title: miRNAs Copy Number Variations repertoire as hallmark indicator of cancer species predisposition

abstract: Aging is one of the hallmarks of multiple human diseases, including cancer. However, the molecular mechanisms associated with high longevity and low cancer incidence percentages characterizing long-living organisms have not been fully understood yet. In this context, we hypothesized that variations in the number of copies (CNVs) of specific genes may protect some species from cancer onset. Based on the statistical comparison of gene copy numbers within the genomes of cancer -prone and -resistant organisms, we identified novel gene targets linked to the tumor predisposition of a species, such as CD52, SAT1 and SUMO protein family members. Furthermore, for the first time, we were able to discover that, considering the entire genome copy number landscape of a species, microRNAs (miRNAs) are among the most significant gene families enriched for cancer progression and predisposition. However, their roles in ageing and cancer resistance from a comparative perspective remains largely unknown. To this end, we identified through bioinformatics analysis, several alterations in miRNAs copy number patterns, represented by duplication of miR-221, miR-222, miR-21, miR-372, miR-30b, miR-30d and miR-31 among others. Therefore, our analysis provides the first evidence that an altered copy number miRNAs signature is able to statistically discriminate species more susceptible to cancer than those that are tumor resistant, helping researchers to discover new possible therapeutic targets involved in tumor predisposition.


title: rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation

abstract:
Knowledge-based statistical potentials have been shown to be rather effective in protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical potentials have been developed for RNA 3D structure evaluation, while their performances are either still at low level for the test datasets from structure prediction models or dependent on the "black-box" process through neural networks. In this work, we have developed an all-atom distance-dependent statistical potential based on residue separation for RNA 3D structure evaluation, namely rsRNASP, which is composed of short- and long-ranged potentials distinguished by residue separation. The extensive examinations against available RNA test datasets show that, rsRNASP has apparently higher performance than the existing statistical potentials for the realistic test datasets with large RNAs from structure prediction models including the newly released RNA-Puzzles dataset, and is comparable to the existing top statistical potentials for the test datasets with small RNAs or near-native decoys. Additionally, rsRNASP is also superior to RNA3DCNN, a recently developed scoring function through 3D convolutional neural networks. rsRNASP and the relevant databases are available at website https://github.com/Tan-group/rsRNASP.

SIGNIFICANCERNAs play crucial roles in catalyzing biochemical reactions and regulating gene expression, and the biological functions of RNAs are generally coupled to their structures. Complementary to experiments, developing computational models to predict RNA 3D structures can be very helpful for understanding RNA biology functions. For a computational model, a reliable energy function is essentially important either for guiding conformational folding or for structure evaluation. For this purpose, we developed a residue-separation-based distance-dependent statistical potential, named rsRNASP which distinguishes the short- and long-ranged interactions, for RNA 3D structure evaluation. Our rsRNASP were examined against extensive test sets and shows overall superior performance over existing top traditional statistical potentials and a recently developed scoring function through 3D convolutional neural networks, especially for realistic test set from various computational structure prediction models.

category: bioinformatics


title: Radial-axial transport coordination enhances sugar translocation in the phloem vasculature of plants

abstract:
Mass transport of photosynthates in the phloem of plants is necessary for describing plant carbon allocation, productivity, and responses to water and thermal stress. Several hypotheses about optimization of phloem structure and function and limitations of phloem transport under drought have been proposed, and tested with models and anatomical data. However, the true impact of radial water exchange of phloem conduits with their surroundings on mass transport of photosynthates has not been addressed. Here, the physics of the Munch mechanism of sugar transport is re-evaluated to include local variations in viscosity resulting from the radial water exchange in two dimensions (axial and radial). Model results show that radial water exchange pushes sucrose away from conduit walls thereby reducing wall frictional stress due to a decrease in sap viscosity and an increase in sugar concentration in the central region of the conduit. These two co-occurring effects lead to increased sugar front speed and axial mass transport across a wide range of phloem conduit lengths. Thus, sugar transport operates more efficiently than predicted by previous models that ignore these two effects. A faster front speed leads to higher phloem resiliency under drought because more sugar can be transported with a smaller pressure gradient.

SummaryThe overall speed of sap increased by including a concentrationdependent viscosity in axial and radial directions.

category: biophysics


title: Lactoferricins access the cytosol of Escherichia coli within few seconds

abstract: We report the real-time response of E. coli to lactoferricin-derived antimicrobial peptides (AMPs) on length-scales bridging microscopic cell-sizes to nanoscopic lipid packing using millisecond time-resolved synchrotron small-angle X-ray scattering. Coupling a multi-scale scattering data analysis to biophysical assays for peptide partitioning revealed that the AMPs rapidly saturate the bacterial envelope and reach the cytosol within less than three seconds--much faster than previously considered. Final cytosolic AMP concentrations of ~ 100 mM suggest an efficient shut-down of metabolism as primary cause for bacterial killing. On the other hand, the damage of the cell envelope is a collateral effect of AMP activity that does not kill the bacteria. This implies that the impairment of the membrane barrier is a necessary but not sufficient condition for microbial killing by lactoferricins. The most efficient AMP studied exceeds others in both speed of reaching cytoplasm and lowest cytosolic peptide concentration.


title: Mechanical characterisation of the developing cell wall layers of tension wood fibres by Atomic Force Microscopy

abstract:
Trees can generate large mechanical stresses at the stem periphery to control the orientation of their axes. This key factor in the biomechanical design of trees, named "maturation stress", occurs in wood fibres during cellular maturation when their secondary cell wall thickens. In this study, the spatial and temporal stiffening kinetics of the different cell wall layers were recorded during fibre maturation on a sample of poplar tension wood using atomic force microscopy. The thickening of the different layers was also recorded. The stiffening of the CML, S1 and S2-layers was initially synchronous with the thickening of the S2 layer and continued a little after the S2-layer reached its final thickness as the G-layer begins to develop. In contrast, the global stiffness of the G-layer, which initially increased with its thickening, was almost stable long before it reached its final maximum thickness. A limited radial gradient of stiffness was observed in the G-layer, but it decreased sharply on the lumen side, where the new sub-layers are deposited during cell wall thickening. Although very similar at the ultrastructural and biochemical levels, the stiffening kinetics of the poplar G-layer appears to be very different from that described in maturing bast fibres.

HighlightNew insights into the changes in mechanical properties within the cell wall of poplar tension wood fibres during maturation have been obtained using atomic force microscopy.


title: Kin discrimination modifies fitness, spatial segregation and matrix sharing between strains with low relatedness in Bacillus subtilis biofilms

abstract:
Microorganisms in nature form multicellular groups called biofilms. In biofilms bacteria embedded in a matrix of extracellular polymeric substances (EPS) interact intensely, due to their proximity to each other. Most studies have investigated genetically homogeneous biofilms, leaving a gap in knowledge on genetically heterogeneous biofilms. Recent insights show that a Gram-positive model bacterium, Bacillus subtilis, discriminates between strains of high (kin) and low (non-kin) phylogenetic relatedness, reflected in merging (kin) and boundaries (non-kin) between swarms. However, it is not clear how kinship between interacting strains affects their fitness, the genotype distribution, and the EPS sharing in floating biofilms (pellicles). To address this gap in knowledge we cultivate B. subtilis strains as mixtures of kin and non-kin strains in static cultures, allowing them to form pellicles. We show here that in non-kin pellicles only one strains fitness was reduced; at the same time, strains segregated into larger patches and exhibited decreased matrix sharing, as compared to kin and isogenic pellicles, in which both strains had comparable colony forming units (CFU) counts and more homogenous cell mixing. Overall, our results emphasize kin discrimination (KD) as a social behavior that shapes fitness, spatial segregation and sharing of the extracellular matrix in genetically heterogenous biofilms of B. subtilis.

IMPORTANCEBiofilm communities have both beneficial and harmful effects on human societies in natural, medical and industrial environments. Bacillus subtilis, a Gram-positive and biotechnologically important bacterium, serves as a model for studying biofilms. Recent studies have shown that this species engages in kin discriminatory behavior during swarming, which may have implications for community assembly, thus being of fundamental importance. Effects of KD on fitness, genotype segregation and matrix sharing in biofilms is not well understood. By using environmental strains with determined kin types and integrated fluorescent reporters we provide evidence that KD involves antagonism of the dominant strain against non-kin, which has important implications for genotype segregation and sharing of matrix polysaccharides between producers and non-producers. Our results reveal novel consequences of KD and are important for advancing our fundamental understanding of microbial sociality, and its role in the assembly of multicellular groups and in the shaping of microbial diversity.

category: ecology


title: Human metapneumovirus P protein independently drives phase separation and recruits N protein to liquid-like inclusion bodies

abstract:
Human metapneumovirus (HMPV) inclusion bodies (IBs) are dynamic structures required for efficient viral replication and transcription. The minimum components needed to form IB-like structures in cells are the nucleoprotein (N) and the tetrameric phosphoprotein (P). HMPV P binds to two versions of N protein in infected cells: C-terminal P residues interact with oligomeric, RNA-bound N (N-RNA), and N-terminal P residues interact with monomeric N (N0) to maintain a pool of protein to encapsidate new RNA. Recent work on other negative-strand viruses has suggested that IBs are liquid-like organelles formed via liquid-liquid phase separation (LLPS). Here, HMPV IBs in infected or transfected cells were shown to possess liquid organelle properties, such as fusion and fission. Recombinant versions of HMPV N and P proteins were purified to analyze the interactions required to drive LLPS in vitro. Purified HMPV P was shown to form liquid droplets in the absence of other protein binding partners, a novel finding compared to other viral systems. Removal of nucleic acid from purified P altered phase separation dynamics, suggesting that nucleic acid interactions also play a role in IB formation. HMPV P also recruits monomeric N (N0-P) and N-RNA to IBs in vitro. These findings suggest that, in contrast to what has been reported for other viral systems, HMPV P acts as a scaffold protein to mediate multivalent interactions with monomeric and oligomeric HMPV N to promote phase separation of IBs.

IMPORTANCEHuman metapneumovirus (HMPV) is a leading cause of respiratory disease among children, immunocompromised individuals, and the elderly. Currently, no vaccines or antivirals are available for treatment of HMPV infections. Cytoplasmic inclusion bodies (IBs), where HMPV replication and transcription occur, represent a promising target for the development of novel antivirals. The HMPV nucleoprotein (N) and phosphoprotein (P) are the minimal components needed for IB formation in eukaryotic cells. However, interactions that regulate the formation of these dynamic structures are poorly understood. Here, we showed that HMPV IBs possess the properties of liquid organelles and that purified HMPV P phase separates independently in vitro. Our work suggests that HMPV P phase separation dynamics are altered by nucleic acid. We provide strong evidence that, unlike results reported from other viral systems, HMPV P alone serves as a scaffold for multivalent interactions with monomeric (N0) and oligomeric (N-RNA) HMPV N for IB formation.

category: microbiology


title: Optogenetic perturbations of RNA expression in tissue space

abstract:
Organoids derived from stem cells become increasingly important to study human development and to model disease. However, methods are needed to control and study spatio-temporal patterns of gene expression in organoids. To this aim, we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes, at single-cell resolution and in programmable spatio-temporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (SHH) signaling in an organoid model for human neurodevelopment. High-resolution spatial transcriptomic and single-cell analyses showed that this local induction was sufficient to generate stereotypically patterned organoids in three dimensions and revealed new insights into SHHs contribution to gene regulation in neurodevelopment.

With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.

category: bioengineering


title: Spatio-temporal, optogenetic control of gene expression in organoids


title: Injectable Liposome Based Supramolecular Hydrogels for the Programmable Release of Multiple Protein Drugs

abstract: Directing and manipulating biological functions is at the heart of next-generation biomedical initiatives such as tissue and immuno-engineering. Yet, the ambitious goal of engineering complex biological networks requires the ability to precisely perturb specific signaling pathways at distinct times and places. Using lipid nanotechnology and the principles of supramolecular self-assembly, we have developed an injectable liposomal nanocomposite hydrogel platform to precisely control drug presentation through programing of the co-release of multiple protein drugs. These liposomal hydrogels exhibited robust shear-thinning and self-healing behaviors enabling facile injectability for local drug delivery applications. By integrating modular lipid nanotechnology into this hydrogel platform, we introduced multiple mechanisms of protein release based on liposome surface chemistry. When injected into immuno-competent mice, these liposomal hydrogels exhibited formulation-dependent rates of dissolution and excellent biocompatibility. To fully validate the utility of this system for multi-protein delivery, we demonstrated the synchronized, sustained, and localized release of IgG antibody and IL-12 cytokine in vivo, despite the significant size differences between these two proteins. Overall, these liposomal nanocomposite hydrogels are a highly modular platform technology with the ability the mediate orthogonal modes of protein release and the potential to precisely coordinate biological cues both in vitro and in vivo.


title: Cytotoxic T-cell-based vaccine against SARS-CoV2: a hybrid immunoinformatic approach

abstract: This paper presents an alternative vaccination platform that provides long-term cellular immune protection mediated by cytotoxic T-cells. The immune response via cellular immunity creates superior resistance to viral mutations, which are currently the greatest threat to the global vaccination campaign. Furthermore, we also propose a safer, more facile and physiologically appropriate immunization method using either intra-nasal or oral administration. The underlying technology is an adaptation of synthetic long peptides (SLPs) previously used in cancer immunotherapy. SLPs comprising HLA class I and class II epitopes are used to stimulate antigen cross-presentation and canonical class II presentation by dendritic cells. The result is a cytotoxic T cell-mediated prompt and specific immune response against the virus-infected epithelia and a rapid and robust virus clearance. Peptides isolated from COVID-19 convalescent patients were screened for the best HLA population coverage and were tested for toxicity and allergenicity. 3D peptide folding followed by molecular docking studies provided positive results, suggesting a favourable antigen presentation.


title: Amino Acid Composition and Charge Based Prediction of Antisepsis Peptides by Random Forest Machine Learning Algorithm

abstract: Sepsis is a severe infectious disease with high mortality, and it occurs when chemicals released in the bloodstream to fight an infection trigger inflammation throughout the body and it can cause a cascade of changes that damage multiple organ systems, leading them to fail, even resulting in death. In order to reduce the possibility of sepsis or infection antiseptics are used and process is known as antisepsis. Antiseptic peptides (ASPs) show properties similar to antigram-negative peptides, antigram-positive peptides and many more. Machine learning algorithms are useful in screening and identification of therapeutic peptides and thus provide initial filters or built confidence before using time consuming and laborious experimental approaches. In this study, various machine learning algorithms like Support Vector Machine (SVM), Random Forest (RF), K-Nearest Neighbour (KNN) and Logistic Regression (LR) were evaluated for prediction of ASPs. Moreover, the characteristics physicochemical features of ASPs were also explored to use them in machine learning. Both manual and automatic feature selection methodology was employed to achieve best performance of machine learning algorithms. A 5-fold cross validation and independent data set validation proved RF as the best model for prediction of ASPs. Our RF model showed an accuracy of 97%, Matthews Correlation Coefficient (MCC) of 0.93, which are indication of a robust and good model. To our knowledge this is the first attempt to build a machine learning classifier for prediction of ASPs.


title: Using causality and correlation analysis to decipher microbial interactions in activated sludge

abstract: Network theory is widely used to understand microbial interactions in activated sludge and numerous other artificial and natural environments. However, when using correlation-based methods, it is not possible to identify the directionality of interactions within microbiota. Based on the classic Granger test of sequencing-based time-series data, a new Microbial Causal Correlation Network (MCCN) was constructed with distributed ecological interaction on the directed, associated links. As a result of applying MCCN to a time series of activated sludge data, we found that the hub species OTU56, classified as belonging the genus Nitrospira, was responsible for completing nitrification in activated sludge, and mainly interacted with Proteobacteria and Bacteroidetes in the form of amensal and commensal relationships, respectively. Phylogenetic tree suggested a mutualistic relationship between Nitrospira and denitrifiers. Zoogloea displayed the highest ncf value within the classified OTUs of the MCCN, indicating that it could be a foundation for activated sludge through forming the characteristic cell aggregate matrices into which other organisms embed during floc formation. Overall, the introduction of causality analysis greatly expands the ability of a network to shed a light on understanding the interactions between members of a microbial community.


title: A structural biology community assessment of AlphaFold 2 applications

abstract: Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods have led to protein structure predictions that have reached the accuracy of experimentally determined models. While this has been independently verified, the implementation of these methods across structural biology applications remains to be tested. Here, we evaluate the use of AlphaFold 2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modelling of interactions; and modelling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modelled when compared to homology modelling, identifying structural features rarely seen in the PDB. AF2-based predictions of protein disorder and protein complexes surpass state-of-the-art tools and AF2 models can be used across diverse applications equally well compared to experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life science research.


title: The Impact of Body Mass Index on Physical Activity and Cardiac Workload

abstract:
BackgroundHaving an abnormal body mass index (BMI) adversely affects cardiac workload and level of physical activity.

ObjectiveTo examine the relationship between cardiac workload, physical activity, Sex, and BMI.

MethodsThe number of steps taken per day (Steps) and minutes per week spent in targeted heart rate zones were collected from primarily first and second year university students (n = 1,801; 62% female) over a standard, 15-week long semester. Other data collected included BMI, Sex, Age, and Class Standing. Sex differences in BMI, Steps, and training heart rate zone (heart rates above 50% of max) minutes (THR) were evaluated, correlations between the study parameters were analyzed, and one-way ANOVA was used to test between competing models. The values p < .05 were considered statistically significant.

ResultsStatistically significant (p < .05) differences between males and females were found for Steps, THR, and BMI. Males were more physically active but spent 18% less time with heart rates above 50% of max. Students who had abnormal BMI values, both low and high, experienced greater cardiac workload (p < .05), even though they were found to be less physically active (p < .05).

ConclusionOur study revealed that university students with abnormal BMI values experienced greater cardiac workload, even though they are less physically active. Thus, physical fitness and healthy lifestyle interventions should also include underweight students in addition to students who are overweight or obese.

category: physiology


title: The longevity response to warm temperature is neurally controlled via regulation of collagen genes

abstract: Studies in diverse species have associated higher temperatures with shorter lifespan and lower temperatures with longer lifespan. However, the mechanisms behind these inverse effects of temperature on longevity are not well understood. Here, we demonstrate that in Caenorhabditis elegans, functional loss of NPR-8, a G protein-coupled receptor related to mammalian neuropeptide Y receptors, increases worm lifespan at 25{degrees}C but not at 20{degrees}C or 15{degrees}C, and that the lifespan increase at 25{degrees}C is regulated by the NPR-8-expressing AWB and AWC chemosensory neurons as well as AFD thermosensory neurons. RNA sequencing revealed that both warm temperature and old age profoundly alter gene expression. Further investigation uncovered that the NPR-8-dependent longevity response to warm temperature is achieved by regulating the expression of a subset of collagen genes. As elevated collagen expression is a common feature of many lifespan-extending interventions and enhanced stress resistance, collagen expression could be critical for healthy aging.


title: The longevity response to warm temperature is neurally controlled via the regulation of collagen genes


title: Computing personalized brain functional networks from fMRI using self-supervised deep learning

abstract: A novel self-supervised deep learning (DL) method is developed for computing bias-free, personalized brain functional networks (FNs) that provide unique opportunities to better understand brain function, behavior, and disease. Specifically, convolutional neural networks with an encoder-decoder architecture are employed to compute personalized FNs from resting-state fMRI data without utilizing any external supervision by optimizing functional homogeneity of personalized FNs in a self-supervised setting. We demonstrate that a DL model trained on fMRI scans from the Human Connectome Project can identify canonical FNs and generalizes well across four different datasets. We further demonstrate that the identified personalized FNs are informative for predicting individual differences in behavior, brain development, and schizophrenia status. Taken together, self-supervised DL allows for rapid, generalizable computation of personalized FNs.

category: neuroscience


title: Backward masking in mice requires visual cortex

abstract: Visual masking is used extensively to infer the timescale of conscious perception in humans; yet the underlying circuit mechanisms are not understood. We describe a robust backward masking paradigm in mice, in which the location of a briefly flashed grating is effectively masked within a 50 ms window after stimulus onset. Optogenetic silencing of visual cortex likewise reduces performance in this window, but response rates and accuracy do not match masking, demonstrating cortical silencing and masking are distinct phenomena. Spiking responses recorded in primary visual cortex (V1) are consistent with masked behavior when quantified over long, but not short, time windows, indicating masking involves further downstream processing. Accuracy and performance can be quantitatively recapitulated by a dual accumulator model constrained by V1 activity. The model and the animal"s performance for the earliest decisions imply that the initial spike or two arriving from the periphery trigger a correct response, but subsequent V1 spikes, evoked by the mask, degrade performance for later decisions. To test the necessity of visual cortex for backward masking, we optogenetically silenced mask-evoked cortical activity which fully restored discrimination of target location. Together, these results demonstrate that mice, like humans, are susceptible to backward visual masking and that visual cortex causally contributes to this process.


title: Flygenvectors: The spatial and temporal structure of neural activity across the fly brain

abstract: What are the spatial and temporal scales of brainwide neuronal activity, and how do activities at different scales interact? We used SCAPE microscopy to image a large fraction of the central brain of adult Drosophila melanogaster with high spatiotemporal resolution while flies engaged in a variety of behaviors, including running, grooming and flailing. This revealed neural representations of behavior on multiple spatial and temporal scales. The activity of most neurons across the brain correlated (or, in some cases, anticorrelated) with running and flailing over timescales that ranged from seconds to almost a minute. Grooming elicited a much weaker global response. Although these behaviors accounted for a large fraction of neural activity, residual activity not directly correlated with behavior was high dimensional. Many dimensions of the residual activity reflect the activity of small clusters of spatially organized neurons that may correspond to genetically defined cell types. These clusters participate in the global dynamics, indicating that neural activity reflects a combination of local and broadly distributed components. This suggests that microcircuits with highly specified functions are provided with knowledge of the larger context in which they operate, conferring a useful balance of specificity and flexibility.


title: Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

abstract: The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features which separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well-distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.


title: Metacommunity research can benefit from including context-dependency

abstract: Context-dependency, C-D, of outcomes occurs when several factors affect a focal metric. Remedies for treating milder cases of C-D are readily available but severe cases, where some contributory factors cause non-linear changes in others, escaped routine scrutiny. This poses a universal challenge to standard research strategies. We suggest that metacommunity framework may be particularly vulnerable because its core notions (habitat structure, dispersal, and species interactions) are functionally entangled. When these notions are generalized to include many species and situations, they become interdependent. To illustrate the significance of such interdependence, we test two hypotheses. One that holding combination of parameters constant in all but one dimension, can alter inference of a study and the second that the severity of context-dependency increases when core metacommunity dimensions interact and transform one another through a variety of mechanisms. The results support these ideas and imply that C-D predicts a dauntingly vast space of possible empirical outcomes and interpretations, most of which can arise from reciprocal interactions among metacommunity core dimensions. We proffer that an adaptable and structured use of macro-variables is a place to start investigating metacommunity mechanisms more efficiently.


title: Simultaneous acoustic monitoring uncovers evidence of biodiversity loss and overlooked temporal variation in a threatened Amazonian bird community

abstract:
O_LIBirds are frequently used as indicator taxon in ecology, but traditional surveys are prone to error and largely inadequate in the dense, speciose tropical forests where they are most needed. Passive acoustic monitoring (PAM) has the potential to address many of these pitfalls, providing unique advantages for both long-term monitoring and rapid biodiversity assessment. Here, we evaluate the effectiveness of PAM for characterizing spatiotemporal variation in avian species richness, diversity, vocal activity, and community composition in the Amazon basin global biodiversity hotspot.
C_LIO_LIWe employed an array of ten autonomous recording units (ARUs) spanning edge, degraded, and interior forest at a reserve on the deforestation frontier of Madre de Dios, Peru, a region featuring some of the richest, most complex avian assemblages on Earth. Recordings from 21 dawn-hours across three days at seven sites were manually annotated by a single observer.
C_LIO_LIARUs and manual annotation performed well as an inventory method, especially for midstory and understory species. Sites in edge and degraded habitats featured significantly lower avian species richness, Shannon diversity, and vocal activity levels than in the forest interior, patterns that replicate the findings of prior high-effort avian censuses in the region. We observed significant temporal variation between days; at all featured sites, vocal activity was highest on January 20th and lowest on January 31st.
C_LIO_LIWe demonstrated that novel annotation-generated metrics can work as effective proxies for abundance data and per-capita song rate, correlating with diversity indices and efficiently characterizing habitats at a level of detail unobtainable with human observers. Generalist species were significantly overrepresented in the soundscapes of interior forest, relative to their contributed share of species richness, and interior specialists were underrepresented, suggesting that the entire 191ha site is degraded. The between-days temporal variation that we documented, almost certainly overlooked without simultaneous monitoring, may obfuscate or distort the results of traditional surveys.
C_LIO_LISynthesis & Applications. We propose that PAM should become a cornerstone of biodiversity research. The standardization advantages demonstrated in this study, permanent storage, multi-taxa applications, and potential of automated identification make bioacoustics an ideal methodological avenue for guiding management and policy under rapid global change.
C_LI


title: Gene flow biases population genetic inference of recombination rate

abstract: Accurate estimates of the rate of recombination are key to understanding a host of evolutionary processes as well as the evolution of recombination rate itself. Model-based population genetic methods that infer recombination rates from patterns of linkage disequilibrium (LD) in the genome have become a popular method to estimate rates of recombination. However, these LD-based methods make a variety of simplifying assumptions about the populations of interest that are often not met in natural populations. One such assumption is the absence of gene flow from other populations. Here, we use forward-time population genetic simulations of isolation-with-migration scenarios to explore how gene flow affects the accuracy of LD-based estimators of recombination rate. We find that moderate levels of gene flow can result in either the overestimation or underestimation of recombination rates by up to 20-50% depending on the timing of divergence. We also find that these biases can affect the detection of interpopulation differences in recombination rate, causing both false positive and false negatives depending on the scenario. We discuss future possibilities for mitigating these biases and recommend that investigators exercise caution and confirm that their study populations meet assumptions before deploying these methods.

category: evolutionary biology


title: Insight into Cross-Amyloid Interactions and Morphologies: Molecular Dynamics Simulations of Model Peptide Fragments of Amyloid-β (Aβ16-22) and Islet Amyloid Polypeptide (IAPP20-29)

abstract:
Amyloid-beta (A{beta}) and islet amyloid polypeptide (IAPP) are small peptides, classified as amyloids, that have the potential to self-assemble and form cytotoxic species, such as small soluble oligomers and large insoluble fibrils. The formation of A{beta} aggregates facilitates the progression of Alzheimers disease (AD), while IAPP aggregates induce pancreatic {beta}-cell apoptosis, leading to exacerbation of Type 2 diabetes (T2D). Cross-amyloid interactions between A{beta} and IAPP have been described both in vivo and in vitro, implying the role of A{beta} or IAPP as modulators of cytotoxic self-aggregation of each peptide, and suggesting that A{beta}-IAPP interactions are a potential molecular link between AD and T2D. Using molecular dynamics simulations, "hot spot" regions of the two peptides were studied to understand the formation of hexamers in a heterogenous and homogenous peptide-containing environment. Systems of only A{beta}(16-22) peptides formed antiparallel, {beta}-barrel-like structures, while systems of only IAPP(20-29) peptides formed stacked, parallel beta strands and had relatively unstable aggregation structures after 2 s of simulation time. Systems containing both A{beta} and IAPP (1:1 ratio) hexamers showed antiparallel, {beta}-barrel-like structures, with an interdigitated arrangement of A{beta}(16-22) and IAPP(20-29). These {beta}-barrel structures have features of cytotoxic amyloid species identified in previous literature. Ultimately, this work seeks to provide atomistic insight into both the mechanism behind cross-amyloid interactions and structural morphologies of these toxic amyloid species.

Statement of SignificanceMolecular knowledge, biophysical characterization, structural morphologies, and formation pathways of amyloid oligomers - specifically low-molecular weight, cross-amyloid oligomers - remain preliminary and undefined. Characterizing interactions between homogenous and heterogenous amyloid oligomers is of great interest given that certain oligomer morphologies contribute to cytotoxicity, eventually resulting in comorbid diseases such as Alzheimers disease (AD) and Type 2 Diabetes Mellitus (T2DM). Utilizing model systems (e.g., fragments of full-length peptides) and molecular dynamics (MD) simulations to probe the biophysical underpinnings of cross-amyloid oligomer structures is the first step in understanding the dynamics, stability, and potential modes of cytotoxicity of these species, providing important insights into targetable biomolecular structures.

category: biochemistry


title: Spontaneous nucleation and fast aggregate-dependent proliferation of α-synuclein aggregates within liquid condensates at physiological pH

abstract: It is well-established that -synuclein aggregation may proceed through an initial lipid-dependent aggregate formation and, if at acidic pH, a subsequent aggregate-dependent proliferation. It has also been recently reported that the aggregation of -synuclein may also take place through an alternative pathway, which takes place within dense liquid condensates produced through liquid-liquid phase separation. The microscopic mechanism of this process, however, remains to be clarified. Here, we developed a fluorescence-based assay to perform a kinetic analysis of the aggregation process of -synuclein within liquid condensates, and applied it to determine the corresponding mechanism of aggregation. Our analysis shows that at pH 7.4 the aggregation process of -synuclein within dense condensates starts with spontaneous primary nucleation followed by rapid aggregate-dependent proliferation. Taken together, these results reveal a highly efficient pathway for the appearance and proliferation of -synuclein aggregates at physiological pH.


title: Atomic-Resolution Prediction of Degrader-mediated Ternary Complex Structures by Combining Molecular Simulations with Hydrogen Deuterium Exchange

abstract: Targeted protein degradation (TPD) has recently emerged as a powerful approach for removing (rather than inhibiting) proteins implicated in diseases. A key step in TPD is the formation of an induced proximity complex where a degrader molecule recruits an E3 ligase to the protein of interest (POI), facilitating the transfer of ubiquitin to the POI and initiating the proteasomal degradation process. Here, we address three critical aspects of the TPD process using atomistic simulations: 1) formation of the ternary complex induced by a degrader molecule, 2) conformational heterogeneity of the ternary complex, and 3) degradation efficiency via the full Cullin Ring Ligase (CRL) macromolecular assembly. The novel approach described here combines experimental biophysical data with molecular dynamics (MD) simulations to accurately predict ternary complex structures at atomic resolution. We integrate hydrogen-deuterium exchange mass spectrometry (HDX-MS, which measures the solvent exposure of protein residues) directly into the MD simulation algorithm to improve the efficiency and accuracy of the ternary structure predictions of the bromodomain of the cancer target SMARCA2 with the E3 ligase VHL, as mediated by three different degrader molecules. The simulations accurately reproduce X-ray crystal structures-including a new structure that we determined in this work (PDB ID: 7S4E)-with root mean square deviations (RMSD) of 1.1 to 1.6 [A]. The simulations also reveal a structural ensemble of low-energy conformations of the ternary complex. Snapshots from these simulations are used as seeds for additional simulations, where we perform 5.7 milliseconds of aggregate simulation time using Folding@home, the worlds largest distributed supercomputer. The detailed free energy surface captures the crystal structure conformation within the low-energy basin and is consistent with solution-phase experimental data (HDX-MS and SAXS). Finally, we graft a structural ensemble of the ternary complexes onto the full CRL and perform enhanced sampling simulations. Our results suggest that differences in degradation efficiency may be related to the proximity distribution of lysine residues on the POI relative to the E2-loaded ubiquitin. We make source code and the simulation and experimental datasets from this work publicly available for researchers to further advance the field of induced proximity modulation.


title: Electrodeformation of White Blood Cells Enriched with Gold Nanoparticles

abstract: The elasticity of white blood cells (WBCs) provides valuable insight into the condition of the cells themselves, the presence of some diseases, as well as immune system activity. In this work, we describe a novel process of refined control of WBCs elasticity through a combined use of gold nanoparticles (AuNPs) and the microelectrode array device. The capture and controlled deformation of gold nanoparticles enriched white blood cells in vitro are demonstrated and quantified. Gold nanoparticles enhance the effect of electrically induced deformation and make the DEP related processes more controllable.


title: Models as games: a novel approach for 'gamesourcing' parameter data and communicating complex models

abstract:
1O_LIModels have become indispensable tools in conservation science in the face of increasingly rapid loss of biodiversity through anthropogenic habitat loss and natural resource exploitation. In addition to their ecological components, accurately representing human decision-making processes in such models is vital to maximise their utility. This can be problematic as modelling complexity increases, making them challenging to communicate and parameterise.
C_LIO_LIGames have a long history of being used as science communication tools, but are less widely used as data collection tools, particularly in videogame form. We propose a novel approach to (1) aid communication of complex social-ecological models, and (2) "gamesource" human decision-making data, by explicitly casting an existing modelling framework as an interactive videogame.
C_LIO_LIWe present players with a natural resource management game as a front-end to a social-ecological modelling framework (Generalised Management Strategy Evaluation, GMSE). Players actions replace a model algorithm making management decisions about a population of wild animals, which graze on crops and can thus lower agricultural yield. A number of non-player agents (farmers) respond through modelled algorithms to the players management, taking actions that may affect their crop yield as well as the animal population. Players are asked to set their own management goal (e.g. maintain the animal population at a certain level or improve yield) and make decisions accordingly. Trial players were also asked to provide any feedback on both gameplay and purpose.
C_LIO_LIWe demonstrate the utility of this approach by collecting and analysing game play data from a sample of trial plays, in which we systematically vary two model parameters, and allowing trial players to interact with the model through the game interface. As an illustration, we show how variations in land ownership and the number of farmers in the system affects decision-making patterns as well as population trajectories (extinction probabilities).
C_LIO_LIWe discuss the potential and limitations of this model-game approach in the light of trial player feedback received. In particular, we highlight how a common concern about the game framework (perceived lack of "realism" or relevance to a specific context) are actually criticisms of the underlying model, as opposed to the game itself. This further highlights both the parallels between games and models, as well as the utility of model-games to aid in communicating complex models. We conclude that videogames may be an effective tool for conservation and natural resource management, and that although they provide a promising means to collect data on human decision-making, it is vital to carefully consider both external validity and potential biases when doing so.
C_LI

category: scientific communication and education


title: An innate immune activation state prior to vaccination predicts responsiveness to multiple vaccines

abstract: Many factors determine whether an individual responding to vaccination will generate an immune response that can lead to protection. Several studies have shown that the pre-vaccination immune state is associated with the antibody response to vaccines. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across a wide variety of vaccines. We leveraged the "Immune Signatures Data Resource" created by the NIH Human Immunology Project Consortium (HIPC) to integrate data from 28 studies involving 13 different vaccines and associate the blood transcriptional status of 820 healthy young adults with their responses. An unsupervised analysis of blood transcriptional profiles across studies revealed three distinct pre-vaccination states, characterized by the differential expression of genes associated with a pro-inflammatory response, cell proliferation, and metabolism alterations downstream of NF{kappa}B and IRF7. Innate and adaptive immune cell subset-specific genes were also associated with the three pre-vaccination states. Importantly, individuals whose pre-vaccination state was enriched in pro-inflammatory response genes known to be downstream of NF{kappa}B tended to have higher serum antibody responses one month after vaccination. A supervised analysis of the same data resulted in a single classifier, also enriched for NF{kappa}B regulated genes, that predicted the antibody response across most of the vaccines. Projection into single-cell RNA-sequencing data suggested that this pre-vaccination state was attributable to the signature of activation of non-classical monocytes and myeloid dendritic cells. Transcriptional signatures of acute responses to bacterial and not viral infections were enriched in the high pro-inflammatory pre-vaccination state and also included NF{kappa}B regulated genes. The pro-inflammatory pre-vaccination state was highly reminiscent of the innate activation state triggered by TLR ligands or adjuvants. These results demonstrate that wide variations in the transcriptional state of the immune system in humans can be a key determinant of responsiveness to vaccination. They also define a transcriptional signature NF{kappa}B activation at baseline, that is associated with a greater magnitude of antibody response to multiple vaccines, and suggest that modulation of the innate immune system by next-generation adjuvants targeting NF{kappa}B before vaccine administration may improve vaccine responsiveness.

category: systems biology


title: A Neuromuscular Model of Human Locomotion Combines Spinal Reflex Circuits with Voluntary Movements

abstract: Existing models of human walking use low-level reflexes or neural oscillators to generate movement. While appropriate to generate the stable, rhythmic movement patterns of steady-state walking, these models lack the ability to change their movement patterns or spontaneously generate new movements in the specific, goal-directed way characteristic of voluntary movements. Here we present a neuromuscular model of human locomotion that bridges this gap and combines the ability to execute goal directed movements with the generation of stable, rhythmic movement patterns that are required for robust locomotion. The model represents goals for voluntary movements of the swing leg on the task level of swing leg joint kinematics. Smooth movements plans towards the goal configuration are generated on the task level and transformed into descending motor commands that execute the planned movements, using internal models. The movement goals and plans are updated in real time based on sensory feedback and task constraints. On the spinal level, the descending commands during the swing phase are integrated with a generic stretch reflex for each muscle. Stance leg control solely relies on dedicated spinal reflex pathways. Spinal reflexes stimulate Hill-type muscles that actuate a biomechanical model with eight internal joints and six free-body degrees of freedom. The model is able to generate voluntary, goal-directed reaching movements with the swing leg and combine multiple movements in a rhythmic sequence. During walking, the swing leg is moved in a goal-directed manner to a target that is updated in real-time based on sensory feedback to maintain upright balance, while the stance leg is stabilized by low-level reflexes and a behavioral organization switching between swing and stance control for each leg. With this combination of reflex-based stance leg and voluntary, goal-directed control of the swing leg, the model controller generates rhythmic, stable walking patterns in which the swing leg movement can be flexibly updated in real-time to step over or around obstacles.


title: KLC4 shapes axon arbors during development and mediates adult behavior

abstract: Development of elaborate and polarized neuronal morphology requires precisely regulated transport of cellular cargos by motor proteins such as kinesin-1. Kinesin-1 has numerous cellular cargos which must be delivered to unique neuronal compartments. The process by which this motor selectively transports and delivers cargo to regulate neuronal morphogenesis is poorly understood. Our work implicates one kinesin light chain subunit, KLC4, as an essential regulator of axon branching and arborization pattern of sensory neurons during development. Using several live imaging approaches in klc4 mutant zebrafish, we show that KLC4 is required for stabilization of nascent axon branches and for proper microtubule (MT) dynamics. Furthermore, KLC4 is required for the contact repulsion necessary for tiling of peripheral axon arbors: in klc4 mutants, peripheral axons showed abnormal fasciculation, a behavior characteristic of central axons, suggesting that KLC4 patterns axonal compartments and helps define axon identity. Finally, we find that klc4 mutant adults show anxiety-like behavior in a novel tank test, implicating klc4 as a novel gene involved in stress response circuits.


title: Distinct brainstem to spinal cord noradrenergic pathways differentially regulate spinal neuronal activity

abstract: Brainstem to spinal cord pathways modulate spinal neuronal activity. We implemented locus coeruleus (LC) targeting strategies by microinjecting CAV-PRS-ChR2 virus in the spinal cord (LC:SC module) or LC (LC:LC module). While activation of both modules inhibited evoked spinal neuronal firing via 1-adrenoceptor-mediated actions, LC:SC opto-activation abolished diffuse noxious inhibitory controls. The LC as a pain generator is likely mechanistically underpinned by maladaptive communication with discrete descending modulatory pathways.


title: Innate immune signaling drives late cardiac toxicity following DNA damaging cancer therapies

abstract: Late cardiac toxicity is a potentially lethal complication of cancer therapy, yet the pathogenic mechanism remains largely unknown, and few treatment options exist. Here we report DNA damaging agents such as radiation and anthracycline chemotherapies induce delayed cardiac inflammation following therapy due to activation of cGAS and STING-dependent type I interferon signaling. Genetic ablation of cGAS-STING-signaling in mice inhibits DNA damage induced cardiac inflammation, rescues late cardiac functional decline, and prevents death from cardiac events. Treatment with a STING antagonist suppresses cardiac interferon signaling following DNA damaging therapies and effectively mitigates cardiotoxicity. These results identify a therapeutically targetable, pathogenic mechanism for one of the most vexing treatment-related toxicities in cancer survivors.

category: immunology


title: Deactivation of SARS-CoV-2 surrogate porcine epidemic diarrhea virus with electron beam irradiation under the cold chain transportation condition

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prevailed all over the world and emerged as a significant public health emergency. The rapid outbreak of SARS-CoV-2 is largely due to its high transmission capacity. Studies implied that the cold chain logistics would be a potential route for the spread of SARS-CoV-2. The low temperature condition of the cold chain is conducive to survival and transmission of virus. Thus, the virus disinfection in cold chain should not be neglected for controlling COVID-19. However, due to the low temperature feature of the cold-chain, the virus disinfecting methods suitable in cold chain are limited. Here the high-energy electron beam irradiation is proposed to disinfect the SARS-CoV-2 in cold chain logistics. We evaluated the impact of high-energy electron beam irradiation on porcine epidemic diarrhea virus (PEDV), an enveloped virus surrogate for SARS-CoV-2, and explored the possible mechanism of the action of high-energy electron beam irradiation on PEDV. The irradiation dose of 10 kGy inactivated 98.1 % PEDV on the both top and bottom surfaces of various packaging materials under cold chain frozen condition. High-energy electron beam inactivated PEDV by inducing damages on viral genome or even capsid.


title: Viroporin activity of SARS-CoV-2 Orf3a and Envelope protein impacts viral pathogenicity

abstract:
COVID-19 is caused by SARS-CoV-2 which has affected nearly 220 million people worldwide and death toll close to 5 million as of present day. The approved vaccines are lifesaving yet temporary solutions to such a devastating pandemic. Viroporins are important players of the viral life cycle of SARS-Cov-2 and one of the primary determinants of its pathogenesis. We studied the two prominent viroporins of SARS-CoV-2 (i) Orf3a and (ii) Envelope (E) protein from a structural point of view. Orf3a has several hotspots of mutations which has been reported in SARS-CoV-2 with respect to SARS-CoV-1. Mutations in SARS-CoV-2 Orf3a channel forming residues enhances the formation of a prominent the inter-subunit channel, which was not present in the SARS-CoV-1 Orf3a. This enhanced structural feature can be correlated with higher channelling activity in SARS-CoV-2 than in SARS-CoV-1. On the other hand, E protein is one of the most conserved protein among the SARS-CoV proteome. We found that the water molecules form networks of electrostatic interactions with the polar residues in the E protein putative wetted condition while no water channel formation was observed in the putative dewetted condition. This aqueous medium mediates the non-selective translocation of cations thus affecting the ionic homeostasis of the host cellular compartments. This ionic imbalance leads to increased inflammatory response in the host cell. Our results shed light into the mechanism of viroporin action, which can be leveraged for the development of antiviral therapeutics. Furthermore, our results corroborate with previously published transcriptomic data from COVID-19 infected lung alveolar cells where inflammatory responses and molecular regulators directly impacted by ion channelling were upregulated. These observations overlap with transcript upregulation observed in diseases having acute lung injury, pulmonary fibrosis and Acute Respiratory Distress Syndrome (ARDS).

One Sentence SummaryMembrane permeation of Orf3a is significantly more in SARS-CoV-2 than in SARS-CoV-1 which might contribute to increased viral contagion.

category: molecular biology


title: Prioritizing candidate peptides for cancer vaccines by PEPPRMINT: a statistical model to predict peptide presentation by HLA-I proteins

abstract: Recent development of cancer immunotherapy has opened unprecedented avenues to eliminate tumor cells using the human immune system. Cancer vaccines composed of neoantigens, or peptides unique to tumor cells due to somatic mutations, have emerged as a promising approach to activate or strengthen the immune response against cancer. A key step to identifying neoantigens is computationally predicting which somatically mutated peptides are presented on the cell surface by a human leukocyte antigen (HLA). Computational prediction relies on large amounts of high-quality training data, such as mass spectrometry data of peptides presented by one of several HLAs in living cells. We developed a complete pipeline to prioritize neoantigens for cancer vaccines. A key step of our pipeline is PEPPRMINT (PEPtide PResentation using a MIxture model and Neural neTwork), a model designed to exploit mass spectrometry data to predict peptide presentation by HLAs. We applied our pipeline to DNA sequencing data of 60 melanoma patients and identified a group of neoantigens that were more immunogenic in tumor cells than in normal cells. Additionally, the neoantigen burden estimated by PEPPRMINT was significantly associated with activity of the immune system, suggesting these neoantigens could induce an immune response.

category: genomics


title: Broadscale evolutionary analysis of eukaryotic DDE transposons

abstract: DDE transposons are widespread selfish genetic elements, often comprising a large proportion of eukaryotic genomic content. DDE transposons have also made important contributions to varied host functions during eukaryotic evolution, and their transposases may be the most abundant and ubiquitous genes in nature. Yet much remains unknown about their basic biology. We employ a broadscale screen of DDE transposase diversity to characterise major evolutionary patterns for all 19 DDE transposon superfamilies. We identify considerable variation in DDE transposon superfamily size, and find a dominant association with animal hosts. While few DDE transposon superfamilies specialise in plants or fungi, the four largest superfamilies contain major plant-associated clades, at least partially underlying their relative success. We recover a pattern of host conservation among DDE transposon lineages, punctuated by occasional horizontal transfer to distantly related hosts. Host range and horizontal transfer are strongly positively correlated with DDE transposon superfamily size, arguing against variation in the capacity for generalism. We find that rates of horizontal transfer decrease sharply with increasing levels of host taxonomy, supporting the existence of host-associated barriers to DDE transposon spread. Overall, despite their relatively simple genetic structure, our results imply that trade-offs in host adaptation are important in defining DDE transposon-host relationships and evolution. In addition, our study provides a phylogenetic framework to facilitate the identification and further analysis of DDE transposons.


title: Double reduction estimation and equilibrium tests in natural autopolyploid populations

abstract: Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the co-migration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate double reduction given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium{chi} 2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. Finally, we highlight the difficulty in distinguishing between random mating and equilibrium in tetraploids at biallelic loci. Our methods are implemented in the hwep R package on GitHub https://github.com/dcgerard/hwep.


title: Drought stress induces morpho-physiological and proteome changes of Pandanus amaryllifolius

abstract: Drought is one of the significant threats to the agricultural sector. However, there is limited knowledge on the plant response to drought stress and post-drought recovery. Pandanus amaryllifolius, a moderate drought-tolerant plant, is well known for its ability to survive in low-level soil moisture conditions. Understanding the molecular regulation of drought stress signaling in this plant could help guide the rational design of crop plants to counter this environmental challenge. This study aimed to determine the morpho-physiological, biochemical and protein changes of P. amaryllifolius in response to drought stress and during recovery. Drought significantly reduced leaf relative water content of P. amaryllifolius. In contrast, relative electrolyte leakage, proline and malondialdehyde contents, and the activities of antioxidant enzymes in the drought-treated and recovered samples were relatively higher than the well-watered sample. The protein changes between drought-stressed, well-watered, and recovered plants were evaluated using tandem mass tags (TMT)-based quantitative proteomics. Of the 1,415 differentially abundant proteins, 74 were significantly altered. The majority of proteins differing between them were related to carbon metabolism, photosynthesis, stress response, and antioxidant activity. This is the first study that reports the protein changes in response to drought stress in Pandanus. The data generated provide an insight into the drought-responsive mechanisms in P. amaryllifolius.

category: plant biology


title: Direct neuronal conversion of microglia/macrophages reinstates neurological function after stroke

abstract: Ischaemic brain injury causes permanent neuronal loss, which often results in persistent severe neurological dysfunctions. Although generating new neurons in the injured brain would be an ideal approach to replenish the lost neurons for repairing the damage, the adult mammalian brain retains only limited neurogenic capability. Here, we show that direct conversion of microglia/macrophages into neurons in the brain has great potential as a therapeutic strategy for ischaemic brain injury. After transient middle cerebral artery occlusion in adult mice, microglia/macrophages converge at the lesion core of the striatum, where neuronal loss is prominent. Targeted expression of a neurogenic transcription factor, NeuroD1, in microglia/macrophages in the injured striatum enables their conversion into induced neuronal cells that functionally integrate into the existing neuronal circuits. Furthermore, NeuroD1-mediated induced neuronal cell generation significantly improves neurological function in the mouse stroke model, and ablation of these cells abolishes the gained functional recovery. Our findings thus demonstrate that neuronal conversion contributes directly to functional recovery after stroke and shed further light on the development of therapies for ischaemic brain injury by in situ neuronal conversion technology.


title: Transient dendritic cell activation diversifies the T cell response to acute infection

abstract:
The precise timing of T cell priming during infection remains unclear. Here, we mapped the cellular dynamics of all immune lineages during acute infection with Listeria monocytogenes (Lm). We identified highly transient DC activation 2 days post-infection that functions as a critical time window for priming effector T cells. Regulation of this transient state was mediated by DC extrinsic IFN{gamma} provided by lymphocytes. Furthermore, antigen-specific T cells that arrive late to the site of priming and miss peak DC activation acquire only memory T cell fates. This temporal regulation of fate is recapitulated by CD8+ DCs ex vivo, suggesting that shifts in activation state of a single antigen presenting cell population alter T cell fates. These results uncover a novel mechanism for temporal regulation of T cell differentiation during a dynamic immune response to acute infection.

One-Sentence SummaryThe immune system generates a balanced protective response through rapidly shifting activation states and recruitment of new cells into an ongoing inflammatory landscape.


title: A CRISPR-Cas9 screen reveals a role for WD repeat-containing protein 81 (WDR81) in the entry of late penetrating viruses

abstract:
Successful initiation of infection by many different viruses requires their uptake into the endosomal compartment. While some viruses exit this compartment early, others must reach the degradative, acidic environment of the late endosome. Mammalian orthoreovirus (reovirus) is one such late penetrating virus. To identify host factors that are important for reovirus infection, we performed a CRISPR-Cas9 knockout (KO) screen that targets over 20,000 genes in fibroblasts derived from the embryos of C57/BL6 mice. We identified seven genes (WDR81, WDR91, RAB7, CCZ1, CTSL, GNPTAB, and SLC35A1) that were required for the induction of cell death by reovirus. Notably, CRISPR-mediated KO of WD repeat-containing protein 81 (WDR81) rendered cells resistant to reovirus infection. Susceptibility to reovirus infection was restored by complementing KO cells with human WDR81. Although the absence of WDR81 did not affect viral attachment efficiency or uptake into the endosomal compartments for initial disassembly, it delayed viral gene expression and diminished infectious virus production. Consistent with the role of WDR81 in impacting the maturation of endosomes, WDR81-deficiency led to the accumulation of reovirus particles in dead-end compartments. Though WDR81 was dispensable for infection by VSV (vesicular stomatitis virus), which exits the endosomal system at an early stage, it was required for VSV-EBO GP (VSV that expresses the Ebolavirus glycoprotein), which must reach the late endosome to initiate infection. These results reveal a broad, previously unappreciated role for WDR81 in promoting the replication of late penetrating viruses.

AUTHOR SUMMARYViruses are obligate intracellular parasites that require the contributions of numerous host factors to complete the viral life cycle. Thus, the host-pathogen interaction can regulate cell death signaling and virus entry, replication, assembly, and egress. Functional genetic screens are useful tools to identify host factors that are important for establishing infection. Such information can also be used to understand cell biology. Notably, genome-scale CRISPR-Cas9 knockout screens are robust due to their specificity and the loss of host gene expression. Mammalian orthoreovirus (reovirus) is a tractable model system to investigate the pathogenesis of neurotropic and cardiotropic viruses. Using a CRISPR-Cas9 screen, we identified WD repeat-containing protein 81 (WDR81) as an essential host factor for reovirus infection of murine cells. Ablation of WDR81 blocked a late step in the viral entry pathway. Further, our work indicates that WDR81 is required for the entry of vesicular stomatitis virus that expresses the Ebolavirus glycoprotein.


title: Inhibition of Kallikrein-related peptidases 7 restrains pancreatic tumor growth through induction of ferroptosis

abstract: Pancreatic cancer is one of the most aggressive and lethal malignancies with extremely poor prognosis, and KLK7 was considered as a potential therapeutic target. In this study, we analyzed the expression of KLK7 in TCGA and GTEx databases and found that KLK7 had a negative correlation to long-term survival rate (>1.5 years) of pancreatic cancer patients. Compound 42 is a coumarinic derivative, a suicide substrate inhibitor of KLK7, which has been proved to inhibit the proliferation of PANC-1 cells in vitro effectively in our previous study. In this study, we further investigated the inhibition ability of Compound 42 in tumor formation and development in CDX and PDX tumor models of pancreatic cancer subsequently. Besides, we studied the inhibitory mechanism of Compound 42 and the result showed that Compound 42 arrested the pancreatic cancer cell cycle in G0/G1 phase and induced ferroptosis through down-regulation of GPX4 protein level and accumulation of iron ion. Thus, these experiments demonstrate that Compound 42, suppressing pancreatic cancer in vivo, is expected to become a novel drug for pancreatic cancer treatment.


title: Using trait data improves correlation between environment and community data only if abundances are considered

abstract:
A straightforward way to explore variation between communities is to calculate dissimilarity indices and relate them with environmental and spatial variables. Communities are most often represented by the (relative) abundances of taxa they comprise; however, more recently, the distribution of traits of organisms included in the communities has been shown more strongly related to ecosystem properties. In this study, we test whether taxon- or trait-based dissimilarity is correlated more tightly with environmental difference and geographical distance and how the abundance scale influences this correlation. Our study system is grassland vegetation in Hungary, where we sampled vegetation plots spanning a long productivity gradient from open dry grasslands to marshes in three sites. We considered three traits for vascular plants: canopy height, specific leaf area and seed mass. We obtained field estimates of normalized vegetation difference index (NDVI) as proxy of productivity (water availability) for each plot. We calculated between-community dissimilarities using a taxon-based and a trait-based index, using raw and square-root transformed abundances and presence/absence data. We fitted distance-based redundancy analysis models with NDVI difference and geographical distance on the dissimilarity matrices and evaluated them using variance partitioning. Then, using the pooled data, we calculated non-metric multidimensional scaling ordinations (NMDS) from all types of dissimilarity matrices and made pairwise comparisons using Procrustes analysis. Data analysis was done separately for the three sites.

We found that taxonomical dissimilarity matches environmental and spatial variables better when presence/absence data is used instead of abundance. This pattern was mainly determined by the increasing variation explained by space at the presence/absence scale. In contrast to this trend, with trait-based dissimilarity, accounting for abundance increased explained variation significantly due to the higher explanatory power of NDVI. With abundance data, considering traits improved environmental matching to a great extent in comparison with taxonomical information. However, with presence/absence data, traits brought no advantage over taxon-based dissimilarity in any respect. Changing the abundance scale caused larger difference between ordinations in the case of trait-based dissimilarity than with taxonomical dissimilarity.

We conclude that considering relevant traits improves environmental matching only if abundances are also accounted for.

Supporting informationAdditional graphs supporting the results are presented as appendix.

Open researchData used in this research are publicly available from Dryad ###link to be supplied upon acceptance###


title: Rapid evolution and strain turnover in the infant gut microbiome

abstract: While the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about the evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from >700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from that of adults. We find evidence for almost 100-fold increase in the rate of evolution and strain turnover in the infant gut compared to healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel in multiple infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.


title: Avian haemosporidians (Plasmodium and Haemoproteus) in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other lineages of the world

abstract: The avian haemosporidians (Plasmodium and Haemoproteus) are widely distributed and may affect the host populations from body damage at individual level to the extinction of a population. The knowledge about their status may help in future avifauna conservation plans. Hence, we examined the avian haemosporidians status, in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India, and their phylogenetic relationships with other known lineages of the world. We used the common genetic marker (Cytochrome b gene fragment of 479 bp) with information on the geographic distribution of parasite and host species available at MalAvi database. The prevalence of avian haemosporidians, from northern, eastern, and southern parts of India and phylogenetic genetic analysis of lineages was carried out to know the genetic relatedness among them at local and world level. The MCC tree revealed six Haemosporidian lineages in which one was common (H_MSP01) and five were unique (H_CYOPOL01, H_CHD01, H_CYORUB01, H_EUMTHA01, and P_GEOCIT01). The avian host richness Index was 2.0852. 9.9%, prevalence of Haemosporidian infection was found in 111 DNA samples belonging to 6 host species. The Haemoproteus prevalence was found to be 9.0 % across five host species (Phylloscopus trochiloides, Cyornis poliogenys, C. hainanus dialilaemus, C. rubeculoides, Eumiyas thalassinus) and Plasmodium prevalence was 0.9% in Geokichla citrina. Spatial phylogeny at global level showed H_MSP01 lineage, found in different host species in India, was genetically related to H. pallidus lineages (COLL2 and PFC1) in parts of Africa, Europe, North America, Malaysia, and Philippines. The Plasmodium lineage (P_GEOCIT01) was related to PADOM16 in Egypt with poor sequence similarity (93.89%). The statistical analysis suggested that the haemosporidians host species distribution range was directly and significantly associated with the altitude, minimum temperature, and relative humidity. H_MSP01 distribution was in accordance with H. pallidus having a wide geographic and host range.

category: genetics


title: Avian haemosporidians (Plasmodium and Haemoproteus) status in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other lineages of the world


title: Ecological and social pressures interfere with homeostatic sleep regulation in the wild

abstract: Sleep is fundamental to the health and fitness of all animals. The physiological importance of sleep is underscored by the central role of homeostasis in determining sleep investment - following periods of sleep deprivation, individuals experience longer and more intense sleep bouts. Yet, most studies of sleep have been conducted in highly controlled settings, disconnected from the ecological and social context that may exert pressures on sleep patterns in conflict with homeostatic regulation. Using tri-axial accelerometry and GPS to track the sleep patterns of a group of wild baboons (Papio anubis) at multiple temporal and spatial scales, we found that ecological and social pressures indeed interfere with homeostatic sleep regulation. Baboons sacrificed time spent sleeping when in less familiar locations and when sleeping in proximity to more group-mates, regardless of how much they had slept the prior night or how much they had physically exerted themselves the preceding day. Moreover, we found that the collective dynamics characteristic of social animal groups persist into the sleep period, as baboons exhibited synchronized patterns of waking throughout the night, particularly with nearby group-mates. Thus, for animals whose fitness depends critically on avoiding predation and developing social relationships, maintaining sleep homeostasis may be only secondary to remaining vigilant when sleeping in risky habitats and interacting with group-mates during the night. Our results highlight the importance of studying sleep in ecologically relevant contexts, where the adaptive function of sleep patterns directly reflect the complex trade-offs that have guided its evolution.

category: animal behavior and cognition


title: G4-Selective Ligand Induced Autophagy

abstract: G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy is a housekeeping cellular homeostatic mechanism and deregulation of autophagy is common in cancer and in neurodegenerative diseases. In this study, we identified the presence of 46 putative G4 sequences in the MTOR gene by use of QGRS mapper tool. We sought to connect these putative G4 sequences to a functional context by leveraging G4-targeting ligands. A G4-selective dimeric carbocyanine dye Bis-4,3 and the porphyrin TMPyP4 were used to affect the replication, transcription and translation of the MTOR gene. The ligand-induced induction of autophagic pathway via MTOR gene regulation was monitored upon treatment of HeLa and SHSY-5Y cells with G4-targeting ligands. The use of Bis-4,3 was compared with the known G4-stabilizing activity of TMPyP4. Our results show that treatment with G4-selective ligands downregulates mTOR activity and leads to the induction of excessive autophagy. This is first report on effect of G4-selective ligands on MTOR regulation and mTOR expression. mTOR being the key negative regulator of autophagy, the current work suggests potential of G4 stabilizing ligands towards induction of autophagy through the downregulation of mTOR.


title: IMCellXMBD: A statistical approach for robust cell identification and quantification from imaging mass cytometry images

abstract: Imaging Mass Cytometry (IMC) has become a useful tool in biomedical research due to its capability to measure over 100 markers simultaneously. Unfortunately, some protein channels in IMC images can be very noisy, which may significantly affect the phenotyping results without proper data processing. We developed IMCellXMBD1, a highly effective and generalizable cell identification and quantification method for IMC images. IMCell performs denoising by subtracting an estimated background noise value from pixel values for each individual protein channel, identifies positive cells from negative cells by comparing the distribution between segmented cells and decoy cells, and normalize the protein expression levels of the identified positive cells for downstream data analysis. Experimental results demonstrate that our method significantly improves the reliability of cell phenotyping which is essential for using IMC in biomedical studies.

category: bioinformatics


title: Elucidation of the molecular interactions that enable stable interaction between HIV protease inhibitor ritonavir and human DNA repair enzyme ALKBH2: a molecular dynamics simulation study

abstract: The human DNA repair enzyme AlkB homologue-2 and 3 (ALKBH2 and ALKKBH3) repairs methyl adducts from genomic DNA. Overexpression of ALKBH2 and ALKBH3 has been implicated in both tumorigenesis and chemotherapy resistance in some cancers, including glioblastoma and renal cancer rendering it a potential therapeutic target and a diagnostic marker. However, no inhibitor is available against these important DNA repair proteins. Intending to repurpose a drug as an inhibitor of ALKBH2/ALKBH3, we performed in silico evaluation of HIV protease inhibitors and identified Ritonavir as an ALKBH2-interacting molecule. Using molecular dynamics simulation, we elucidated the molecular details of Ritonavir-ALKBH2 interaction. The present work highlights that Ritonavir might be used to target the ALKBH2-mediated DNA alkylation repair.


title: Efficient Differentially Private Methods for a Transmission Disequilibrium Test in Genome Wide Association Studies

abstract: To achieve the provision of personalized medicine, it is very important to investigate the relationship between diseases and human genomes. For this purpose, large-scale genetic studies such as genome-wide association studies are often conducted, but there is a risk of identifying individuals if the statistics are released as they are. In this study, we propose new efficient differentially private methods for a transmission disequilibrium test, which is a family-based association test. Existing methods are computationally intensive and take a long time even for a small cohort. Moreover, for approximation methods, sensitivity of the obtained values is not guaranteed. We present an exact algorithm with a time complexity of [O](nm) for a dataset containing n families and m single nucleotide polymorphisms (SNPs). We also propose an approximation algorithm that is faster than the exact one and prove that the obtained scores sensitivity is 1. From our experimental results, we demonstrate that our exact algorithm is 10, 000 times faster than existing methods for a small cohort with 5, 000 SNPs. The results also indicate that the proposed method is the first in the world that can be applied to a large cohort, such as those with 106 SNPs. In addition, we examine a suitable dataset to apply our approximation algorithm. Supplementary materials are available at https://github.com/ay0408/DP-trio-TDT.


title: The interplay of supercoiling and thymine dimers inDNA

abstract: AO_SCPLOWBSTRACTC_SCPLOWThymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here we introduce a model of thymine dimers in the oxDNA forcefield, parametrised by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.

category: biophysics


title: Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14-3-3 ζ Protein

abstract: Mutation of an invariant aspartate residue in the binding pocket of 14-3-3{zeta} isoform to alanine dramatically reduced phosphopeptide binding and induced opening of the binding pocket. Here we use extensive molecular dynamics simulations to understand the role of D124 residue in ligand binding. The simulations show that in the absence of phosphopeptide, the D124A mutation leads to binding pocket reorganization including widening up of the binding pocket at the major groove and repositioning of N173, a key residue that interacts with the main chain of phosphopeptide. These structural changes would interfere with the efficient binding of the peptide, corroborating the experimental observations. Both gain and loss of electrostatic interactions in the form of salt bridges strongly indicate a rearrangement of the network of interactions within the binding pocket. Limited proteolysis coupled mass spectrometry (lip-MS) of the apo and holo forms of WT and mutant protein shows a peptide binding helix otherwise buried in the WT protein was particularly accessible to trypsin in the apo form of the mutant protein and the region was mapped to 158-186 amino acid residues of 14-3-3{zeta}). These results further confirm the dynamic nature of D124A mutant. Unlike other basic residues, the invariant D124 facilitates peptide binding by maintaining the geometry of interacting residues and by enforcing the structural integrity of amphipathic pocket.


title: Lomitapide, a cholesterol-lowering drug, is an anticancer agent that induces autophagic cell death via inhibiting mTOR

abstract: Autophagy is a biological process that maintains cellular homeostasis and regulates the internal cellular environment. Hyperactivating autophagy to trigger cell death has been a suggested therapeutic strategy for cancer treatment. Mechanistic target of rapamycin (mTOR) is a crucial protein kinase that regulates autophagy; therefore, using a structure-based virtual screen analysis, we identified lomitapide, a cholesterol-lowering drug, as a potential mTOR complex 1 (mTORC1) inhibitor. Our results showed that lomitapide directly inhibits mTORC1 in vitro and induces autophagy-dependent cancer cell death by decreasing mTOR signaling, thereby inhibiting the downstream events associated with increased LC3 conversion in various cancer cells (e.g., HCT116 colorectal cancer cells) and tumor xenografts. Lomitapide also significantly suppresses the growth and viability along with elevated autophagy in patient-derived colorectal cancer organoids. Furthermore, a combination of lomitapide and immune checkpoint blocking antibodies synergistically inhibits tumor growth in murine MC-38 or B16-F10 pre-clinical syngeneic tumor models. These results elucidates the direct, tumor-relevant immune-potentiating benefits of mTORC1 inhibition by lomitapide, which complement the current immune checkpoint blockade. This study highlights the potential repurposing of lomitapide as a new therapeutic option for cancer treatment.

category: cancer biology


title: The scratch-digging lifestyle of the Permian "microsaur" Batropetes as a model for the exaptative origin of jumping locomotion in frogs

abstract:
Recent studies have shown that the Triassic stem-frog Triadobatrachus lacked the ability to jump off, but nonetheless had the forelimb strength to withstand the impact of landing from a jump. We propose a hypothesis to resolve this pseudoparadox: the strengthened forelimbs are former adaptations to forelimb-based digging that later made jumping possible by exaptation.

Micro-CT data from a skeleton of Batropetes palatinus reveal thin cortical bone, confirming Batropetes as terrestrial. Combining adaptations to walking and digging, confirmed by statistical analyses, Batropetes is thought to have searched for food in leaf litter or topsoil. We interpret Batropetes as having used one forelimb at a time to shove leaf litter aside. Batropetes may thus represent an analog or possibly a homolog of the digging stage that preceded the origin of Salientia.

We discuss the possibility of homology with the digging lifestyles of other "microsaurs" and other amphibians.

category: paleontology


title: scoMorphoFISH: A Deep-Learning enabled toolbox for single-cell single-mRNA quantification and correlative (ultra-)morphometry

abstract: Increasing the information depth of single kidney biopsies can improve diagnostic precision, personalized medicine and accelerate basic kidney research. Until now, information on mRNA abundance and morphologic analysis has been obtained from different samples, missing out on the spatial context and single-cell correlation of findings. Herein, we present scoMorphoFISH, a modular toolbox to get spatial single-cell single-mRNA expression data optimized for routinely generated kidney biopsies. Deep-Learning was used to virtually dissect tissue sections in tissue compartments and cell types to which single-cell expression data was assigned. Furthermore, we show correlative and spatial single-cell expression quantification with super-resolved podocyte foot process morphometry on the same histological section. In contrast to bulk analysis methods, this approach will help to identify local transcription changes even in less frequent kidney cell types on a spatial single-cell level with single-mRNA resolution. As this method performs well with standard formalin-fixed paraffin-embedded samples and we provide pretrained DL-networks embedded in a comprehensive image analysis workflow, this method can be applied immediately in a variety of settings.

category: pathology


title: Cell and circuit origins of fast network oscillations in the mammalian main olfactory bulb

abstract: Neural synchrony generates fast network oscillations throughout the brain, including the main olfactory bulb (MOB), the first processing station of the olfactory system. Identifying the mechanisms synchronizing neurons in the MOB will be key to understanding how network oscillations support the coding of a high-dimensional sensory space. Here, using paired recordings and optogenetic activation of glomerular sensory inputs in MOB slices, we uncovered profound differences in principal mitral cell (MC) vs. tufted cell (TC) spike-time synchrony: TCs robustly synchronized across fast- and slow-gamma frequencies, while MC synchrony was weaker and concentrated in slow-gamma frequencies. Synchrony among both cell types was enhanced by shared glomerular input but was independent of intraglomerular lateral excitation. Cell-type differences in synchrony could also not be traced to any difference in the synchronization of synaptic inhibition. Instead, greater TC than MC synchrony paralleled the more periodic firing among resonant TCs than MCs and emerged in patterns consistent with densely synchronous network oscillations. Collectively, our results thus reveal a mechanism for parallel processing of sensory information in the MOB via differential TC vs. MC synchrony, and further contrast mechanisms driving fast network oscillations in the MOB from those driving the sparse synchronization of irregularly-firing principal cells throughout cortex.


title: GABAB receptor/HCN channel complexes in VTA dopamine neurons limit synaptic inhibition and prevent anxiety-like behavior

abstract: Aversive stimuli inhibiting dopamine neurons in the ventral tegmental area (DAVTA neurons) induce anxiety-like behaviors. The inhibition of DAVTA neurons is prolonged by GABAB receptor (GBR)-activated K+-currents, which exhibit a rapid desensitization of unknown physiological relevance. We now report that GBRs associate via auxiliary KCTD16 subunits with HCN channels, which facilitates activation of hyperpolarization- activated currents (Ih) by GBR-activated K+ currents. Activation of Ih underlies rapid K+ current desensitization in DAVTA neurons and limits GBR-mediated inhibition. Disruption of the GBR/HCN complex in KCTD16-/- mice or blockade of Ih prolongs optogenetically driven inhibition of DAVTA neuron firing. KCTD16-/- mice exhibit an increased anxiety-like behavior in response to stressful stimuli, which is reproduced by in vivo CRISPR/Cas9-mediated KCTD16 ablation in DAVTA neurons or intra-VTA infusion of HCN antagonist to wild-type mice. Our data reveal that GBR-induced Ih protect DAVTA neurons from prolonged GBR- mediated inhibition in response to stressors, which moderates anxiety-like behaviors.


title: Age-Related Differences in Reward-Based Modulation of Sequential Reaching Performance

abstract: Reward can increase the speed and accuracy of movements in both simple and sequential reaching tasks. Two mechanisms are thought to be responsible for this: an increase in maximum velocity, due to increased muscle stiffness, resulting in faster, but energetically inefficient, individual movements; or coarticulation - the blending of sub-movements into single, smoother, more energetically efficient movements. Older adults have shown reduced sensitivity to reward in decision paradigms, but there is little research relating reward and motor performance in older adults. Using a novel online sequential reaching task, we compared the effects of reward on motor performance between young (18-23 years) and older (65-79 years) participants. We found that movement time decreased across training in all groups, and reward invigorated this decrease in both age groups. This suggests that reward is a viable facilitator of motor performance to compensate for age-related motor decline and has the potential for use in the design of rehabilitation programmes for age-related motor deficits or disease.


title: Tuft cell-produced cysteinyl leukotrienes and IL-25 synergistically drivelung type 2 inflammation

abstract:
Aeroallergen sensing by airway epithelial cells can trigger pathogenic immune responses leading to chronic type 2 inflammation, the hallmark of airway diseases such as asthma. Airway tuft cells are specialized chemosensory epithelial cells and the dominant source of the epithelial cytokine IL-25 in the trachea and of cysteinyl leukotrienes (CysLTs) in the naive murine nasal mucosa. The interaction of IL-25 and CysLTs and the contribution of tuft cell-derived CysLTs to the development of allergen-triggered inflammation in the airways has not been clarified. Here we show that inhalation of LTC4 in combination with a subthreshold dose of IL-25 leads to dramatic synergistic induction of type 2 inflammation throughout the lungs, causing rapid eosinophilia, dendritic cell (DC) and inflammatory type 2 innate lymphoid cell (ILC2) expansion, and goblet cell metaplasia. While lung eosinophilia is dominantly mediated through the classical CysLT receptor CysLT1R, type 2 cytokines and activation of innate immune cells require signaling through both CysLT1R and CysLT2R. Tuft cell-specific deletion of the terminal enzyme requisite for CysLT production, Ltc4s, was sufficient to reduce both the innate immune response in the lung - eosinophilia, KLRG1+ ILC2 activation and DC recruitment - and the systemic immune response in the draining lymph nodes after inhalation of the mold aeroallergen Alternaria. Our findings identify surprisingly potent synergy of CysLTs and IL-25 downstream of aeroallergen-trigged activation of airway tuft cells leading to a highly polarized type 2 immune response and further implicate airway tuft cells as powerful modulators of type 2 immunity in the lungs.

One Sentence SummaryTuft cells produce two highly synergistic mediators: LTC4 and IL-25 to cooperatively induce allergen-driven airway inflammation.


title: Tuft cell-produced cysteinyl leukotrienes and IL-25 synergistically initiate lung type 2 inflammation


title: Human neutrophils are not activated by Zika virus but reduce the infection of susceptible cells

abstract: Zika virus (ZIKV) emergence highlighted the need for a deeper understanding on virus-host interaction to pave the development of antiviral therapies. The present work aimed to address the response of neutrophils during ZIKV infection. Neutrophils are an important effector cell in innate immunity involved in the host response to neurotropic arboviruses. Our results indicate that human neutrophils were not permissive to Asian or African ZIKV strains replication. Indeed, after stimulation with ZIKV, neutrophils were not primed against the virus as evaluated by the absence of CD11b modulation, secretion of inflammatory cytokines and granule content, production of reactive oxygen species and neutrophil extracellular traps formation. Overall, neutrophils did not affect ZIKV infectivity. Moreover, ZIKV infection of primary innate immune cells in vitro did not trigger neutrophil migration. However, neutrophil co-cultured with ZIKV susceptible cells (A549) resulted in lower frequencies of infection on A549 cells by cell-to-cell contact. In vivo, neutrophil depletion from immunocompetent mice did not affect ZIKV spreading to the draining lymph nodes. The data suggest human neutrophils do not play a per se antiviral role against ZIKV, but these cells might participate in an infected environment shaping the ZIKV infection in other target cells.