title: Inactivation of the Hippo Tumor Suppressor Pathway Promotes Melanoma

abstract: Human melanomas are commonly driven by activating mutations in BRAF, which promote melanocyte proliferation through constitutive stimulation of the MAPK pathway. However, oncogenic BRAF alone is insufficient to promote melanoma; instead, its expression merely induces a transient burst of proliferation that ultimately ceases with the development of benign nevi (i.e. moles) comprised of growth-arrested melanocytes. The tumor suppressive mechanisms that induce this melanocytic growth arrest remain poorly understood. Recent modeling studies have suggested that the growth arrest of nevus melanocytes is not solely due to oncogene activation in individual cells, but rather due to cells sensing and responding to their collective overgrowth, similar to what occurs in normal tissues. This cell growth arrest is reminiscent of the arrest induced by activation of the Hippo tumor suppressor pathway, which is an evolutionarily conserved pathway known to regulate organ size. Herein, we demonstrate that oncogenic BRAF signaling activates the Hippo pathway in vitro, which leads to inhibition of the pro-growth transcriptional co-activators YAP and TAZ, ultimately promoting the growth arrest of melanocytes. We also provide evidence that the Hippo tumor suppressor pathway is activated in growth-arrested nevus melanocytes in vivo, both from single-cell sequencing of mouse models of nevogenesis and human tissue samples. Mechanistically, we observe that oncogenic BRAF promotes both ERK-dependent alterations in the actin cytoskeleton and whole-genome-doubling events, and that these two effects independently promote Hippo pathway activation. Lastly, we demonstrate that abrogation of the Hippo pathway, via melanocyte-specific deletion of the Hippo kinases Lats1/2, enables oncogenic BRAF-expressing melanocytes to bypass nevus formation, thus leading to the rapid onset of melanoma with 100% penetrance. This model is clinically relevant, as co-heterozygous loss of LATS1/2 is observed in [~]15% of human melanomas. Collectively, our data reveal that the Hippo pathway enforces the stable growth arrest of nevus melanocytes and therefore represents a critical and previously unappreciated barrier to melanoma development.


title: Bacteriostatic antibiotics promote the evolution of CRISPR-Cas immunity

abstract: Phage therapy can be used in combination with antibiotics to combat infections with bacterial pathogens1-3. However, bacteria can rapidly evolve phage resistance via receptor mutation, or using their CRISPR-Cas adaptive immune systems4, which insert short phage-derived sequences into CRISPR loci in the bacterial genome5 to guide sequence-specific cleavage of cognate sequences6. Unlike CRISPR-Cas immunity, mutation of the phage receptor leads to attenuated virulence when the opportunistic pathogen Pseudomonas aeruginosa is infected with its phage DMS3vir7, which underscores the need to predict how phage resistance evolves under clinically relevant conditions. Here, using eight antibiotics with various modes of action, we show that bacteriostatic antibiotics (which inhibit cell growth without killing) specifically promote evolution of CRISPR-Cas immunity in P. aeruginosa by slowing down phage development and providing more time for cells to acquire phage-derived sequences and mount an immune response. Our data show that some antimicrobial treatments can contribute to the evolution of phage-resistant pathogens with high virulence.

category: microbiology


title: CFTR corrector efficacy is associated with occupancy of distinct binding sites

abstract: CFTR misfolding due to cystic fibrosis causing mutations can be corrected with small molecules designated as correctors. VX-809, an investigational corrector compound, is believed to bind CFTR directly to either the first membrane-spanning domain (MSD1) and/or the first nucleotide-binding domain (NBD1). Blind docking onto the 3D structures of these domains, followed by molecular dynamics (MD) simulations, revealed the presence of two potential VX-809 binding sites which, when mutated, abrogated corrector rescue. Mutations altering protein maturation are also shown to be not equally sensitive to the occupancy of the two sites by VX-809, with the most frequent mutation F508del requiring integrity of both sites and allosteric coupling with the F508del region while L206W only requires the integrity of the MSD1 site. A network of charged amino acids in the lasso Lh2 helix and the intracellular loops ICL1 and ICL4 is involved in the allostery between MSD1 and NBD1. Corrector VX-445, which is used in combination in clinics with VX-661, a structurally close analog of VX-809, to fully correct F508del, is also shown to occupy two potential binding sites on MSD1 and NBD1, the latter being shared with VX-809. In conclusion, VX-809 and VX-445 appear to bind different CFTR domains to alleviate specific folding defects. These results provide new insights into therapeutics understanding and may help the development of efficient corrector combinations.

category: molecular biology


title: The encephalomyocarditis virus Leader promotes the release of virions inside extracellular vesicles via the induction of secretory autophagy

abstract: Naked viruses can escape host cells before the induction of lysis via release in extracellular vesicles (EVs). These nanosized EVs cloak the secreted virus particles in a host-derived membrane, which alters virus-host interactions that affect infection efficiency and antiviral immunity. Currently, little is known about the viral and host factors regulating this form of virus release. Here, we assessed the role of picornavirus security proteins by studying the encephalomyocarditis virus (EMCV) Leader protein. EV release upon infection with wildtype virus or a Leader-deficient mutant was characterized at the single particle level using high-resolution flow cytometry. Inactivation of the Leader abolished EV induction during infection and strongly reduced EV-enclosed virus release. We demonstrate that the Leader promotes the release of virions within EVs by stimulating a secretory arm of autophagy. This newly discovered role of the EMCV Leader adds to the variety of mechanisms via which this protein affects virus-host interactions. Moreover, these data provide first evidence for a crucial role of non-structural viral proteins in the non-lytic release of picornaviruses via packaging in EVs.

category: cell biology


title: The adenoviral E1B-55k protein introduced to immortalize HEK293 cells mediates accumulation of key WNT/β-catenin signaling proteins in large cytoplasmic aggregates and influences the activity of WNT/β-catenin signaling.

abstract: HEK293 cells are one of the most widely used cell lines in research and HEK293 cells are frequently used as an in vitro model for studying the WNT signaling pathway. The HEK293 cell line was originally established by transfection of human embryonic kidney cells with sheared adenovirus 5 DNA and it is known that that HEK293 cells stably express the adenoviral E1A and E1B-55k proteins. Here we show that HEK293 cells display an unexpected distribution of key components of the WNT/{beta}-catenin signaling pathway where AXIN1, APC, DVL2 and tankyrase are all co-localized in large spherical cytoplasmic aggregates. The cytoplasmic aggregates are enclosed by a narrow layer of the adenoviral E1B-55k protein. Reduction of E1B-55k protein levels leads to disappearance of the cytoplasmic aggregates thus corroborating an essential role of the E1B-55k protein in mediating the formation of the aggregates. Furthermore, HEK293 cells with reduced E1B-55k protein levels display reduced levels of transcriptional activation of WNT/{beta}-catenin signaling upon stimulation by the Wnt3A agonist. The demonstrated influence of the E1B-55k protein on the cellular localization of WNT/{beta}-catenin signaling components and on transcriptional regulation of WNT/{beta}-catenin signaling asks for caution in the interpretation of data derived from the HEK293 cell line.


title: The adenoviral E1B-55k protein present in HEK293 cells mediates abnormal accumulation of key WNT signaling proteins in large cytoplasmic aggregates.


title: Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing

abstract: Microbial communities in many environments include distinct lineages of closely related organisms which have proved challenging to separate in metagenomic assembly, preventing generation of complete metagenome-assembled genomes (MAGs). The advent of long and accurate HiFi reads presents a possible means to address this challenge by generating complete MAGs for nearly all sufficiently abundant bacterial genomes in a microbial community. We present a metagenomic HiFi assembly of a complex microbial community from sheep fecal material that resulted in 428 high-quality MAGs from a single sample, the highest resolution achieved with metagenomic deconvolution to date. We applied a computational approach to separate distinct haplotype lineages and identified haplotypes of hundreds of variants across hundreds of kilobases of genomic sequence. Analysis of these haplotypes revealed 220 lineage-resolved complete MAGs, including 44 in single circular contigs, and demonstrated improvement in overall assembly compared to error-prone long reads. We report the characterization of multiple, closely-related microbes within a sample with potential to improve precision in assigning mobile genetic elements to host genomes within complex microbial communities.


title: The Mediator tail module cooperates with proneural factors to determine fate identity in Glioblastoma.

abstract: Glioblastoma stem cells (GSCs) exhibit latent neuronal lineage differentiation potential governed by the proneural transcription factor Achaete-scute homolog 1 (ASCL1) and harnessing and promoting terminal neuronal differentiation has been proposed as a novel therapeutic strategy. Here, using a genome-wide CRISPR suppressor screen we identified genes required for ASCL1-mediated neuronal differentiation. This approach revealed a specialized function of the Mediator complex tail module and of its subunits MED24 and MED25 for this process in GSCs, human fetal neural stem cells and pluripotent stem cells. We show that upon induction of neuronal differentiation MED25 is recruited to genomic loci co-occupied by ASCL1 to regulate neurogenic gene expression programs. MED24 and MED25 are sufficient to induce neuronal differentiation in GSC cultures and to mediate neuronal differentiation in multiple contexts. Collectively our data expand our understanding of the mechanisms underlying directed terminal neuronal differentiation in brain tumor stem cells and point to a unique function of the Mediator tail in neuronal reprogramming.


title: Identification of organ-specific transcriptomic shifts in the vasculature during systemic inflammation using TrendCatcher

abstract: Studying temporal gene expression shifts during disease progression provides important insights into the biological mechanisms that distinguish adaptive and maladaptive responses. Existing tools for the analysis of time course transcriptomic data are not designed to optimally identify distinct temporal patterns when analyzing dynamic differentially expressed genes (DDEGs). Moreover, there is a lack of methods to assess and visualize the temporal progression of biological pathways mapped from time course transcriptomic datasets. In this study, we developed an open-source R package TrendCatcher (https://github.com/jaleesr/TrendCatcher), which applies the smoothing spline ANOVA model and break point searching strategy to identify and visualize distinct dynamic transcriptional gene signatures and biological processes from longitudinal datasets. We used TrendCatcher to perform a systematic temporal analysis of COVID-19 peripheral blood transcriptomes, including bulk RNA-seq and scRNA-seq time course data. TrendCatcher uncovered the early and persistent activation of neutrophils and coagulation pathways as well as impaired type I interferon (IFN-I) signaling in circulating cells as a hallmark of patients who progressed to severe COVID-19, whereas no such patterns were identified in individuals receiving SARS- CoV-2 vaccinations or patients with mild COVID-19. These results underscore the importance of systematic temporal analysis to identify early biomarkers and possible pathogenic therapeutic targets.


title: Systematic temporal analysis of transcriptomes using TrendCatcher identifies early and persistent neutrophil activation as an early hallmark of severe COVID-19

category: bioinformatics


title: Systematic temporal analysis of peripheral blood transcriptomes using TrendCatcher identifies early and persistent neutrophil activation as a hallmark of severe COVID-19


title: Adaptive radiation and burst speciation of hillstream cyprinid fish <Garra> in African river

abstract: Adaptive radiation of fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that also riverine and stream environments provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeastern Asia to Western Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have been found among these new species in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra ( thick-lipped and  predatory) that were not described before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intra-basin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide SNP data, mtDNA was unable to identify any genetic structure suggesting a recent and rapid speciation event. Furthermore, we found evidence for a hybrid origin of the novel  thick-lipped phenotype, as being the result of the hybridization of two other sympatrically occurring species. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly adaptively radiated in a riverine environment, and that this radiation was promoted by the evolution of novel feeding strategies.

category: evolutionary biology


title: The central nucleus of the amygdala and gustatory cortex assess affective valence during CTA learning and expression in male and female rats

abstract: This study evaluated behavior (Boost(R) intake, LiCl-induced behaviors, ultrasonic vocalizations (USVs), task performance) and c-Fos activation during conditioned taste aversion (CTA), the reinforced task (Boost(R) task) and control task (cage only) to understand how male and female rats balance the relative danger or safety of a stimulus in learning and performing a task. Females drank more Boost(R) than males but showed similar aversive behaviors after LiCl treatment. Males produced 55 kHz USVs (indicating positive valence) when anticipating Boost(R) and inhibited these calls after pairing with LiCl. Females produced 55 kHz USVs based on their estrous cycle but were more likely to make 22 kHz USVs than males (indicating negative valence) after pairing with LiCl. c-Fos responses were similar in males and females after Boost(R) or LiCl. Females engaged the gustatory cortex and ventral tegmental area more than males during the Boost(R) task and males engaged the amygdala more than females in both the reinforcing and devalued tasks. Network analysis of correlated c-Fos responses across brain regions identified two unique networks characterizing the Boost(R) and LiCl (CTA) tasks, in both of which the VTA played a central role. RNAscope identified a population of D1-receptor expressing cells in the CeA that responded to Boost(R) and D2 receptor-expressing cells that responded to LiCl. The present study suggests that males and females differentially process the affective valence of a stimulus to produce the same goal-directed behavior.

category: animal behavior and cognition


title: The Immune landscape of solid pediatric tumors.

abstract:
BackgroundImmunotherapy is quickly coming to the forefront of cancer treatment; however, the implementation of immunotherapy in solid pediatric cancers, which classically display a low mutational load, is hindered by insufficient understanding of the determinants of cancer immune responsiveness in children. In order to better understand tumor-host interplay, we sought to characterize solid pediatric cancers based on immunological parameters using analytes extracted from gene expression data.

MethodsWe used RNAseq data from the publicly available TARGET studies for five pediatric solid tumor types (408 patients): Wilms tumor (WT), neuroblastoma (NBL), osteosarcoma (OS), clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor of the kidney (RT). We assessed the performance of previously identified immune signatures like the Immunologic Constant of Rejection (ICR), which captures an active Th1/cytotoxic response associated with favorable prognosis and responsiveness to immunotherapy. We also performed gene set enrichment analysis (ssGSEA) and clustering, using more than 100 immune signatures to define immune subtypes in pediatric tumors and compared the overall survival across subtypes. The expression of immune checkpoints and enrichment of oncogenic pathways were also assessed across the immune subtypes.

ResultsThe five tumor types showed distinct ICR score distributions. A higher ICR score was associated with better survival in OS and NBL-HR-MYCN_NA, but with poorer survival in WT. The clustering of immune signatures revealed the same five principal modules observed in adult solid tumors: Wound Healing, TGF-B signaling, IFN-G signaling, Macrophages, and Lymphocytes. These modules clustered pediatric patients into six immune subtypes (S1-S6) with distinct survival outcomes. The S2 cluster showed the best overall survival and was characterized by low enrichment of the wound healing signature, high Th1, low Th2. Conversely, cluster S4 showed the worst survival and highest enrichment of wound healing signature, low Th1, and high Th2. Furthermore, the upregulation of the WNT/Beta-catenin pathway is associated with unfavorable outcomes and lack of T-cell infiltration in OS.

ConclusionsWe demonstrated that extracranial solid pediatric tumors could be classified according to their immune disposition, unveiling similarity with adults tumors. Immunological parameters might be explored to refine diagnostic and prognostic biomarkers and to identify potential immune-responsive tumors.

category: cancer biology


title: A short report on optimization of nucleic acid probes by DNA microarray synthesis and next generation sequencing

abstract: This manuscript has been withdrawn by bioRxiv as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author

category: synthetic biology


title: Immunomodulatory Therapy with Glatiramer Acetate Reduces Endoplasmic Reticulum Stress and Mitochondrial Dysfunction in Experimental Autoimmune Encephalomyelitis

abstract: Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are found in lesions of multiple sclerosis (MS) and of experimental autoimmune encephalomyelitis (EAE), an animal model of MS, and may contribute to the neuronal loss that underlies permanent impairment. These pathological changes are due to the neuroinflammation that characterizes MS and the strong interplay between the ER and mitochondria. We investigated whether immunomodulatory drug glatiramer acetate (GA) can reduce these changes in the spinal cords of chronic EAE mice by using routine histology, immunostaining, and electron microscopy. EAE spinal cord tissue exhibited increased infiltration/inflammation (upregulation of proinflammatory cytokines), demyelination, mitochondrial dysfunction (increased fission, decreased fusion, and increased biogenesis), ER stress, downregulation of NAD+ dependent pathways, and increased neuronal death. GA reversed these pathological changes, suggesting that immunomodulating therapy can attenuate ER stress, mitochondrial dysfunction, apoptotic cell death, and demyelination in the CNS and increase NAD+ utilizing activities by suppressing neuroinflammation.

category: neuroscience


title: Heme oxygenase limits mycobacterial infection-induced ferroptosis

abstract: Iron homeostasis is essential for both sides of the host-pathogen interface. Restricting access of iron slows bacterial growth while iron is also a necessary co-factor for host immunity. Heme oxygenase 1 (HMOX1) is a critical regulator of iron homeostasis that catalyses the liberation of iron during degradation of heme. It is also a stress-responsive protein that can be rapidly upregulated and confers protection to the host. Although a protective role of HMOX1 has been demonstrated in a variety of diseases, the role of HMOX1 in Mycobacterium tuberculosis infection is equivocal across experiments with different host-pathogen combinations. Here we use the natural host-pathogen pairing of the zebrafish-Mycobacterium marinum infection platform to study the role of zebrafish heme oxygenase in mycobacterial infection. We identify zebrafish Hmox1a as the relevant functional paralog of mammalian HMOX1 and demonstrate a conserved role for Hmox1a in protecting the host from mycobacterial infection. Using genetic and chemical tools, we show zebrafish Hmox1a protects the host against mycobacterial infection by reducing infection-induced iron accumulation and ferroptosis.

category: immunology


title: Real-time HRMAS 13C NMR of obligately anaerobic cells identifies new metabolic targets in the pathogen Clostridioides difficile

abstract: Anaerobic microbial metabolism drives critical aspects of host-microbiome interactions and supports many economically important industrial applications. Yet, the metabolic pathways of anaerobic bacteria and their associated constraints for maintaining energy and redox balance are often poorly described. We employ High-Resolution Magic Angle Spinning Carbon-13 (13C) Nuclear Magnetic Resonance spectroscopy with dynamic flux balance analysis to resolve real-time metabolism in living cells of the obligately anaerobic pathogen Clostridioides difficile. Using 13C-labeled carbon sources, we elaborate the time-dependent progression of reductive and oxidative anaerobic fermentation pathways. Analyses identified new integration points for redox and nitrogen coupling between carbohydrate and amino acid metabolism, particularly in the production of 13C-alanine from 13C-glucose to provide an ammonia sink from co-occurring amino acid fermentation. Analyses conducted in the presence or absence of selenium, a required co-factor for the proline Stickland reductase, demonstrate further capacity to modulate cellular metabolism and resulting metabolites. Findings informed a genome-scale metabolic model of C. difficile, identifying alanine and associated electron carrier pools as critical metabolic integration points in energy flow and biomass expansion. We illustrate use of HRMAS NMR as a new analytical platform to resolve complex interactions in anaerobic metabolism and inform new metabolic targets to counter C. difficile infections.


title: Kaposi's Sarcoma-associated Herpesvirus vFLIP Promotes MEndT to Generate Hybrid M/E State for Tumorigenesis

abstract:
Kaposis sarcoma (KS) is an angioproliferative and invasive tumor caused by Kaposis sarcoma-associated herpesvirus (KSHV). The cellular origin of KS tumor cells remains contentious. Recently, evidence has accrued indicating that KS may arise from KSHV-infected mesenchymal stem cells (MSCs) through mesenchymal-to-endothelial transition (MEndT), but the transformation process has been largely unknown. In this study, we investigated the KSHV-mediated MEndT process and found that KSHV infection rendered MSCs incomplete endothelial lineage differentiation and formed hybrid mesenchymal/endothelial (M/E) state cells characterized by simultaneous expression of mesenchymal markers PDGFRA/Nestin and endothelial markers PDPN/CD31. The hybrid M/E cells have acquired high tumorigenic properties in vitro and the potential to form KS-like tumors after transplanted in mice under renal capsules. These results faithfully recapitulate Kaposis sarcoma where proliferating KS spindle-shaped cells and the cells that line KS-specific aberrant vessels were also found to exhibit a hybrid M/E state. Furthermore, the genetic analysis identified KSHV-encoded FLICE inhibitory protein (vFLIP) as a crucial regulator controlling KSHV-induced MEndT and generating hybrid M/E state cells for tumorigenesis. Overall, KSHV-mediated MEndT that transforms MSCs to tumorigenic hybrid M/E state cells driven by vFLIP is an essential event in Kaposis sarcomagenesis.

Author SummaryKaposis sarcoma manifests as multifocal lesions with spindle cell proliferation, intense angiogenesis, and erythrocyte extravasation. Although the origin and true malignant nature of KS remains contentious, it is established that KSHV infection with concomitant viral oncogene expression in normal cell progenitors causes KS. The mechanism of KSHV oncogenesis could be revealed through reproduction of KS by infection of normal cells. This study reports that the KSHV infection of mesenchymal stem cells initiates mesenchymal-to-endothelial transition (MEndT) that generates mesenchymal/endothelial (M/E) hybrid state cells. The hybrid M/E cells acquired high tumorigenic properties, including tumor initiation, angiogenesis, migration, and the potential to form KS-like tumors after transplanted in mice. This finding faithfully recapitulates Kaposis sarcoma where proliferating KS spindle cells and the cells that line KS-specific aberrant vessels are also found to exhibit the hybrid M/E state. We also found that KSHV-encoded viral FLICE inhibitory protein (vFLIP) plays a crucial role in promoting MEndT and the generation of M/E state cells. These results provide a new layer of evidence for MSCs being the cell source of KS spindle cells and reveal novel insight into KS pathogenesis and viral tumorigenesis.


title: Fitness costs of female choosiness in a socially monogamous songbird

abstract: Female mate choice is thought to be responsible for the evolution of many extravagant male ornaments and displays, but the costs of being too selective may hinder the evolution of choosiness. Selection against choosiness should be strongest in socially monogamous mating systems, because females may end up without a partner and forego reproduction, especially when many females prefer the same few partners (frequency-dependent selection). Here we quantify the fitness costs of having mating preferences that are difficult to satisfy. We capitalise on the recent discovery that female zebra finches (Taeniopygia guttata) prefer males of familiar song dialect. We measured female fitness in captive breeding colonies in which one third of females were given ample opportunity to choose a mate of their preferred dialect (two thirds of all males;  relaxed competition), while two thirds of the females had to compete over a limited pool of mates they preferred (one third of all males;  high competition). As expected, social pairings were strongly assortative with regard to song dialect. In the high-competition group, 26% of the females remained unpaired, yet they still obtained relatively high fitness by using brood parasitism as an alternative reproductive tactic. Another 31% of high-competition females paired disassortatively for song dialect. These females showed increased levels of extra-pair paternity, mostly with same-dialect males as sires, suggesting that preferences were not abolished after social pairing. However, females that paired disassortatively for song dialect did not have lower reproductive success. Overall, females in the high-competition group reached equal fitness as those that experienced relaxed competition. Our study suggests that alternative reproductive tactics such as egg dumping can help overcome the frequency-dependent costs of being highly selective in a monogamous mating system, thereby facilitating the evolution of female choosiness.


title: Population genomics of Pocillopora corals: insights from RAD-sequencing

abstract: Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.


title: Meta-imputation of transcriptome from genotypes across multiple datasets using summary-level data.

abstract:
Transcriptome wide association studies (TWAS) can be used as a powerful method to identify and interpret the underlying biological mechanisms behind GWAS by mapping gene expression levels with phenotypes. In TWAS, gene expression is often imputed from individual-level genotypes of regulatory variants identified from external resources, such as Genotype-Tissue Expression (GTEx) Project. In this setting, a straightforward approach to impute expression levels of a specific tissue is to use the model trained from the same tissue type. When multiple tissues are available for the same subjects, it has been demonstrated that training imputation models from multiple tissue types improves the accuracy because of shared eQTLs between the tissues and increase in effective sample size. However, existing joint-tissue methods require access of genotype and expression data across all tissues. Moreover, they cannot leverage the abundance of various expression datasets across various tissues for non-overlapping individuals.

Here, we explore the optimal way to combine imputed levels across training models from multiple tissues and datasets in a flexible manner using summary-level data. Our proposed method (SWAM) combines arbitrary number of transcriptome imputation models to linearly optimize the imputation accuracy given a target tissue. By integrating models across tissues and/or individuals, SWAM can improve the accuracy of transcriptome imputation or to improve power to TWAS without having to access each individual-level dataset. To evaluate the accuracy of SWAM, we combined 49 tissue-specific gene expression imputation models from the GTEx Project as well as from a large eQTL study of Depression Susceptibility Genes and Networks (DGN) Project and tested imputation accuracy in GEUVADIS lymphoblast cell lines samples. We also extend our meta-imputation method to meta-TWAS to leverage multiple tissues in TWAS analysis with summary-level statistics. Our results capitalize on the importance of integrating multiple tissues to unravel regulatory impacts of genetic variants on complex traits.

Author SummaryThe gene expression levels within a cell are affected by various factors, including DNA variation, cell type, cellular microenvironment, disease status, and other environmental factors surrounding the individual. The genetic component of gene expression is known to explain a substantial fraction of transcriptional variation among individuals and can be imputed from genotypes in a tissue-specific manner, by training from population-scale transcriptomic profiles designed to identify expression quantitative loci (eQTLs). Imputing gene expression levels is shown to help understand the genetic basis of human disease through Transcriptome-wide association analysis (TWAS) and Mendelian Randomization (MR).

However, it has been unclear how to integrate multiple imputation models trained from individual datasets to maximize their accuracy without having to access individual genotypes and expression levels that are often protected for privacy concerns. We developed SWAM (Smartly Weighted Averaging across Multiple datasets), a meta-imputation framework which can accurately impute gene expression levels from genotypes by integrating multiple imputation models without requiring individual-level data. Our method examines the similarity or differences between resources and borrowing information most relevant to the tissue of interest. We demonstrate that SWAM outperforms existing single-tissue and multi-tissue imputation models and continue to increase accuracy when integrating additional imputation models.

category: genomics


title: Population structure and association mapping for hundred seed weight in mungbean minicore

abstract: Mungbean is an important legume rich in protein and carbohydrates. It is cultivated mostly in south to south east Asia and east Africa. One of the important yield contributing traits in mungbean is 100 seed weight. Variation for this trait is available in the mungbean germplasm, and to facilitate improvement of this trait through breeding, genome-wide association mapping for 100 seed weight was carried out in the World Vegetable Center mungbean minicore collection. A total of 24,870 single nucleotide polymorphic markers were tested for association with 100 see weight in plants grown in Pakistan, Bangladesh, Myanmar and Taiwan and candidate loci associated with seed weight on chromosomes 1, 4, 6, 8 and 9 were identified. None of the QTLs was stable across all environments, but loci on chromosomes 4 and 8 were significant in Pakistan and Bangladesh and other loci on chromosome 8 were significantly associated in plants grown in Myanmar and Taiwan.


title: Pannexin 3 deletion reduces fat accumulation and inflammation in a sex-specific manner

abstract:
BackgroundPannexin 3 (PANX3), is a channel-forming glycoprotein that enables nutrient-induced inflammation in vitro, and genetic linkage data suggests it regulates body mass index. Here, we characterized inflammatory and metabolic parameters in global Panx3 knockout (KO) mice in the context of forced treadmill running (FEX) and high fat diet (HFD).

MethodsC57BL/6N (WT) and KO mice were randomized to either a FEX running protocol or no running (SED) from 24 until 30 weeks of age. Body weight was measured biweekly, and body composition was measured at 24 and 30 weeks of age. Male WT and KO mice were fed a HFD from 12 - 28 weeks of age. Metabolic organs were analyzed for a panel of inflammatory markers and PANX3 expression.

ResultsIn females there were no significant differences in body composition between genotypes, which could be due to the lack of PANX3 expression in female white adipose tissue, while male KOs fed a chow diet had lower body weight, and lower fat mass at 24 and 30 weeks of age, which was reduced to the same extent as 6 weeks of FEX in WT mice. Additionally, male KO mice exhibited significantly lower expression of multiple pro-inflammatory genes in white adipose tissue compared to WT mice. While on a HFD body weight differences were insignificant, in KO mice, multiple inflammatory genes were significantly differently expressed in quadriceps muscle and white adipose tissue resulting in a more anti-inflammatory phenotype compared to WT mice. The lower fat mass in male KO mice may be due to significantly fewer adipocytes in their subcutaneous fat compared to WT mice. Mechanistically, adipose stromal cells (ASCs) cultured from KO mice grow significantly slower than WT ASCs.

ConclusionPANX3 is expressed in male adult mouse adipose tissue and may regulate adipocyte numbers, influencing fat accumulation and inflammation.

category: physiology


title: Visualization of Arabidopsis root system architecture in 3D by refraction-contrast X-ray micro-computed tomography

abstract: Plant roots change their morphological traits in order to adapt themselves to different environmental conditions, resulting in alteration of the root system architecture. To understand this mechanism, it is essential to visualize morphology of the entire root system. To reveal effects of long-term alteration of gravity environment on root system development, we have performed an experiment in the International Space Station using Arabidopsis (Arabidopsis thaliana (L.) Heynh.) plants and obtained dried root systems grown in rockwool slabs (mineral wool substrate). X-ray computer tomography (CT) technique using an industrial X-ray scanner has been introduced for the purpose to visualize root system architecture of crop species grown in soil in 3D non-invasively. In the case of the present study, however, root system of Arabidopsis is composed of finer roots compared with typical crop plants and rockwool is also composed of fibers having similar dimension to that of the roots. A higher spatial resolution imaging method is required for distinguishing roots from rockwool. Therefore, in the present study, we tested refraction-contrast X-ray micro-CT using coherent X-ray optics available at the beamline BL20B2 of the synchrotron radiation facility SPring-8. Using this technique, both the primary and the secondary roots were successfully identified in the tomographic slices, clearly distinguished from the individual rockwool fibers and resulting in successful tracing of these roots from their basal regions. This newly-developed technique should contribute to elucidate the effect of microgravity on Arabidopsis root system architecture in space.

category: plant biology


title: Probing pathophysiology of extracellular cGAMP with substrate-selective ENPP1

abstract: The biology of the immune second messenger cGAMP depends on its cellular localization. cGAMP, which is synthesized in response to cytosolic double-stranded DNA, also exists in the extracellular space as a paracrine immunotransmitter that enhances the anticancer immune response. However, the role of extracellular cGAMP is unexplored outside of cancer due to a lack of tools to systemically manipulate it. The extracellular enzyme ENPP1, the only known hydrolase of cGAMP, is a promising target. However, because ENPP1 also degrades extracellular ATP, using genetic knockouts of ENPP1 to study extracellular cGAMP leads to confounding effects. Here we report the H362A point mutation in ENPP1, the dominant cGAMP hydrolase, which selectively abolishes ENPP1s ability to degrade cGAMP, while retaining activity toward other substrates. H362 is not necessary for binding cGAMP or the catalytically-essential zinc atoms but instead supports the in-line reaction geometry. H362 is evolutionarily conserved down to bacteria, suggesting an ancient origin for extracellular cGAMP biology. Enpp1H362A mice do not display the systemic calcification seen in Enpp1-/- mice, highlighting the substrate-specific phenotype of ENPP1. Remarkably, Enpp1H362A mice were resistant to HSV-1 infection, demonstrating the antiviral role of endogenous extracellular cGAMP. The ENPP1H362A mutation is the first genetic tool to enable exploration of extracellular cGAMP biology in a wide range of tissues and diseases.


title: Evaluation of genotoxic and cytogenetic effects of saponins and aluminum hydroxide adjuvant on viral vaccine

abstract: Bovine papillomavirus (BPV) is the etiological agent of bovine papillomatosis, infectious disease characterized by the presence of benign tumors that can progress to malignancy. The phylogenetic classification of the PVs is performed based on the sequence homology of the Open Reading Frame L1, the most conserved among different viral serotypes. Given the immunogenicity of saponins, it,s has been used as a candidate as adjuvant use. For this reason, the safety of using saponin as an adjuvant has to be better determined to human or veterinary vaccine use. So, this study aimed to evaluate the mutagenic and genotoxic effect of saponins in comparison with the adjuvant widely used aluminum hydroxide using an isolated and purified L1 protein from BPV as model. In this study, genomic lesions, which after processed without repair can result in mutations, were detected by comet assay. Possible damages to genetic material caused by structural chromosomal changes (clastogenesis), as well as chromosomal losses (aneugenesis) were evaluated by the micronucleus test. Both tests were done on polychromatic erythrocytes and Vero cells. The evaluation of apoptosis and necrosis of treated Vero cells was made by Annexin V / PI staining and flow cytometry. The two vaccine products (L1 +Saponin and L1 + Aluminum Hydroxide) showed damages compatible with the positive control in the comet assay and both slightly elevated the micronucleus levels, in the Cell Viability Assay the results with Aluminum Hydroxide were satisfactory, characterizing Aluminum Hydroxide as a safer adjuvant according to the proposed tests, better than the saponins. Some fractions of the saponin extract separated by High Performance Liquid Chromatography were evaluated against genotoxic activity by comet assay, and their identities were confirmed by similarity to the reference standard by mass spectrometry.


title: Capacity to erase gene occlusion is a defining feature distinguishing naive from primed pluripotency

abstract: Pluripotent stem cells can exist in either the naive state representing a developmental blank slate or the downstream primed state poised for differentiation. Currently, known differences between these two states are mostly phenomenological, and none can adequately explain why the two states should differ in developmental priming. Gene occlusion is a mode of epigenetic inactivation that renders genes unresponsive to their cognate transcriptional activators. It plays a crucial role in lineage restriction. Here, we report that a defining feature distinguishing the two pluripotent states lies in the ability of naive but not primed cells to erase occlusion. This "deocclusion" capacity requires Esrrb, a gene expressed only in the naive but not primed state. Notably, Esrrb silencing in the primed state is itself due to occlusion. Collectively, our data argue that the Esrrb-dependent deocclusion capacity in naive cells is key for sustaining naive pluripotency, and the loss of this capacity in the primed state via the occlusion of Esrrb poises cells for differentiation.


title: Volumetric alteration of olfactory bulb and immune-related molecular changes in olfactory epithelium in first episode psychosis patients

abstract:
BackgroundOlfactory dysfunction has been reproducibly reported in patients with psychosis, including first episode psychosis (FEP) patients. Consistently, structural abnormalities in the olfactory bulb (OB), a key region of the peripheral olfactory system, have also been reported in psychotic disorders. Meanwhile, air pollution and viral infections in the upper respiratory tract, including those of SARS-CoV-2, are reportedly risk factors for brain dysfunction and mental disorders. These risk factors can disturb the olfactory epithelium (OE) that is located adjacent to the OB and connected via direct neuronal projections. Nevertheless, it is unknown how a disturbance of the OE possibly affects the OB in the pathophysiological context of psychotic disorders.

MethodsWe examined the volume of the OB in FEP patients and healthy controls from 3 Tesla magnetic resonance imaging and molecular expression profiles of olfactory neuronal cells (ONCs) enriched from freshly biopsied OE.

ResultsWe observed a reduction of the OB volume in FEP patients compared with healthy controls. We also observed a significant alteration in gene expression profiles in the ONCs from FEP patients, supporting the pathological changes in the OE. Among such molecular changes, immune-related molecules and pathways were underscored in association with the OB volume changes in FEP patients.

ConclusionsOur data support the OB and OE pathologies in FEP patients. Immune-related molecular changes in the OE can biologically link adverse factors in the nasal cavity, such as air pollution and viral infection, with the OB structural change, both of which have been reported for psychotic disorders.


title: Monotreme middle ear is not primitive for Mammalia

abstract: The study on evolution of the mammalian middle ear has been fueled by continuous discoveries of Mesozoic fossils in the last two decades. Wang et al.1 recently reported a specimen of Vilevolodon diplomylos (IMMNH-PV01699)2 that adds to the increasing knowledge about the auditory apparatus of  haramiyidans, an extinct Mesozoic group of mammaliaforms. The authors hypothesized that a middle ear with a monotreme-like incus and malleus and incudomallear articulation was primitive for mammals, which challenges the convention that the monotreme middle ear is specialized3 or autapomorphic4 in mammals. We raise concerns about terminology and identification of the incus presented by Wang et al. and show that their analysis does not support their hypothesis; instead, it supports the one by Mao et al.5,6.

category: paleontology


title: Genetic network regulating visual acuity makes limited contribution to visually guided eye emmetropization

abstract:
During postnatal development, the eye undergoes a refinement process whereby optical defocus guides eye growth towards sharp vision in a process of emmetropization. Optical defocus activates a signaling cascade originating in the retina and propagating across the back of the eye to the sclera. Several observations suggest that visual acuity might be important for optical defocus detection and processing in the retina; however, direct experimental evidence supporting or refuting the role of visual acuity in refractive eye development is lacking. Here, we used genome-wide transcriptomics to determine the relative contribution of the retinal genetic network regulating visual acuity to the signaling cascade underlying visually guided eye emmetropization.

Our results provide evidence that visual acuity is regulated at the level of molecular signaling in the retina by an extensive genetic network. The genetic network regulating visual acuity makes relatively small contribution to the signaling cascade underlying refractive eye development. This genetic network primarily affects baseline refractive eye development and this influence is primarily facilitated by the biological processes related to melatonin signaling, nitric oxide signaling, phototransduction, synaptic transmission, and dopamine signaling. We also observed that the visual-acuity-related genes associated with the development of human myopia are chiefly involved in light perception and phototransduction. Our results suggest that the visual-acuity-related genetic network primarily contributes to the signaling underlying baseline refractive eye development, whereas its impact on visually guided eye emmetropization is modest.

category: systems biology


title: Cortical Surface-Informed Volumetric Spatial Smoothing of fMRI Data via Graph Signal Processing

abstract: Conventionally, as a preprocessing step, functional MRI (fMRI) data are spatially smoothed before further analysis, be it for activation mapping on task-based fMRI or functional connectivity analysis on resting-state fMRI data. When images are smoothed volumetrically, however, isotropic Gaussian kernels are generally used, which do not adapt to the underlying brain structure. Alternatively, cortical surface smoothing procedures provide the benefit of adapting the smoothing process to the underlying morphology, but require projecting volumetric data on to the surface. In this paper, leveraging principles from graph signal processing, we propose a volumetric spatial smoothing method that takes advantage of the gray-white and pial cortical surfaces, and as such, adapts the filtering process to the underlying morphological details at each point in the cortex.


title: Using spatially-explicit plant competition models to optimise crop productivity in intercropped systems

abstract: Intercropping, by capitalizing on positive biodiversity-productivity relationships, represents a promising option to increase agricultural sustainability. However, the complexity and context-dependency of plant-plant interactions can make it challenging for farmers to find suitable crop combinations. Furthermore, intercropping is usually implemented with standard inter-row spacing and plant densities based on monoculture practices, which might not be the ideal configuration to maximise yield. Therefore, here we present a spatially-explicit method based on plant ecological interaction models that allowed to optimize crop species combinations and spatial configurations for maximal yield in intercropped systems. We tested this method with three crop species, namely oat, lupin, and camelina. In a first step, field experiments in which crop density was varied provided us with indications on which species would compete more with each other. The results showed us that oat and camelina strongly competed with each other. In addition, the distance experiments allowed us to understand how the changes in yield associated with the presence of neighbours vary with distance. This allowed us to find the sets of parameters (identity of neighbours, sowing density, distances between individuals) that optimises intercrop yield (measured as Land Equivalent Ratio [LER]) for the three considered species. Specifically, we show that alternating rows of species led to higher LERs than a homogeneous species mixing. In addition, for each spatial configuration considered, we provide indications for the optimal inter- and intra-row distances and information about relative yield losses with suboptimal planting patterns. By modelling crop yield from simple and reproducible density and distance experiments, our results allow to optimize crop mixtures in terms of species combinations and spatial configurations.

category: ecology


title: Metabarcoding and ecological interaction networks for selecting candidate biological control agents

abstract:
O_LIClassical biological control can be used to decrease the density of invasive species to below an acceptable ecological and economic threshold. Natural enemies specific to the invasive species are selected from its native range and released into the invaded range. This approach has drawbacks, despite the performance of specificity tests to ensure its safety, because the fundamental host range defined under controlled conditions does not represent the actual host range in natura, and these tests omit indirect interactions within community.
C_LIO_LIWe focus on Sonchus oleraceus (Asteraceae), a weed species originating from Western Palearctic that is invasive worldwide and notably in Australia. We explore how analyses of interaction network within its native range can be used to 1) inventory herbivores associated to the target plant, 2) characterize their ecological host ranges, and 3) guide the selection of candidate biocontrol agents considering interactions with species from higher trophic levels. Arthropods were collected from plant community sympatric to S. oleraceus, in three bioclimatic regions, and interactions were inferred by a combination of molecular and morphological approaches.
C_LIO_LIThe networks reconstructed were structured in several trophic levels from basal species (diversified plant community), to intermediate and top species (herbivorous arthropods and their natural enemies). The subnetwork centered on S. oleraceus related interactions contained 116 taxa and 213 interactions. We identified 47 herbivores feeding on S. oleraceus, 15 of which were specific to the target species (i.e. Generality value equal to 1). Some discrepancies with respect to published findings or conventional specificity tests suggested possible insufficient sampling effort for the recording of interactions or the existence of cryptic species. Among potential candidate agents, 6 exhibited interactions with natural enemies.
C_LIO_LISynthesis and applications: Adopting a network approach as prerequisite step of the CBC program can provide a rapid screening of potential agents to be tested in priority. Once ecological host range defined, we suggest that priority should be given to agent predated by a minimum species, and, when they exist, to an agent that possesses enemies from the most distant taxonomical group from those occurring in the range of introduction.
C_LI


title: The gut parasite Nosema ceranae impairs olfactory learning in bumblebees

abstract: Pollinators are exposed to numerous parasites and pathogens when foraging on flowers. These biological stressors may affect critical cognitive abilities required for foraging. Here, we tested whether exposure to Nosema ceranae, one of the most widespread parasite of honey bees also found in wild pollinators, impacts cognition in bumblebees. We investigated different forms of olfactory learning and memory using conditioning of the proboscis extension reflex. Seven days after feeding parasite spores, bumblebees showed lower performance in absolute and differential learning, and reversal learning than controls. Long-term memory was also slightly reduced. The consistent effect of N. ceranae exposure across different types of olfactory learning indicates that its action was not specific to particular brain areas or neural processes. We discuss the potential mechanisms by which N. ceranae impairs bumblebee cognition and the broader consequences for populations of pollinators.


title: Changes in Iris Stiffness and Permeability in Primary Angle Closure Glaucoma

abstract:
PurposeTo evaluate the biomechanical properties of the iris by evaluating iris movement during pupil constriction and to compare such properties between healthy and primary angle-closure glaucoma (PACG) subjects.

MethodsA total of 140 subjects were recruited for this study. In a dark room, the anterior segments of one eye per subject were scanned using anterior segment optical coherence tomography (AS-OCT, SS-1000 CASIA, Tomey Corporation, Nagoya, Japan) imaging during induced pupil constriction with an external white light source of 1700 lux. Using a custom segmentation code, we automatically isolated the iris segments from the AS-OCT images, which were then discretized and transformed into a three-dimensional point cloud. For each iris, a finite element (FE) mesh was constructed from the point cloud, and an inverse FE simulation was performed to match the clinically observed iris constriction in the AS-OCT images. Through this optimization process, we were able to identify the elastic modulus and permeability of each iris.

ResultsFor all 140 subjects (95 healthy and 45 PACG of Indian/Chinese ethnicity, Age: 60.2{+/-}8.7 for PACG subjects and 57.7{+/-}10.1 for healthy subjects), the simulated deformation pattern of the iris during pupil constriction matched well with OCT images. We found that the iris stiffness was higher in PACG than in healthy controls (24.5{+/-}8.4 kPa vs 17.1{+/-}6.6 kPa with 40 kPa of active stress specified in the sphincter region; p < 0.001), whereas iris permeability was lower (0.41{+/-}0.2 mm2/kPa.s vs 0.55{+/-}0.2 mm2/kPa.s; p = 0.142).

ConclusionThis study suggests that the biomechanical properties of the iris in PACG are different from those in healthy controls. An improved understanding of the biomechanical behavior of the iris may have implications for the understanding and management of angle-closure glaucoma.

category: bioengineering


title: Biological mechanisms of aging predict age-related disease multimorbidities in patients

abstract: Genetic, environmental and pharmacological interventions into the aging process can confer resistance to a multiple age-related diseases in laboratory animals, including rhesus monkeys. These findings imply that mechanisms of aging might contribute to patterns of multimorbidity in humans, and hence could be targeted to prevent multiple conditions simultaneously. To address this question, we text mined 917,645 literature abstracts followed by manual curation, and found strong, non-random associations between age-related diseases and aging mechanisms, confirmed by gene set enrichment analysis of GWAS data. Integration of these associations with clinical data from 3.01 million patients showed that age-related diseases associated with each of five aging mechanisms were more likely than chance to be present together in patients. Genetic evidence revealed that innate and adaptive immunity, the intrinsic apoptotic signalling pathway and activity of the ERK1/2 pathway played a significant role across multiple aging mechanisms and multiple, diverse age-related diseases. Mechanisms of aging therefore contribute to multiple age-related diseases and to patterns of human age-related multimorbidity, and could potentially be targeted to prevent more than one age-related condition in the same patient.


title: Inferring Gene Regulatory Networks from Single Cell RNA-seq Temporal Snapshot Data Requires Higher Order Moments

abstract:
Single cell RNA-sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. To date, this aspiration remains unrealised due to technical- and computational challenges. In this work, we focus on the latter, which is under-represented in the literature.

We took a systemic approach by subdividing the GRN inference into three fundamental components: the data pre-processing, the feature extraction, and the inference. We saw that the regulatory signature is captured in the statistical moments of scRNA-seq data, and requires computationally intensive minimisation solvers to extract. Furthermore, current data pre-processing might not conserve these statistical moments.

Though our moment-based approach is a didactic tool for understanding the different compartments of GRN inference, this line of thinking-finding computationally feasible multi-dimensional statistics of data-is imperative for designing GRN inference methods.


title: BigBrainWarp: Toolbox for integration of BigBrain 3D histology with mutlimodal neuroimaging

abstract: AO_SCPLOWBSTRACTC_SCPLOWNeuroimaging stands to benefit from emerging ultrahigh-resolution histological atlases of the human brain; the first of which is "BigBrain". Ongoing research aims to characterise regional differentiation of cytoarchitecture with BigBrain and to optimise registration of BigBrain with standard neuroimaging templates. Together, this work paves the way for multi-scale investigations of brain organisation. However, working with BigBrain can present new challenges for neuroimagers, including dealing with cellular resolution neuroanatomy and complex transformation procedures. To simplify workflows and support adoption of best practices, we developed BigBrainWarp, a toolbox for integration of BigBrain with multimodal neuroimaging. The primary BigBrainWarp function wraps multiple state-of-the-art deformation matrices into one line of code, allowing users to easily map data between BigBrain and standard MRI spaces. Additionally, the toolbox contains ready-to-use cytoarchitectural features to improve accessibility of histological information. The present article discusses recent contributions to BigBrain-MRI integration and demonstrates the utility of BigBrainWarp for further investigations.


title: BigBrainWarp: Toolbox for integration of BigBrain 3D histology with multimodal neuroimaging


title: Can you affect me? The influence of vitality forms on action perception and motor response

abstract: During the interaction with others, action, speech, and touches can communicate positive, neutral, or negative attitudes. Offering an apple can be gentle or rude, a caress can be kind or rushed. These subtle aspects of social communication have been named vitality forms by Daniel Stern. Although they characterize all human interactions, to date it is not clear whether vitality forms expressed by an agent affect the action perception and the motor response of the receiver. To this purpose, we carried out a psychophysics study aiming to investigate how perceiving different vitality forms can influence cognitive and motor tasks performed by participants. In particular, participants were stimulated with requests made through a physical contact or vocally and conveying rude or gentle vitality forms, and then they were asked to estimate the end of a passing action observed in a monitor (action estimation task) or to perform an action in front of it (action execution task) with the intention to pass an object to the other person presented in the video. Results showed that the perception of different vitality forms influences both the estimated duration of the action and the motor response of participants, suggesting how these forms of communication can positively or negatively affect our behavior.


title: Functional architecture of neural circuits for leg proprioception in Drosophila

abstract: To effectively control their bodies, animals rely on feedback from proprioceptive mechanosensory neurons. In the Drosophila leg, different proprioceptor subtypes monitor joint position, movement direction, and vibration. Here, we investigate how these diverse sensory signals are integrated by central proprioceptive circuits. We find that signals for leg joint position and directional movement converge in second-order neurons, revealing pathways for local feedback control of leg posture. Distinct populations of second-order neurons integrate tibia vibration signals across pairs of legs, suggesting a role in detecting external substrate vibration. In each pathway, the flow of sensory information is dynamically gated and sculpted by inhibition. Overall, our results reveal parallel pathways for processing of internal and external mechanosensory signals, which we propose mediate feedback control of leg movement and vibration sensing, respectively. The existence of a functional connectivity map also provides a resource for interpreting connectomic reconstruction of neural circuits for leg proprioception.


title: Young Adults Recruit Similar Motor Modules Across Walking, Turning, and Chair Transfers

abstract:
Moving about in the world during daily life requires executing and successfully shifting between a variety of functional tasks, such as arising from a chair or bed, walking, turning, and navigating stairs, etc. Moreover, moving about during daily life requires not only navigating between different functional tasks but also performing these tasks in the presence of mental distractions. However, little is known about underlying neuromuscular control for executing and shifting between these different tasks. In this study, we investigated muscle coordination across walking, turning, and chair transfers by applying motor module (aka muscle synergy) analysis to the Timed-Up-and-Go (TUG) test with and without a secondary cognitive dual task. We found that healthy young adults recruit a small set of common motor modules across the subtasks of the TUG test and that their composition is robust to cognitive distraction. Instead, cognitive distraction impacted motor module activation timings such that they became more consistent. This work is the first to demonstrate motor module generalization across multiple tasks that are both functionally different and crucial for healthy mobility. Overall, our results suggest that the central nervous system may draw from a "library" of modular control strategies to navigate the variety of movements and cognitive demands required of daily life.

New & NoteworthyWe demonstrated that healthy young adults recruit a small set of motor modules across subtasks of the Timed-Up-and-Go test (i.e., walking, turning, and chair transfers). Moreover, we showed that motor module composition, but not activation timing, is robust to cognitive distractions. These results support the hypothesis that healthy young adults recruit from a "library" of motor modules and modulate their activation timing to meet the different mechanical and cognitive demands required to navigate daily life.


title: Autonomic arousals contribute to brain fluid pulsations during sleep

abstract:
During sleep, slow waves of neuro-electrical activity engulf the human brain and aid in the consolidation of memories. Recent research suggests that these slow waves may also promote brain health by facilitating the removal of metabolic waste, possibly by orchestrating the pulsatile flow of cerebro-spinal fluid (CSF) through local neural control over vascular tone. To investigate the role of slow waves in the generation of CSF pulsations, we analyzed functional MRI data obtained across the full sleep-wake cycle and during a respiratory task during wakefulness. This revealed a novel generating mechanism that relies on the autonomic regulation of cerebral vascular tone without requiring slow electrocortical activity or even sleep. Therefore, the role of CSF pulsations in brain waste clearance may, in part, depend on proper autoregulatory control of cerebral blood flow.

One-Sentence SummaryAutonomic regulation of cerebral vascular tone mediates CSF flow and may contribute to brain waste clearance.


title: Cellular Bases of Olfactory Circuit Assembly Revealed by Systematic Time-lapse Imaging

abstract: Neural circuit assembly features simultaneous targeting of numerous neuronal processes from constituent neuron types, yet the dynamics is poorly understood. Here, we use the Drosophila olfactory circuit to investigate dynamic cellular processes by which olfactory receptor neurons (ORNs) target axons precisely to specific glomeruli in the ipsi- and contralateral antennal lobes. Time-lapse imaging of individual axons from 28 ORN types revealed a rich diversity in extension speed, innervation timing, and ipsilateral branch locations, and identified that ipsilateral targeting occurs via stabilization of transient interstitial branches. Fast imaging using adaptive optics- corrected lattice light-sheet microscopy showed that upon approaching target, many ORN types exhibit "exploring branches" consisted of parallel microtubule-based terminal branches emanating from an F-actin-rich hub. Antennal nerve ablations uncovered essential roles for bilateral interactions in contralateral target selection, and for ORN axons to facilitate dendritic refinement of postsynaptic partner neurons. Altogether, these observations provide cellular bases for wiring specificity establishment.


title: A Discriminative Characterization of Heschl's Gyrus Morphology using Spectral Graph Features

abstract: Heschls Gyrus (HG), which hosts the primary auditory cortex, exhibits large variability not only in size but also in its gyrification patterns, within (i.e., between hemispheres) and between individuals. Conventional structural measures such as volume, surface area and thickness do not capture the full morphological complexity of HG, in particular, with regards to its shape. We present a method for characterizing the morphology of HG in terms of Laplacian eigenmodes of surface-based and volume-based graph representations of its structure, and derive a set of spectral graph features that can be used to discriminate HG subtypes. We applied this method to a dataset of 177 adults previously shown to display considerable variability in the shape of their HG, including data from amateur and professional musicians, as well as non-musicians. Results show the superiority of the proposed spectral graph features over conventional ones in differentiating HG subtypes, in particular, single HG versus Common Stem Duplications (CSDs). We anticipate the proposed shape features to be found beneficial in the domains of language, music and associated pathologies, in which variability of HG morphology has previously been established.


title: Strategic infarct locations for post-stroke depressive symptoms: a lesion- and disconnection-symptom mapping study

abstract:
BackgroundDepression is the most common neuropsychiatric complication after stroke. Infarct location is associated with post-stroke depressive symptoms (PSDS), but it remains debated which brain structures are critically involved. We performed a large-scale lesion-symptom mapping study to identify infarct locations, and white matter disconnections, associated with PSDS.

MethodsWe included 553 patients (age 69{+/-}11 years, 42% female) with acute ischemic stroke. PSDS were measured using the 30-item Geriatric Depression Scale (GDS-30). Multivariable support vector regression (SVR)-based analyses were performed both at the level of individual voxels (SVR-VLSM) and predefined regions of interest (SVR-ROI) to relate infarct location to PSDS. We externally validated our findings in an independent stroke cohort (N=459). Finally, disconnectome-based analyses were performed using SVR-VLSM, in which white matter fibers disconnected by the infarct were analyzed instead of the infarct itself. Results: Infarcts in the right amygdala, right hippocampus and right pallidum were consistently associated with PSDS (permutation-based p<0.05) in SVR-VLSM and SVR-ROI. External validation (N=459) confirmed the association between infarcts in the right amygdala and pallidum, but not the right hippocampus, and PSDS. Disconnectome-based analyses revealed that disconnections in the right parahippocampal white matter, right thalamus and pallidum, and right anterior thalamic radiation were significantly associated (permutation-based p<0.05) with PSDS.

ConclusionsInfarcts in the right amygdala and pallidum, and disconnections of right limbic and frontal cortico-basal ganglia-thalamic circuits, are associated with PSDS. Our findings provide a comprehensive and integrative picture of strategic infarct locations for PSDS, and shed new light on pathophysiological mechanisms of depression after stroke.


title: Local rather than global H3K27me3 dynamics associates with differential gene expression in Verticillium dahliae

abstract: Differential growth conditions typically trigger global transcriptional responses in filamentous fungi. Such fungal responses to environmental cues involve epigenetic regulation, including chemical histone modifications. It has been proposed that conditionally expressed genes, such as those that encode secondary metabolites but also effectors in pathogenic species, are often associated with a specific histone modification, lysine27 methylation of H3 (H3K27me3). However, thus far no analyses on the global H3K27me3 profiles have been reported under differential growth conditions in order to assess if H3K27me3 dynamics governs differential transcriptional. Using ChIP- and RNA-sequencing data from the plant pathogenic fungus Verticillium dahliae grown in three in vitro cultivation media, we now show that a substantial number of the identified H3K27me3 domains globally display stable profiles among these growth conditions. However, we do observe local quantitative differences in H3K27me3 ChIP-seq signal that associate with a subset of differentially transcribed genes between media. Comparing the in vitro results to expression during plant infection suggests that in planta-induced genes may require chromatin remodelling to achieve expression. Overall, our results demonstrate that some loci display H3K27me3 dynamics associated with concomitant transcriptional variation, but many differentially expressed genes are associated with stable H3K27me3 domains. Thus, we conclude that while H3K27me3 is required for transcriptional repression, it does not appear that transcriptional activation requires global erasure of H3K27me3. We propose that the H3K27me3 domains that do not undergo dynamic methylation may contribute to transcription through other mechanisms or may serve additional genomic regulatory functions.

category: microbiology


title: Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions

abstract:
The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that "naturalized" populations of E. faecalis exist in the extraenteric environment in a viable but not culturable (VBNC) state. The extent to which these naturalized or VBNC E. faecalis can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and qPCR counts. However, the enteric isolates exhibited a spike in rRNA:rDNA ratios between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential expression of genes thought to be related to habitat adaptation in the accompanying mesocosm metatranscriptomes when compared between environmental and enteric isolates. Overall, our results provide novel information on how rRNA levels may vary over different metabolic states (i.e., alive vs. VBNC) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring.

IMPORTANCEEnterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, some species within this group can enter an inactive, viable but not culturable (VBNC) state that make it difficult to accurately quantify during routine monitoring. Furthermore, lower-risk, environmental enterococci strains may also confound water quality estimates. We developed an rRNA:rDNA viability assay for E. faecalis (a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested here; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher risk) fecal pollution because rRNA levels significantly decreased after one week in all isolates.


title: The human innate immune protein calprotectin elicits a multi-metal starvation response in Pseudomonas aeruginosa

abstract:
To combat infections, the mammalian host limits availability of essential transition metals such as iron (Fe), zinc (Zn), and manganese (Mn) in a strategy termed "nutritional immunity". The innate immune protein calprotectin (CP) contributes to nutritional immunity by sequestering these metals to exert antimicrobial activity against a broad range of microbial pathogens. One such pathogen is Pseudomonas aeruginosa, which causes opportunistic infections in vulnerable populations including individuals with cystic fibrosis. CP was previously shown to withhold Fe(II) and Zn(II) from P. aeruginosa and induce Fe- and Zn-starvation responses in this pathogen. In this work, we performed quantitative, label-free proteomics to further elucidate how CP impacts metal homeostasis pathways in P. aeruginosa. We report that CP induces an incomplete Fe-starvation response, as many Fe-containing proteins that are repressed by Fe limitation are not affected by CP treatment. The Zn-starvation response elicited by CP seems to be more complete than the Fe-starvation response and includes increases in Zn transporters and Zn-independent proteins. CP also induces the expression of membrane-modifying proteins, and metal-depletion studies indicate this response results from the sequestration of multiple metals. Moreover, the increased expression of membrane-modifying enzymes upon CP treatment correlates with increased resistance to polymyxin B. Thus, response of P. aeruginosa to CP treatment includes both single and multi-metal starvation responses and includes many factors related to virulence potential, broadening our understanding of this pathogens interaction with the host.

ImportanceTransition metals are critical for growth and infection by all pathogens, and the innate immune system withholds these metals from pathogens to limit their growth in a strategy termed "nutritional immunity". While multi-metal depletion by the host is appreciated, the majority of metal depletion studies have focused on individual metald. Here we use the innate immune protein calprotectin (CP), which complexes with several metals including iron (Fe), zinc (Zn), and manganese (Mn), and the opportunistic pathogen Pseudomonas aeruginosa to investigate multi-metal starvation. Using an unbiased label-free proteomics response, we demonstrate that multi-metal withholding by CP induces a regulatory response that is not merely additive of individual metal starvation responses, including the induction of Lipid A modification enzymes.


title: Combined effect of cell geometry and polarity domains determines the orientation of unequal division

abstract:
Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s).

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/442692v1_ufig1.gif" ALT="Figure 1">
View larger version (75K):
org.highwire.dtl.DTLVardef@4b0e87org.highwire.dtl.DTLVardef@1a6fdbdorg.highwire.dtl.DTLVardef@5ca0ddorg.highwire.dtl.DTLVardef@1450e61_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightO_LISpindle tilting in anisotropic cell shape induces unequal cell division
C_LIO_LICortical polarity domain can exert attractive or repulsive effect on spindle
C_LIO_LICell geometry and polarity domain cooperate to position the spindle
C_LIO_LICell geometry modulates the effect of polarity domain
C_LI


title: Hierarchical Bayesian Model for Estimating Migratory Bird Harvest in Canada

abstract: The Canadian Wildlife Service (CWS) requires reliable estimates of the harvest of migratory game birds, including waterfowl, to effectively manage populations of these hunted species. The National Harvest Survey is an annual survey of hunters who purchase Canadas mandatory migratory game bird hunting permit, integrating information from a survey of hunting activity with information from a separate survey of species composition in the harvest. We use these survey data to estimate the number of birds harvested for each species, as well as hunting activity metrics such as the number of active hunters and days spent hunting. The analytical methods used to generate these estimates have not changed since the survey was first designed in the early 1970s. Here we describe a new hierarchical Bayesian integrated model, which replaces the series of ratio estimators that comprised the old model. We are now using this new model to generate estimates for migratory bird harvests as of the 2019-2020 hunting season, and to generate updated estimates for all earlier years. The hierarchical Bayesian model uses over-dispersed Poisson distributions to model mean hunter activity and harvest (zero inflated Poisson and zero truncated Poisson, respectively). It also includes multinomial distributions to model some key components including, variation in total harvest across periods of the hunting season, the species composition of the harvest within each of those periods, and the age and sex composition in the harvests of a given species. We estimated the parameters of the Poisson and the multinomial distributions for each year as random effects using first-difference time-series. This time-series component allows the model to share information across years and reduces the sensitivity of the estimates to annual sampling noise. The new model estimates are generally very similar to those from the old model, particularly for the species that occur most commonly in the harvest, and so the results do not suggest any major changes to harvest management decisions and regulations. However, estimates for all species from the new model are more precise and less susceptible to annual sampling error, particularly for species that occur less commonly in the harvest (e.g., sea ducks and other species of conservation concern). This new model, with its hierarchical Bayesian framework, will also facilitate future improvements and elaborations, allowing the incorporation of prior information from the rich literature and knowledge in game bird management and biology.


title: Hierarchical Bayesian Integrated Model for Estimating Migratory Bird Harvest in Canada


title: Cross-fitted instrument: a blueprint for one-sample Mendelian Randomization

abstract:
Bias from weak instruments may undermine the ability to estimate causal effects in instrumental variable regression (IVR). We present here a simple solution for handling weak instrument bias by introducing a new type of instrumental variable called  cross-fitted instrument (CFI). CFI splits the data at random and estimates the impact of the instrument on the exposure in each partition. The estimates are then used to perform an IVR on each partition. We adapt CFI to Mendelian randomization (MR) and term this adaptation  Cross-Fitting for Mendelian Randomization (CFMR). A major advantage of CFMR is its use of all the available data to select genetic instruments, as opposed to traditional two-sample MR where a large part of the data is only used for instrument selection. Consequently, CFMR has the potential to enhance the power of MR in a meta-analysis setting by enabling an unbiased one-sample MR to be performed in each cohort prior to meta-analyzing the results across all the cohorts. In a similar fashion, CFMR enables a cross-ethnic MR analysis by accounting for ethnic heterogeneity, which is particularly important in consortia-led meta-analyses where the participating cohorts might be of different ethnicities. To our knowledge, there are currently no MR approach that can account for such heterogeneity. Finally, CFMR enables the application of MR to exposures that are rare or difficult to measure, which would normally preclude their analysis in the regular two-sample MR setting.

Key messagesO_LIWe develop a new method to enable an unbiased one-sample Mendelian Randomization.
C_LIO_LIThe new method provides the same power as the standard two-sample Mendelian Randomization approach and does not require summary statistics from a genome-wide association study in an independent cohort.
C_LIO_LIOur approach enables a cross-ethnic instrumental variable regression to account for heterogeneity in a sample consisting of multiple ethnicities.
C_LI


title: Explainable Sleep Stage Classification with Multimodal Electrophysiology Time-series

abstract: Many automated sleep staging studies have used deep learning approaches, and a growing number have used multimodal data to improve their classification performance. However, few studies using multimodal data have provided model explainability. Some have used traditional ablation approaches that "zero out" a modality. However, the samples that result from this ablation are unlikely to be found in real electroencephalography (EEG) data, which could adversely affect the importance estimates that result. Here, we train a convolutional neural network for sleep stage classification with EEG, electrooculograms (EOG), and electromyograms (EMG) and propose an ablation approach that replaces each modality with values that approximate the line-related noise commonly found in electrophysiology data. The relative importance that we identify for each modality is consistent with sleep staging guidelines, with EEG being important for most sleep stages and EOG being important for Rapid Eye Movement (REM) and nonREM stages. EMG showed low relative importance across classes. A comparison of our approach with a "zero out" ablation approach indicates that while the importance results are consistent for the most part, our method accentuates the importance of modalities to the model for the classification of some stages like REM (p < 0.05). These results suggest that a careful, domain-specific selection of an ablation approach may provide a clearer indicator of modality importance. Further, this study provides guidance for future research on using explainability methods with multimodal electrophysiology data.


title: Convergence Assessment for Bayesian Phylogenetic Analysis using MCMC simulation

abstract:
O_LIPosterior distributions are commonly approximated by samples produced from a Markov chain Monte Carlo (MCMC) simulation. Every MCMC simulation has to be checked for convergence, i.e., that sufficiently many samples have been obtained and that these samples indeed represent the true posterior distribution.
C_LIO_LIHere we develop and test different approaches for convergence assessment in phylogenetics. We analytically derive a threshold for a minimum effective sample size (ESS) of 625. We observe that only the initial sequence estimator provides robust ESS estimates for common types of MCMC simulations (autocorrelated samples, adaptive MCMC, Metropolis-Coupled MCMC). We show that standard ESS computation can be applied to phylogenetic trees if the tree samples are converted into traces of absence/presence of splits.
C_LIO_LIConvergence in distribution between replicated MCMC runs can be assessed with the Kolmogorov-Smirnov test. The commonly used potential scale reduction factor (PSRF) is biased when applied to skewed posterior distribution. Additionally, we analytically derive the expected difference between split frequencies (EDSF) and show that it depends on the true frequency of a split. Hence, the average standard deviation of split frequencies is too simplistic and the EDSF should be used instead to check for convergence in split frequencies.
C_LIO_LIWe implemented the methods described here in the open-source R package Convenience (https://github.com/lfabreti/convenience), which allows users to easily test for convergence using output from standard phylogenetic inference software.
C_LI


title: Rpl24Bst mutation suppresses colorectal cancer by promoting eEF2 phosphorylation via eEF2K

abstract: Increased protein synthesis supports the rapid proliferation associated with cancer. The Rpl24Bst mutant mouse reduces the expression of the ribosomal protein RPL24 and has been used to suppress translation and limit tumorigenesis in multiple mouse models of cancer. Here we show that Rpl24Bst also suppresses tumorigenesis and proliferation in a model of colorectal cancer with two common patient mutations, Apc and Kras. In contrast to previous reports, Rpl24Bst mutation has no effect on ribosomal subunit abundance but suppresses translation elongation through phosphorylation of eEF2, reducing protein synthesis by 40% in tumour cells. Ablating eEF2 phosphorylation in Rpl24Bst mutant mice by inactivating its kinase, eEF2K, completely restores the rates of elongation and protein synthesis. Furthermore, eEF2K activity is required for the Rpl24Bst mutant to suppress tumorigenesis. This work demonstrates that elevation of eEF2 phosphorylation is an effective means to suppress colorectal tumorigenesis with two driver mutations. This positions translation elongation as a therapeutic target in colorectal cancer, as well as other cancers where the Rpl24Bst mutation has a tumour suppressive effect in mouse models.


title: Electronic nicotine delivery systems exhibit reduced bronchial epithelial cells toxicity compared to cigarette: The Replica Project

abstract: Cigarette smoking is the leading cause of preventable deaths worldwide. Electronic Nicotine Delivery Systems (ENDS) may reduce health risks associated with chronic exposure to smoke and their potential benefits have been the matter of intense scientific debate. Here we replicated three key published studies from the Tobacco Industry on cytotoxic and inflammatory effects of cigarette smoke and ENDS aerosol in an independent multicentric study. We aimed to establish the reliability of results and the robustness of conclusions by replicating the authors experimental protocols and further validating them with different techniques. We exposed human bronchial epithelial cell (NCI-H292) to cigarette smoke and to aerosol from ENDS. All the exposure were conducted at air-liquid interface to assess cytotoxicity effects of smoke and aerosol. Moreover, we aimed to assess different inflammatory mediators release (IL-6, IL-8 and MMP-1) from cells exposed to whole smoke and to smoke without particulate matter (vapor phase). We were able to replicate the results obtained in the original studies on cytotoxicity confirming that almost 80% of the cytotoxic effect of smoke is due to the vapor phase of smoke. Moreover, our results substantiated the reduced cytotoxic effects of ENDS aerosol in respect to cigarette smoke. However, our data are significantly different from the original ones in terms of inflammatory and remodeling activity triggered by smoke. Taken all together, the data obtained independently in different laboratories clearly demonstrate the reduced toxicity of ENDS products compared to cigarettes and thus providing a valuable tool to the harm reduction strategies in smokers.

category: pharmacology and toxicology


title: A Bivalent Chromatin Controls Timing of Expression of Camalexin Biosynthesis Genes in Response to a Pathogen Signal in Arabidopsis

abstract: Temporal dynamics of gene expression underpins the responses to internal and environmental stimuli. In eukaryotes, regulation of gene induction includes changing chromatin states at the target genes, and recruitment of the transcriptional machinery that includes transcription factors. As one of the most potent specialized metabolites in Arabidopsis thaliana, camalexin can be rapidly induced by bacterial and fungal infections. Though several transcription factors controlling camalexin biosynthesis genes have been characterized, it remains unknown how the rapid activation of genes in this pathway upon a pathogen signal happens. By combining publicly available epigenomic data with in vivo chromatin mapping, we found that camalexin biosynthesis genes are marked with two epigenetic modifications with opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation), to form a bivalent chromatin. Mutants with reduced H3K27m3 or H3K18ac showed that both modifications were required to determine the timing of gene expression and metabolite accumulation at an early stage of the stress response. Our study indicates that this type of bivalent chromatin, which we name a kairostat, plays an important role controlling the timely induction of gene expression upon stimuli in plants.


title: Cell-type-specific silence in thalamocortical circuits precedes hippocampal sharp-wave ripples.

abstract: Memory consolidation requires the encoding of neocortical memory traces, which is thought to occur during hippocampal oscillations called sharp-wave ripples (SWR). Evidence suggests that the hippocampus communicates memory-related neural patterns across distributed cortical circuits via its major output pathways. Here, we sought to understand how this information is processed in the retrosplenial cortex (RSC), a primary target circuit. Using patch-clamp recordings from mice during quiet wakefulness, we found that SWR-aligned synaptic modulation is widespread but weak, and that spiking responses are sparse. However, using cell type and projection-specific two-photon calcium imaging and optogenetics, we show that, starting 1-2 seconds before SWR, superficial inhibition in RSC is reduced, along with thalamocortical input. We propose that pyramidal dendrites experience a period of decreased local inhibition and subcortical interference in a seconds-long time window preceding hippocampal SWR. This may aid communication of weak and sparse SWR-aligned excitation between the hippocampus and neocortex, and promote the selective strengthening of memory-related connections.


title: Binding the acoustic features of an auditory source through temporal coherence

abstract: Numerous studies have suggested that the perception of a target sound source can only be segregated from a complex acoustic background if the acoustic features underlying its perceptual attributes (e.g., pitch, location, and timbre) induce temporally modulated responses that are mutually correlated, and that are uncorrelated from those of other sources in the mixture. This "temporal coherence" hypothesis asserts that listening attentively to one or a subset of attributes of a target source enhances their neural responses and concomitantly enhances all other coherent responses, thus binding them together while simultaneously suppressing the incoherent responses to the background features. Here we report on EEG measurements in human subjects engaged in various sound segregation tasks that demonstrate rapid binding among the temporally coherent features of the attended source regardless of their identity, harmonic relationship, or frequency separation, thus confirming the key role temporal coherence plays in the organization of auditory scenes.


title: Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making

abstract: Optimality analysis of value-based decisions in binary and multi-alternative choice settings predicts that reaction times should be sensitive only to differences in stimulus magnitudes, but not to overall absolute stimulus magnitude. Yet experimental work in the binary case has shown magnitude sensitive reaction times, and theory shows that this can be explained by switching from linear to geometric time costs, but also by nonlinear subjective utility. Thus disentangling explanations for observed magnitude sensitive reaction times is difficult. Here for the first time we extend the theoretical analysis of geometric time-discounting to ternary choices, and present novel experimental evidence for magnitude-sensitivity in such decisions, in both humans and slime moulds. We consider the optimal policies for all possible combinations of linear and geometric time costs, and linear and nonlinear utility; interestingly, geometric discounting emerges as the predominant explanation for magnitude sensitivity.


title: Metamodal Coupling of Vibrotactile and Auditory Speech Processing Systems Through Matched Stimulus Representations

abstract: It has been postulated that the brain is organized by "metamodal", sensory-independent cortical modules implementing particular computations, leading to the intriguing hypothesis that brain areas can perform tasks (such as word recognition) not just in "standard" sensory modalities but also in novel sensory modalities. Yet, evidence for this theory, especially in neurotypical subjects, has been variable. We hypothesized that effective metamodal engagement of a brain area requires congruence between the novel and standard sensory modalities not only at the task level (e.g., "word recognition") but critically also a match at the algorithmic level (in Marrs terminology), i.e., at the level of neural representation of the information of interest. To test this hypothesis, we trained participants to recognize vibrotactile versions of auditory words using two encoding schemes. The vocoded approach preserved the dynamics and representational similarities of auditory speech while the token-based approach used an abstract phoneme-based code. Although both groups learned the vibrotactile word recognition task, only in the vocoded group did trained vibrotactile stimuli recruit the auditory speech network and lead to increased coupling between somatosensory and auditory speech areas. In contrast, the token-based encoding appeared to rely on paired-associate learning. Thus, matching neural input representations is a critical factor for assessing and leveraging the metamodal potential of cortical modules.