title: Cotranslational folding of a periplasmic protein domain in Escherichia coli

abstract: In Gram-negative bacteria, periplasmic domains in inner membrane proteins are cotranslationally translocated across the inner membrane through the SecYEG translocon. To what degree such domains also start to fold cotranslationally is generally difficult to determine using currently available methods. Here, we apply Force Profile Analysis (FPA) - a method where a translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide - to follow the cotranslational translocation and folding of the large periplasmic domain of the E. coli inner membrane protease LepB in vivo. Membrane insertion of LepBs two N-terminal transmembrane helices is initiated when their respective N-terminal ends reach 45-50 residues away from the peptidyl transferase center (PTC) in the ribosome. The main folding transition in the periplasmic domain involves all but the ~15 most C-terminal residues of the protein and happens when the C-terminal end of the folded part is ~70 residues away from the PTC; a smaller putative folding intermediate is also detected. This implies that wildtype LepB folds post-translationally in vivo, and shows that FPA can be used to study both co- and post-translational protein folding in the periplasm.


title: Hepatocyte nuclear factor 4a and glucocorticoid receptor coordinately regulate lipid metabolism in mice fed a high-fat-high-sugar diet

abstract: Hepatocyte nuclear factor 4 (HNF4) and glucocorticoid receptor (GR), master regulators of liver metabolism, are down-regulated in fatty liver diseases. The present study was aimed to elucidate the role of down-regulation of HNF4 and GR in fatty liver and hyperlipidemia. Adult mice with liver-specific heterozygote and knockout (knockout) of HNF4 were fed a low-fat diet (LFD) or a high-fat-high-sugar diet (HFHS) for 15 days. Compared to LFD-fed mice, HFHS-fed wildtype mice had hepatic induction of lipid catabolic genes and down-regulation of lipogenic genes. Compared to HFHS-fed wildtype mice, HNF4 heterozygote mice had down-regulation of lipid catabolic genes, induction of lipogenic genes, and increased hepatic and blood levels of lipids, whereas HNF4 knockout mice had mild hypolipidemia, down-regulation of lipid-efflux genes, but induction of genes for uptake/storage of lipids. Sterol-regulatory-element-binding protein-1c (SREBP-1C), a master lipogenic regulator, was induced in HFHS-fed HNF4 heterozygote mice. In reporter assays, HNF4 potently inhibited the transactivation of mouse and human SREBP-1C promoter by liver X receptor. Surprisingly, nuclear GR proteins were gene-dosage-dependently decreased in HNF4 heterozygote and knockout mice. HFHS-fed mice with liver-specific knockout of GR had increased hepatic lipids and induction of SREBP-1C and PPAR{gamma}. In reporter assays, GR and HNF4 synergistically/additively induced lipid catabolic genes. Phosphorylation of AMP-activated protein kinase (AMPK), a key GR modulator, was dramatically decreased in HNF4 knockout mice. Thus, cooperative induction of lipid catabolic genes and suppression of lipogenic genes by HNF4 and GR, modulated by AMPK, may mediate the early resistance to HFHS-induced fatty liver and hyperlipidemia.

category: molecular biology


title: Capacity of countries to reduce biological invasions

abstract: The extent and impacts of biological invasions on biodiversity are largely shaped by an array of socio-ecological predictors, which exhibit high variation among countries. Yet a global synthetic perspective of how these factors vary across countries is currently lacking. Here, we investigate how a set of five socio-ecological predictors (Governance, Trade, Environmental Performance, Lifestyle and Education, Innovation) explain i) country-level established alien species (EAS) richness of eight taxonomic groups, and ii) country capacity to prevent and manage biological invasions and their impacts. Trade and Governance together best predicted the average EAS richness, increasing variance explained by up to 54% compared to models based on climatic and spatial variables only. Country-level EAS richness increased strongly with Trade, whereas high level of Governance resulted in lower EAS richness. Historical (1996) levels of Governance and Trade better explained response variables than current (2015) levels. Thus, our results reveal a historical legacy of these two predictors with profound implications for the future of biological invasions. We therefore used Governance and Trade to define a two-dimensional socio-economic space in which the position of a country captures its capacity to address issues of biological invasions. Our results provide novel insights into the complex relationship between socio-ecological predictors and biological invasions. Further, we highlight the need for designing better policies and management measures for alien species, and for integrating biological invasions in global environmental scenarios.

category: ecology


title: Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function

abstract: The circadian clock is an important adaptation to life on earth. Here, we use machine learning to predict complex temporal circadian gene expression patterns in Arabidopsis. Most significantly, we classify circadian genes using DNA sequence features generated from public genomic resources, with no experimental work or prior knowledge needed. We use model explanation to rank DNA sequence features, observing transcript-specific combinations of potential circadian regulatory elements that discriminate temporal phase of expression. Model interpretation/explanation provides the backbone of our methodological advances, giving insight into biological processes and experimental design. Next, we use model interpretation to optimize sampling strategies when we predict circadian transcripts using reduced numbers of transcriptomic timepoints, saving both time and money. Finally, we predict the circadian time from a single transcriptomic timepoint, deriving novel marker transcripts that are most impactful for accurate prediction, this could facilitate the identification of altered clock function from existing datasets.

category: genomics


title: Cancer relevance of human genes

abstract:
BackgroundIt is unclear how many of genes contribute to the biology of cancer. We hypothesize that genes that interact with core cancer gene (CCG) in a protein-protein interaction network (PPI) may have functional importance.

MethodsWe categorized genes into 1- (n=6791), 2- (n=7724), 3- (n=1587), and >3-steps (n=362) removed from the nearest CCG in the STRING PPI and demonstrate that the cancer-biology related functional contribution of the genes in these different neighborhood categories decreases as their distance from the CCGs increases.

ResultsGenes closer to cancer genes manifest greater connectedness in the network, show greater importance in maintaining cell viability in a broad range of cancer cells in vitro, are also under greater negative germline selection pressure in the healthy populations, and have higher somatic mutation frequency and cancer effect.

ConclusionsApproximately 70% of human genes are 1 or 2 steps removed from cancer genes in protein network and show functional importance in cancer-biology. These results suggest that the universe of cancer-relevant genes extends to thousands of genes that can contribute functional effects when dysregulated.


title: NeuroSCORE: A Genome-wide Omics-Based Model to Identify Candidate Disease Genes of the Central Nervous System

abstract: To identify and prioritize candidate disease genes of the central nervous system (CNS) we created the Neurogenetic Systematic Correlation of Omics-Related Evidence (NeuroSCORE). We used five genome-wide metrics highly associated with neurological phenotypes to score 19,598 protein-coding genes. Genes scored one point per metric, resulting in a range of scores from 0-5. Approximately 13,000 genes were then paired with phenotype data from the Online Mendelian Inheritance in Man (OMIM) database. We used logistic regression to determine the odds ratio of each metric and compared genes scoring 1+ to cause a known CNS-related phenotype compared to genes that scored zero. We tested NeuroSCORE using microarray copy number variants (CNVs) in case-control cohorts, mouse model phenotype data, and gene ontology (GO) and pathway analyses. NeuroSCORE identified 8,296 genes scored [≥]1, of which 1,580 are "high scoring" genes (scores [≥]3). High scoring genes are significantly associated with CNS phenotypes (OR=5.5, p<2x10-16), enriched in case CNVs, and enriched in mouse ortholog genes associated with behavioral and nervous system abnormalities. GO and pathway analyses showed high scoring genes were enriched in chromatin remodeling, mRNA splicing, dendrite development, and neuron projection. OMIM has no phenotype for 1,062 high scoring genes (67%). Top scoring genes include ANKRD17, CCAR1, CLASP1, DOCK9, EIF4G2, G3BP2, GRIA1, MAP4K4, MARK2, PCBP2, RNF145, SF1, SYNCRIP, TNPO2, and ZSWIM8. NeuroSCORE identifies and prioritizes CNS-disease candidate genes, many not yet associated with any phenotype in OMIM. These findings can help direct future research and improve molecular diagnostics for individuals with neurological conditions.


title: An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

abstract: The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with experimental data. Its regulation appears to be implemented in part through chromosomal localization, as rRNA genes are typically closer to the origin of replication than tRNA genes and thus have increasingly higher gene dosage at faster growth. At the highest growth rates in E. coli, the tRNA/rRNA ratio appears to be regulated entirely through this effect.

category: systems biology


title: Discovery of fungal-specific targets and inhibitors using chemical phenotyping of pathogenic spore germination

abstract: There is a critical need for new antifungal drugs; however, the lack of available fungal-specific targets is a major hurdle in the development of antifungal therapeutics. Spore germination is a differentiation process absent in humans that could harbor uncharacterized fungal-specific targets. To capitalize on this possibility, we developed novel phenotypic assays to identify and characterize inhibitors of spore germination of the human fungal pathogen Cryptococcus. Using these assays, we carried out a high throughput screen of ~75,000 drug-like small molecules and identified and characterized 191 novel inhibitors of spore germination, many of which also inhibited yeast replication and demonstrated low cytotoxicity against mammalian cells. Using an automated, microscopy-based, quantitative germination assay (QGA), we discovered that germinating spore populations can exhibit unique phenotypes in response to chemical inhibitors. Through the characterization of these spore population dynamics in the presence of the newly identified inhibitors, we classified 6 distinct phenotypes based on differences in germination synchronicity, germination rates, and overall population behavior. Similar chemical phenotypes were induced by inhibitors that targeted the same cellular function or had shared substructures. Leveraging these features, we used QGAs to identify outliers among compounds that fell into similar structural groups and thus refined relevant structural moieties, facilitating target identification. This approach led to the identification of complex II of the electron transport chain as the putative target of a promising structural cluster of germination inhibitory compounds. These inhibitors showed high potency against Cryptococcus spore germination, while maintaining low cytotoxicity against mammalian cells, making them prime candidates for development into novel antifungal therapeutics.

category: microbiology


title: Landscape composition mediates suppression of major pests by natural enemies in conventional cruciferous vegetables

abstract:
BackgroundConservation biological control provides an environment-friendly approach to improve the efficacy of natural enemies. Although numerous studies have demonstrated the potential of semi-natural habitats in promoting biological control in organic or unsprayed agroecosystems, few studies were conducted in conventional agricultural fields. In this study, we investigated the effects of landscape composition on the major pests of cruciferous vegetables and on the assemblages of their natural enemies in southeastern China.

ResultsHabitat diversity, particularly increasing grassland proportion in the landscape, had a positive impact in controlling both small-sized pests (aphids, leaf miners, thrips and flea beetles) and Plutella xylostella. This increasing proportion also promoted greater abundance and diversity of canopy-dwelling predators, more forests supported a higher diversity of airborne enemies (parasitoids and canopy-dwelling predators) as well as a higher abundance of ground-dwelling predators. A general increase in habitat diversity was beneficial to parasitoids and ground-dwelling predators. Additionally, the proportion of forest, grassland, and non-cruciferous vegetable area, as well as habitat diversity, affected the compositions of natural enemy communities. Moreover, inconsistent effects of non-cruciferous and grassland habitats were found between sampling regions for small-sized pests and canopy-dwelling predators. Moreover, the scale at which pests and natural enemies abundance and richness responded most to landscape composition varied with their feeding range and dispersal ability.

ConclusionOur study provides evidence that increasing the amount of semi-natural habitats and habitat diversity can result in lower pest and higher natural enemy abundance in conventional cruciferous agroecosystems. Regional conditions and spatial scales also should be considered in designing the agricultural landscape mosaic.


title: Sex pheromone signal and stability covary with fitness

abstract: If sexual signals are costly to produce or maintain, covariance between signal expression and fitness is expected. This signal-fitness covariance is important evolutionarily, because it can contribute to the maintenance of genetic variation in signal traits, despite selection from mate preferences. Chemical signals, such as moth sex pheromones, have traditionally been assumed to be stereotypical species-recognition signals, but their relationship with fitness is unclear. Here we test the hypothesis that for chemical signals that are primarily used for conspecific mate finding, there is covariation between signal properties and fitness in the noctuid moth Heliothis subflexa. Additionally, as moth signals are synthesized de novo every night throughout the females reproductive life, the maintenance of the signal can be costly. Therefore, we also hypothesized that fitness covaries with signal stability (i.e. the lack of intra-individual variation over time). We measured among- and within-individual variation in pheromone amount and composition as well as fecundity, fertility, and fitness in two independent groups of females that differed in the time in between two consecutive pheromone samples. In both groups, we found reproductive success and longevity to be correlated with pheromone amount, composition, and stability, supporting both our hypotheses. This study is the first to report a correlation between fitness and sex pheromone composition in moths, solidifying previous indications of condition-dependent moth pheromones and highlighting how signal-fitness covariance may contribute to heritable variation in chemical signals both among and within individuals.

category: evolutionary biology


title: Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis

abstract: Dosage compensation (DC) is a mechanism by which X chromosome transcription is equalized in the somatic cells of both males and females. In male fruit flies, expression levels of the X-chromosome are increased two-fold to compensate for their single X chromosome. In testis, dosage compensation is thought to cease during meiosis, however, the timing and degree of the resulting transcriptional suppression is difficult to separate from global meiotic downregulation of each chromosome. To address this, we analyzed testis single-cell RNA-sequencing (scRNA-seq) data from two Drosophila melanogaster strains. We found evidence that the X chromosome is equally transcriptionally active as autosomes in somatic and pre-meiotic cells, and less transcriptionally active than autosomes in meiotic and post-meiotic cells. In cells experiencing dosage compensation, close proximity to MSL (male-specific lethal) chromatin entry sites (CES) correlates with increased X chromosome transcription. We found low or undetectable level of germline expression of most msl genes, mle, roX1 and roX2 via sequencing or RNA-FISH, and no evidence of germline nuclear roX1/2 localization. Our results suggest that, although DC occurs in somatic and premeiotic germ cells in Drosophila testis, there might be non-canonical factors involved in the dosage compensation. The single-cell expression patterns and enrichment statistics of detected genes can be explored interactively in our database: https://zhao.labapps.rockefeller.edu/gene-expr/.

category: genetics


title: Depth Dataset Using Microsoft Kinect-v2

abstract: In biomedical imaging studies, numerous methods have been used to capture human data, mostly by using magnetic resonance imaging (MRI) and computed tomography (CT). However, due to being inexpensive and accessibility of Microsoft Kinect, its usage has been significantly increased in recent years. In this study, we aimed to represent the procedure of data acquisition, which includes a set of depth images from individuals back surfaces. The goal of image acquisition is to investigate spinal deformities and landmark detection of the back surface. Traditional imaging systems are challenging, most notably because of ionized beams in the data acquisition process, which has not been solved yet. Indeed, noninvasiveness is the most crucial advantage of our study. Our imaging system was set in a dim laboratory, and the University approved the ethical letter of Medical Sciences before data acquisition. After that, the subjects (total 105; 50 women and 55 men) were recruited, and data images were captured from the back surface. Then, we increased the imaging data size by using the augmentation method to use deep learning methods in future works. Finally, this Dataset leads us to the desired output in our study procedure.

category: bioengineering


title: Temporo-cerebellar connectivity underlies timing constraints in audition

abstract:
The flexible and efficient adaptation to dynamic, rapid changes in the auditory environment likely involves generating and updating of internal models. Such models arguably exploit connections between the neocortex and the cerebellum, supporting proactive adaptation. Here we test the functional mechanisms associated with temporo-cerebellar connectivity, verifying these mechanisms for speech sounds. First, we identify lesion-specific deficits for the encoding of short timescale spectro-temporal non-speech and speech properties in patients with left posterior temporal cortex stroke. Second, using lesion-guided probabilistic tractography in healthy participants, we reveal bidirectional temporo-cerebellar connectivity with cerebellar dentate nuclei and crura I/II. These findings imply that the encoding and modeling of rapidly modulated auditory spectro-temporal properties engage a temporo-cerebellar interface. The data further support the conjecture that proactive adaptation to a dynamic environment via internal models is a generalizable principle.

Significance StatementAsymmetric sampling in time, the principle of duration-sensitive hemispheric specialization of the cerebral cortex in the sensory decomposition of sound, is a widely tested hypothesis in auditory neuroscience. This functional organization is mirrored in the cerebellar cortex, implicated in the internal forward-modeling of sensory feedback that arises from motor actions. The potential structural and functional integration of these systems is not well understood. Using a unique combination of causal lesion-symptom mapping in persons with temporal lobe damage and diffusion-weighted magnetic resonance neuroimaging in healthy persons, we identify one key missing link and provide evidence for cross-lateral temporo-cerebellar connectivity using probabilistic white matter fiber tractography. These cerebellar-pontine-temporal cortex connections not only support asymmetric sampling in time but also establish the basis for a generalizable role of cerebellar forward-modeling in sensation beyond the monitoring of sensory feedback in the motor domain.

category: neuroscience


title: Delayed auditory encoding and variable representation of stimulus regularity in cerebellar lesion patients

abstract: The dynamic and fleeting nature of sound necessitates the rapid encoding and use of information distributed over time. Here we investigated cerebellar contributions to these abilities. We measured EEG from cerebellar patients and healthy controls while they listened to "oddball" sound sequences consisting of infrequent pitch-deviant and frequent standard tones. Inter-stimulus-intervals were temporally regular (600 ms) or irregular (200-1000 ms). This allowed probing early event-related potentials (ERP; P50, N100) that reflect repetitive and changing stimulus characteristics in temporally regular or less (irregular) predictable sequences. Further, time-frequency data provided an index of temporal processing variability at the stimulation frequencies. We expected that cerebellar lesions lead to aberrant encoding and use of auditory information, reflected in the ERP morphology of peak amplitudes, latencies and typical suppression effects linked to stimulus predictability. Results confirm longer P50 peak latencies in patients and variable processing at stimulation frequencies covarying with the location of cerebellar damage. These findings further support the idea that the cerebellum might play a generalizable role in the encoding of auditory stimulation over time.


title: Comparing Methods for Species Tree Estimation With Gene Duplication and Loss

abstract: Species tree inference from gene trees is an important part of biological research. One confounding factor in estimating species trees is gene duplication and loss which can lead to gene trees with multiple copies of the same gene. In recent years there have been several new methods developed to address this problem that have substantially improved on earlier methods; however, the best performing methods (ASTRAL-Pro, ASTRID-multi, and FastMulRFS) have not yet been directly compared. In this study, we compare ASTRAL-Pro, ASTRID-multi, and FastMulRFS under a wide variety of conditions. Our study shows that while all three have very good accuracy, nearly the same under many conditions, ASTRAL-Pro and ASTRID-multi are more reliably accurate than FastMuLRFS, and that ASTRID-multi is often faster than ASTRAL-Pro. The datasets generated for this study are freely available in the Illinois Data Bank at https://databank.illinois.edu/datasets/IDB-2418574


title: Huntingtin CAG expansion impairs germ layer patterning in synthetic human gastruloids through polarity defects.

abstract: Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG repeats in the Huntingtin gene (HTT). While HD has been shown to have a developmental component, how early during human embryogenesis the HTT-CAG expansion can cause embryonic defects remains unknown. Here, we demonstrate a specific and highly reproducible CAG length-dependent phenotypic signature in a synthetic model for human gastrulation derived from human embryonic stem cells (hESCs). Specifically, we observed a reduction in the extension of the ectodermal compartment that is associated with enhanced ACTIVIN signaling. Surprisingly, rather than a cell-autonomous effect, tracking the dynamics of TGF{beta} signaling demonstrated that HTT-CAG expansion perturbs the spatial restriction of ACTIVIN response. This is due to defects in the apicobasal polarization in the context of the polarized epithelium of the gastruloid, leading to ectopic subcellular localization of TGF{beta} receptors. This work refines the earliest developmental window for the prodromal phase of HD to the first two weeks of human development as modeled by our gastruloids.

category: developmental biology


title: A behavioral syndrome linking boldness and flexibility facilitates invasion success in sticklebacks

abstract: For a species to expand its range, it needs to be good at dispersing and also capable of exploiting resources and adapting to different environments. Therefore, behavioral and cognitive traits could play key roles in facilitating invasion success. Here, we show that dispersing sticklebacks are bold, while sticklebacks that have recently established in a new region are flexible. Moreover, boldness and flexibility are negatively correlated with one another at the individual, family and population levels. Multiple lines of evidence suggest that the divergence in boldness and flexibility is likely to be evolutionary in origin. If boldness is favored in invaders during the initial dispersal stage, while flexibility is favored in recent immigrants during the establishment stage, then the link between boldness and flexibility could generate positive correlations between successes during both dispersal and establishment, and therefore play a key role in facilitating colonization success in sticklebacks and other organisms.

category: animal behavior and cognition


title: Expansion of cortical layers 2 and 3 in human left temporal cortex associates with verbal intelligence

abstract: The expansion of supragranular cortical layers is thought to have enabled evolutionary development of human cognition and language. However, whether increased volume of supragranular cortical layers can actually support greater cognitive and language abilities in humans has not been demonstrated. Here, we find that subjects with higher general and verbal intelligence test (VIQ) scores have selectively expanded layers 2 and 3 only in the left temporal cortex, an area associated with language and IQ-test performance. This expansion is accompanied by lower neuron densities and larger cell-body size. Furthermore, individuals with higher VIQ scores had neurons with larger dendritic trees in left temporal cortex, potentially impacting their function. Indeed, neurons of subjects with higher VIQ scores had faster action potential upstroke kinetics, which improves information processing. These data show that expansion of supragranular layer volume, cortical and cellular micro-architecture and function are associated with improved verbal mental ability in human subjects.


title: TNF signalling fine-tunes Langerhans cell transcriptional programmes mediating adaptive immunity.

abstract: Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels, coordinating both immunogenic and tolerogenic immune responses. To determine molecular switches directing induction of LC immune activation, we performed mathematical modelling of gene regulatory networks identified by single cell RNA sequencing of LCs exposed to TNF, a key pro-inflammatory signal produced by the skin. Our approach delineated three programmes of LC phenotypic activation (immunogenic, tolerogenic or ambivalent), and confirmed that TNF enhanced LC immunogenic programming. Through regulon analysis followed by mutual information modelling, we identified IRF1 as the key transcription factor for the regulation of immunogenicity in LCs. Application of a mathematical toggle switch model, coupling IRF1 with tolerance-inducing transcription factors, determined the key set of transcription factors regulating the switch between tolerance and immunogenicity, and correctly predicted LC behaviour in LCs derived from different body sites. Our findings provide a mechanistic explanation of how combinatorial interactions between different transcription factors can coordinate specific transcriptional programmes in human LCs, interpreting the microenvironmental context of the local tissue microenvironments.


title: Ex vivo delivery of regulatory T cells for control of alloimmune priming in the donor lung

abstract:
Survival after lung transplantation (LTx) is hampered by uncontrolled inflammation and alloimmunity. Regulatory T cells (Tregs) are being studied for post-implantation cell therapy in solid organ transplantation. Whether these systemically administered Tregs can function at the appropriate location and time is an important concern. We hypothesized that in vitro expanded, recipient-derived Tregs can be delivered to donor lungs prior to LTx via ex vivo lung perfusion (EVLP), maintaining their immunomodulatory ability.

In a rat model, Wistar Kyoto (WKy) CD4+CD25high Tregs were expanded in vitro prior to EVLP. Expanded Tregs were administered to Fisher 344 (F344) donor lungs during EVLP; left lungs were transplanted into WKy recipients. Treg localization and function post-transplant were assessed. In a proof-of-concept experiment, cryopreserved expanded human CD4+CD25+CD127low Tregs were thawed and injected into discarded human lungs during EVLP. Rat Tregs entered the lung parenchyma and retained suppressive function. Expanded Tregs had no adverse effect on donor lung physiology during EVLP; lung water as measured by wet- to-dry weight ratio was reduced by Treg therapy. The administered cells remained in the graft at 3 days post-transplant where they reduced activation of intragraft effector CD4+ T cells; these effects were diminished by day 7. Human Tregs entered the lung parenchyma during EVLP where they expressed key immunoregulatory molecules (CTLA4+, 4-1BB+, CD39+, and CD15s+). Pre-transplant Treg administration can inhibit alloimmunity within the lung allograft at early time points post- transplant. Our organ-directed approach has potential for clinical translation.

category: immunology


title: HGC: fast hierarchical clustering for large-scale single-cell data

abstract:
Clustering is a key step in revealing heterogeneities in single-cell data. Cell heterogeneity can be explored at different resolutions and the resulted varying cell states are inherently nested. However, most existing single-cell clustering methods output a fixed number of clusters without the hierarchical information. Classical hierarchical clustering provides dendrogram of cells, but cannot scale to large datasets due to the high computational complexity. We present HGC, a fast Hierarchical Graph-based Clustering method to address both problems. It combines the advantages of graph-based clustering and hierarchical clustering. On the shared nearest neighbor graph of cells, HGC constructs the hierarchical tree with linear time complexity. Experiments showed that HGC enables multiresolution exploration of the biological hierarchy underlying the data, achieves state-of-the-art accuracy on benchmark data, and can scale to large datasets. HGC is freely available for academic use at https://www.github.com/XuegongLab/HGC.

Contactzhangxg@tsinghua.edu.cn, stevenhuakui@gmail.com

category: bioinformatics


title: Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data

abstract:
SAD phasing can be challenging when the signal-to-noise ratio is low. In such cases, having an accurate estimate of substructure content can determine whether or not the substructure of anomalous scatterer positions can successfully be determined. We propose a likelihood-based target function to accurately estimate the strength of the anomalous scattering contribution directly from measured intensities, determining a complex correlation parameter relating the Bijvoet mates as a function of resolution. This gives a novel measure of intrinsic anomalous signal. The SAD likelihood target function also accounts for correlated errors in the measurement of intensities from Bijvoet mates, which can arise from the effects of radiation damage. When the anomalous signal is assumed to come primarily from a substructure comprised of one anomalous scatterer with a known value of f" and when the protein composition of the crystal is estimated correctly, the refined complex correlation parameters can be interpreted in terms of the atomic content of the primary anomalous scatterer, before the substructure is known. The maximum likelihood estimation of substructure content was tested on a curated database of 357 SAD cases with useful anomalous signal. The prior estimates of substructure content are highly correlated to the content determined by phasing calculations, with a correlation coefficient (on a log-log basis) of 0.72.

SynopsisAn intensity-based likelihood method is provided to estimate scattering from an anomalous substructure considering the effect of measurement errors in Bijvoet pairs and correlations between those errors.

category: biophysics


title: Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

abstract: DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn which is slightly different from that of native B-form DNA (10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.


title: The Human walking kinematic model combined with upper and lower limb movement

abstract: The purpose of this study is to build a relatively complete human walking kinematic model. This model is combined with the rolling-foot model (lower limb) and multi-rod swinging model (upper limb) connected by COM. We calculated the velocity of COM and other critical joints of the upper limb by marker point capture experiment using the high-speed camera. This research shows that the hand joint velocity measured through the experiment can achieve high coincidence with that calculated by the theoretical model given specific inputs. Moreover, the common pattern of upper limb angles is also studied for an accurate description. The proposed kinematic model is expected to forecast desired motion intention for better compliance by the rehabilitation and assistive robots.


title: Structure of human Nav1.5 reveals the fast inactivation-related segments as a mutational hotspot for the Long QT Syndrome

abstract: Nav1.5 is the primary voltage-gated Na+ (Nav) channel in the heart. Mutations of Nav1.5 are associated with various cardiac disorders exemplified by the type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). E1784K is a common mutation that has been found in both LQT3 and BrS patients. Here we present the cryo-EM structure of the human Nav1.5-E1784K variant at an overall resolution of 3.3 [A]. Structural mapping of 91 and 178 point mutations that are respectively associated with LQT3 and BrS reveals a unique distribution pattern for LQT3 mutations. Whereas the BrS mutations spread evenly on the structure, LQT3 mutations are mainly clustered to the segments in repeats III and IV that are involved in gating, voltage-sensing, and particularly inactivation. A mutational hotspot involving the fast inactivation segments is identified and can be mechanistically interpreted by our "door wedge" model for fast inactivation. The structural analysis presented here, with a focus on the impact of disease mutations on inactivation and late sodium current, establishes a structure-function relationship for the mechanistic understanding of Nav1.5 channelopathies.


title: Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)

abstract: Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3 untranslated regions (3UTRs) of mRNA, but the identity of functional targets remains unknown. Here we used iCLIP to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of target mRNAs largely in 3UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more "U/TAG" motifs compared to targets bound non-productively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute MSI2 loss. Eukaryotic elongation factor 3A (EIF3A) was determined to be an immediate, direct target. We propose that MSI2 down-regulation of EIF3A amplifies these effects on the proteome. Our results also underscore the challenges in defining functional targets of RBP since mere binding does not imply a discernible functional interaction.

category: cancer biology


title: NEDD4 Regulates Ubiquitination and Stability of the Cell adhesion Molecule IGPR-1 via Lysosomal Pathway

abstract: The cell adhesion molecule immunoglobulin and proline-rich receptor-1 (IGPR-1) regulates various critical cellular processes including, cell-cell adhesion, mechanosensing and autophagy. However, the molecular mechanisms governing IGPR-1 cell surface expression levels remains unknown. In the present study, we used an in vitro ubiquitination assay and identified ubiquitin E3 ligase NEDD4 and the ubiquitin conjugating enzyme UbcH6 involved in the ubiquitination of IGPR-1. In vitro GST-pulldown and in vivo co-immunoprecipitation assays demonstrated that NEDD4 binds to IGPR-1. Over-expression of wild-type NEDD4 downregulated IGPR-1 and deletion of WW domains (1-4) of NEDD4 revoked its effects on IGPR-1. Similarly, knockdown of NEDD4 increased IGPR-1 levels in A375 melanoma cells. Furthermore, deletion of 57 amino acids encompassing polyproline rich (PPR) motif on the C-terminus of IGPR-1 nullified the binding of NEDD4 with IGPR-1. Moreover, we demonstrate that NEDD4 promotes K48- and K63-dependent polyubiquitination of IGPR-1. The NEDD4-mediated polyubiquitination of IGPR-1 stimulated lysosomal degradation of IGPR-1 as the treatment of cells with the lysosomal inhibitors, bafilomycine and ammonium chloride increased IGPR-1 levels in the HEK-293 cells ectopically expressing IGPR-1 and in multiple human skin melanoma cell lines. Hence, these findings suggest that ubiquitin E3 ligase NEDD4 is a key regulator of IGPR-1 with a significant implication in the therapeutic targeting of IGPR-1.

category: cell biology


title: Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1

abstract: In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.


title: Adaptive maternal effects in early life history traits help to maintain ecological resilience in novel environments for two contrasting Senecio species

abstract: Maternal effects can maintain fitness across environmental conditions regularly experienced by a population. However, the consequences of maternal effects for ecological resilience in novel environments remain poorly understood. We produced seeds by breeding field-collected individuals of two closely related, but ecologically distinct, species of Sicilian daisy (Senecio, Asteraceae) in a quantitative genetics design. Using siblings of the same families, we quantified seedling root morphology in the laboratory, and planted seeds at four elevations that included the native elevation of each species. Seedling survival of both species was high at their native elevations, but declined at the novel elevation furthest from their native range, demonstrating adaptive divergence. Seedling development rate changed with elevation similarly for both species, and aligned with selection for faster development at lower elevation and slower development at higher elevation. Selection on paternal (sire) variance in development rate was consistent across elevation, and opposed phenotypic selection in the novel elevations. By contrast, selection on maternal variance in development rate changed with elevation and aligned with the direction of selection at both the native and novel elevations, suggesting that maternal effects underlying plasticity in development rate can increase fitness in novel environments. Selection on root morphology was only strong for the high elevation species, and occurred in the direction of the native phenotype for maternal variance, but not for sire variance. Together, these results suggest that maternal variation in development time plasticity and root architecture can increase ecological resilience in novel habitats, despite theory suggesting that they may reduce fitness in such situations.


title: Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies

abstract: The increasing prevalence of SARS-CoV-2 variants with mutations in the spike protein has raised concerns that recovered individuals may not be protected from reinfection and that current vaccines will become less effective. The B.1.1.7 isolate identified in the United Kingdom and B.1.351 isolate identified in the Republic of South Africa encode spike proteins with multiple mutations in the S1 and S2 subunits. In addition, variants have been identified in Columbus, Ohio (COH.20G/677H), Europe (20A.EU2) and in domesticated minks. Analysis by antibody neutralization of pseudotyped viruses showed that convalescent sera from patients infected prior to the emergence of the variant viruses neutralized viruses with the B.1.1.7, B.1.351, COH.20G/677H Columbus Ohio, 20A.EU2 Europe and mink cluster 5 spike proteins with only a minor decrease in titer compared to that of the earlier D614G spike protein. Serum specimens from individuals vaccinated with the BNT162b2 mRNA vaccine neutralized D614G virus with titers that were on average 7-fold greater than convalescent sera. Vaccine elicited antibodies neutralized virus with the B.1.1.7 spike protein with titers similar to D614G virus and neutralized virus with the B.1.351 spike with, on average, a 3-fold reduction in titer (1:500), a titer that was still higher than the average titer with which convalescent sera neutralized D614G (1:139). The reduction in titer was attributable to the E484K mutation in the RBD. The B.1.1.7 and B.1.351 viruses were not more infectious than D614G on ACE2.293T cells in vitro but N501Y, an ACE2 contacting residue present in the B.1.1.7, B.1.351 and COH.20G/677H spike proteins caused higher affinity binding to ACE2, likely contributing to their increased transmissibility. These findings suggest that antibodies elicited by primary infection and by the BNT162b2 mRNA vaccine are likely to maintain protective efficacy against B.1.1.7 and most other variants but that the partial resistance of virus with the B.1.351 spike protein could render some individuals less well protected, supporting a rationale for the development of modified vaccines containing E484K.


title: A human antibody with blocking activity to RBD proteins of multiple SARS-CoV-2 variants including B.1.351 showed potent prophylactic and therapeutic efficacy against SARS-CoV-2 in rhesus macaques

abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease-2019 (COVID-19), interacts with the host cell receptor angiotensin-converting enzyme 2 (hACE2) via its spike 1 protein for infection. After the virus sequence was published, we identified two potent antibodies against SARS-CoV-2 RBD from antibody libraries using a phage-to-yeast (PtY) display platform in only 10 days. Our lead antibody JMB2002, now in a phase I clinical trial, showed broad-spectrum in vitro blocking activity against hACE2 binding to the RBD of multiple SARS-CoV-2 variants including B.1.351 that was reportedly much more resistant to neutralization by convalescent plasma, vaccine sera and some clinical stage neutralizing antibodies. Furthermore, JMB2002 has demonstrated complete prophylactic and potent therapeutic efficacy in a rhesus macaque disease model. Prophylactic and therapeutic countermeasure intervention of SARS-CoV-2 using JMB2002 would likely slow down the transmission of currently emerged SARS-CoV-2 variants and result in more efficient control of the COVID-19 pandemic.


title: Long non-coding RNAs bind to proteins relevant to the ethanol tolerance in yeast: a systems biology view

abstract: The ethanol disturbs the cell cycle, transcription, translation, protein folding, cell wall, membranes, and many Saccharomyces cerevisiae metabolic processes. Long non-coding RNAs (lncRNAs) are regulatory molecules binding onto the genome or proteins. The number of lncRNAs described for yeast is still scarce, and little is known concerning their roles in the system. There is a lack of knowledge concerning how lncRNAs are responsive to the ethanol tolerance in yeast and whether they act in this tolerance. Hence, by using RNA-Seq data from S. cerevisiae strains with different ethanol tolerance phenotypes, we found the severe ethanol responsive lncRNAs. We modeled how they participate in the ethanol tolerance by analyzing lncRNA-protein interactions. The results showed that the EtOH tolerance responsive lncRNAs, in both higher tolerant and lower tolerant phenotypes, work on different pathways: cell wall, cell cycle, growth, longevity, cell surveillance, ribosome biogenesis, intracellular transport, trehalose metabolism, transcription, and nutrient shifts. In summary, lncRNAs seems to interconnect essential systems modules to overcome the ethanol stress. Finally, here we also found the most extensive catalog of lncRNAs in yeast.


title: Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants.

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with amino-acid substitutions and deletions in spike protein (S) can reduce the effectiveness of monoclonal antibodies (mAbs) and may compromise immunity induced by vaccines. We report a polyclonal, fully human, anti-SARS-CoV-2 immunoglobulin produced in transchromosomic bovines (Tc-hIgG-SARS-CoV-2) hyperimmunized with two doses of plasmid DNA encoding the SARS-CoV-2 Wuhan strain S gene, followed by repeated immunization with S protein purified from insect cells. The resulting Tc-hIgG-SARS-CoV-2, termed SAB-185, efficiently neutralizes SARS-CoV-2, and vesicular stomatitis virus (VSV) SARS-CoV-2 chimeras in vitro. Neutralization potency was retained for S variants including S477N, E484K, and N501Y, substitutions present in recent variants of concern. In contrast to the ease of selection of escape variants with mAbs and convalescent human plasma, we were unable to isolate VSV-SARS-CoV-2 mutants resistant to Tc-hIgG-SARS-CoV-2 neutralization. This fully human immunoglobulin that potently inhibits SARS-CoV-2 infection may provide an effective therapeutic to combat COVID-19.


title: Targeting CTP Synthetase 1 to Restore Interferon Induction and Impede Nucleotide Synthesis in SARS-CoV-2 Infection

abstract: The newly emerged SARS-CoV-2 caused a global pandemic with astonishing mortality and morbidity. The mechanisms underpinning its highly infectious nature remain poorly understood. We report here that SARS-CoV-2 exploits cellular CTP synthetase 1 (CTPS1) to promote CTP synthesis and suppress interferon (IFN) induction. Screening a SARS-CoV-2 expression library identified ORF7b and ORF8 that suppressed IFN induction via inducing the deamidation of interferon regulatory factor 3 (IRF3). Deamidated IRF3 fails to bind the promoters of classic IRF3-responsible genes, thus muting IFN induction. Conversely, a shRNA-mediated screen focused on cellular glutamine amidotransferases corroborated that CTPS1 deamidates IRF3 to inhibit IFN induction. Functionally, ORF7b and ORF8 activate CTPS1 to promote de novo CTP synthesis while shutting down IFN induction. De novo synthesis of small-molecule inhibitors of CTPS1 enabled CTP depletion and IFN induction in SARS-CoV-2 infection, thus impeding SARS-CoV-2 replication. Our work uncovers a strategy that a viral pathogen couples immune evasion to metabolic activation to fuel viral replication. Inhibition of the cellular CTPS1 offers an attractive means for developing antiviral therapy that would be resistant to SARS-CoV-2 mutation.


title: Intraspecific trait changes have large impacts on community functional composition but do not affect ecosystem function

abstract:
O_LIPlant functional traits can provide a more mechanistic understanding of community responses to global change and effects on ecosystem functions. In particular, nitrogen enrichment shifts trait composition by promoting dominance of fast growing, acquisitive plants (with high specific leaf area [SLA] and low leaf dry matter content [LDMC]), and such fast species have higher aboveground biomass production. Changes in mean trait values can be due to a shift in species identity, a shift in species relative abundance and/or a shift in intraspecific trait values. However, we do not know the relative importance of these three shifts in determining responses to global change and effects on function.
C_LIO_LIWe quantified the relative importance of composition, abundance and intraspecific shifts in driving variation in SLA and LDMC. We collected leaf samples in a large grassland experiment, which factorially manipulates functional composition (slow vs. fast species), plant species richness, nitrogen enrichment and foliar fungal pathogen removal. We fitted structural equation models to test the relative importance of abundance shifts, intraspecific shifts and sown trait composition in contributing to overall variation in community weighted mean traits and aboveground and belowground biomass production.
C_LIO_LIWe found that intraspecific shifts were as important as abundance shifts in determining community weighted mean traits, and even had large effects relative to a wide initial gradient in trait composition. Intraspecific trait shifts resulted in convergence towards intermediate SLA, in diverse communities, although convergence was reduced by nitrogen addition and enhanced by pathogen removal. In contrast, large intraspecific shifts in LDMC were not influenced by the treatments. Belowground biomass was reduced by SLA and increased by LDMC, while aboveground biomass increased in communities dominated by high SLA species. However, despite large intraspecific trait shifts, intraspecific variation in these traits had no effect on above or belowground biomass production.
C_LIO_LIOur results add to a growing body of literature showing large intraspecific trait variation and emphasise the importance of using field sampled data to determine community composition. However, they also show that intraspecific variation does not affect ecosystem functioning and therefore trait response-effect relationships may differ between vs. within species.
C_LI


title: Mendelian Randomization Analysis Using Multiple Biomarkers of an Underlying Common Exposure

abstract: Mendelian Randomization (MR) analysis is increasingly popular for testing the causal effect of exposures on disease outcomes using data from genome-wide association studies. In some settings, the underlying exposure, such as systematic inflammation, may not be directly observable, but measurements can be available on multiple biomarkers, or other types of traits, that are co-regulated by the exposure. We propose method MRLE, which tests the significance for, and the direction of, the effect of a latent exposure by leveraging information from multiple related traits. The method is developed by constructing a set of estimating functions based on the second-order moments of summary association statistics, under a structural equation model where genetic variants are assumed to have indirect effects through the latent exposure and potentially direct effects on the traits. Simulation studies showed that MRLE has well-controlled type I error rates and increased power compared to single-trait MR tests under various types of pleiotropy. Applications of MRLE using genetic association statistics across five inflammatory biomarkers (CRP, IL-6, IL-8, TNF- and MCP-1) provided evidence for potential causal effects of inflammation on increased risk of coronary artery disease, colorectal cancer and rheumatoid arthritis, while standard MR analysis for individual biomarkers often failed to detect consistent evidence for such effects.


title: Exercise Attenuates Sickness Behavior And Protects Against Dopaminergic Impairment Induced By Neuroinflammation

abstract: Neuroinflammation affects dopamine metabolism and produces a set of symptoms known as sickness behavior, including fever, anhedonia, anorexia, weight loss, decreased sociability and mobility, and cognitive impairment. Motor and cognitive impairments related to sickness behavior are associated with dopamine (DA) metabolism imbalance in the prefrontal cortex. Lipopolysaccharide (LPS) administration induces neuroinflammation and causes sickness behavior in mice, while physical exercise has anti-inflammatory properties and may attenuate sickness behavior and DA impairment. We investigated the effect of exercise on DA levels and sickness behavior induced by LPS in mice. Adult Swiss male mice (8-10 weeks, 47.1 {+/-} 0.7 g, n=495) performed six weeks of voluntary exercise in free-running wheels (RW group) or had the blocked wheel in their cages (sedentary, SED group). After six weeks of exercise, both groups received an intraperitoneal injection (i.p.) of either saline (SAL) or LPS (0.33 mg/kg, i.p.). All animals were submitted to behavioral tests for sickness behavior assessment (fatigue, locomotion, anhedonia, and social interaction). Neuroinflammation markers and DA metabolism were assessed in the prefrontal cortex. LPS administration provoked anorexia, body weight loss, impaired motor function, social withdrawal, and anhedonia. This sickness behavior was accompanied by reduced cortical DA metabolism and its metabolite, 3,4-dihydroxyphenylacetic acid (DOPAC). Neuroinflammation was confirmed through increased levels of the proinflammatory cytokines IL-1{beta} and IL-6. Inflammation was also confirmed in the blood by an increased content of IL-1{beta}. Physical exercise intervention prevented animals from neurochemical, biochemical, and behavioral alterations. These findings provide new evidence of physical exercises potential as an environmental approach to treating neuroinflammatory conditions.


title: A vascularized tumoroid model for studying human glioblastoma angiogenesis

abstract: Glioblastoma (GBM) angiogenesis is critical for tumor growth and recurrence, making it a compelling therapeutic target. Here, a disease-relevant, vascularized tumoroid in vitro model with stem-like features and stromal surrounds is reported. The model is used to recapitulate how individual components of the GBMs complex brain microenvironment such as hypoxia, vasculature-related stro-mal cells and growth factors support GBM angiogenesis. It is scalable, tractable, cost-effective and can be used with biologically-derived or biomimetic matrices. Patient-derived primary GBM cells are found to closely participate in blood vessel formation in contrast to a GBM cell line containing differentiated cells. Exogenous growth factors amplify this effect under normoxia but not at hypoxia suggesting that a significant amount of growth factors is already being produced under hypoxic conditions. Under hypoxia, primary GBM cells and umbilical vein endothelial cells are found to strongly co-localize in a mosaic pattern to form sprouting vascular networks, with GBM cells acquiring an endothelial-like behaviour, which has been reported to occur in vivo. These findings demonstrate that our 3D tumoroid in vitro model exhibits biomimetic attributes that may permit its use as a preclinical model in studying microenvironment cues of tumor angiogenesis.


title: A vascularized tumoroid model for human glioblastoma angiogenesis


title: Densified Collagen Tubular Grafts for Human Tissue Replacement and Disease Modelling Applications

abstract: Fabrication of tubular grafts de novo has been limited by the ability to produce constructs which fulfil the mechanical and biological requirements for implantation and function. In this work, we present a novel method for the formation of densified collagen hydrogel tubular grafts on the scale of human-sized vessels. The seamless, densified collagen hydrogel tubes are highly customisable in terms of luminal diameter and wall thickness; here we report tubes with luminal diameters 1-5 mm and wall thicknesses of 0.2-3 mm. Using genipin as a biocompatible crosslinker, we eliminate the acid solubility and swelling of the collagen, while increasing the strength of the tubes. While the materials-based method of manufacture enables acellular grafts to be generated rapidly, the cell-compatible densification method enables a high density and uniformly distributed population of cells to be incorporated into the walls of the construct, as well as onto the luminal surface. Additionally, we report a method for generating tubes consisting of distinct cell domains in the walls. The cellular configurations at the boundary between the cell populations may be useful for disease modelling applications. We also demonstrate a method for luminal surface patterning of collagen tubes.


title: Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins

abstract: Finding optimal parameters for force fields used in molecular simulation is a challenging and time-consuming task, partly due to the difficulty of tuning multiple parameters at once. Automatic differentiation presents a general solution: run a simulation, obtain gradients of a loss function with respect to all the parameters, and use these to improve the force field. This approach takes advantage of the deep learning revolution whilst retaining the interpretability and efficiency of existing force fields. We demonstrate that this is possible by parameterising a simple coarse-grained force field for proteins, based on training simulations of up to 2,000 steps learning to keep the native structure stable. The learned potential matches chemical knowledge and PDB data, can fold and reproduce the dynamics of small proteins, and shows ability in protein design and model scoring applications. Problems in applying differentiable molecular simulation to all-atom models of proteins are discussed along with possible solutions. The learned potential, simulation scripts and training code are made available at https://github.com/psipred/cgdms.


title: Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility

abstract: Combining samples for genetic association is standard practice in human genetic analysis of complex traits, but is rarely undertaken in rodent genetics. Here, using 23 phenotypes and genotypes from two independent laboratories, we obtained a sample size of 3,076 commercially available outbred mice and identified 70 loci, more than double the number of loci identified in the component studies. Fine-mapping in the combined sample reduced the number of likely causal variants, with a median reduction in set size of 51%, and indicated novel gene associations, including Pnpo, Ttll6 and GM11545 with bone mineral density, and Psmb9 with weight. However replication at a nominal threshold of 0.05 between the two component studies was surprisingly low, with less than a third of loci identified in one study replicated in the second. In addition to overestimates in the effect size in the discovery sample (Winners Curse), we also found that heterogeneity between studies explained the poor replication, but the contribution of these two factors varied among traits. Available methods to control Winners Curse were contingent on the power of the discovery sample, and depending on the method used, both overestimated and underestimated the true effect. Leveraging these observations we integrated information about replication rates, confounding, and Winners Curse corrected estimates of power to assign variants to one of four confidence levels. Our approach addresses concerns about reproducibility, and demonstrates how to obtain robust results from mapping complex traits in any genome-wide association study.


title: epitopepredict: A tool for integrated MHC binding prediction

abstract: A key step in the cellular adaptive immune response is the presentation of antigen to T cells. During this process short peptides processed from self or foreign proteins may be presented on the surface bound to MHC molecules for binding to T cell receptors. Those that bind and activate an immune response are called epitopes. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics which allows in silico screening of peptides before experiments are performed. The most effective approach is to estimate the binding affinity of a given peptide fragment to MHC class I or II molecules. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open source license from https://github.com/dmnfarrell/epitopepredict


title: The local topological free energy of the SARS-CoV-2 Spike protein

abstract: The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its spike protein. Understanding protein rearrangement and identifying specific residues where mutations affect protein rearrangement has attracted a lot of attention for drug development. We use a mathematical method introduced in [9] to associate a local topological/geometrical free energy along the SARS-CoV-2 spike protein backbone. Our results show that the total local topological free energy of the SARS-CoV-2 spike protein monotonically decreases from pre-to post-fusion and that its distribution along the protein domains is related to their activity in protein rearrangement. By using density functional theory (DFT) calculations with inclusion of solvent effects, we show that high local topological free energy conformations are unstable compared to those of low topological free energy. By comparing to experimental data, we find that the high local topological free energy conformations in the spike protein are associated with mutations which have the largest experimentally observed effect to protein rearrangement.


title: Insights on SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival

abstract:
Recent mutations on the receptor binding domain (RBD) of the SARS-CoV-2s spike protein have been manifested as the major cause of the wide and rapid spread of the virus. Especially, the variant B.1.351 in South Africa with the hallmark of triple mutations (N501Y, K417N and E484K) is worrisome. Quickly after the outbreak of this new variant, several studies showed that both N501Y and E484K can enhance the binding between RBD and the human ACE2 receptor. However, the mutation K417N seems to be unfavorable because it removes one interfacial salt-bridge. So far, it is still not well understood why the K417N mutation is selected in the viral evolution. Here, we show that despite the loss in the binding affinity (1.48 kcal/mol) between RBD and ACE2 the K417N mutation abolishes a buried interfacial salt-bridge between RBD and the neutralizing antibody CB6 and thus substantially reduces their binding energy by 9.59 kcal/mol, facilitating the variants to efficiently elude CB6 (as well as many other antibodies). Thus, when proliferating from person to person the virus might have adapted to the human immune system through evasive mutations. Taking into account limited and relevant experimental works in the field, we show that our theoretical predictions are consistent with existing experimental findings. By harnessing the revealed molecular mechanism for variants, it becomes feasible to redesign therapeutic antibodies accordingly to make them more efficacious.

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title: Drug Conjugates of Antagonistic RSPO4 Mutant For Simultaneous Targeting of LGR4/5/6 for Cancer Treatment

abstract: LGR4-6 (Leucine-rich repeating containing, G-protein-coupled receptors 4, 5, and 6) are three related receptors with distinct roles in organ development and stem cell survival. All three receptors are upregulated in gastrointestinal cancers to different levels, and LGR5 has been shown to be enriched in cancer stem cells. Antibody-drug conjugates (ADCs) targeting LGR5 showed robust antitumor effect in vivo but could not eradicate tumors due to plasticity of LGR5-positive cancer cells. As LGR5-negative cells often express LGR4 or LGR6 or both, we reasoned that simultaneous targeting of all three LGRs may provide a more effective approach. R-spondins (RSPOs) bind to LGR4-6 with high affinity and potentiate Wnt signaling. We identified an RSPO4 mutant (Q65R) that retains potent LGR binding but no longer potentiates Wnt signaling. The RSPO4 mutant was fused to the N-terminus of human IgG1-Fc to create a peptibody which was then conjugated with cytotoxins monomethyl auristatin or duocarmycin by site-specific conjugation. The resulting peptibody drug conjugates (PDCs) showed potent cytotoxic effects on cancer cell lines expressing any LGR in vitro and suppressed tumor growth in vivo without inducing intestinal enlargement or other adverse effects. These results suggest that RSPO-derived PDCs may provide a novel approach to the treatment of cancers with high LGR expression.

category: pharmacology and toxicology


title: Targeting interleukin-1 for reversing fat browning and muscle wasting in infantile nephropathic cystinosis

abstract:
BackgroundCtns-/- mice, a mouse model of infantile nephropathic cystinosis, exhibit hypermetabolism with adipose tissue browning and profound muscle wasting. Inflammatory cytokines such as IL-1 trigger inflammatory cascades and play an important role in the pathogenesis of cachexia. Anakinra is an FDA-approved IL-1 receptor antagonist that blocks IL-1 signaling and may provide targeted novel therapy.

MethodsCtns-/- mice were bred to Il6 -/- and Il1{beta} -/- mice. Ctns-/- mice and wild type control were treated with anakinra (2.5 mg.kg.day, IP) or saline as vehicle for 6 weeks. We quantitated total fat mass and studied expression of molecules regulating adipose tissue browning. We measured gastrocnemius weight, total lean mass content, muscle function (grip strength and rotarod activity), muscle fiber size, muscle fatty infiltration and expression of molecules regulating muscle metabolism. We also evaluated the effects of anakinra on the muscle transcriptome.

ResultsIl-1{beta} deficiency or treatment with anakinra normalized food intake and weight gain, fat and lean mass content, metabolic rate and muscle function in Ctns-/- mice. Anakinra also diminished molecular perturbations of energy homeostasis in adipose tissue and muscle, specifically, aberrant expression of beige adipose cell biomarkers (UCP-1, CD137, Tmem26 and Tbx1) and molecules implicated in adipocyte tissue browning (Cox2/Pgf2, Tlr2, Myd88 and Traf6) in inguinal white adipose tissue in Ctns-/- mice. Moreover, anakinra normalized gastrocnemius weight and fiber size as well as attenuated muscle fat infiltration in Ctns-/- mice. This was accompanied by correction of the increased muscle wasting signaling pathways (increased protein content of ERK1/2, JNK, p38 MAPK and NF-{kappa}B p65 and gene expression of Atrogin-1 and Myostatin) and the decreased myogenesis process (decreased gene expression of MyoD and Myogenin) in gastrocnemius of Ctns-/- mice. Finally, anakinra normalized or attenuated 12 of those top 20 differentially expressed muscle genes in Ctns-/- mice.

ConclusionsAnakinra attenuates adipose tissue browning and muscle wasting in Ctns-/- mice. IL-1 receptor blockade may represent a novel targeted treatment for cachexia in patients with infantile nephropathic cystinosis.

category: physiology


title: Elephant seal muscle cells adapt to sustained glucocorticoid exposure by shifting their metabolic phenotype

abstract: Elephant seals experience natural periods of prolonged food deprivation while breeding, molting, and undergoing postnatal development. Prolonged food deprivation in elephant seals increases circulating glucocorticoids without inducing muscle atrophy, but the cellular mechanisms that allow elephant seals to cope with such conditions remain elusive. We generated a cellular model and conducted transcriptomic, metabolic, and morphological analyses to study how seal cells adapt to sustained glucocorticoid exposure. Seal muscle progenitor cells differentiate into contractile myotubes with a distinctive morphology, gene expression profile, and metabolic phenotype. Exposure to dexamethasone at three ascending concentrations for 48h modulated the expression of 6 clusters of genes related to structural constituents of muscle and pathways associated with energy metabolism and cell survival. Knockdown of the glucocorticoid receptor (GR) and downstream expression analyses corroborated that GR mediates the observed effects. Dexamethasone also decreased cellular respiration, shifted the metabolic phenotype towards glycolysis, and induced mitochondrial fission and dissociation of mitochondria-ER interactions without decreasing cell viability. Knockdown of DDIT4, a GR target involved in the dissociation of mitochondria-ER membranes, recovered respiration and modulated antioxidant gene expression. These results show that adaptation to sustained glucocorticoid exposure in elephant seal myotubes involves a metabolic shift toward glycolysis, which is supported by alterations in mitochondrial morphology and a reduction in mitochondria-ER interactions, resulting in decreased respiration without compromising cell survival.


title: C-bouton components on rat extensor digitorum longus motoneurons are resistant to chronic functional overload

abstract: Mammalian motor systems adapt to the demands of their environment. For example, muscle fibre types change in response to increased load or endurance demands. However, for adaptations to be effective, motoneurons must adapt such that their properties match those of the innervated muscle fibres. We used a rat model of chronic functional overload to assess adaptations to both motoneuron size and a key modulatory synapse responsible for amplification of motor output, C-boutons. Overload of Extensor Digitorum Longus (EDL) muscles was induced by removal of their synergists, Tibialis Anterior (TA) muscles. Following 21 days survival, EDL muscles showed an increase in fatigue resistance and a decrease in force output, indicating a shift to a slower phenotype. These changes were reflected by a decrease in motoneuron size. However, C-bouton complexes remained largely unaffected by overload. The C-boutons themselves, quantified by expression of vesicular acetylcholine transporter, were similar in size and density in the control and overload conditions. Expression of the post-synaptic voltage-gated potassium channel (KV2.1) was also unchanged. Small conductance calcium activated potassium channels (SK3) were expressed in most EDL motoneurons, despite this being an almost exclusively fast motor pool. Overload induced a decrease in the proportion of SK3+ cells, however there was no change in density or size of clusters. We propose that reductions in motoneuron size may promote early recruitment of EDL motoneurons, but that C-bouton plasticity is not necessary to increase the force output required in response to muscle overload.


title: Transsynaptic N-cadherin adhesion complexes control presynaptic vesicle and bulk endocytosis at physiological temperature

abstract: At mammalian glutamatergic synapses, most basic elements of synaptic transmission have been shown to be modulated by specific transsynaptic adhesion complexes. However, although crucial for synapse homeostasis, a physiological regulation of synaptic vesicle endocytosis by adhesion molecules has not been firmly established. The homophilic adhesion protein N-cadherin is localized at the peri-active zone, where the highly temperature dependent endocytosis of vesicles occurs. Here, we demonstrate an important modulatory role of N-cadherin in endocytosis at near physiological temperature by synaptophysin-pHluorin imaging. Different modes of endocytosis including bulk endocytosis were dependent on N-cadherin expression and function. N-cadherin modulation was mediated by actin filaments, because actin polymerization rescued the knockout induced endocytosis defect. Using super-resolution imaging, we found a strong recruitment of N-cadherin to glutamatergic synapses upon massive vesicle release, which might in turn enhance vesicle endocytosis. This provides a novel, adhesion protein mediated mechanism for efficient coupling of exo- and endocytosis.


title: Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation

abstract: Escherichia coli is a Gram-negative bacterium that colonizes the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and some commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here we examine SslE from the E. coli Waksman and H10407 strains and reveal that it has a novel and dynamic structure. In response to acidification within mature biofilms we show how SslE forms a unique functional aggregate that interacts with cellulose and regulates the distribution of exopolysaccharides in macrocolony biofilms. Our data indicates that the spatial organization of SslE polymers and local pH are critical for biofilm maturation and SslE is a key factor that drives persistence of SslE-secreting bacteria during acidic stress.


title: Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors

abstract: Microbial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of all non-ribosomal peptides (NRP) produced by B. subtilis clade, we revealed that they acted either synergistically or additively to effectively eliminate phylogenetically distinct competitors. All four major NRP biosynthetic clusters were also imperative for the survival of B. subtilis in a complex community extracted from the rhizosphere. The production of NRP came with a fitness cost manifested in growth inhibition, rendering NRP synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, NRP production was only induced by the presence of peptidoglycan cue from a sensitive competitor. These results experimentally demonstrate a general ecological concept - closely related communities ("self") are favoured during competition, due to compatibility in attack and defence mechanisms.


title: β-Catenin and canonical Wnts control two separate pattern formation systems in Hydra: Insights from mathematical modelling

abstract: Formation of the body axes and the subsequent formation of the apical termini are fundamental steps during animal development. Nuclear {beta}-catenin and canonical Wnt3 have been identified as major players in both these processes in Hydra. Based on molecular knowledge of canonical Wnt signalling directly linking nuclear {beta}-catenin and Wnt3 activity, de novo axis formation and head formation have frequently been assumed to be part of the same pattern formation system. In this study, we investigated this relationship by combining new model simulations with available experimental results. We demonstrated that nuclear {beta}-catenin and Wnt3 likely contribute to two distinct de novo pattern formation systems in Hydra, organizing development and differentiation on two different spatial scales. In particular, the results suggested that nuclear {beta}-catenin acts at the scale of the whole body to control axis formation, whereas canonical Wnt3 signalling is involved in a downstream pathway responsible for small-scale patterning of the head. These results suggest that the underlying mechanisms may also be more complex than previously assumed in other animals where axis formation has been ascribed to canonical Wnt signalling.


title: β-catenin and canonical Wnts in Hydra pattern formation: Insights from mathematical modelling into two distinct systems


title: Cardiac and behavioural responses to hypoxia and warming in free-swimming gilthead seabream Sparus aurata

abstract:
Cardiac and behavioural responses to hypoxia and warming were investigated in free-swimming gilthead seabream Sparus aurata equipped with biologging tags in the peritoneal cavity. After suitable recovery in a holding tank, heart rate (fH) and the variance of tri-axial body acceleration (VARm) were logged during exposure to stepwise progressive hypoxia or warming, comparing when either swimming in a tank or confined to individual respirometer chambers. When undisturbed under control conditions (normoxia, 21 {degrees}C), mean fH was significantly lower in tank than respirometers. In progressive hypoxia (100 - 15% oxygen saturation), mean fH in the tank was significantly lower than respirometers at oxygen levels until 40%, with significant bradycardia in both holding conditions below this. Mean VARm was low and invariant in hypoxia. Warming (21 to 31 {degrees}C) caused progressive tachycardia with no differences in fH between holding conditions. Mean VARm was, however, significantly higher in the tank during warming, with a positive relationship between VARm and fH across all temperatures. Therefore, spontaneous activity contributed to raising fH of fish in the tank during warming. Mean fH in respirometers had a highly significant linear relationship with mean rates of oxygen uptake, considering data from hypoxia and warming together. The high fH of confined S. aurata indicates that static respirometry techniques may bias estimates of metabolic traits in some fish species. Biologging on free-swimming fish revealed novel information about cardiac responses to environmental stressors, which may be closer to responses exhibited by fish in their natural environment.

SUMMARY STATEMENTImplantable biologgers were used to provide the first measurements of cardiac responses to hypoxia and warming in a free-swimming fish, revealing that confinement in respirometer chambers raises heart rate, with consequences for estimates of metabolic rates.


title: The hepatocyte insulin receptor is required to program rhythmic gene expression and the liver clock

abstract:
In mammalian cells, gene expression is rhythmic and sensitive to various environmental and physiological stimuli. A circadian clock system helps to anticipate and synchronize gene expression with daily stimuli including cyclic light and food intake, which control the central and peripheral clock programs, respectively. Food intake also regulates insulin secretion. How much insulin contributes to the effect of feeding on the entrainment of the clock and rhythmic gene expression remains to be investigated.

An important component of insulin action is mediated by changes in insulin receptor (IR)-dependent gene expression. In the liver, insulin at high levels controls the transcription of hundreds of genes involved in glucose homeostasis to promote energy storage while repressing the expression of gluconeogenic genes. In type 2 diabetes mellitus (T2DM), selective hepatic insulin resistance impairs the inhibition of hepatic glucose production while promoting lipid synthesis. This pathogenic process promoting hyperlipidemia as well as non-alcoholic fatty liver diseases.

While several lines of evidence link such metabolic diseases to defective control of circadian homeostasis, the hypothesis that IR directly synchronizes the clock has not been studied in vivo. Here, we used conditional hepatocyte-restricted gene deletion to evaluate the role of IR in the regulation and oscillation of gene expression as well as in the programming of the circadian clock in adult mouse liver.


title: The role of IL-1 in adipose browning and muscle wasting in CKD-associated cachexia

abstract: Cytokines such as IL-6, TNF- and IL-1{beta} trigger inflammatory cascades which may play a role in the pathogenesis of chronic kidney disease (CKD)-associated cachexia. CKD was induced by 5/6 nephrectomy in mice. We studied energy homeostasis in Il1{beta}-/-/CKD, Il6-/-/CKD and Tnf-/-/CKD mice and compared with wild type (WT)/CKD controls. Parameters of cachexia phenotype were completely normalized in Il1{beta}-/-/CKD mice but were only partially rescued in Il6-/-/CKD and Tnf-/-/CKD mice. We tested the effects of anakinra, an IL-1 receptor antagonist, on CKD-associated cachexia. WT/CKD mice were treated with anakinra (2.5 mg.kg.day, IP) or saline for 6 weeks and compared with WT/sham controls. Anakinra normalized food intake and weight gain, fat and lean mass content, metabolic rate and muscle function, and also attenuated molecular perturbations of energy homeostasis in adipose tissue and muscle in WT/CKD mice. Anakinra attenuated browning of white adipose tissue in WT/CKD mice. Moreover, anakinra normalized gastrocnemius weight and fiber size as well as attenuated muscle fat infiltration in WT/CKD mice. This was accompanied by correcting the increased muscle wasting signaling pathways while promoting the decreased myogenesis process in gastrocnemius of WT/CKD mice. We performed qPCR analysis for the top 20 differentially expressed muscle genes previously identified via RNAseq analysis in WT/CKD mice versus controls. Importantly, 17 differentially expressed muscle genes were attenuated in anakinra treated WT/CKD mice. In conclusion, IL-1 receptor antagonism may represent a novel targeted treatment for adipose tissue browning and muscle wasting in CKD.


title: Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks and plastoglobular functions

abstract:
Plastoglobules (PGs) are dynamic protein-lipid micro-compartments in plastids enriched for isoprenoid-derived metabolites. Chloroplast PGs support formation, remodeling and controlled dismantling of thylakoids during developmental transitions and environmental responses. However, the specific molecular functions of most PG proteins are still poorly understood. This study harnesses recent co-mRNA expression from ATTED-II using combined microarray and RNAseq information on an updated inventory of 34 PG proteins, as well as proteomics data across 30 Arabidopsis tissue types from ATHENA. Hierarchical clustering based on relative abundance for the PG proteins across non-photosynthetic and photosynthetic tissue types showed their coordinated protein accumulation across Arabidopsis parts, tissue types, development and senescence. We generated multiple mRNA-based networks by applying different coefficient thresholds; functional enrichment was determined for each network and PG gene. Combined analysis of these stringency networks identified a central hub and four peripheral modules. Enrichment of specific nuclear transcription factors (e.g. Golden2-like) and support for cross-talk between PGs and the plastid gene expression was observed, and specific ABC1 kinases seem part of a light signaling network. Examples of other specific findings are that FBN7b is involved with upstream steps of tetrapyrrole biosynthesis and that ABC1K9 is involved in starch metabolism.

HighlightThe plastoglobular proteome shows coherent tissue-specific accumulation, whereas combined analysis of transcriptional co-expression networks, at different stringencies and following in-depth functional annotation, associate selected plastoglobular proteins to specific metabolic functions.

category: plant biology


title: Rational Design of Programmable Monodisperse Semi-Synthetic Protein Nanomaterials Containing Engineered Disulfide Functionality

abstract: The reversible nature of disulfide functionality has been exploited to design intelligent materials such as nanocapsules, micelles, vesicles, inorganic nanoparticles, peptide and nucleic acid nanodevices. However, to our knowledge, there are no reports on design of semi-synthetic protein assemblies containing an engineered disulfide bond. Towards that end, herein, we disclose a new chemical methodology for the construction redox-sensitive protein assemblies using monodisperse facially amphiphilic protein-dendron bioconjugates. The disulfide functionality is strategically placed between the dendron and protein domains. The custom designed bioconjugates self-assembled into nanoscopic objects of a defined size dictated by the nature of dendron domain. The stimuli-responsive behavior of the protein assemblies is demonstrated using a suitable redox trigger.

category: synthetic biology


title: Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

abstract: Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF CRX in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences.

category: systems biology


title: Neuronal Switching Between Single- and Dual-Network Activity via Modulation of Intrinsic Membrane Properties

abstract:
Oscillatory networks underlie rhythmic behaviors (e.g. walking, chewing), and complex behaviors (e.g. memory formation, decision making). Flexibility of oscillatory networks includes neurons switching between single- and dual-network participation, even generating oscillations at two distinct frequencies. Modulation of synaptic strength can underlie this neuronal switching. Here we ask whether switching into dual-frequency oscillations can also result from modulation of intrinsic neuronal properties. The isolated stomatogastric nervous system of male Cancer borealis crabs contains two well-characterized rhythmic feeding-related networks (pyloric, [~]1 Hz; gastric mill, [~]0.1 Hz). The identified modulatory projection neuron MCN5 causes the pyloric-only LPG neuron to switch to dual pyloric/gastric mill bursting. Bath applying the MCN5 neuropeptide transmitter Gly1-SIFamide only partly mimics the LPG switch to dual activity, due to continued LP neuron inhibition of LPG. Here, we find that MCN5 uses a co-transmitter, glutamate, to inhibit LP, unlike Gly1-SIFamide excitation of LP. Thus, we modeled the MCN5-elicited LPG switching with Gly1-SIFamide application and LP photoinactivation. Using hyperpolarization of pyloric pacemaker neurons and gastric mill network neurons, we found that LPG pyloric-timed oscillations require rhythmic electrical synaptic input. However, LPG gastric mill-timed oscillations do not require any pyloric/gastric mill synaptic input and are voltage dependent. Thus, we identify modulation of intrinsic properties as an additional mechanism for switching a neuron into dual-frequency activity. Instead of synaptic modulation switching a neuron into a second network as a passive follower, modulation of intrinsic properties could enable a switching neuron to become an active contributor to rhythm generation in the second network.

Significance StatementNeuromodulation of oscillatory networks can enable network neurons to switch from sing<bacle- to dual-network participation, even when two networks oscillate at distinct frequencies. We used small, well-characterized networks to determine whether modulation of synaptic strength, an identified mechanism for switching, is necessary for dual-network recruitment. We demonstrate that rhythmic electrical synaptic input is required for continued linkage with a "home" network, but that modulation of intrinsic properties is sufficient to switch a neuron into dual-frequency oscillations, linking it to a second network. Neuromodulator-induced switches in neuronal participation between networks occurs in motor, cognitive, and sensory networks. Our study highlights the importance of considering intrinsic properties as a pivotal target for enabling parallel participation of a neuron in two oscillatory networks.


title: Somatostatin-positive Interneurons Contribute to Seizures in SCN8A Epileptic Encephalopathy

abstract: SCN8A epileptic encephalopathy is a devastating epilepsy syndrome caused by mutant SCN8A which encodes the voltage-gated sodium channel NaV1.6. To date, it is unclear if and how inhibitory interneurons, which express NaV1.6, influence disease pathology. We found that selective expression of the R1872W mutation in somatostatin (SST) interneurons was sufficient to convey susceptibility to audiogenic seizures. SST interneurons from mutant mice were hyperexcitable but hypersensitive to action potential failure via depolarization block under normal and seizure-like conditions. Remarkably, GqDREADD-mediated activation of wild-type SST interneurons resulted in prolonged electrographic seizures and was accompanied by SST hyperexcitability and depolarization block. Aberrantly large persistent sodium currents, a hallmark of SCN8A mutations, were observed and were found to contribute directly to aberrant SST physiology in computational and pharmacological experiments. These novel findings demonstrate a critical and previously unidentified contribution of SST interneurons to seizure generation not only in SCN8A encephalopathy, but epilepsy in general.


title: Self-assembling SARS-CoV-2 nanoparticle vaccines targeting the S protein induces protective immunity in mice

abstract: The spike (S), a homotrimer glycoprotein, is the most important antigen target in the research and development of SARS-CoV-2 vaccine. There is no doubt that fully simulating the advanced structure of this homotrimer in the subunit vaccine development strategy is the most likely way to improve the immune protective effect of the vaccine. In this study, the preparation strategies of S protein receptor-binding domain (RBD) trimer, S1 region trimer, and ectodomain (ECD) trimer nanoparticles were designed based on ferritin nanoparticle self-assembly technology. The Bombyx mori baculovirus expression system was used to prepare these three nanoparticle vaccines with high expression levels in the silkworm. The immune results of mice show that the nanoparticle vaccine prepared by this strategy can not only induce an immune response by subcutaneous administration but also effective by oral administration. Given the stability of these ferritin-based nanoparticles vaccine, easy-to-use and low-cost oral immunization strategy can make up for the vaccination blind areas caused by the shortage of ultralow-temperature equipment and medical resources in underdeveloped areas. And the oral vaccine is also a very potential candidate to cut off the spread of SARS-CoV-2 in domestic and farmed animals, especially in stray and wild animals.


category: microbiology


title: Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata

abstract: We used network methods to analyze transcriptomic and polar metabolomic data generated from the stress resistant stony coral Montipora capitata. Corals were exposed to ambient or thermal stress conditions over a five-week period that coincided with a mass spawning event of this species. Gene co-expression networks showed that the early thermal stress response involves downregulation of growth and DNA replication, whereas signaling and the immune response are strongly upregulated. Later stages are dominated by suppression of metabolite transport and biomineralization and enhanced expression of transcriptional regulators. Integration of gene-metabolite data demonstrates that the major outcome of the thermal treatment is activation of animal redox stress pathways with detoxification of reactive oxygen species being dominant. Differential regulation of the highly conserved cytochrome P450 gene family was of particular interest with downregulation of CYP1A1, involved in progesterone metabolism, potentially explaining the attenuated mass spawning observed during the sampling period.

category: genomics


title: Optical regulation of endogenous RhoA reveals switching of cellular responses by signal amplitude

abstract: How protein signaling networks respond to different input strengths is an important but poorly understood problem in cell biology. For example, the small GTPase RhoA regulates both focal adhesion (FA) growth or disassembly, but whether RhoA serves as a switch selecting between cellular outcomes, or if outcomes are simply modulated by additional factors in the cell, is not clear. Here, we develop a photoswitchable RhoA guanine exchange factor, psRhoGEF, to precisely control endogenous RhoA activity. We also develop a FRET-based biosensor to allow visualization of RhoA activity together with psRhoGEF control. Using these new optical tools, we discover that low levels of RhoA activation preferentially induce FA disassembly in a Src-dependent manner, while high levels induce both FA growth and disassembly in a ROCK-dependent manner. Thus, rheostatic control of RhoA activation with photoswitchable RhoGEF reveals that cells can use signal amplitude to produce multiple responses to a single biochemical signal.


title: Optical regulation of endogenous RhoA reveals selection of cellular responses by signal amplitude