunology


title: GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology

abstract:
Different regions of the gastrointestinal tract have distinct digestive and absorptive functions, which may be locally disrupted by infection or autoimmune disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. Here, we used mouse models, transcriptomics, and immune profiling to show that regional epithelial expression of the transcription factor GATA4 prevented adherent bacterial colonization and inflammation in the proximal small intestine by regulating retinol metabolism and luminal IgA. Loss of epithelial GATA4 expression increased mortality in mice infected with Citrobacter rodentium. In active celiac patients with villous atrophy, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. This study reveals broad impacts of GATA4-regulated intestinal regionalization and highlights an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.

One-sentence summaryEpithelial GATA4 regulates intestinal regionalization of bacterial colonization, metabolic pathways, and tissue immunity.


title: Dormant spores sense amino acids through the B subunits of their germination receptors

abstract: Bacteria from the orders Bacillales and Clostridiales differentiate into stress-resistant spores that can remain dormant for years, yet rapidly germinate upon nutrient sensing. How spores monitor nutrients is poorly understood but in most cases requires putative membrane receptors. The prototypical receptor from Bacillus subtilis consists of three proteins (GerAA, GerAB, GerAC) required for germination in response to L-alanine. GerAB belongs to the Amino Acid-Polyamine-Organocation superfamily of transporters. Using evolutionary co-variation analysis, we provide evidence that GerAB adopts a structure similar to an L-alanine transporter from this superfamily. We show that mutations in gerAB predicted to disrupt the ligand-binding pocket impair germination, while mutations predicted to function in L-alanine recognition enable spores to respond to L-leucine or L-serine. Finally, substitutions of bulkier residues at these positions cause constitutive germination. These data suggest that GerAB is the L-alanine sensor and that B subunits in this broadly conserved family function in nutrient detection.

category: microbiology


title: Genetically distant bacteriophages elicit unique genomic changes in Enterococcus faecalis

abstract:
The human microbiota harbors diverse bacterial and bacteriophage (phage) communities. Bacteria evolve to overcome phage infection, thereby driving phage evolution to counter bacterial resistance. Understanding how phages promote genetic alterations in medically relevant bacteria is important as phages continue to become established biologics for the treatment of multidrug-resistant (MDR) bacterial infections. Before phages are used as standalone or combination antibacterial therapies, we must obtain a deep understanding of the molecular mechanisms of phage infection and how host bacteria alter their genomes to become resistant. We performed coevolution experiments using a single Enterococcus faecalis strain and two distantly related phages, to determine how phage pressure impacts the evolution of the E. faecalis genome. Whole genome sequencing revealed mutations previously demonstrated to be essential for phage infection. We also identified mutations in several genes previously unreported to be associated with phage infection in E. faecalis. Intriguingly, there was only one shared mutation in the E. faecalis genome in response to each of the two phages tested, demonstrating that infection by genetically distinct phages results in different host responses. This study shows that infection of the same host by disparate phages leads to evolutionary trajectories that result in distinct genetic changes. This implies that bacteria respond to phage pressure through host responses that are tailored to specific phages. This work serves as the basis for the study of E. faecalis genome evolution during phage infection and will inform the design of future therapeutics, such as phage cocktails, intended to target MDR E. faecalis.

IMPORTANCEStudies characterizing the genome evolution of bacterial pathogens following phage selective pressure are lacking. Phage therapy is experiencing a rebirth in Western medicine. Such studies are critical for understanding how bacteria subvert phage infection and how phages evolve to counter such mutations. This study utilizes comparative genomic analyses to demonstrate how a pathogenic strain of Enterococcus faecalis responds to infection by two genetically distant phages. We show that genetic alterations in the E. faecalis genome accumulate in a manner that is specific to the infecting phage with little to no overlap in shared fixed mutations. This suggests that bacterial genome evolution in response to phage infection is uniquely tied to phage genotype, and sets a precedence for investigations into how phages drive bacterial genome evolution relevant to phage therapeutic applications.


title: The return of the rings: evolutionary role of aromatic residues in liquid-liquid phase separation

abstract: Aromatic residues appeared relatively late in the evolution of protein sequences. They stabilize the hydrophobic core of globular proteins and are typically absent from intrinsically disordered regions (IDRs). However, recent advances in protein liquid-liquid phase separation (LLPS) studies have shown that aromatic residues in IDRs often act as important "stickers", promoting multivalent interactions and the formation of higher-order oligomers. To reconcile this apparent contradiction, we compared levels of sequence disorder in RNA binding proteins and the human proteome and found that aromatic residues appear more frequently than expected in the IDRs of RNA binding proteins, which are often found to undergo LLPS. Phylogenetic analysis shows that aromatic residues are highly conserved among chordates, highlighting their importance in LLPS-driven functional assembly. These results suggest therefore that aromatic residues have contributed twice to evolution: in stabilizing structured proteins and in the assembly of biomolecular condensates.

category: molecular biology


title: Climate-driven variation in biotic interactions provides a narrow and variable window of opportunity for an insect herbivore at its ecological margin

abstract:
Climate-driven geographic range shifts have been associated with transitions between dietary specialism and generalism at range margins. The mechanisms underpinning these often transient niche breadth modifications are poorly known, but utilisation of novel resources likely depends on phenological synchrony between the consumer and resource. We use a climate-driven range and host shift by the butterfly Aricia agestis to test how climate-driven changes in host phenology and condition affect phenological synchrony, and consider implications for host use.

Our data suggest that the perennial plant which was the primary host before range expansion is a more reliable resource than the annual Geraniaceae upon which the butterfly has become specialised in newly colonised parts of its range. In particular, climate-driven phenological variation in the novel host Geranium dissectum generates a narrow and variable  window of opportunity for larval productivity in summer. Therefore, although climatic change may allow species to shift hosts and colonise novel environments, specialisation on phenologically-limited hosts may not persist at ecological margins as climate change continues. We highlight the potential role for phenological (a)synchrony in determining lability of consumer-resource associations at range margins, and the importance of considering causes of synchrony in biotic interactions when predicting range shifts.

category: ecology


title: Temperature predicts leaf shape in palms (Arecaceae)

abstract: Leaves display a remarkable variety of shapes, each potentially relevant to the function of these organs and with potential ecological advantages in certain climates. Studies correlating leaf shape with either climate or allometric constraints (how size and shape relate) focus on intraspecific variation or model organisms, and the drivers of leaf shape at a macroecological scale remain poorly known. Here, we determine associations between climatic and allometric factors with the evolution of leaf shape in a lineage with one of the highest diversities of leaf shape known, the palms (family Arecaceae). We apply a Bayesian phylogenetic mixed model to test for associations with leaf shapes (entire, pinnate, palmate, and costapalmate). We further reconstruct the ancestral leaf shape in palms using multistate speciation and extinction models. We find that high mean annual temperature correlates with dissected shapes. The ancestral leaf shape is entire, and pinnate lineages originated multiple independent times after transitions into polymorphism (species with entire or pinnate individuals). Finally, we compared the frequency of shapes with global temperatures through time through the Cenozoic. Although mean annual temperature has a positive effect on leaf dissection, the relative frequency of pinnate lineages increased as global temperatures cooled through time, potentially through colonization of open more seasonal habitats. Dissection could therefore be beneficial at high temperatures, where other leaf shaped lineages would be highly vulnerable under increased global warming. This study contributes to the understanding of leaf shape evolution and its drivers.

category: evolutionary biology


title: Regulation Mechanisms of the Dual ATPase in KaiC

abstract:
KaiC is a dual ATPase, with one active site in its N-terminal domain and another in its C-terminal domain, that drives the circadian clock system of cyanobacteria through sophisticated coordination of the two sites. To elucidate the coordination mechanism, we studied the contribution of the dual ATPase activities in the ring-shaped KaiC hexamer and these structural bases for activation and inactivation. At the N-terminal active site, a lytic water molecule is sequestered between the N-terminal domains, and its reactivity to ATP is controlled by the quaternary structure of the N-terminal ring. The C-terminal ATPase activity is regulated mostly by water-incorporating voids between the C-terminal domains, and the size of these voids is sensitive to phosphoryl modification of S431. The N-terminal ATPase activity inversely correlates with the affinity of KaiC for KaiB, a clock protein constitutes the circadian oscillator together with KaiC and KaiA, and the complete dissociation of KaiB from KaiC requires KaiA-assisted activation of the dual ATPase. Delicate interactions between the N-terminal and C-terminal rings make it possible for the components of the dual ATPase to work together, thereby driving the assembly and disassembly cycle of KaiA and KaiB.

Significance StatementKaiC, a core clock protein in the cyanobacterial circadian clock system, hydrolyzes ATP at two distinct sites in a slow but ordered manner to measure the circadian time scale. We used biochemical and structural biology techniques to characterize the properties and interplay of dual ATPase active sites. Our results show that the N-terminal and C-terminal ATPases communicate with each other through an interface between the N-terminal and C-terminal domains in KaiC. The dual ATPase sites are regulated rhythmically in a concerted or opposing manner dependent on the phase of the circadian clock system, controlling the affinities of KaiC for other clock proteins, KaiA and KaiB.

category: biochemistry


title: Defined microenvironments trigger in vitro gastrulation in human pluripotent stem cells

abstract: Embryogenesis is orchestrated through local morphogen gradients and endometrial constraints that give rise to the three germ layers in a well-defined assembly. In vitro models of embryogenesis have been demonstrated by treating pluripotent stem cells in adherent or suspension culture with soluble morphogens and small molecules, which leads to tri-lineage differentiation. However, treatment with exogenous agents override the subtle spatiotemporal changes observed in vivo that ultimately underly the human body plan. Here we demonstrate how microconfinement of pluripotent stem cells on hydrogel substrates catalyses gastrulation-like events without the need for supplements. Within six hours of initial seeding, cells at the boundary show elevated cytoskeletal tension and yes-associated protein (YAP) activity, which leads to changes in cell and nuclear morphology, epithelial to mesenchymal transition, and emergence of defined patterns of primitive streak containing SRY-Box Transcription Factor 17 (SOX17)+ T/BRACHYURY+ cells. Immunofluorescence staining, transcript analysis, and the use of pharmacological modulators reveal a role for mechanotransduction-coupled non-canonical wingless-type (WNT) signalling in promoting epithelial to mesenchymal transition and multilayered organization within the colonies. These microscale gastruloids were removed from the substrate and encapsulated in 3D hydrogels, where biomaterials properties correspond to maintenance and spatial positioning of the primitive streak. Together, this approach demonstrates how materials alone can nurture embryonic gastrulation, thereby providing an in vitro model of early development.

category: bioengineering


title: Hotmelt tissue adhesive with supramolecularly-controlled sol-gel transition for preventing postoperative abdominal adhesion

abstract: Postoperative adhesion is a serious and frequent complication, but there is currently no reliable anti-adhesive barrier available due to low tissue adhesiveness, undesirable chemical reactions, and poor operability. Here, we report a single-syringe hotmelt tissue adhesive to prevent postoperative abdominal adhesions. Through the augmentation of intermolecular hydrogen bonding by conjugation of the ureidopyrimidinone unit to tendon-derived gelatin, the sol-gel transition behavior of gelatin was supramolecularly-controlled, which provided a hotmelt tissue adhesive that dissolves upon warming over 40 {degrees}C and glues at 37 {degrees}C. This functionalization improved the key features necessary for an anti-adhesive barrier, including bulk mechanical strength, tissue adhesive properties, underwater stability, and anti-adhesive property. This hotmelt tissue adhesive with excellent tissue adhesiveness, biocompatibility, and operability has enormous potential to prevent postoperative complications.


title: Large1 Gene Transfer in Older myd Mice with Severe Muscular Dystrophy Restores Muscle Function and Greatly Improves Survival

abstract: Muscular dystrophy is a progressive and ultimately lethal neuromuscular disease due to lack of therapeutic options that restore muscle function. Gene editing and gene transfer hold great promise as therapies for various neuromuscular diseases when administered prior to the onset of severe clinical symptoms. However, the efficacy of these strategies for restoring neuromuscular function and improving survival in the late stages of muscular dystrophy with severe muscle pathophysiology is unknown. Dystroglycanopathies are muscular dystrophies characterized by extensive skeletal muscle degeneration and, in many cases, are accompanied by eye and brain abnormalities. Thus far, mutations in at least eighteen human genes are known to cause dystroglycanopathies, including those in the like-acetylglucosaminyltransferase-1 (LARGE1) gene. LARGE1 encodes a xylosyl- and glucuronosyltransferase that modifies -dystroglycan (-DG) with matriglycan, a linear repeating disaccharide of alternating xylose and glucuronic acid that binds to the laminin G-like domains of extracellular matrix proteins with high affinity. Largemyd/Largemyd (myd) mice lack expression of Large1, and exhibit severe skeletal muscle pathophysiology, impaired mobility, and a drastically reduced lifespan (50% survivorship at 35 weeks of age). Here, we show that systemic delivery of AAV2/9 CMV Large1 (AAVLarge1) in >34-week-old myd mice with advanced disease restores matriglycan expression, attenuates skeletal muscle pathophysiology, improves motor and respiratory function, and normalizes systemic metabolism, which collectively and dramatically extends survival. Our results demonstrate that in a mouse model of muscular dystrophy, skeletal muscle function can be restored, illustrating its remarkable plasticity, and that survival can be greatly improved even after the onset of severe skeletal muscle pathophysiology.

category: physiology


title: Recording true oxygen reduction capacity during photosynthetic electron transfer in Arabidopsis thylakoids and intact leaves

abstract:
Reactive oxygen species (ROS) are generated in electron transport processes of living organisms in oxygenic environments. Chloroplasts are plant bioenergetics hubs where imbalances between photosynthetic inputs and outputs drive ROS generation upon changing environmental conditions. Plants have harnessed various site-specific thylakoid membrane ROS products into environmental sensory signals. Our current understanding of ROS production in thylakoids suggests that oxygen (O2) reduction takes place at numerous components of the photosynthetic electron transfer chain (PETC). To refine models of site- specific O2 reduction capacity of various PETC components in isolated thylakoids, the stoichiometry of oxygen production and consumption reactions, associated with H2O2 accumulation, was quantified using membrane inlet mass spectrometry and specific inhibitors. Combined with P700 spectroscopy and electron paramagnetic resonance spin trapping, we demonstrate that electron flow to PSI is essential for H2O2 accumulation during light-induced photosynthetic electron transport process. Further leaf disc measurements provided clues that H2O2 from PETC has a potential of increasing mitochondrial respiration and CO2 release.

One sentence summaryPhotosynthetically derived H2O2 only accumulates at Photosystem I and may trigger cooperation with mitochondria during stress

category: plant biology


title: The plastoglobule-localized AtABC1K6 is a Mn2+-dependent protein kinase necessary for timely transition to reproductive growth

abstract:
The Absence of bc1 Complex (ABC1) is an ancient, atypical protein kinase family that emerged prior to the archaeal-eubacterial divergence. Loss-of-function mutants in ABC1 genes are linked to respiratory defects in microbes and humans, and to compromised photosynthetic performance and stress tolerance in plants. However, demonstration of protein kinase activity remains elusive, hampering their study. Here, we investigate a homolog from Arabidopsis thaliana, AtABC1K6, and demonstrate in vitro protein kinase activity as autophosphorylation, which we replicate with a human ABC1 ortholog. We show that AtABC1K6 protein kinase activity requires an atypical buffer composition, including Mn2+ as divalent cation co-factor and a low salt concentration. AtABC1K6 associates with plastoglobule lipid droplets of A. thaliana chloroplasts, along with five paralogs. Protein kinase activity associated with isolated A. thaliana plastoglobules was inhibited at higher salt concentrations, but could accommodate Mg2+ as well as Mn2+, indicating salt sensitivity, but not the requirement for Mn2+, may be a general characteristic of ABC1s. Loss of functional AtABC1K6 impairs the developmental transition from vegetative to reproductive growth. This phenotype is complemented by the wild-type sequence of AtABC1K6 but not by a kinase-dead point mutant in the unique Ala-triad of the ATP-binding pocket, demonstrating the physiological relevance of the proteins kinase activity. We suggest that ABC1s are bona fide protein kinases with a unique regulatory mechanism. Our results open the door to detailed functional and mechanistic studies of ABC1s and plastoglobules.

SIGNIFICANCE STATEMENTThe Absence of bc1 Complex (ABC1) is an ancient, atypical protein kinase family with enigmatic physiological roles in a wide range of species including plants, humans and microbes. While mutants demonstrate their critical role for organismal survival, their study has been severely hampered by the previous inability to determine catalytic function. Here, we demonstrate in vitro protein kinase activity with an A. thaliana homolog, AtABC1K6. Loss of functional AtABC1K6 impairs the developmental transition from vegetative to reproductive growth. The lack of phenotypic complementation with a kinase-dead point mutant demonstrates the physiological relevance of the proteins kinase activity. Our results present the experimental means to investigate the targets, functions, and regulation of ABC1s.


title: Motor learning selectively strengthens cortical and striatal synapses of motor engram neurons

abstract:
Learning and consolidation of new motor skills require adaptations of neuronal activity and connectivity in the motor cortex and striatum, two key motor regions of the brain. Yet, how neurons undergo synaptic changes and become recruited during motor learning to form a memory engram remains an open question. Here, we train mice on a single-pellet reaching motor learning task and use a genetic approach to identify and manipulate behavior-relevant neurons selectively in the primary motor cortex (M1). We find that the degree of reactivation of M1 engram neurons correlates strongly with motor performance. We further demonstrate that learning-induced dendritic spine reorganization specifically occurs in these M1 engram neurons. In addition, we find that motor learning leads to an increase in the number and strength of outputs from M1 engram neurons onto striatal spiny projection neurons (SPNs) and that these synapses form local clusters along SPN dendrites. These results identify a highly specific synaptic plasticity during the formation of long-lasting motor memory traces in the corticostriatal circuit.

HIGHLIGHTS- Motor performance is correlated with the reactivation of motor engram neurons
- Motor learning increases spine density and new spine survival selectively on M1 engram neurons
- Motor learning strengthens motor engram outputs to the striatum
- M1 engram outputs converge onto clusters of dendritic spines on striatal spiny projection neurons


title: Bladder tissue-resident memory T cells are necessary and sufficient to mediate immunity to recurrent UTI

abstract: Urinary tract infection (UTI) is one of the most prevalent human bacterial infections. Due to the rapid rise of multidrug-resistant uropathogens in global circulation, new therapeutic approaches, including vaccines and immunotherapy, are urgently needed. However, the development of these therapies is impeded by an incomplete understanding of how memory develops during UTI. Here, we found that reducing bacteria load early in infection, by reducing the quantity of bacteria used for infection or with antibiotics, completely abrogated the protective memory response. As we observed that a mixed T helper cell polarization bias, comprised of Th1, Th2, and Th17 T cells, develops, we hypothesized that reducing antigen load likely altered T helper cell polarization. Surprisingly, T helper cell polarization was unchanged in these scenarios, however, we identified a population of tissue resident memory (TRM) T cells that was significantly reduced in the absence of sufficient antigen, supporting that this population is necessary for protection. To demonstrate that they are sufficient for memory against recurrent UTI, we depleted circulating and lymph node-resident T cells, and observed that mice were still protected against a second infection. Our findings uncover an unappreciated mechanism of immunity to UTI and key role for TRM cells in the memory response to bacterial infection in the bladder, providing a target for non-antibiotic-based immunotherapy and/or new vaccine strategies to improve the response to UTI.


title: Multi-omics of host-microbiome interactions in short- and long-term Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

abstract: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system, debilitating disability manifesting as severe fatigue and post-exertional malaise. The chronic dysfunctions in ME/CFS are increasingly recognized as significant health factors with potential parallels with  long COVID. However, the etiology of ME/CFS remains elusive with limited high-resolution human studies. In addition, reliable biomarker-based diagnostics have not been well-established, but may assist in disease classification, particularly during different temporal phases of the disease. Here, we performed deep multi- omics (shotgun metagenomics of gut microbiota and plasma metabolomics) and clinical phenotyping of healthy controls (n=79) vs. two cohorts of ME/CFS patients - those with short-term disease (<4 years, n=75), and patients with long-term disease (>10y, n=79). Overall, ME/CFS was characterized by reduced gut microbiome diversity and richness with high heterogeneity, and depletion of sphingomyelins and short-chain fatty acids in the plasma. We found significant differences when stratifying by cohort; short-term ME/CFS was associated with more microbial dysbiosis, but long-term ME/CFS was associated with markedly more severe phenotypic and metabolic abnormalities. We identified a reduction in the gene-coding capacity (and relative abundance of butyrate producers) of microbial butyrate biosynthesis together with a reduction in the plasma concentration of butyrate, especially in the short-term group. Global co-association and detailed gene pathway correlation analyses linking the microbiome and metabolome identified additional potential biological mechanisms underlying host-microbiome interactions in ME/CFS, including bile acids and benzoate pathways. Finally, we built multiple state-of-the-art classifiers to identify microbes, microbial gene pathways, metabolites, and clinical features that individually or together, were most able to differentiate short or long-term MECFS, or MECFS vs. healthy controls. Taken together, our study presents the highest resolution, multi-cohort and multi- omics analysis to date, providing an important resource to facilitate mechanistic hypotheses of host-microbiome interactions in ME/CFS.


title: No robust coexistence in a canonical model of plant-soil feedbacks

abstract: Plant-soil feedbacks (PSFs) are considered a key mechanism generating frequency-dependent dynamics in plant communities. Negative feedbacks, in particular, are often invoked to explain coexistence and the maintenance of diversity in species-rich communities. However, the primary modeling framework used to study PSFs considers only two plant species, and we lack clear theoretical expectations for how these complex interactions play out in communities with natural levels of diversity. Here, we demonstrate that this canonical model for PSFs is equivalent to a well-studied model from evolutionary game theory, and use this equivalence to characterize the dynamics with an arbitrary number of plant species. Surprisingly, we find that coexistence of more than two species is virtually impossible, suggesting that alternative theoretical frameworks are needed to describe feedbacks observed in diverse natural communities. Drawing on our analysis, we discuss future directions for PSF models and implications for experimental study of PSF-mediated coexistence in the field.


title: Sciara coprophila larvae upregulate DNA repair pathways and downregulate developmental regulators in response to ionizing radiation

abstract: Robust DNA damage prevention and repair strategies are crucial to faithful reproduction and inheritance of the genetic material. Although many molecular pathways that respond to DNA damage are well conserved through evolution, the quality and effectiveness of these systems can vary between species. Studies dating back for nearly a century document that the dark-winged fungus gnat Sciara coprophila (Order: Diptera; sub-order: Nematocera) is relatively resistant to irradiation-induced mutations that cause visible phenotypes when compared to the fruit fly Drosophila melanogaster (Order: Diptera; sub-order: Brachycera). However, the molecular responses to irradiation for S. coprophila have yet to be analyzed. To address this gap, we first characterized the effects of ionizing radiation on S. coprophila throughout its life cycle. Our data show that developing S. coprophila embryos are highly sensitive to even low doses of gamma-irradiation, whereas larvae can tolerate up to 80 Gy and still retain their ability to develop to adulthood with a developmental delay of 5 to 8 extra days in the larval stage. To survey the genes involved in the early transcriptional response to irradiation, we compared RNA-seq profiles of larvae with and without radiation treatment. Our analysis showed that 327 genes are differentially expressed in irradiated larvae, with 232 genes upregulated and 95 genes downregulated relative to controls. The upregulated genes were enriched for DNA damage response genes, including those involved in DNA repair, cell cycle arrest, and apoptosis, whereas the down-regulated genes were enriched for developmental regulators, consistent with the developmental delay observed in irradiated larvae. Thus, our study has laid the groundwork to further dissect how Sciara copes with radiation-induced damage.

category: genomics


title: Cephalopod Retinal Development Shows Vertebrate-like Mechanisms of Neurogenesis

abstract: Neurogenesis, the regulation of cellular proliferation and differentiation in the developing nervous system, is the process that underlies the diversity of size and cell type found in animal nervous systems. Our understanding of how this process has evolved is limited because of the lack of high resolution data and live-imaging methods across species. The retina is a classic model for the study of neurogenesis in vertebrates and live-imaging of the retina has shown that during development, progenitor cells are organized in a pseudostratified neuroepithelium and nuclei migrate in coordination with the cell cycle along the apicobasal axis of the cell, a process called interkinetic nuclear migration. Eventually cells delaminate and differentiate within the boundaries of the epithelium. This process has been considered unique to vertebrates and thought to be important in maintaining organization during the development of a complex nervous system. Coleoid cephalopods, including squid, cuttlefish and octopus, have the largest nervous system of any invertebrate and convergently-evolved camera-type eyes, making them a compelling comparative system to vertebrates. Here we have pioneered live-imaging techniques to show that the squid, Doryteuthis pealeii, displays cellular mechanisms during cephalopod retinal neurogenesis that are hallmarks of vertebrate processes. We find that retinal progenitor cells in the squid undergo interkinetic nuclear migration until they exit the cell cycle, we identify retinal organization corresponding to progenitor, post-mitotic and differentiated cells, and we find that Notch signaling regulates this process. With cephalopods and vertebrates having diverged 550 million years ago, these results suggest that mechanisms thought to be unique to vertebrates may be common to highly proliferative neurogenic primordia contributing to a large nervous system.

category: developmental biology


title: Coevolution of brain size and longevity in parrots

abstract: Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the Cognitive Buffer Hypothesis, which proposes that increased cognitive abilities enable longer life spans, and the Expensive Brain Hypothesis, which holds that increases in life span are caused by prolonged developmental time of, and increased parental investment in, large brained offspring. We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using a principled Bayesian approach that addresses data uncertainty and imputation of missing values, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction. Our results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans.


title: Coevolution of relative brain size and life expectancy in parrots


title: Mesodiencephalic junction Gabaergic inputs are processed separately from motor cortical inputs in the basilar pons

abstract: The basilar pontine nuclei (bPN) receive inputs from the entire neocortex and constitute the main source of mossy fibers to the cerebellum. Despite their critical position in the cortico-cerebellar pathway, it remains unclear if and how the bPN process inputs. An important unresolved question is whether the bPN strictly receives excitatory inputs or also receives inhibitory inputs. In the present study, we identified the mesodiencephalic junction as a prominent source of GABAergic afferents to the bPN. We combined optogenetics and whole-cell patch clamp recordings and confirmed that the bPN indeed receives monosynaptic GABA inputs from this region. Furthermore, we found no evidence that these inhibitory inputs converge with motor cortex (M1) inputs at the single neuron level. We also found no evidence of any connectivity between bPN neurons, suggesting the absence of a local circuit. Finally, rabies tracings revealed that GABAergic MDJ neurons themselves receive prominent inputs from neocortical output neurons. Our data indicates that inhibition from the MDJ, and excitation from the neocortex remain separate streams of information through the bPN. It is therefore unlikely that inhibition in the bPN has a gating function, but rather shapes an appropriate output of the bPN during behavior.


title: Insights into Early Word Comprehension: Tracking the Neural Representations of Word Semantics in Infants.

abstract: AO_SCPLOWBSTRACTC_SCPLOWInfants start developing rudimentary language skills and can start understanding simple words well before their first birthday [Bergelson and Swingley, 2012]. This development has also been shown primarily using Event Related Potential (ERP) techniques to find evidence of word comprehension in the infant brain [Parise and Csibra, 2012, Friedrich and Friederici, 2010]. While these works validate the presence of semantic representations of words (word meaning) in infants, they do not tell us about the mental processes involved in the manifestation of these semantic representations or the content of the representations. To this end, we use a decoding approach where we employ machine learning techniques on Electroencephalography (EEG) data to predict the semantic representations of words found in the brain activity of infants. We perform multiple analyses to explore word semantic representations in two groups of infants (9-month-old and 12-month-old). Our analyses show significantly above chance decodability of overall word semantics, word animacy, and word phonetics. As we analyze brain activity, we observe that participants in both age groups show signs of word comprehension immediately after word onset, marked by our models significantly above chance word prediction accuracy. We also observed strong neural representations of word phonetics in the brain data for both age groups, some likely correlated to word decoding accuracy and others not. Lastly, we discover that the neural representations of word semantics are similar in both infant age groups. Our results on word semantics, phonetics, and animacy decodability, give us insights into the evolution of neural representation of word meaning in infants.


title: Differential regulation of cranial and cardiac neural crest by Serum Response Factor

abstract: Serum response factor (SRF) is an essential transcription factor that influences many cellular processes including cell proliferation, migration, and differentiation. SRF directly regulates and is required for immediate early gene (IEG) and actin cytoskeleton-related gene expression. SRF coordinates these competing transcription programs through discrete sets of cofactors, the Ternary Complex Factors (TCFs) and Myocardin Related Transcription Factors (MRTFs). The relative contribution of these two programs to in vivo SRF activity and mutant phenotypes is not fully understood. To study how SRF utilizes its cofactors during development, we generated a knock-in SrfI allele in mice harboring point mutations that disrupt SRF-MRTF-DNA complex formation but leave SRF-TCF activity unaffected. Homozygous SrfI/I mutants die at E10.5 with notable cardiovascular phenotypes, and neural crest conditional mutants succumb at birth to defects of the cardiac outflow tract but display none of the craniofacial phenotypes associated with complete loss of SRF in that lineage. Our studies further support an important role for MRTF mediating SRF function in cardiac neural crest and suggest new mechanisms by which SRF regulates transcription during development.


title: First evidence towards chemical self-recognition in a gecko

abstract: Self-recognition is the ability to recognise stimuli originating from oneself. Humans and most great apes show evidence of true self-recognition in the mirror test. They use their reflection to remove a mark that is only visible in the mirror. Not all animals, however, rely primarily on vision. In lizards, chemical cues are important in social interactions. A number of lizard species show chemical self-recognition but it has never been investigated in a gecko species. Here, we test the tokay gecko (Gekko gecko) a territorial species with parental care on their ability to discriminate their own skin and faecal chemicals from those of same-sex, unfamiliar conspecifics. Geckos show a higher response rate towards chemicals from unfamiliar individuals compared to self-produced chemicals and a water control. Lizards showed self-directed behaviour, responded stronger to skin chemicals and females responded more than males. Our study provides first evidence towards self-recognition and for a social function of chemical present on faeces in tokay geckos but further tests are needed to confirm true self-recognition. Tokay geckos are an excellent model species to investigate individual recognition to demonstrate more sophisticated social cognitive abilities than have previously been attributed to reptiles.

category: animal behavior and cognition


title: TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis

abstract: Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression through controlling chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease-like state that contributes to an exacerbated sensitivity to autophagy inducers.

category: cancer biology


title: Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer's disease mouse model

abstract: Deposition of amyloid beta (A{beta}) along with glia cell-mediated neuroinflammation are prominent pathogenic hallmarks of Alzheimers disease (AD). In recent years, impairment of autophagy has been found to be another important feature, contributing to AD progression and aging. Therefore, we assessed the effect of the autophagy activator Spermidine, a small body-endogenous polyamine often used as dietary supplement and known to promote longevity, on glia cell-mediated neuroinflammation. Spermidine reduced TLR3- and TLR4- mediated inflammatory processes in microglia and astrocytes by decreasing cytotoxicity, inflammasome activity and NF-{kappa}B signaling. In line with these anti-inflammatory effects, oral treatment of the amyloid prone AD-like APPPS1 mice with Spermidine reduced neuroinflammation and neurotoxic soluble A{beta}. Mechanistically, single nuclei sequencing revealed microglia as one of the main targets of Spermidine treatment, with increased expression of genes implicated in cell motility and phagocytosis. Thus, Spermidine provides a promising therapeutic potential to target glia cells in AD progression.


title: WGS analysis of Listeria monocytogenes from rural, urban, and farm environments in Norway: Genetic diversity, persistence, and relation to clinical and food isolates

abstract:
Listeria monocytogenes is a ubiquitous environmental bacterium associated with a wide variety of natural and man-made environments, such as soil, vegetation, livestock, food processing environments, and urban areas. It is also among the deadliest foodborne pathogens, and knowledge about its presence and diversity in potential sources is crucial to effectively track and control it in the food chain. Isolation of L. monocytogenes from various rural and urban environments showed higher prevalence in agricultural and urban developments than in forest or mountain areas, and that detection was positively associated with rainfall. Whole genome sequencing (WGS) was performed for the collected isolates and for L. monocytogenes from Norwegian dairy farms and slugs, in total 218 isolates. The data was compared with available datasets from clinical and food associated sources in Norway collected within the last decade. Multiple examples of clusters of isolates with 0-8 wgMLST allelic differences were collected over time in the same location, demonstrating persistence of L. monocytogenes in natural, urban and farm environments. Furthermore, several clusters with 6-20 wgMLST allelic differences containing isolates collected across different locations, times and habitats were identified, including nine clusters harbouring clinical isolates. The most ubiquitous clones found in soil and other natural and animal ecosystems (CC91, CC11, and CC37) were distinct from clones predominating among both clinical (CC7, CC121, CC1) and food (CC9, CC121, CC7, CC8) isolates. The analyses indicated that ST91 was more prevalent in Norway than other countries and revealed a high proportion of the hypovirulent ST121 among Norwegian clinical cases.

ImportanceListeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment. For effective management, both public health authorities and food producers need reliable tools for source tracking, surveillance, and risk assessment. For this, whole genome sequencing (WGS) is regarded as the present and future gold standard. In the current study, we use WGS to show that L. monocytogenes can persist for months and years in natural, urban and dairy farm environments. Notably, clusters of almost identical isolates, with genetic distances within the thresholds often suggested for defining an outbreak cluster, can be collected from geographically and temporally unrelated sources. The work highlights the need for a greater knowledge of the genetic relationships between clinical isolates and isolates of L. monocytogenes from a wide range of environments, including natural, urban, agricultural, livestock, food production, and food processing environments, in order to correctly interpret and use results from WGS analyses.


title: Presence of Toxoplasma gondii tissue cysts in human semen

abstract:
Toxoplasma gondii is a widely prevalent protozoan parasite in human populations. This parasite is thought to be primarily transmitted through undercooked meat and contamination by cat feces. Here, we demonstrate that Toxoplasma gondii cysts can be found within human semen, thus suggesting a potential for sexual transmission. We visualized Toxoplasma gondii cysts in ejaculates of immune-competent and latently infected human volunteers. We confirmed the encystment by probing transcription of a bradyzoite-specific gene in these structures. These observations extend previous observations of the parasite in semen of several non-human host species, including rats, dogs, and sheep. Toxoplasma gondii infection is a clinically significant infection, in view of its high prevalence, its purported role in neuropsychiatric disorders such as schizophrenia, as well as in the more serious form of congenital toxoplasmosis. Our demonstration of intact Toxoplasma gondii cysts in the ejaculate supports the possibility of sexual transmission of the parasite and provides an impetus for further investigations.

ImportanceToxoplasma gondii is recognized as one of the five infections that can harm fetal health. There is also emerging evidence that toxoplasmosis is related to the development of neuropsychiatric disorders. In this context, the current report includes visual evidence of Toxoplasma gondii cyst presence in the semen of human males. It is thus plausible that this clinically significant infection can be sexually transmitted. The existence of sexual transmission in a population, and its relative importance vis-a-vis other transmission routes, remains undetermined. These possibilities are of acute relevance to human health in the context of sexual health and pregnancy management.


title: Listeria monocytogenes GlmR is an accessory uridyltransferase essential for cytosolic survival and virulence

abstract:
The cytosol of eukaryotic host cells is an intrinsically hostile environment for bacteria. Understanding how cytosolic pathogens adapt to and survive in the cytosol is critical to developing novel therapeutic interventions for these pathogens. The cytosolic pathogen Listeria monocytogenes requires glmR (previously known as yvcK), a gene of unknown function, for resistance to cell wall stress, cytosolic survival, inflammasome avoidance and ultimately virulence in vivo. A genetic suppressor screen revealed that blocking utilization of UDP-GlcNAc by a non-essential wall teichoic acid decoration pathway restored resistance to cell wall stress and partially restored virulence of {Delta}glmR mutants. In parallel, metabolomics revealed that {Delta}glmR mutants are impaired in the production of UDP-GlcNAc, an essential peptidoglycan and wall teichoic acid (WTA) precursor. We next demonstrated that purified GlmR can directly catalyze the synthesis of UDP-GlcNAc from GlcNAc-1P and UTP, suggesting that it is an accessory uridyltransferase. Biochemical analysis of GlmR orthologues suggest that uridyltransferase activity is conserved. Finally, mutational analysis resulting in a GlmR mutant with impaired catalytic activity demonstrated that uridyltransferase activity was essential to facilitate cell wall stress responses and virulence in vivo. Taken together these studies indicate that GlmR is an evolutionary conserved accessory uridyltransferase required for cytosolic survival and virulence of L. monocytogenes.

ImportanceBacterial pathogens must adapt to their host environment in order to cause disease. The cytosolic bacterial pathogen Listeria monocytogenes requires a highly conserved protein of unknown function, GlmR (previously known as YvcK) to survive in the host cytosol. GlmR is important for resistance to some cell wall stresses and is essential for virulence. The {Delta}glmR mutant is deficient in production of an essential cell wall metabolite, UDP-GlcNAc, and suppressors which increase metabolite levels also restore virulence. Purified GlmR can directly catalyze the synthesis of UDP-GlcNAc and this enzymatic activity is conserved in pathogens from Firmicutes and Actinobacteria phyla. These results highlight the importance accessory cell wall metabolism enzymes in responding to cell wall stress in a variety of bacterial pathogens.


title: Weakly migratory metastatic breast cancer cells activate fibroblasts via microvesicle-Tg2 to facilitate dissemination and metastasis

abstract: Cancer cell migration is highly heterogeneous, and the migratory capability of cancer cells is thought to be an indicator of metastatic potential. It is becoming clear that a cancer cell does not have to be inherently migratory to metastasize, with weakly migratory cancer cells often found to be highly metastatic. However, the mechanism through which weakly migratory cells escape from the primary tumor remains unclear. Here, utilizing phenotypically sorted highly and weakly migratory breast cancer cells, we demonstrate that weakly migratory metastatic cells disseminate from the primary tumor via communication with stromal cells. While highly migratory cells are capable of single cell migration, weakly migratory cells rely on cell-cell signaling with fibroblasts to escape the primary tumor. Weakly migratory cells release microvesicles rich in tissue transglutaminase 2 (Tg2) which activate fibroblasts and lead weakly migratory cancer cell migration in vitro. These microvesicles also induce tumor stiffening and fibroblast activation in vivo and enhance the metastasis of weakly migratory cells. Our results identify microvesicles and Tg2 as potential therapeutic targets for metastasis and reveal a novel aspect of the metastatic cascade in which weakly migratory cells release microvesicles which activate fibroblasts to enhance cancer cell dissemination.


title: Plasticity in stomatal behavior across a gradient of water supply is consistent among field-grown maize inbred lines with varying stomatal patterning

abstract:
Stomata regulate leaf CO2 assimilation (A) and water loss. The Ball-Berry and Medlyn models predict stomatal conductance (gs) with a slope parameter (m or g1) that reflects sensitivity of gs to A, atmospheric CO2 and humidity, and is inversely related to water use efficiency (WUE). This study addressed knowledge gaps about what the values of m and g1 are in C4 crops under field conditions, as well as how they vary among genotypes and with drought stress. m and g1 were unexpectedly consistent in four inbred maize genotypes across a gradient of water supply. This was despite genotypic variation in stomatal patterning, A and gs. m and g1 were strongly correlated with soil water content, moderately correlated with pre-dawn leaf water potential ({Psi}pd), and weakly correlated with midday leaf water potential ({Psi}md). This implied that m and g1 respond to long-term water supply more than short-term drought stress. The conserved nature of m and g1 across anatomically diverse genotypes and water supplies suggests there is flexibility in structure-function relationships underpinning WUE. This evidence can guide simulation of maize gs across a range of water supply in the primary maize growing region and inform efforts to improve WUE.

Summary statementParameter values for models simulating stomatal conductance were unexpectedly consistent for anatomically and physiologically diverse genotypes of the model C4 crop maize when they were grown across a range of water supplies in the field.


title: DNA methylation patterns differ between free-living Rhizobium leguminosarum RCAM1026 and bacteroids formed in symbiosis with pea (Pisum sativum L.)

abstract: Rhizobium leguminosarum (Rl) is a common name for several genospecies of rhizobia able to form nitrogen-fixing nodules on the roots of pea (Pisum sativum L.) and undergo terminal differentiation into a symbiotic form called bacteroids. In this work, we compared the genomes of the free-living and differentiated forms of the Rl strain RCAM1026 using Oxford Nanopore long reads. No significant genome rearrangements were observed, but the relative abundances of replicons were different between the cell states. GANTC, GGCGCC and GATC methylated motifs have been found in the genome, along with genes for methyltransferases with matching predicted targets. Methylation patterns for the GANTC and GATC motives differed significantly depending on the cell state, which indicates their possible connection to the regulation of symbiotic differentiation. The GGCGCC motif was completely methylated in both bacteria states, and, apparently, is a target for the modification-restriction system. Currently, the methylation patterns in symbiotic bacteria are not extensively studied, so a further investigation of the topic coupled with gene expression data is needed to elucidate the function of differential methylation in terminal differentiation of R. leguminosarum and other rhizobia.


title: Tubular lysosome induction couples animal starvation to healthy aging

abstract:
Dietary restriction promotes longevity via autophagy activation. However, changes to lysosomes underlying this effect remain unclear. Using the nematode Caenorhabditis elegans, we show that induction of autophagic tubular lysosomes, which occurs upon dietary restriction or mTOR inhibition, is a critical event linking reduced food intake to lifespan extension. We find that starvation induces tubular lysosomes not only in affected individuals but also in well-fed descendants, and the presence of gut tubular lysosomes in well-fed progeny is predictive of enhanced lifespan. Furthermore, we demonstrate that expression of Drosophila SVIP, a tubular-lysosome activator in flies, artificially induces tubular lysosomes in well-fed worms and improves C. elegans health in old age. These findings identify tubular lysosomes as a new class of lysosomes that couples starvation to healthy aging.

One-Sentence SummaryTubular lysosome induction promotes healthy aging.

category: cell biology


title: Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

abstract: The origin of plants and their colonization of land resulted in the transformation of the terrestrial environment. Here we investigate the evolution of the land plants (embryophytes) and their two main lineages, the tracheophytes (vascular plants) and bryophytes (non-vascular plants). We used new fossil calibrations, relative lineage dating implied by horizontal gene transfer, and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes and bryophytes as monophyletic sister groups that diverged during the Cambrian, 515-494 Ma. The embryophyte stem is characterised by a burst of gene innovation, while bryophytes subsequently experienced a no less dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses confirm that extant tracheophytes and bryophytes are both highly derived; as a result, understanding the origin of land plants requires tracing character evolution across the diversity of modern lineages.


title: The impact of epistasis in the heterosis and combining ability analyses

abstract:
The current theoretical knowledge concerning the influence of epistasis on heterosis is based on simplified multiplicative model. The objective of this study was to assess the impact of epistasis in the heterosis and combining ability analyses, assuming additive model, hundreds of genes, linkage disequilibrium (LD), dominance, and seven types of digenic epistasis. We developed the quantitative genetics theory for supporting the simulation of the individual genotypic values in nine populations, the selfed populations, the 36 interpopulation crosses, 180 doubled haploids (DHs) and their 16,110 crosses, assuming 400 genes in 10 chromosomes of 200 cM. Epistasis only affects population heterosis if there is LD. Only additive x additive and dominance x dominance epistasis can affect the components of the heterosis and combining ability analyses of populations. Both analyses can lead to completely wrong inferences regarding the identification of the superior populations, the populations with greater differences of gene frequencies, and the populations with maximum variability, when the number of interacting genes and the magnitude of the epistatic effects are high. There was a decrease in the average heterosis by increasing the number of epistatic genes and the magnitude of their epistatic effects. The same results are generally true for the combining ability analysis of DHs. Surprisingly, the combining ability analyses of subsets of 20 DHs showed no significant average impact of epistasis on the identification of the most divergent ones, even assuming a high number of epistatic genes and great magnitude of their effects. However, a significant negative effect can occur.

Statements and DeclarationsThe author has no relevant financial or non-financial interests to disclose. The author has no competing interests to declare that are relevant to the content of this article. The author certifies that he has no affiliations with or involvement in any organization or entity with any financial interest or non-financial interest in the subject matter or materials discussed in this manuscript. The author has no financial or proprietary interests in any material discussed in this article.

category: genetics


title: Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation

abstract: In less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands of strains in a single study. There are now hundreds of thousands of genomes available even for a single bacterial species and the number of genomes is expected to continue to increase at an accelerated pace given the advances in sequencing technology and widespread genomic surveillance initiatives. This explosion of data calls for innovative methods to enable rapid exploration of the structure of a population based on different data modalities, such as multiple sequence alignments, assemblies and estimates of gene content across different genomes. Here we present Mandrake, an efficient implementation of a dimensional reduction method tailored for the needs of large-scale population genomics. Mandrake is capable of visualising population structure from millions of whole genomes and we illustrate its usefulness with several data sets representing major pathogens. Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application (https://gtonkinhill.github.io/mandrake-web/).


title: FITTING OF HYPERELASTIC CONSTITUTIVE MODELS IN DIFFERENT SHEEP HEART REGIONS BASED ON BIAXIAL MECHANICAL PROPERTIES

abstract: Heart failure remains one of the leading causes of death especially among people over the age of 60 years worldwide. To develop effective therapy and suitable replacement materials for the heart muscle it is necessary to understand its biomechanical behaviour under load. This paper investigates the passive mechanical response of the sheep myocardia excised from three different regions of the heart. Due to the relatively higher cost and huge ethical demands in acquisition and testing of real animal heart models, this paper evaluates the fitting performances of five different constitutive models on the myocardial tissue responses. Ten sheep were sacrificed, and their hearts excised and transported within 3h to the testing biomechanical laboratory. The upper sections of the hearts above the short axes were carefully dissected out. Tissues were dissected from the mid-sections of the left ventricle, mid-wall and right ventricle for each heart. The epicardia and endocardia were then carefully sliced off each tissue to leave the myocardia. Stress-strain curves were calculated, filtered and resampled. The results show that Choi-Vito model was found to provide the best fit to the LV, the polynomial (Anisotropic) model to RV, the Four-Fiber Family model to RV, Holzapfel (2000) to RV, Holzapfel (2005) to RV and the Fung model to LV.


title: Computational Fontan Analysis: Preserving accuracy while expediting workflow

abstract:
BackgroundPost-operative outcomes of the Fontan operation have been linked to graft shape after implantation. Computational fluid dynamics (CFD) simulations are used to explore different surgical options. The objective of this study is to perform a systematic in vitro validation for investigating the accuracy and efficiency of CFD simulation to predict Fontan hemodynamics.

MethodsCFD simulations were performed to measure indexed power loss (iPL) and hepatic flow distribution (HFD) in 10 patient-specific Fontan models, with varying mesh and numerical solvers. The results were compared with a novel in vitro flow loop setup with 3D printed Fontan models. A high-resolution differential pressure sensor was used to measure the pressure drop for validating iPL predictions. Microparticles with particle filtering system were used to measure HFD. The computational time was measured for a representative Fontan model with different mesh sizes and numerical solvers.

ResultsWhen compared to in vitro setup, variations in CFD mesh sizes had significant effect on HFD (p = 0.0002) but no significant impact on iPL (p = 0.069). Numerical solvers had no significant impact in both iPL (p = 0.50) and HFD (P = 0.55). A transient solver with 0.5 mm mesh size requires computational time 100 times more than a steady solver with 2.5 mm mesh size to generate similar results.

ConclusionsThe predictive value of CFD for Fontan planning can be validated against an in vitro flow loop. The prediction accuracy can be affected by the mesh size, model shape complexity and flow competition.

category: bioinformatics


title: Alu-mediated weak CEBPA binding and slow B cell transdifferentiation in human

abstract: Many developmental and differentiation processes take substantially longer in human than in mouse. To investigate the molecular mechanisms underlying this phenomenon, here we have specifically focused on the transdifferentiation from B cells to macrophages. The process is triggered by exactly the same molecular mechanism -- the induction by the transcription factor (TF) CEBPA -- but takes three days in mouse and seven in human (1, 2). In mouse, the speed of this process is known to be associated with Myc expression (3). We found that in this species, CEBPA binds strongly to the Myc promoter, efficiently down-regulating Myc. In human, in contrast, CEBPA does not bind this promoter, and MYC is indirectly and more slowly down-regulated. Attenuation of CEBPA binding is not specific to the MYC promoter, but a general trait of the human genome across multiple biological conditions. We traced back weak CEBPA binding to the primate-specific Alu repeat expansion. Many Alu repeats carry strong CEBPA binding motifs, which sequester CEBPA, and attenuate CEBPA binding genome-wide. We observed similar CEBPA and MYC dynamics in natural processes regulated by CEBPA, suggesting that CEBPA attenuation could underlie the longer duration in human processes controlled by this factor. Our work highlights the highly complex mode in which biological information is encoded in genome sequences, evolutionarily connecting, in an unexpected way, lineage-specific transposable element expansions to species-specific changes in developmental tempos.


title: Detecting ice artefacts in processed macromolecular diffraction data with machine learning

abstract:
Contamination with diffraction from ice crystals can negatively affect, or even impede macromolecular structure determination and therefore, detecting the resulting artefacts in diffraction data is crucial. However, once the data have been processed, it can be very difficult to automatically recognize this problem. To address this, a set of convolutional neural networks named Helcaraxe has been developed which can detect ice diffraction artefacts in processed diffraction data from macromolecular crystals. The networks outperform previous algorithms and will be available as part of the AUSPEX webserver and CCP4-distributed software.

SynopsisA program utilizing artificial learning and convolutional neural networks, named Helcaraxe, has been developed which can detect ice crystal artefacts in processed macromolecular diffraction data with unprecedented accuracy.

category: biophysics


title: Longitudinal to transverse metachronal wave transitions in an in-vitro model of ciliated bronchial epithelium

abstract: Myriads of cilia beat on ciliated epithelia, which are ubiquitous in life. When ciliary beats are synchronized, metachronal waves emerge, whose direction of propagation depends on the living system in an unexplained way. We show on a reconstructed human bronchial epithelium in-vitro that the direction of propagation is determined by the ability of mucus to be transported at the epithelial surface. Numerical simulations show that longitudinal waves maximise the transport of mucus while transverse waves, observed when the mucus is rigid and still, minimize the energy dissipated by the cilia.


title: Effect of eribulin on angiogenesis and endothelial adhesion molecules.

abstract:
Tumor vasculature is an important component of the tumor microenvironment and deeply affect anticancer immune response. Eribulin is a non taxane inhibitor of the mitotic spindle. However, off-target effect interfering with the tumor vasculature have been reported. The mechanisms responsible of this effect is not clear.

We designed an in vitro study to investigate the effect of eribulin on neo-angiogenesis and on the adhesion molecules ICAM-1 and VCAM-1, with or without TGF-{beta}. We also investigated the effects of paclitaxel and vinorelbine in the same experimental conditions.

Eribulin was able to up-regulate the epithelial markers VE-cadherin and CD-31 in the HUVEC and tube formation in HUVEC cultured in Matrigel. The drug effectively arrested tube formation even in presence of TGF-{beta}. Eribulin counteracted the TGF-{beta} induced change in cell shape from the endothelial cobblestone-like morphology to an elongated spindle-shaped morphology that is characteristic of EndMT.

We also observed that eribulin is able to upregulate ICAM-1 and to counteract its downregulation induced by TGF-{beta}.

In this study, eribulin was able to inhibit the vasculature remodeling and the downregulation of ICAM-1 induced by TGF-{beta}. These effects might have important therapeutic consequence if the drug will be administered with immunotherapy.


title: Inhibition of Metastatic Uveal Melanoma Cell Proliferation by the Histone Deacetylase 6 Inhibitor, Ricolinostat, is Linked to Altered Microphthalmia-associated Transcription Factor and Phospho-ERK Expression

abstract:
Metastatic uveal melanoma (MUM) is characterized by poor patient survival. Unfortunately, current treatment options demonstrate limited benefits. In this study, we evaluate the efficacy of ACY-1215, a histone deacetylase 6 inhibitor (HDAC6i), to attenuate MUM cell growth in vitro and in vivo, and elucidate the underlying molecular mechanisms. Treatment of OMM2.5 MUM cells with ACY-1215 resulted in a significant (p = 0.0001), dose-dependent reduction in cell survival and proliferation in vitro, and in vivo regression of primary OMM2.5 xenografts in zebrafish larvae. Furthermore, flow cytometry analysis revealed that ACY-1215 significantly arrested the OMM2.5 cell cycle in S phase (p = 0.0006) following 24 hours of treatment and significant apoptosis was triggered in a time- and dose-dependent manner (p = <0.0001). Additionally, ACY-1215 treatment resulted in a significant reduction in OMM2.5 p-ERK expression levels. Through proteome-profiling, attenuation of the microphthalmia-associated transcription factor (MITF) signaling pathway was linked to the observed anti-cancer effects of ACY-1215. In agreement, pharmacological inhibition of MITF signaling with ML329, significantly reduced OMM2.5 cell survival and viability in vitro (p = 0.0001) and in vivo (p = 0.0006). Our findings provide evidence that ACY-1215 and ML329 are efficacious against growth and survival of MUM cells and are potential therapeutic options for MUM.

Simple SummaryUveal melanoma (UM) is the most common adult eye cancer. UM originates in the iris, ciliary body, or choroid (collectively known as the uvea), in the middle layer of the eye. This first or primary UM is treated by targeting the cancer cells using ocular radiation implants or by surgical removal of the eye. However, when UM spreads to the liver and other parts of the body, patients have a poor survival prognosis. Unfortunately, there are no effective treatment options for UM that has spread. Our aim is to help identify effective treatments for UM cancer that has spread. In our study, we identified that the drug ACY-1215 prevents the growth of UM cells from the liver. Our study has found a promising treatment approach for advanced UM.


title: Repeated exposure to chlorpyrifos is associated with a dose-dependent chronic neurobehavioral deficit in adult rats

abstract: Organophosphate (OP) chemicals include commonly used pesticides and also chemical warfare agents, and mechanistically they are potent inhibitors of the cholinesterase (ChE) enzyme. While a chronic low-dose OP exposure does not produce acute cholinergic crises, epidemiological studies report long-term neuropsychiatric issues including depression and cognitive impairments in OP-exposed individuals. Chlorpyrifos (CPF) is one of the most widely used pesticides worldwide. Multiple laboratory studies have reported on either the long-term behavioral effect of a single, high-dose CPF or studied sub-chronic behavioral effects particularly the motor and cognitive effects of repeated low-dose CPF exposure. However, studies on chronic mood and depression-related morbidities following repeated sub-threshold CPF doses that would mimic occupationally-relevant OP exposures are lacking. Here, adult male rats were injected with CPF (1, 3, 5, or 10 mg/kg/d, s.c.) for 21-days. Dependent on the CPF dose, ChE activity was inhibited approximately 60-80% in the blood and about 20-50% in the hippocampus at 2-days after the end of CPF exposures. Following an 11-week washout period, CPF-treated rats exhibited a dose-dependent increase in signs of anhedonia (sucrose preference test), anxiety (open-field and elevated plus-maze), and despair (forced swim test) despite a complete recovery of ChE activity at this stage. We speculate that both cholinergic and non-cholinergic mechanisms could play a role in the development of chronic OP-related depressive outcomes. The proposed CPF exposure paradigm could provide an ideal model to further study molecular mechanisms underlying cause and effect relationships between environmental OP exposures and the development of chronic behavioral deficits.

category: pharmacology and toxicology


title: A novel approach in heart-rate-variability analysis

abstract: Heart-rate variability (HRV), measured by the fluctuation of beat-to-beat intervals, has been growingly considered the most important hallmark of heart rate (HR) time series. HRV can be characterized by various statistical measures both in the time and frequency domains, or by nonlinear methods. During the past decades, an overwhelming amount of HRV data has been piled up in the research community, but the individual results are difficult to reconcile due to the different measuring conditions and the usually HR-dependent statistical HRV-parameters applied. Moreover, the precise HR-dependence of HRV parameters is not known. Using data gathered by a wearable sensor of combined heart-rate and actigraphy modalities, here, we introduce a novel descriptor of HRV, based on a modified Poincare plot of 24-h RR-recordings. We show that there exists a - regressive biexponential - HRV versus HR "master" curve ("M-curve") that is highly conserved for a healthy individual on short and medium terms (on the hours to months scale, respectively). At the same time, we reveal how this curve is related to age in the case of healthy people, and establish alterations of the M-curves of heart-attack patients. A stochastic neuron model accounting for the observed phenomena is also elaborated, in order to facilitate physiological interpretation of HRV data. Our novel evaluation procedure applied on the time series of interbeat intervals allows the description of the HRV(HR) function with unprecedented precision. To utilize the full strength of the method, we suggest a 24-hour-long registration period under natural, daily-routine circumstances (i.e., no special measuring conditions are required). By establishing a patients M-curve, it is possible to monitor the development of his/her status over an extended period of time. On these grounds, the new method is suggested to be used as a competent tool in future HRV analyses for both clinical and training applications, as well as for everyday health promotion.


title: The Loroxanthin cycle: A new type of xanthophyll cycle in green algae (Chlorophyta)

abstract: Xanthophyll cycles have proven to be major contributors to photoacclimation for many organisms. This work describes a light-driven xanthophyll cycle operating in the chlorophyte Chlamydomonas reinhardtii and involving the xanthophylls Lutein (L) and Loroxanthin (Lo). Pigments were quantified during a switch from high to low light and at different time points from cells grown in Day/night cycle. Trimeric LHCII was purified from cells acclimated to high or low light and their pigment content and spectroscopic properties were characterized. The Lo/(L+Lo) ratio in the cells varies by a factor of 10 between cells grown in low or high light leading to a change in the Lo/(L+Lo) ratio in trimeric LHCII from 0.5 in low light to 0.07 in high light. Trimeric LhcbMs binding Loroxanthin have 5{+/-}1% higher excitation energy transfer from carotenoid to Chlorophyll as well as higher thermo- and photostability than trimeric LhcbMs that only bind Lutein. The Loroxanthin cycle operates on long time scales (hours to days) and likely evolved as a shade adaptation. It has many similarities with the Lutein-epoxide - Lutein cycle of plants.


title: Extrinsic motivators drive children's cooperation to conserve forests

abstract:
Forests are essential common-pool resources. It is increasingly critical to nurture a lifelong concern for forest health both locally and globally. Here, in two experiments, we demonstrate that school age children (6-18 yrs. old; N>1000;) of three nationalities (China, D. R. Congo and U.S.) do not have levels of intrinsic motivation to allow for successful cooperation in common-pool goods games requiring them to maintain a forest. We instead find that the size, timing, and certainty of receiving individual payoffs from cooperation significantly boost the odds of successful conservation efforts. We also provide evidence that the experience of playing this game increases longer term motivation to conserve forests. Results have implications for designing policy and curriculum to encourage collective action for forest conservation.

One Sentence SummaryExtrinsic motivation boosts concern for forests among children and adolescents in the United States, China, and the Democratic Republic of the Congo.

category: scientific communication and education


title: Neural population dynamics underlying evidence accumulation in multiple rat brain regions

abstract: Accumulating evidence in service of sensory decision making is a core cognitive function. However, previous work has focused either on the dynamics of neural activity during decision-making or on models of evidence accumulation governing behavior. We unify these two perspectives by introducing an evidence-accumulation framework that simultaneously describes multi-neuron population spiking activity and dynamic stimulus-driven behavior during sensory decision-making. We apply our method to behavioral choices and neural activity recorded from three brain regions -- the posterior parietal cortex (PPC), the frontal orienting fields (FOF), and the anterior-dorsal striatum (ADS) -- while rats performed a pulse-based accumulation task. The model accurately captures the relationship between stimuli and neural activity, the coordinated activity of neural populations, and the distribution of animal choices in response to the stimulus. Model fits show strikingly distinct accumulation models expressed within each brain region, and that all differ strongly from the accumulation strategy expressed at the level of choices. In particular, the FOF exhibited a suboptimal  primacy strategy, where early sensory evidence was favored. Including neural data in the model led to improved prediction of the moment-by-moment value of accumulated evidence and the intended--and ultimately made--choice of the animal. Our approach offers a window into the neural representation of accumulated evidence and provides a principled framework for incorporating neural responses into accumulation models.

category: neuroscience


title: Spontaneous emergence of topologically robust grid cell modules: A multiscale instability theory

abstract: The grid cell system is a paradigmatic example of the computational advantages of modular representations. Modular grid responses emerge along a strip of cortex with smooth gradients in several biophysical properties, within days of eye opening in juvenile animals. The mechanisms underlying this emergence are unknown. We show that multiple spatially and functionally discrete grid modules can spontaneously self-organize from lateral interactions that are continuously graded in scale, when combined with a fixed-scale interaction. We derive a comprehensive analytic theory to reveal that modularization through this mechanism is highly generic and robust. It predicts that each term in the sequence of grid period ratios should be distinct and furnishes values that are invariant to microscopic details about dynamics and connectivity, resulting in the most accurate match to data to date. Altogether, this work reveals novel self-organization mechanisms by which simple local interactions and smooth gradients may interact to produce macroscopic modular organization.


title: From smooth cortical gradients to discrete modules: spontaneous and topologically robust emergence of modularity in grid cells


title: From smooth cortical gradients to discrete modules: A biologically plausible mechanism for the self-organization of modularity in grid cells


title: Reversing anterior insular cortex neuronal hypoexcitability attenuates compulsive behavior in juvenile rats

abstract: Development of self-regulatory competencies during adolescence is partially dependent on normative brain maturation. Here we report that juvenile rats as compared to adults exhibit impulsive and compulsive-like behavioral traits, the latter being associated with lower expression of mRNA levels of the immediate early gene zif268 in the anterior insula (AI). This observation suggests that deficits in AI function in juvenile rats could explain their immature pattern of interoceptive cue integration in rational decision-making and compulsive phenotype. In support of this, here we report hypoexcitability of juvenile layer-V pyramidal neurons in the AI, concomitant with reduced glutamatergic synaptic input to these cells. Chemogenetic activation of the AI attenuated the compulsive trait suggesting that delayed maturation of the AI results in suboptimal integration of sensory and cognitive information in adolescents and this contributes to inflexible behaviors in specific conditions of reward availability.


title: Cortical adaptation to sound reverberation

abstract: In almost every natural environment, sounds are reflected by nearby objects, producing many delayed and distorted copies of the original sound, known as reverberation. Our brains usually cope well with reverberation, allowing us to recognize sound sources regardless of their environments. In contrast, reverberation can cause severe difficulties for speech recognition algorithms and hearing-impaired people. The present study examines how the auditory system copes with reverberation. We trained a linear model to recover a rich set of natural, anechoic sounds from their simulated reverberant counterparts. The model neurons achieved this by extending the inhibitory component of their receptive filters for more reverberant spaces, and did so in a frequency-dependent manner. These predicted effects were observed in the responses of auditory cortical neurons of ferrets in the same simulated reverberant environments. Together, these results suggest that auditory cortical neurons adapt to reverberation by adjusting their filtering properties in a manner consistent with dereverberation.


title: Absolute quantitation of serum antibody reactivity using the Richards growth model for antigen microspot titration

abstract: In spite of its pivotal role in the characterization of humoral immunity, there is no accepted method for the absolute quantitation of antigen specific serum antibodies. We devised a novel method to quantify polyclonal antibody reactivity, which exploits protein microspot assays and employs a novel analytical approach. Microarrays with a density series of disease specific antigen were treated with different serum dilutions and developed for IgG and IgA binding. By fitting binding data of both dilution series to a product of two generalized logistic functions, we obtained estimates of antibody reactivity of two immunoglobulin classes simultaneously. These estimates are the antigen concentrations required for reaching the inflection point of thermodynamic activity coefficient of antibodies and the limiting activity coefficient of antigen. By providing universal chemical units, this approach may improve standardization of serological testing, the quality control of antibodies and the quantitative mapping of antibody-antigen interaction space.

category: immunology


title: Genetic evidence for signal transduction within the Bacillus subtilis GerA germinant receptor

abstract:
Bacterial spores can rapidly exit dormancy through the process of germination. This process begins with the activation of nutrient receptors embedded in the spore membrane. The prototypical germinant receptor in Bacillus subtilis responds to L-alanine and is thought to be a complex of proteins encoded by the genes in the gerA operon: gerAA, gerAB, and gerAC. The GerAB subunit has recently been shown to function as the nutrient sensor, but beyond contributing to complex stability, no additional functions have been attributed to the other two subunits. Here, we investigate the role of GerAA. We resurrect a previously characterized allele of gerA (termed gerA*) that carries a mutation in gerAA and show it constitutively activates germination even in the presence of a wild-type copy of gerA. Using an enrichment strategy to screen for suppressors of gerA*, we identified mutations in all three gerA genes that restore a functional receptor. Characterization of two distinct gerAB suppressors revealed that one (gerAB-E105K) reduces the GerA complexs ability to respond to L-alanine, while another (gerAB-F259S) disrupts the germinant signal downstream of L-alanine recognition. These data argue against models in which GerAA is directly or indirectly involved in germinant sensing. Rather, our data suggest that GerAA is responsible for transducing the nutrient signal sensed by GerAB. While the steps downstream of gerAA have yet to be uncovered, these results validate the use of a dominant-negative genetic approach in elucidating the gerA signal transduction pathway.

ImportanceEndospore formers are a broad group of bacteria that can enter dormancy upon starvation and exit dormancy upon sensing the return of nutrients. How dormant spores sense and respond to these nutrients is poorly understood. Here, we identify a key step in the signal transduction pathway that is activated after spores detect the amino acid L-alanine. We present a model that provides a more complete picture of this process that is critical for allowing dormant spores to germinate and resume growth.

category: microbiology


title: RACK1 associates with RNA-binding proteins Vigilin and SERBP1 to control dengue virus replication

abstract: Dengue virus (DENV), a re-emerging virus transmitted by Aedes mosquitoes, causes severe pathogenesis in humans. No effective treatment is available against this virus. We recently identified the scaffold protein RACK1 as a component of the DENV replication complex, a macromolecular complex essential for viral genome amplification. Here, we show that RACK1 is important for DENV infection. RACK1 mediates DENV replication through binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to a loss-of-function screen identified the RNA binding proteins Vigilin and SERBP1 as DENV host dependency factors. Vigilin and SERBP1 interact with DENV viral RNA (vRNA), forming a ternary complex with RACK1 to mediate viral replication. Overall, our results indicate that RACK1 recruits Vigilin and SERBP1, linking the DENV vRNA to the translation machinery for optimal translation and replication.


title: Modelling human zygotic genome activation in 8C-like cells in vitro

abstract:
The remodelling of the epigenome and transcriptome of the fertilised oocyte to establish totipotency in the zygote and developing embryo is one of the most critical processes in mammalian embryogenesis. Zygotic or embryonic genome activation (ZGA, EGA) in the 2-cell embryo in mouse, and the 8-cell embryo in humans, constitutes the first major wave of transcription. Failure to initiate ZGA leads to developmental defects, and contributes to the high attrition rates of human pre-implantation embryos. Due to limitations in cell numbers and experimental tractability, the mechanisms that regulate human embryonic genome activation in the totipotent embryo remain poorly understood. Here we report the discovery of human 8-cell like cells (8CLCs) specifically among naive embryonic stem cells, but not primed pluripotent cells. 8CLCs express ZGA marker genes such as ZSCAN4, LEUTX and DUXA and their transcriptome closely resembles that of the 8-cell human embryo. 8-cell like cells reactivate 8-cell stage specific transposable elements such as HERVL and MLT2A1 and are characterized by upregulation of the DNA methylation regulator DPPA3. 8CLCs show reduced SOX2 protein, and can be identified based on expression of the novel ZGA-associated protein markers TPRX1 and H3.Y in vitro. Overexpression of the transcription factor DUX4. as well as spliceosome inhibition increase ZGA-like transcription and enhance TPRX1+ 8CLCs formation. Excitingly, the in vitro identified 8CLC marker proteins TPRX1 and H3.Y are also expressed in 8-cell human embryos at the time of genome activation and may thus be relevant in vivo. The discovery of 8CLCs provides a unique opportunity to model and manipulate human ZGA-like transcriptional programs in vitro, and might provide critical functional insights into one of the earliest events in human embryogenesis in vivo.

HighlightsO_LIZGA markers and transposable elements are expressed in 8CLCs among naive human stem cells
C_LIO_LIThe transcription factor DUX4 and spliceosome inhibition induce ZGA-like transcription
C_LIO_LI8CLC marker proteins TPRX1 and H3.Y are expressed in nuclei of 8-cell human embryos
C_LIO_LI8CLCs serve as a novel in vitro model for human ZGA
C_LI

category: molecular biology


title: Reproduction, seasonal morphology, and juvenile growth in three Malagasy fruit bats

abstract: The island nation of Madagascar is home to three endemic species of Old World Fruit Bat in the family Pteropodidae: Pteropus rufus, Eidolon dupreanum, and Rousettus madagascariensis, all three of which are IUCN Red Listed under some category of threat. To inform conservation efforts to model population viability for these threatened species, as well understand the mechanisms underpinning persistence of several potentially zoonotic pathogens hosted by these bats, we here define the seasonal limits of a staggered annual birth pulse across the three species. Our field studies in central-eastern Madagascar indicate that this annual birth pulse takes place in September/October for P. rufus, November for E. dupreanum, and December for R. madagascariensis. Juvenile development periods vary across the three Malagasy pteropodids, resulting in near-synchronous weaning of pups for all species in late January-February at the height of the fruiting season for Madagascar, a pattern characteristic of most mammalian frugivores on the island. We here document the size range in morphological traits for the three Malagasy fruit bat species; these traits span the range of those known for pteropodids more broadly, with P. rufus and E. dupreanum among the larger of recorded species and R. madagascariensis among the smaller. All three species demonstrate subtle sexual dimorphism in observed traits with larger-bodied males vs. females. We explore seasonal variation in adult body condition by comparing observed body mass with body mass predicted by forearm length, demonstrating that pregnant females add weight during staggered gestation periods and males lose weight during the nutritionally-deficit Malagasy winter. Finally, we quantify forearm, tibia, and ear length growth rates in juvenile bats, demonstrating both faster growth and more protracted development times for the largest P. rufus species. The longer development period for the already-threatened P. rufus further jeopardizes this species conservation status as human hunting of bats for subsistence is particularly detrimental to population viability during reproductive periods. The more extreme seasonal variation in the mass to forearm relationship for P. rufus may also modulate immune function, an important consideration given these bats roles as reservoir hosts for several high profile viral families known to cause severe disease in humans. Our work highlights the importance of longitudinal field studies in collecting critical data for mammalian conservation efforts and human public health alike.

category: ecology