title: The Similarity Structure of Real-World Memories

abstract:
How do we mentally organize our memories of life events? Two episodes may be connected because they share a similar location, time period, activity, spatial environment, or social and emotional content. However, we lack an understanding of how each of these dimensions contributes to the perceived similarity of two life memories. We addressed this question with a data-driven approach, eliciting pairs of real-life memories from participants. Participants annotated the social, purposive, spatial, temporal, and emotional characteristics of their memories. We found that the overall similarity of memories was influenced by all of these factors, but to very different extents. Emotional features were the most consistent single predictor of overall memory similarity. Memories with different emotional tone were reliably perceived to be dissimilar, even when they occurred at similar times and places and involved similar people; conversely, memories with a shared emotional tone were perceived as similar even when they occurred at different times and places, and involved different people. A predictive model explained over half of the variance in memory similarity, using only information about (i) the emotional properties of events and (ii) the primary action or purpose of events. Emotional features may make an outsized contribution to event similarity because they provide compact summaries of an events goals and self-related outcomes, which are critical information for future planning and decision making. Thus, in order to understand and improve real-world memory function, we must account for the strong influence of emotional and purposive information on memory organization and memory search.

SignificanceOur brains enable us to understand and act within the present, informed by previous, related life experience. But how are our life experiences organized so that one event can be related to another? Theories have suggested that we use spatiotemporal, social, causal, purposive, and emotional dimensions to inter-relate our memories; however, these organizing principles are usually studied using impersonal laboratory stimuli. Here, we mapped and modeled the connections between peoples own annotated life memories. We found that life events are linked by a variety of factors, but are predominantly connected in memory by their primary activity and emotional character. This highlights a need for theories of memory organization and retrieval to better account for the role of high-level actions and emotions.


title: In Silico: Mutagenicity and carcinogenicity prediction of Sugar substitutes

abstract: Sugar substitutes are mostly artificial, man-made industrial products used as additives in food and beverages. Most of these substances flow through the digestive tract and food chains to become emerging organic contaminants in various abiotic and biotic environmental media. Here, we predict the mutagenicity and carcinogenicity of commonly used sugar substitutes using the in silico based methods. The simplified molecular-input line-entry system (SMILES) of sugar substitutes were obtained from the PubChem database for the toxicity predictions. Here, sixteen sugar substitutes tested out of these four compounds Glucin (GLU), and 5-nitro-2-propoxyaniline (P-4000), SCL, Ace were predicted as mutagens by using in silico tools such as LAZAR, pKCSM, and Toxtree. Based on the predicted results GLU and P-4000 were predicted as carcinogenic sugar substitutes.

category: bioengineering


title: SAILER: Scalable and Accurate Invariant Representation Learning for Single-Cell ATAC-Seq Processing and Integration

abstract:
MotivationSingle-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) provides new opportunities to dissect epigenomic heterogeneity and elucidate transcriptional regulatory mechanisms. However, computational modelling of scATAC-seq data is challenging due to its high dimension, extreme sparsity, complex dependencies, and high sensitivity to confounding factors from various sources.

ResultsHere we propose a new deep generative model framework, named SAILER, for analysing scATAC-seq data. SAILER aims to learn a low-dimensional nonlinear latent representation of each cell that defines its intrinsic chromatin state, invariant to extrinsic confounding factors like read depth and batch effects. SAILER adopts the conventional encoder-decoder framework to learn the latent representation but imposes additional constraints to ensure the independence of the learned representations from the confounding factors. Experimental results on both simulated and real scATAC-seq datasets demonstrate that SAILER learns better and biologically more meaningful representations of cells than other methods. Its noise-free cell embeddings bring in significant benefits in downstream analyses: Clustering and imputation based on SAILER result in 6.9% and 18.5% improvements over existing methods, respectively. Moreover, because no matrix factorization is involved, SAILER can easily scale to process millions of cells. We implemented SAILER into a software package, freely available to all for large-scale scATAC-seq data analysis.

AvailabilityThe software is publicly available at https://github.com/uci-cbcl/SAILER

Contactjingz31@uci.edu and xhx@uci.edu

category: bioinformatics


title: ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders

abstract:
MotivationSingle-cell RNA sequencing (scRNAseq) technologies allow for measurements of gene expression at a single-cell resolution. This provides researchers with a tremendous advantage for detecting heterogeneity, delineating cellular maps, or identifying rare subpopulations. However, a critical complication remains the low number of single-cell observations due to limitations by the rarity of a subpopulation, tissue degradation, or cost. This absence of sufficient data may cause inaccuracy or irreproducibility of downstream analysis. In this work, we present ACTIVA (Automated Cell-Type-informed Introspective Variational Autoencoder): a novel framework for generating realistic synthetic data using a single-stream adversarial variational autoencoder conditioned with cell-type information. Within a single framework, ACTIVA can generate data representative of the entire population, or specific subpopulations on demand, as opposed to two separate models (such as scGAN and cscGAN). Data generation and augmentation with ACTIVA can enhance scRNAseq pipelines and analysis, such as benchmarking new algorithms, studying the accuracy of classifiers, and detecting marker genes. ACTIVA will facilitate analysis of smaller datasets, potentially reducing the number of patients and animals necessary in initial studies.

ResultsWe train and evaluate models on multiple public scRNAseq datasets. In comparison to GAN-based models (scGAN and cscGAN), we demonstrate that ACTIVA generates cells that are more realistic and harder for classifiers to identify as synthetic, which also have better pair-wise correlations between genes. We show that data augmentation with ACTIVA significantly improves the classification of rare subtypes (more than 45% improvement compared to not augmenting and 4% better than cscGAN) all while reducing training time by an order of magnitude in comparison to both models.

Availability of data and codeLinks to raw, pre- and post-processed data, source code and tutorials are available at https://github.com/SindiLab.

Supplementary informationSupplementary material can be found as a separate file with the same pre-print submission.


title: Improving antibody thermostability based on statistical analysis of sequence and structural consensus data

abstract: The use of Monoclonal Antibodies (MAbs) as therapeutics has been increasing over the past 30 years due to their high specificity and strong affinity towards the target. One of the major challenges towards their use as drugs is their low thermostability, which impacts both efficacy as well as manufacturing and delivery. To aid the design of thermally more stable mutants, consensus sequence-based method has been widely used. These methods typically have a success rate of about 50% with maximum melting temperature increment ranging from 10 to 32{degrees}C. In order to improve the prediction performance, we have developed a new and fast MAbs specific method by adding a 3D structural layer to the consensus sequence method. This is done by analyzing the close-by residue pairs which are conserved in more than eight hundred MAbs 3D structures. Major advantage of this structural level assessment is in significantly reducing the false positives by almost half from the consensus sequence method alone. In summary, combining consensus sequence and structural residue pair covariance methods, we developed an inhouse application for predicting human MAb thermostability to guide protein engineers to design more stable molecules. This application has shown success in designing MAb engineering panels in multiple biologics programs.


title: Inference of an integrative network for Rheumatoid Arthritis combining data-driven machine learning approaches and a state-of-the-art mechanistic disease map

abstract:
Rheumatoid arthritis (RA) is a multifactorial, complex autoimmune disease that involves various genetic, environmental and epigenetic factors. Systems biology approaches provide the means to study complex diseases through the integration of different layers of biological information. Combining multiple data types can help compensate for missing or conflicting information and limit the possibility of false positives. In this work, we aim to unravel mechanisms governing the regulation of key transcription factors in RA and derive patient-specific models to gain more insights into the disease heterogeneity and the response to treatment.

We first make use of publicly available transcriptomic datasets (peripheral blood) relative to RA and machine learning to create an RA specific transcription factor (TF) co-regulatory network. The TF cooperativity network is subsequently enriched in signalling cascades and upstream regulators using a state-of-the-art, RA-specific molecular map. The integrative network is then used as a template to analyze patients data regarding their response to anti-TNF treatment and identify master regulators and upstream cascades affected by the treatment. We use the Boolean formalism to simulate in silico subparts of the integrated network and identify combinations and conditions that can switch on or off the identified TFs, mimicking the effects of single and combined perturbations.


title: Inference of an integrative, executable network for Rheumatoid Arthritis combining data-driven machine learning approaches and a state-of-the-art mechanistic disease map


title: ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity

abstract:
ObjectiveIn hepatocytes, peroxisome proliferator-activated receptor  (PPAR) acts as a lipid sensor that regulates hepatic lipid catabolism during fasting and orchestrates a genomic response required for whole-body homeostasis. This includes the biosynthesis of ketone bodies and the secretion of the starvation hormone fibroblast growth factor 21 (FGF21). Several lines of evidence suggest that adipose tissue lipolysis contributes to this specific process. However, whether adipose tissue lipolysis is a dominant signal for the extensive remodeling of liver gene expression dependent on PPAR has not been investigated.

MethodsFirst, using mice lacking adipose tissue lipolysis through adipocyte-specific deletion of adipose triglyceride lipase (ATGL), we characterized the responses dependent on adipocyte ATGL during fasting. Next, we performed liver whole genome expression analysis in fasted mice upon deletion of adipocyte ATGL or hepatocyte PPAR. Finally, we tested the consequences of hepatocyte-specific PPAR deficiency during pharmacological induction of adipocyte lipolysis with a {beta}3-adrenergic receptor agonist.

ResultsIn the absence of ATGL in adipocytes, ketone body and FGF21 productions were impaired in response to starvation. Liver transcriptome analysis revealed that adipocyte ATGL is critical for regulation of hepatic gene expression during fasting and highlighted a strong enrichment in PPAR target genes in this condition. Genome expression analysis confirmed that a large set of fasting-induced genes are sensitive to both ATGL and PPAR. Adipose tissue lipolysis induced by acute activation of the {beta}3-adrenergic receptor also triggered PPAR-dependent responses in the liver, supporting a role for adipocyte-derived fatty acids as dominant signals for hepatocyte PPAR activity. In addition, the absence of hepatocyte PPAR altered brown adipose tissue (BAT) morphology and reduced UCP1 expression upon stimulation of the {beta}3-adrenergic receptor. In agreement with this finding, mice lacking hepatocyte PPAR showed decreased tolerance to acute cold exposure.

ConclusionsThese results underscore the central role of hepatocyte PPAR in the sensing of adipocyte-derived fatty acids and reveal that its activity is essential for full activation of BAT. Intact PPAR activity in hepatocytes is required for cross-talk between adipose tissues and the liver during fat mobilization during fasting and cold exposure.

category: physiology


title: Mentorship as a strategy to improve research ability of students and young researchers in Africa: an exploratory study and initial findings on the CORE Africa Research Mentorship Scheme

abstract:
Mentorship provides an opportunity to support skill development, improve research ability, promote interest in research and offer career advice. The need for research mentorship in Africa is well-recognised. However, there is scarce literature on the development of such programmes and their potential impacts on students and young researchers in Africa (SYRIA). This study documents the development of the CORE Africa Research Mentorship Scheme (CARMS), and reports the outcomes and challenges experienced over a two-year period, from 2018 to 2020.

41 mentors and mentees from Cameroon, Uganda and Nigeria participated in the programme. Mentors were based in Africa and the UK, while mentees were all based in Africa. Mentees gained knowledge and skills in various research areas including proposal writing, research methods, data analysis, report writing and research publication. Nine mentees gained their first research publication through the CARMS and three successfully completed their first grant proposal. Three mentees were supported by their mentor to develop PhD research proposals and five others gained skills that helped them secure paid research jobs. Eleven mentees have  graduated from the programme, seven of which are currently enrolled as trainee mentors. Mentees appreciated the opportunity to improve on their research skills and felt that the programme gave them a  safe environment to freely express their concerns.

Main challenges encountered were: difficulty finding suitable mentors, communication barriers, poorly defined mentorship goals, dealing with mentees lack of knowledge/experience of  basic research concepts and funding limitations. This programme had several positive impacts on the knowledge and skills of mentees and demonstrates the importance of mentorship in research capacity strengthening. Sustaining such programmes requires investments in training and development, to ensure that mentees are continuously and adequately supported.

category: scientific communication and education


title: Predicting multimodal MRI outcomes in children with neurodevelopmental conditions following MRI simulator training

abstract: Pediatric brain imaging holds significant promise for understanding neurodevelopment. However, the requirement to remain still inside a noisy, enclosed scanner remains a challenge. Verbal or visual descriptions of the process, and/or practice in MRI simulators are the norm in preparing children. Yet, the factors predictive of successfully obtaining neuroimaging data remain unclear. We examined data from 250 children (6-12 years, 197 males) with autism and/or attention-deficit/hyperactivity disorder. Children completed systematic MRI simulator training aimed to habituate to the scanner environment and minimize head motion. An MRI session comprised multiple structural, resting-state, task and diffusion scans. Of the 201 children passing simulator training and attempting scanning, nearly all (94%) successfully completed the first structural scan in the sequence, and 88% also completed the following resting state fMRI scan. The number of successful scans decreased as the sequence progressed. Multivariate analyses revealed that age was the strongest predictor of successful scans in the session, with younger children having lower success rates. After age, sensorimotor atypicalities contributed most to prediction. Results provide insights on factors to consider in designing pediatric brain imaging protocols.

category: neuroscience


title: Multiple Monkey Pose Estimation Using OpenPose

abstract: This paper proposes a system for pose estimation on monkeys, in diverse and challenging scenarios, and under complex social interactions by using OpenPose. In comparison to most animals used for research, Monkeys present additional difficulties for pose estimation. Multiple degrees of freedom, unique complex postures, intricated social interactions, among others. Our monkey OpenPose trained model is robust against these difficulties. It achieves similar performance as in human pose estimation models, and it can run in Realtime.


title: Protein domain patterns reveal a functional diversity of the archaeal Cdv system and give insights into the origin of the eukaryotic ESCRT system

abstract: The Endosomal Sorting Complex Required for Transport (ESCRT) system is a multi-protein machinery that is involved in cell division of both Eukaryotes and Archaea. This spread across super-phyla suggests that a precursor ESCRT machinery existed already at an evolutionary early stage of life, making it a promising candidate for the (re)construction of a minimal cell division machinery. There are, however, only few experimental data about ESCRT machineries in Archaea, due to high technical challenges in cultivation and microscopy. Here, we analyse the proteins of archaeal ESCRT machineries bioinformatically on a domain level, to enable mechanistical comparison without such challenging experiments. First, we infer that there are at least three different cell division mechanisms utilizing ESCRT proteins in archaea, probably similar in their constriction mechanisms but different in membrane tethering. Second, we show that ESCRT proteins in Asgard archaea are highly similar to eukaryotic ESCRT proteins, strengthening the recently developed idea that all Eukaryotes descended from archaea. Third, we reconstruct a plausible evolutionary development of ESCRT machineries and suggest that a simple ESCRT-based constriction machinery existed in the last archaeal common ancestor. These findings not only give very interesting insights into the evolution of cell division in Archaea and Eukaryotes, but also reveal new research avenues by suggesting hypothesis-driven experiments for both, cell biology and bottom-up synthetic biology.

category: molecular biology


title: Tracing back variations in archaeal cell division to protein domain architectures


title: deepManReg: a deep manifold-regularized learning model for improving phenotype prediction from multi-modal data

abstract: The biological processes from genotype to phenotype are complex involving multi-scale mechanisms. Increasing multi-modal data enables deeper understanding of underlying complex mechanisms in various phenotypes. However, integrating and interpreting such large-scale multi-modal data remains challenging, especially given highly heterogeneous, nonlinear relationships across modalities. To address this, we developed an interpretable regularized learning model, deepManReg to predict phenotypes from multi-modal data. First, deepManReg employs deep neural networks to learn cross-modal manifolds and then align multi-modal features onto a common latent space. This space aims to preserve both global consistency and local smoothness across modalities and reveal higher-order nonlinear cross-modal relationships. Second, deepManReg uses cross-modal manifolds as a feature graph to regularize the classifiers for improving phenotype predictions and also prioritizing the multi-modal features and cross-modal interactions for the phenotypes. We applied deepManReg to recent single cell multi-modal data such as Patch-seq data including transcriptomics and electrophysiology for neuronal cells in the mouse brain. We show that deepManReg significantly improves predicting cellular phenotypes and also prioritizing genes and electrophysiological features for the phenotypes. Finally, deepManReg is open-source and general for phenotype prediction from multi-modal data. deepManReg is open-source available at https://github.com/daifengwanglab/deepManReg.


title: Predicting cross-tissue hormone-gene relations usingbalanced word embeddings

abstract:
MotivationLarge volumes of biomedical literature present an opportunity to build whole-body human models comprising both within-tissue and across-tissue interactions among genes. Current studies have mostly focused on identifying within-tissue or tissue-agnostic associations, with a heavy emphasis on associations among disease, genes and drugs. Literature mining studies that extract relations pertaining to inter-tissue communication, such as between genes and hormones, are solely missing.

ResultsWe present here a first study to identify from literature the genes involved in inter-tissue signaling via a hormone in the human body. Our models BioEmbedS and BioEmbedS-TS respectively predict if a hormone-gene pair is associated or not, and whether an associated gene is involved in the hormones production or response. Our models are classifiers trained on word embeddings that we had carefully balanced across different strata of the training data such as across production vs. response genes of a hormone (or) well-studied vs. poorly-represented hormones in the literature. Model training and evaluation are enabled by a unified dataset called HGv1 of ground-truth associations between genes and known endocrine hormones that we had compiled. Our models not only recapitulate known gene mediators of tissue-tissue signaling (e.g., at average 70.4% accuracy for BioEmbedS), but also predicts novel genes involved in inter-tissue communication in humans. Furthermore, the species-agnostic nature of our ground-truth HGv1 data and our predictive modeling approach, demonstrated concretely using human data and generalized to mouse, hold much promise for future work on elucidating inter-tissue signaling in other multi-cellular organisms.

AvailabilityProposed HGv1 dataset along with our models predictions, and the associated code to reproduce this work are available respectively at https://cross-tissue-signaling.herokuapp.com/, and https://github.com/BIRDSgroup/BioEmbedS.

Contactnmanik@cse.iitm.ac.in


title: A systematic analysis of genetically regulated differences in gene expression and the role of co-expression networks across 16 psychiatric disorders and substance use phenotypes

abstract: Genome-wide association studies (GWASs) have identified thousands of risk loci for many psychiatric and substance use phenotypes, however the biological consequences of these loci remain largely unknown. We performed a transcriptome-wide association study of 10 psychiatric disorders and 6 substance use phenotypes (collectively termed "mental health phenotypes") using expression quantitative trait loci data from 532 prefrontal cortex samples. We estimated the correlation due to predicted genetically regulated expression between pairs of mental health phenotypes, and compared the results with the genetic correlations. We identified 1,645 genes with at least one significant trait association, comprising 2,176 significant associations across the 16 mental health phenotypes of which 572 (26%) are novel. Overall, the transcriptomic correlations for phenotype pairs were significantly higher than the respective genetic correlations. For example, attention deficit hyperactivity disorder and autism spectrum disorder, both childhood developmental disorders, showed a much higher transcriptomic correlation (r=0.84) than genetic correlation (r=0.35). Finally, we tested the enrichment of phenotype-associated genes in gene co-expression networks built from prefrontal cortex. Phenotype-associated genes were enriched in multiple gene co-expression modules and the implicated modules contained genes involved in mRNA splicing and glutamatergic receptors, among others. Together, our results highlight the utility of gene expression data in the understanding of functional gene mechanisms underlying psychiatric disorders and substance use phenotypes.


title: SynthQA - Hierarchical Machine Learning-based Protein Quality Assessment

abstract:
MotivationIt has been a challenge for biologists to determine 3D shapes of proteins from a linear chain of amino acids and understand how proteins carry out lifes tasks. Experimental techniques, such as X-ray crystallography or Nuclear Magnetic Resonance, are time-consuming. This highlights the importance of computational methods for protein structure predictions. In the field of protein structure prediction, ranking the predicted protein decoys and selecting the one closest to the native structure is known as protein model quality assessment (QA), or accuracy estimation problem. Traditional QA methods dont consider different types of features from the protein decoy, lack various features for training machine learning models, and dont consider the relationship between features. In this research, we used multi-scale features from energy score to topology of the protein structure, and proposed a hierarchical architecture for training machine learning models to tackle the QA problem.

ResultsWe introduce a new single-model QA method that incorporates multi-scale features from protein structures, utilizes the hierarchical architecture of training machine learning models, and predicts the quality of any protein decoy. Based on our experiment, the new hierarchical architecture is more accurate compared to traditional machine learning-based methods. It also considers the relationship between features and generates additional features so machine learning models can be trained more accurately. We trained our new tool, SynthQA, on the CASP dataset (CASP10 to CASP12), and validated our method on 33 targets from the latest CASP 14 dataset. The result shows that our method is comparable to other state-of-the-art single-model QA methods, and consistently outperforms each of the 14 used features.

Availabilityhttps://github.com/Cao-Labs/SynthQA.git

Contactcaora@plu.edu


title: A neuronal social trait space for first impressions in the human amygdala and hippocampus

abstract: People instantaneously evaluate faces with significant agreement on evaluations of social traits. However, the neural basis for such rapid spontaneous face evaluation remains largely unknown. Here, we recorded from 490 neurons in the amygdala and hippocampus in 5 neurosurgical patients and show that amygdala and hippocampal neurons encode a social trait space. We further investigated the temporal evolution and modulation on the social trait representation, and we employed encoding and decoding models to reveal the critical social traits for the trait space. We also recorded from another 259 neurons and replicated our findings using different social traits. Lastly, the neuronal social trait space may have a behavioral consequence likely involved in the abnormal processing of social information in autism. Together, our results suggest that there exists a neuronal population code for a comprehensive social trait space in the human amygdala and hippocampus that underlie spontaneous first impressions.


title: Single Molecule Mass Photometry Reveals Dynamic Oligomerization of Plant and Human Peroxiredoxins for Functional Conservation and Diversification

abstract: Single molecule mass photometry was used to study the dynamic equilibria of the ubiquitous and highly abundant 2-Cysteine peroxiredoxins (2-CysPRX). 2-CysPRXs adopt distinct functions in all cells dependent on their oligomeric conformation ranging from dimers to decamers and high molecular weight aggregates (HMW). The oligomeric state depends on the redox state of their catalytic cysteinyl residues. To which degree they interconvert, how the interconversion is regulated, and how the oligomerisation propensity is organism specific remains, however, poorly understood. The dynamics differs between wild-type and single point mutants affecting the oligomerization interfaces, with concomitant changes to function. Titrating concentration and redox state of Arabidopsis thaliana and human 2-CysPRXs revealed features conserved among all 2-CysPRX and clear differences concerning oligomer transitions, the occurrence of transition states and the formation of HMW which are associated with chaperone activity or storage. The results indicate functional differentiation of human 2-CysPRXs. Our results point to a diversified functionality of oligomerization for 2-CysPRXs and illustrate the power of mass photometry to non-invasively quantify oligomer distributions in a redox environment. This knowledge is important to fully address and model PRX function in cell redox signaling e.g., in photosynthesis, cardiovascular and neurological diseases or carcinogenesis.

category: biochemistry


title: Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

abstract:
O_LISilphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and has a sporophytic self-incompatibility system--the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species.
C_LIO_LIWe used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we identified potential gene candidates using synteny analysis with the annual sunflower (Helianthus annuus) genome.
C_LIO_LIOur linkage map contains 198 SNP markers and resolved into the correct number of linkage groups. We were able to successfully map the S-locus and identify several potential gene candidates in the sunflower syntenic region.
C_LIO_LIOur method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than previous studies, and could be readily be applied to other species. Our best gene candidate appears to be worthy of future work in S. integrifolium and other Asteraceae species.
C_LI

category: plant biology


title: MicroRNA775 and target Galactosyltransferase (GALT9) module regulates recovery from submergence induced senescence by modulating SAGs in Arabidopsis thaliana

abstract: Submergence induced hypoxic condition is one of the abiotic stresses which negatively affects the plant growth and development, and causes early onset of senescence. Hypoxic conditions ateres the expression of a number of non-coding microRNAs (miRNAs), besides protein-coding genes. However, the molecular function of stress-induced miRNA in submergence induced physiological or developmental changes and recovery remains to be understood. The expression of miR775 is highly induced under hypoxic stress conditions. Here, we show that miR775 is a potential post-transcriptional regulator number of targets, including Galactosyltransferase (GALT9). The expression of miR775 and target GALT9 was significantly induced and reduced respectively at 24 hours of submergence. The overexpression of miR775 (miR775-Oe) confers enhanced recovery from submergence stress and reduced accumulation of ROS, in contrast to wild type and endogenous target mimic of miR775 (MIM775) Arabidopsis plants. We observed a similar recovery phenotype in case of target galt9 mutant plants, indicating the role of miR775-GALT9 module in recovery from submergence. Further, we showed that the expression of SENESCENCE ASSOCIATED GENES (SAGs), such as SAG12, SAG29, and ORE1. was increased in MIM775 and reduced in miR775-Oe and galt9 plants. Thus, our results suggest that miR775-GALT9 module plays a crucial role in the recovery from submergence by modulating the expression of SAGs through differential accumulation of ROS.


title: STARCH SYNTHASE 4 is required for normal starch granule initiation in amyloplasts of wheat endosperm

abstract:
O_LIStarch granule initiation is poorly understood at the molecular level. The glucosyltransferase, STARCH SYNTHASE 4 (SS4), plays a central role in granule initiation in Arabidopsis leaves, but its function in cereal endosperms is unknown. We investigated the role of SS4 in wheat, which has a distinct spatiotemporal pattern of granule initiation during grain development.
C_LIO_LIWe generated TILLING mutants in tetraploid wheat (Triticum turgidum) that are defective in both SS4 homoeologs. The morphology of endosperm starch was examined in developing and mature grains.
C_LIO_LISS4 deficiency led to severe alterations in endosperm starch granule morphology. During early grain development, while the wild type initiated single  A-type granules per amyloplast, most amyloplasts in the mutant formed compound granules due to multiple initiations. This phenotype was similar to mutants deficient in B-GRANULE CONTENT 1 (BGC1). SS4 deficiency also reduced starch content in leaves and pollen grains.
C_LIO_LIWe propose that SS4 and BGC1 are required for the proper control of granule initiation during early grain development that leads to a single A-type granule per amyloplast. The absence of either protein results in a variable number of initiations per amyloplast and compound granule formation.
C_LI


title: Wild to domesticates: genomes of edible diploid bananas hold traces of several undefined genepools

abstract: This study is an unprecedent exploration of the diversity of 226 diploid bananas genotyped with restriction-site-associated DNA sequencing data (RADseq) to clarify the processes that led to the creation of edible diploid AA bananas. This wide set included 72 seedy bananas, mostly M. acuminata from different genepools, and 154 edible, i.e. parthenocarpic and sterile, AA accessions obtained from genebanks and recent collecting missions. We highlighted the geographic organisation of the diversity of edible AAs and confirmed the admixed nature of many and further conducted introgressions tests within AAs from South East Asia and New Guinea. Lastly, taking advantage of the presence of an important number of M. acuminata ssp. banksii (22) and of AA from Papua New Guinea (76) in the set, we investigated the patterns of differentiation between wild and cultivated bananas seemingly belonging to the same genepool. We discovered a few cultivated AAs that may be of pure origins both in South-East Asia and in New Guinea. We also detected two undefined parental genepools in South East Asia for which regions of origin could be Thailand and a region between north Borneo and the Philippines, respectively. Finally, we suggest the existence of a third genepool in New Guinea island that might be a source population for both edible AAs and the local M. acuminata ssp. banksii.


title: Geography, not host identity, shapes bacterial community in reindeer lichens

abstract:
Background and AimsTremendous progress have been recently achieved in host-microbe research, however, there is still a surprising lack of knowledge in many taxa. Despite its dominance and crucial role in boreal forest, reindeer lichens have until now received little attention. We characterize, for the first time, the bacterial community of four species of reindeer lichens from Eastern North Americas boreal forests. We analysed the effect of two factors (host-identity and geography) in the bacterial community composition, we verified the presence of a common core bacteriota and identified the most abundant core taxa.

MethodsMorphological and molecular lichen species delimitation was performed based on the ITS region. The bacterial community of around 200 lichen samples was characterised using the 16S rRNA gene.

Key ResultsOur results showed that host-lichen identity does not determine bacterial community composition in reindeer lichens, but we confirmed the influence of geography in shaping the diversity and abundance of bacteria associated to the species Cladonia stellaris from lichen woodlands. We also revealed that reindeer lichens share a reduced common core bacteriota composed exclusively by Proteobacteria.

ConclusionsThe bacterial community in reindeer lichens is not host-selective. Northern lichen woodlands exhibit a significant higher diversity and abundance of bacteria associated to Cladonia stellaris. Nevertheless, the specific role of those bacteria as well as the process of host colonization remains to be determined. Elucidating these two aspects would be key to have a better understanding of the whole boreal ecosystems. The reduced and not diverse core bacteriota of reindeer lichens might be due to the larger size of our study area. The presence of the species Methylorosula polaris in the core bacteriota is evident and might have a particular importance for reindeer lichens.


title: Mixology: a tool for calculating required masses and volumes for laboratory solutions

abstract: We have created a tool to calculate the amount of each ingredient required to make up a custom solution with defined concentrations. It can convert between many kinds of volumetric, mass and concentration units. This includes the ability to convert between molarities and mass-based concentrations, using molecular masses retrieved from the ChEBI database. Mixology can be accessed at http://mixology.science.


title: Multimodal sensorimotor integration of visual and kinaesthetic afferents modulates motor circuits in humans

abstract: Optimal motor control requires the effective integration of multi-modal information. Visual information of movement performed by others even enhances potentials in the upper motor neurons, through the mirror-neuron system. On the other hand, it is known that motor control is intimately associated with afferent proprioceptive information. Kinaesthetic information is also generated by passive, external-driven movements. In the context of sensory integration, its an important question, how such passive kinaesthetic information and visually perceived movements are integrated. We studied the effects of visual and kinaesthetic information in combination, as well as isolated, on sensorimotor-integration - compared to a control condition. For this, we measured the change in the excitability of motor cortex (M1) using low-intensity TMS. We hypothesised that both visual motoneurons and kinaesthetic motoneurons could enhance the excitability of motor responses. We found that passive wrist movements increase the motor excitability, suggesting that kinaesthetic motoneurons do exist. The kinaesthetic influence on the motor threshold was even stronger than the visual information. Moreover, the simultaneous visual and passive kinaesthetic information increased the cortical excitability more than each of them independently. Thus, for the first time, we found evidence for the integration of passive kinaesthetic- and visual-sensory stimuli.


title: An engineered multifunctional protein tag for advanced fluorescence imaging

abstract: Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we present the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of live-cell compatible fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. We showed that the ability to tune the fluorescence color and properties through simple molecular modulation provides an unprecedent experimental versatility for imaging proteins in live cells, including delicate cultured hippocampal neurons, and in multicellular organisms. The ability to tune the spectral properties and fluorescence performance enables to match the spectral specifications and requirements of the most advanced imaging techniques, and allowed us to achieve efficient stimulated emission depletion (STED) nanoscopy of fusion proteins in live cells and live primary cultured neurons.


title: Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging


title: Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytes

abstract:
A primary limitation in the clinical application of pluripotent stem cell derived cardiomyocytes (PSC-CMs) is the failure of these cells to achieve full functional maturity. In vivo, cardiomyocytes undergo numerous adaptive changes during perinatal maturation. By contrast, PSC-CMs fail to fully undergo these developmental processes, instead remaining arrested at an embryonic stage of maturation. To date, however, the precise mechanisms by which directed differentiation differs from endogenous development, leading to consequent PSC-CM maturation arrest, are unknown. The advent of single cell RNA-sequencing (scRNA-seq) has offered great opportunities for studying CM maturation at single cell resolution. However, perinatal cardiac scRNA-seq has been limited owing to technical difficulties in the isolation of single CMs. Here, we used our previously developed large particle fluorescence-activated cell sorting approach to generate an scRNA-seq reference of mouse in vivo CM maturation with extensive sampling of perinatal time periods. We subsequently generated isogenic embryonic stem cells and created an in vitro scRNA-seq reference of PSC-CM directed differentiation. Through trajectory reconstruction methods, we identified a perinatal maturation program in endogenous CMs that is poorly recapitulated in vitro. By comparison of our trajectories with previously published human datasets, we identified a network of nine transcription factors (TFs) whose targets are consistently dysregulated in PSC-CMs across species. Notably, we demonstrated that these TFs are only partially activated in common ex vivo approaches to engineer PSC-CM maturation. Our study represents the first direct comparison of CM maturation in vivo and in vitro at the single cell level, and can be leveraged towards improving the clinical viability of PSC-CMs.

Significance StatementThere is a significant clinical need to generate mature cardiomyocytes from pluripotent stem cells. However, to date, most differentiation protocols yield phenotypically immature cardiomyocytes. The mechanisms underlying this poor maturation state are unknown. Here, we used single cell RNA-sequencing to compare cardiomyocyte maturation pathways in endogenous and pluripotent stem cell-derived cardiomyocytes. We found that in vitro, cardiomyocytes fail to undergo critical perinatal gene expression changes necessary for complete maturation. We found that key transcription factors regulating these changes are poorly expressed in vitro. Our study provides a better understanding of cardiomyocyte maturation both in vivo and in vitro, and may lead to improved approaches for engineering mature cardiomyocytes from stem cells.

category: cell biology


title: Comprehensive molecular features of polycystic ovary syndrome revealed by transcriptome analysis of oocytes and cumulus cells

abstract: PCOS is typically characterized by polycystic ovarian morphology, hyperandrogenism, ovulatory dysfunction and infertility. Furthermore, PCOS patients undergoing ovarian stimulation have more oocytes, however, poor quality of oocytes lead to lower fertilization and implantation rates, decreased pregnancy and increased miscarriage rates. Our study suggests that global gene expression and cell to cell interactions of oocytes and CCs are significantly altered in women with PCOS. Noticeably, genes related to microtubules such as TUBB8 and TUBA1C are abnormally highly expressed in PCOS oocytes, reducing oocyte quality. The pattern of transposable element expression distinguishes PCOS from Control oocytes, implying the role of transposable elements in the occurrence of PCOS.


title: Effects of conjugated linoleic acid on proliferation and differentiation of bovine intramuscular preadipocyte in vitro

abstract: Conjugated linoleic acid (CLA), a mixture of isomers of linoleic acid, has previously been shown to be able to increase intramuscular fat content in vivo and stimulate adipogenesis in intramuscular preadipocytes in vitro in pig. Unfortunately, there is little data to evaluate the effect of CLA on proliferation and differentiation of bovine intramuscular preadipocytes. This study investigated the regulation by CLA in proliferation and differentiation of bovine intramuscular preadipocytes. The results demonstrated that CLA significantly induced the expression of PPAR{gamma} and C/EBP mRNA of bovine intramuscular preadipocytes as well as the accumulation of lipid in cultured intramuscular preadipocytes. Additionally, CLA significantly decreased the cell proportion of phase G0/G1, and remarkably increased the proportion of phase S+G2/M. Collectively, these results suggest that CLA promotes bovine intramuscular preadipocyte proliferation and differentiation.


title: SiCEP3, a C-terminally encoded peptides from Setaria italica, promotes ABA import and signaling pathway

abstract:
C-terminally encoded peptides (CEPs) are small peptides, typically post-translationally modified, and highly conserved in many species. CEPs are known to play roles in inhibition of plant growth and regulation of development, but the mechanisms are not well understood. In this study, we searched for CEP peptides in foxtail millet (Setaria italica). The 14 peptides we identified are divided into two subfamilies. The transcripts of most SiCEPs were more abundant in roots than in other tissues. SiCEP3, SiCEP4, and SiCEP5 were also expressed at high levels in panicles. Moreover, expression of all SiCEPs was induced by biotic stress and phytohormones. SiCEP3 overexpression and application of biosynthetic SiCEP3 both inhibited the growth of seedlings. In the presence of ABA, growth inhibition and ABA content of seedlings increased with the concentration of SiCEP3. Transcripts encoding two ABA transporters and one ABA receptor were induced by SiCEP3, ABA, and the two in combination. Further analysis revealed that SiCEP3 promoted ABA transport via NRT1.2 and ABCG40. In addition, SiCEP3, ABA, or the combination inhibited the kinase activities of CEP receptors CEPR1/2. Taken together, our results indicated that the CEP-CEPR module mediates ABA signaling by regulating ABCG40, NRT1.2, and PYL4 in planta.

HighlightSiCEP3, a C-terminally encoded peptide, can promote ABA import and signaling pathway by inhibiting the kinase activity of its receptors under abiotic stress in Setaria italica.


title: Successful spermatogonial stem cells transplantation within Pleuronectiformes: first breakthrough at inter-family level in marine fish

abstract: As a promising biotechnology, fish germ cell transplantation shows potentials in conservation germplasm resource, propagation of elite species, and generation of transgenic individuals. In this study, we successfully transplanted the Japanese flounder (P. olivaceus), summer flounder (P. dentatus), and turbot (S. maximus) spermatogonia into triploid Japanese flounder larvae, and achieved high transplantation efficiency of 100%, 75-95% and 33-50% by fluorescence tracking and molecular analysis, respectively. Eventually, donor-derived spermatozoa produced offspring by artificial insemination. We only found male and intersex chimeras in inter-family transplantations, while male and female chimeras in both intra-species and intra-genus transplantations. Moreover, the intersex chimeras could mature and produce turbot functional spermatozoa. We firstly realized inter-family transplantation in marine fish species. These results demonstrated successful spermatogonial stem cells transplantation within Pleuronectiformes, suggesting the germ cells migration, incorporation and maturation within order were conserved across a wide range of teleost species.

category: developmental biology


title: Zebrafish spinal cord oligodendrocyte formation requires boc function

abstract: The axis of the vertebrate neural tube is patterned, in part, by a ventral to dorsal gradient of Shh signaling. In the ventral spinal cord, Shh induces concentration-dependent expression of transcription factors, subdividing neural progenitors into distinct domains that subsequently produce distinct neuronal and glial subtypes. In particular, progenitors of the pMN domain express the bHLH transcription factor Olig2 and produce motor neurons followed by oligodendrocytes, the myelinating glial cell type of the central nervous system. In addition to its role in patterning ventral progenitors, Shh signaling must be maintained through development to specify pMN progenitors for oligodendrocyte fate. Using a forward genetic screen in zebrafish for mutations that disrupt development of oligodendrocytes, we identified a new mutant allele of boc, which encodes a type I transmembrane protein that functions as a coreceptor for Shh. Embryos homozygous for the bocco25 allele, which creates a missense mutation in a Fibronectin type III domain that binds Shh, have normally patterned spinal cords but fail to maintain pMN progenitors, resulting in a deficit of oligodendrocytes. Using a sensitive fluorescent detection method for in situ RNA hybridization, we found that spinal cord cells express boc in a graded fashion that is inverse to the gradient of Shh signaling activity and that boc function is necessary to maintain pMN progenitors by shaping the Shh signaling gradient.


title: Annelids win again: the first evidence of Hox antisense transcription in Spiralia.

abstract: To date it is becoming more and more obvious that multiple non-coding RNAs, once considered to be transcriptional noise, play a huge role in gene regulation during animal ontogenesis. Hox genes are key regulators of embryonic development, growth and regeneration of all bilaterian animals. It was shown that mammalian Hox loci are transcribed in both directions and noncoding RNAs maintain and control the normal functioning of Hox clusters. We revealed antisense transcripts of most of Hox genes in two lophotrochozoans, errant annelids Alitta virens and Platynereis dumerilii. It is for the first time when non-coding RNAs associated with Hox genes are found in spiralian animals. All these asRNAs can be referred to as natural antisense transcripts (NATs). We analyzed the expression of all detected NATs using sense probes to their Hox mRNAs during larval and postlarval development and regeneration by whole mount in situ hybridization (WMISH). We managed to clone several asRNAs (Avi-antiHox4-1, Avi-antiHox4-2 and Avi-antiHox5) of these annelids and analyzed their expression patterns as well. Our data indicate variable and complicated interplay between sense and antisense Hox transcripts during development and growth of two annelids. The presence of Hox antisense transcription in the representatives of different bilaterian clades (mammals, myriapods and annelids) and similar expression relationships in sense-antisense pairs suggest that this can be the ancestral feature of Hox cluster regulation.


title: First 'Comprehensive' Annotation of Leucine-Rich Repeat-Containing Receptors in Rice

abstract: Rice plays an essential food security role for more than half of the worlds population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large Leucine-Rich Repeat (LRR)-containing receptor (LRR-CR) subfamilies: the LRR-Receptor-Like Kinase (RLK), LRR-Receptor-Like Protein (RLP) and Nucleotide-binding LRR Receptor (NLR) subfamilies. Using LRRprofiler, a pipeline we developed to annotate and classify those proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies we observed for LRR-CR gene models led us to perform in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a Nipponbare closely related cultivar, using an optimised strategy. Here we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to  functional and  structural annotations, we propose the community to adopt this new approach, which we call  comprehensive annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR in order to promote their use in breeding future resilient varieties.

category: genomics


title: A New 'Comprehensive' Annotation of Leucine-Rich Repeat-Containing Receptors in Rice


title: Multiscale mechanics and temporal evolution of vimentin intermediate filament networks

abstract: The cytoskeleton, an intricate network of protein filaments, motor proteins, and crosslinkers, largely determines the mechanical properties of cells. Among the three filamentous components, F-actin, microtubules, and intermediate filaments (IFs), the IF network is by far the most extensible and resilient to stress. We present a multiscale approach to disentangle the three main contributions to vimentin IF network mechanics - single filament mechanics, filament length, and interactions between filaments - including their temporal evolution. Combining particle tracking, quadruple optical trapping and computational modeling, we derive quantitative information on the strength and kinetics of filament interactions. Specifically, we find that hydrophobic contributions to network mechanics enter mostly via filament elongation kinetics, whereas electrostatics have a direct influence on filament-filament interactions. These results indicate that cells might need to explicitly suppress attractive interactions to re-organize the extremely stable cellular vimentin network.

category: biophysics


title: Disrupted Surfaces of Porous Membranes Reduce Nuclear YAP Localization through Diminished Cell Spreading and Enhance Adipogenesis

abstract:
The disrupted surface of porous membranes, commonly used in tissue-chip and cellular co-culture systems, is known to weaken cell-substrate interactions. Here, we investigated whether disrupted surfaces of membranes with micron and sub-micron scale pores affect YAP localization and differentiation of adipose-derived stem cells (ADSCs). We found that these substrates reduce YAP nuclear localization through decreased cell spreading, consistent with reduced cell-substrate interactions, and in turn enhance adipogenesis, while decreasing osteogenesis.

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title: Disrupted Surfaces of Porous Membranes Reduce Nuclear YAP Localization and Enhance Adipogenesis through Morphological Changes


title: Matrix-Bound Growth Factors are Released upon Cartilage Compression by an Aggrecan-Dependent Sodium Flux that is Lost in Osteoarthritis

abstract:
Articular cartilage is a dense extracellular matrix-rich tissue that degrades following chronic mechanical stress, resulting in osteoarthritis (OA). The tissue has low intrinsic repair especially in aged and osteoarthritic joints. Here we describe three pro-regenerative factors; fibroblast growth factor 2 (FGF2), connective tissue growth factor, bound to transforming growth factor-beta (CTGF-TGF{beta}), and hepatoma-derived growth factor (HDGF), that are rapidly released from the pericellular matrix (PCM) of articular cartilage upon mechanical injury. All three growth factors bound heparan sulfate, and were displaced by exogenous NaCl. We hypothesised that sodium, sequestered within the aggrecan-rich matrix, was freed by injurious compression, thereby enhancing the bioavailability of pericellular growth factors. Indeed, growth factor release was abrogated when cartilage aggrecan was depleted by IL-1 treatment, and in severely damaged human osteoarthritic cartilage. A flux in free matrix sodium upon mechanical compression of cartilage was visualised by 23Na magnetic resonance imaging (MRI) just below the articular surface. This corresponded to a region of reduced tissue stiffness, measured by scanning acoustic microscopy and second harmonic generation microscopy, and where Smad2/3 was phosphorylated upon cyclic compression. Our results describe a novel intrinsic repair mechanism, controlled by matrix stiffness and mediated by the free sodium concentration, in which heparan sulfate-bound growth factors are released from cartilage upon injurious load. They identify aggrecan as a depot for sequestered sodium, explaining why osteoarthritic tissue loses its ability to repair. Treatments that restore matrix sodium to allow appropriate release of growth factors upon load are predicted to enable intrinsic cartilage repair in osteoarthritis.

Significance StatementOsteoarthritis is the most prevalent musculoskeletal disease, affecting 250 million people worldwide 1. We identify a novel intrinsic repair response in cartilage, mediated by aggrecan-dependent sodium flux, and dependent upon matrix stiffness, which results in the release of a cocktail of pro-regenerative growth factors after injury. Loss of aggrecan in late-stage osteoarthritis prevents growth factor release and likely contributes to disease progression. Treatments that restore matrix sodium in osteoarthritis may recover the intrinsic repair response to improve disease outcome.


title: Sterols lower energetic barriers of membrane bending and fission necessary for efficient clathrin mediated endocytosis

abstract: As the principal internalization mechanism in mammalian cells, clathrin-mediated endocytosis (CME) is critical for cellular signal transduction, receptor recycling, and membrane homeostasis. Acute depletion of cholesterol disrupts CME, motivating analysis of CME dynamics in the context of disrupted cholesterol synthesis, sterol specificity, mechanisms involved, and relevance to disease pathology. Using genome-edited cell lines, we demonstrate that inhibition of post-squalene cholesterol biosynthesis as observed in inborn errors of cholesterol metabolism, results in striking immobilization of CME and impaired transferrin uptake. Imaging of membrane bending dynamics and CME pit ultrastructure revealed prolonged clathrin pit lifetimes and accumulation of shallow clathrin-coated structures that scaled with diminishing sterol abundance. Moreover, fibroblasts derived from Smith-Lemli-Opitz syndrome subjects displayed reduced CME function. We conclude that sterols lower the energetic costs of membrane bending during pit formation and vesicular scission during CME and suggest reduced CME contributes to cellular phenotypes observed within disorders of cholesterol metabolism.


title: Molecular profiling of retinal pigment epithelial cell differentiation for therapeutic use

abstract: Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, detailed single cell mapping of the transient cellular and molecular dynamics from the pluripotent state to mature RPE has not been performed. Here we conduct single-cell transcriptomic analyses of 25,718 cells during differentiation as well as in embryonic and adult retina references, revealing differentiation progression through an un-expected initial cell diversification recapitulating early embryonic development before converging towards an RPE lineage. We also identified NCAM1 to track and capture an intermediate retinal progenitor with the potential to give rise to multiple neuroepithelial lineages. Finally, we profiled hESC-RPE cells after subretinal transplantation into the rabbit eye, uncovering robust in vivo maturation towards an adult state. Our detailed evaluation of hESC-RPE differentiation supports the development of safe and efficient pluripotent stem cell-based therapies for AMD.


title: The role of Gdf5 in the development of the zebrafish fin endoskeleton

abstract:
BackgroundThe development of the vertebrate limb skeleton requires a complex interaction of multiple factors to facilitate correct shaping and positioning of bones and joints. Growth and differentiation factor 5 (Gdf5), a member of the transforming growth factor-beta family (TGF-{beta}) is involved in patterning appendicular skeletal elements including joints. Expression of gdf5 in zebrafish has been detected within the first pharyngeal arch jaw joint, fin mesenchyme condensations and segmentation zones in median fins, however little is known about the functional role of Gdf5 outside of Amniota.

ResultsWe generated CRISPR/Cas9 knockout of gdf5 in zebrafish and analysed the resulting phenotype at different developmental stages. Homozygous gdf5 mutant zebrafish displayed changes in segmentation of the endoskeletal disc and, in consequence, loss of posterior radials in the pectoral fins. Mutant fish also displayed affected organisation and length of skeletal elements in the median fins, however joint formation and mineralisation process seemed unaffected.

ConclusionsOur study demonstrates the importance of Gdf5 for the paired and median fin endoskeleton development in zebrafish and reveals that the severity of the effect increases from anterior to posterior side of the elements. Our findings are consistent with phenotypes observed in human and mouse appendicular skeleton in response to Gdf5 knockout, suggesting a broadly conserved role for Gdf5 in Osteichthyes.


title: From heterogeneous datasets to predictive models of embryonic development

abstract: Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing, and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here we use data from our work on signal-dependent gene repression in the Drosophila embryo to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation, and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.


title: Midkine-a regulates the formation of a fibrotic scar during zebrafish heart regeneration

abstract: The adult zebrafish heart regenerates after injury, unlike the hearts of mammals. Heart cryoinjury triggers the formation of a fibrotic scar that gradually degrades, leading to regeneration. Midkine-a (Mdka) is a multifunctional cytokine that is activated after cardiac injury. Here, we investigated the role of mdka in zebrafish heart regeneration. We show that mdka expression is strongly induced at 1-day post cryoinjury (dpci) throughout the epicardium, whereas by 7 dpci expression has become restricted to epicardial cells covering the injured area. To study the role of mdka in heart regeneration, we generated mdka-knock out (KO) zebrafish strains. Analysis of injured hearts showed that loss of mdka decreased endothelial cell proliferation and resulted in a blockade of heart regeneration characterized by retention of a collagenous scar. Transcriptional analysis revealed increases in collagen transcription and TGF{beta} signalling activity. These results reveal a critical role for mdka in fibrosis regulation during heart regeneration.


title: Cardiac progenitors auto-regulate second heart field cell fate via Wnt secretion

abstract:
Proper heart formation requires coordinated development of two anatomically distinct groups of cells - the first and second heart fields (FHF and SHF). Given that congenital heart defects are often restricted to derivatives of the FHF or SHF, it is crucial to understand the mechanisms controlling their development. Wnt signaling has previously been implicated in SHF proliferation; however, the source of Wnts remains unknown. Through comparative gene analysis, we found upregulation of Wnts and Wnt receptor/target genes in the FHF and SHF, respectively, raising the possibility that early cardiac progenitors may secrete Wnts to influence SHF cell fate. To probe this further, we deleted Wntless (Wls), a gene required for Wnt ligand secretion, in various populations of precardiac cells. Deletion of Wls in Mesp1+ cells resulted in formation of a single chamber heart with left ventricle identity, implying compromised SHF development. This phenotype was recapitulated by deleting Wls in cells expressing Islet1, a pan-cardiac marker. Similarly, Wls deletion in cells expressing Nkx2.5, a later-expressed pan-cardiac marker, resulted in hypoplastic right ventricle, a structure derived from the SHF. However, no developmental defects were observed when deleting Wls in SHF progenitors. To gain mechanistic insights, we isolated Mesp1-lineage cells from developing embryos and performed single-cell RNA-sequencing. Our comprehensive single cell transcriptome analysis revealed that Wls deletion dysregulates developmental trajectories of both anterior and posterior SHF cells, marked by impaired proliferation and premature differentiation. Together, these results demonstrate a critical role of local precardiac mesodermal Wnts in SHF fate decision, providing fundamental insights into understanding heart field development and chamber formation.

Significance StatementThere is significant interest in understanding the mechanisms underlying heart formation to develop treatments and cures for patients suffering from congenital heart disease. In particular, we were interested in the intricacies of first (FHF) and second heart field (SHF) development, as many congenital heart defects present with heart field-specific etiologies. Here, we uncovered a novel relationship between specified cardiac progenitor cells and second heart field progenitors. Through genetic manipulation of Wnt secretion in developing mouse embryos, we identified a population of cardiac progenitor cells that acts as a local source of Wnts which are necessary for proper SHF development. Our single cell transcriptomic analysis of developing anterior mesoderm showed cardiac progenitor-secreted Wnts function through regulation of differentiation and proliferation among SHF progenitors. Thus, this study provides insight into the source and timing of Wnts required for SHF development, and points to the crucial role of co-developing cell populations in heart development.


title: linc2function: A deep learning model to identify and assign function to long noncoding RNA (lncRNA)

abstract:
MotivationLncRNAs are much more versatile and are involved in many regulatory roles inside the cell than previously believed. Existing databases lack consistencies in lncRNA annotations, and the functionality of over 95% of the known lncRNAs are yet to be established. LncRNA transcript identification involves discriminating them from their coding counterparts, which can be done with traditional experimental approaches, or via in silico methods. The later approach employs various computational algorithms, including machine learning classifiers to predict the lncRNA forming potential of a given transcript. Such approaches provide an economical and faster alternative to the experimental methods. Current in silico methods mainly use primary-sequence based features to build predictive models limiting their accuracy and robustness. Moreover, many of these tools make use of reference genome based features, in consequence making them unsuitable for non-model species. Hence, there is a need to comprehensively evaluate the efficacy of different predictive features to build computational models. Additionally, effective models will have to provide maximum prediction performance using the least number of features in a species-agnostic manner.

It is popularly known in the protein world that "structure is function". This also applies to lncRNAs as their functional mechanisms are similar to those of proteins. Generally, lncRNA function by structurally binding to its target proteins or nucleic acid forming complexes. The secondary structures of the lncRNAs are modular providing interaction sites for their interactome made of DNA, RNA, and proteins. Through these interactions, they epigenetically regulate cellular biology, thereby forming a layer of genomic programming on top of the coding genes. We demonstrate that in addition to using transcript sequence, we can provide comprehensive functional annotation by collating their interactome and secondary structure information.

ResultsHere, we evaluated an exhaustive list of sequence-based, secondary-structure, interactome, and physicochemical features for their ability to predict the lncRNA potential of a transcript. Based on our analysis, we built different machine learning models using optimum feature-set. We found our model to be on par or exceeding the execution of the state-of-the-art methods with AUC values of over 0.9 for a diverse collection of species tested. Finally, we built a pipeline called linc2function that provides the information necessary to functionally annotate a lncRNA conveniently in a single window.

AvailabilityThe source code is accessible use under MIT license in standalone mode, and as a webserver (https://bioinformaticslab.erc.monash.edu/linc2function).


title: Enabling technology for microbial source tracking based on transfer learning: From ontology-aware general knowledge to context-aware expert systems

abstract: Microbial source tracking quantifies the potential origin of microbial communities, facilitates better understanding of how the taxonomic structure and community functions were formed and maintained. However, previous methods involve a tradeoff between speed and accuracy, and have encountered difficulty in source tracking under many context-dependent settings. Here, we present EXPERT for context-aware microbial source tracking, in which we adopted a Transfer Learning approach to profoundly elevate and expand the applicability of source tracking, enabling biologically informed novel microbial knowledge discovery. We demonstrate that EXPERT can predict microbial sources with performance superior to other methods in efficiency and accuracy. More importantly, we demonstrate EXPERTs context-aware ability on several applications, including tracking the progression of infant gut microbiome development and monitoring the changes of gut microbiome for colorectal cancer patients. Broadly, transfer learning enables accurate and context-aware microbial source tracking and has the potential for novel microbial knowledge discovery.


title: EXPERT: Transfer Learning-enabled context-aware microbial source tracking


title: Deciphering active prophages from metagenomes

abstract: Temperate phages (prophages) are ubiquitous in nature and persist as dormant components of host cells (lysogenic stage) before activating and lysing the host (lytic stage). Actively replicating prophages contribute to central community processes, such as enabling bacterial virulence, manipulating biogeochemical cycling, and driving microbial community diversification. Recent advances in sequencing technology have allowed for the identification and characterization of diverse phages, yet no approaches currently exist for identifying if a prophage has activated. Here, we present PropagAtE (Prophage Activity Estimator), an automated software tool for estimating if a prophage is in the lytic or lysogenic stage of infection. PropagAtE uses statistical analyses of prophage-to-host read coverage ratios to decipher actively replicating prophages, irrespective of whether prophages were induced or spontaneously activated. We demonstrate that PropagAtE is fast, accurate and sensitive, regardless of sequencing depth. Application of PropagAtE to prophages from 348 complex metagenomes from human gut, murine gut and soil environments identified distinct spatial and temporal prophage activation signatures, with the highest proportion of active prophages in murine gut samples. Among the soil habitats evaluated (bog, fen and palsa), we identified unique populations of Myxococcales, Acetobacteraceae and Acidimicrobiaceae prophages to be active in fen, palsa and bog habitats, respectively. Within the human gut, 11 prophage populations, some encoding the sulfur metabolism gene cysH or a rhuM-like virulence factor, were consistently present over time but not active. Overall, PropagAtE will facilitate accurate representations of viruses in microbiomes by associating prophages with their active roles in shaping microbial communities in nature.


title: Nephrotoxicity of the BRAF-kinase inhibitor Vemurafenib isdriven by off-target Ferrochelatase inhibition

abstract:
A multitude of disease and therapy related factors drive the frequent development of renal disorders in cancer patients. Along with chemotherapy, the newer targeted therapeutics can also cause renal dysfunction through on and off-target mechanisms. Interestingly, among the small-molecule inhibitors approved for the treatment of cancers that harbor BRAF-kinase activating mutations, vemurafenib can trigger tubular damage and acute kidney injury (AKI). To investigate the underlying mechanisms, here, we have developed cell culture and mouse models of vemurafenib nephrotoxicity. Our studies show that at clinically relevant concentrations vemurafenib induces cell-death in transformed and primary murine and human renal tubular epithelial cells (RTEC). In mice, two weeks of daily vemurafenib treatment causes moderate AKI with histopathological characteristics of RTEC injury. Importantly, RTEC-specific BRAF gene deletion did not influence renal function under normal conditions or alter the severity of vemurafenib-associated renal impairment. Instead, we found that inhibition of ferrochelatase (FECH), an enzyme involved in heme biosynthesis contributes to vemurafenib nephrotoxicity. FECH overexpression protected RTECs and conversely FECH knockdown increased the sensitivity to vemurafenib nephrotoxicity. Collectively, these studies suggest that vemurafenib-associated RTEC dysfunction and nephrotoxicity is BRAF-independent and caused in part by off-target FECH inhibition.

Translational StatementBRAF is the most frequently mutated protein kinase and a critical oncogenic driver in human cancers. In melanoma and other cancers with BRAF activating mutations, BRAF targeted small-molecule therapeutics such as vemurafenib, and dabrafenib have shown remarkable clinical benefits. However, recent clinical studies have shown that a significant number of patients that receive vemurafenib develop AKI through mechanisms that remain unknown. The present study describes the development of novel experimental models of vemurafenib nephrotoxicity and reveals the underlying off-target mechanisms that contribute to renal injury.

category: pharmacology and toxicology


title: Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity

abstract: Acute ozone (O3) exposure is associated with multiple adverse cardiorespiratory outcomes, the severity of which varies across human populations and rodent models from diverse genetic backgrounds. However, molecular determinants of response, including biomarkers that distinguish which individuals will develop more severe injury and inflammation (i.e., high responders), are poorly characterized. Here, we exposed adult, female and male mice from 6 strains, including 5 Collaborative Cross (CC) strains, to filtered air (FA) or 2 ppm O3 for 3 hours, and measured several inflammatory and injury parameters 21 hours later. Additionally, we collected airway macrophages and performed RNA-seq analysis to investigate influences of strain, treatment, and strain-by-treatment interactions on gene expression as well as transcriptional correlates of lung phenotypes. Animals exposed to O3 developed airway neutrophilia and lung injury, with varying degrees of severity. We identified many genes that were altered by O3 exposure across all strains, and examination of genes whose expression was influenced by strain-by-treatment interactions revealed prominent differences in response between the CC017/Unc and CC003/Unc strains, which were low- and high-responders, respectively (as measured by cellular inflammation and injury). Further investigation of this contrast indicated that baseline gene expression differences likely contribute to their divergent post-O3 exposure transcriptional responses. We also observed alterations in chromatin accessibility that differed by strain and with strain-by-treatment interactions, lending further plausibility that baseline differences can modulate post-exposure responses. Together, these results suggest that aspects of the respiratory response to O3 exposure may be mediated through altered airway macrophage transcriptional signatures, and further confirms the importance of gene-by-environment interactions in mediating differential responsiveness to environmental agents.


title: Atg8 licenses adipokine nuclear exit

abstract:
Adipokines released from the adipocytes function as a systemic adipometer; they impinge on neural circuits to signal nutrient status. On starvation, adipokines must be retained to signal energy deficit; else, it significantly reduces starvation survival. But how fat cells retain adipokines is unclear. Here, we demonstrate that Atg8, a cell-intrinsic autophagy factor, regulates the starvation-induced acute retention of the Leptin Drosophila ortholog Upd2. We show that on starvation, as a direct consequence of Atg8s lipidation, Upd2 accumulates in the nucleus. We illustrate that Upd2s nuclear retention is critical to fat mobilization and increased starvation resilience. Furthermore, nuclear Upd2 promotes the expression of a secreted innate immune gene signature. This hints at an unanticipated connection between adipokine nuclear retention and increased innate immunity. In conclusion, we propose that, during starvation, Atg8s role is not just limited to autophagy but is critical for withholding adipokines in the nucleus to promote starvation resilience.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/428913v5_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1826425org.highwire.dtl.DTLVardef@17cca52org.highwire.dtl.DTLVardef@1c70ac7org.highwire.dtl.DTLVardef@94a024_HPS_FORMAT_FIGEXP  M_FIG C_FIG O_LIIn fed state Upd2 requires Atg8 for nuclear exit and cytosolic localization.
C_LIO_LIAtg8s lipidation on starvation results in Upd2s nuclear accumulation.
C_LIO_LIUpd2 nuclear retention on starvation increases fat mobilization and post-starvation hunger.
C_LIO_LIOn starvation Upd2 nuclear retention increases expression of a secreted innate immune signature.
C_LI


title: Atg8 licenses adipokine nuclear exit


title: Atg8 licenses adipokine nuclear exit


title: NUCLEAR RETENTION OF LEPTIN/UPD2 REGULATES ORGANISMAL RESILIENCE TO NUTRIENT EXTREMES


title: Precise, 3-D optogenetic control of the diameter of single arterioles

abstract: Modulation of brain arteriole diameter is critical for maintenance of cerebral blood pressure and control of hyperemia during regional neural activity. However, studies of hemodynamic function in health and disease have lacked a method to control and monitor blood flow with high spatiotemporal resolution. Here, we describe a new all-optical approach to precisely control and monitor arteriolar contractility in vivo using combined two-photon optogenetics and imaging. The expression of the excitatory opsin, ReaChR, in vascular smooth muscle cells enabled rapid and repeated vasoconstriction following brief light pulses. Targeted two-photon activation of ReaCHR using a spatial light modulator (SLM) produced highly localized constrictions when targeted to individual arteries within the neocortex. We demonstrate the utility of this method for examining arteriole contractile dynamics and creating transient blood flow reductions. Additionally, we show that optogenetic constriction can offset or completely block sensory stimulus evoked vasodilation, providing a valuable tool to dissociate blood flow changes from neural activity.


title: Mutagenesis of the Ammonium Transporter AcAmt Reveals a Reproductive Role and a Novel Ammonia-Sensing Mechanism in the Malaria Vector Mosquito Anopheles coluzzii

abstract:
Anopheline mosquitoes are the sole vectors of malaria and rely on olfactory cues for host seeking in which ammonia derived from human sweat plays an essential role. To investigate the function of the Anopheles coluzzii ammonium transporter (AcAmt) in the mosquito olfactory system, we generated an AcAmt null mutant line using CRISPR/Cas9. AcAmt-/- mutants displayed a series of novel phenotypes compared with wild-type mosquitoes including significantly lower insemination rates during mating and increased mortality during eclosion. Furthermore, AcAmt-/- males showed significantly lower sugar consumption while AcAmt-/- females and pupae displayed significantly higher ammonia levels than their wild-type counterparts. Surprisingly, in contrast to previous studies in Drosophila that revealed that the mutation of the ammonium transporter (DmAmt) induces a dramatic reduction of ammonia responses in antennal coeloconic sensilla, no significant differences were observed across a range of peripheral sensory neuron responses to ammonia and other odorants between wild-type and AcAmt-/- females. Taken together, these data support the existence of a unique ammonia-sensing mechanism in mosquitoes and that the ammonium transporter may be an important molecular target for vector control.

Key MessagesO_LIMutagenesis of An. coluzzii ammonium transporter AcAmt followed by comprehensive electrophysiological investigation suggest a novel ammonia-sensing pathway in Anopheles mosquitoes.
C_LIO_LIAcAmt-/- mutants displayed significant deficiencies in reproduction and eclosion, which are likely due to elevated ammonia levels and reduced ability of sugar feeding.
C_LIO_LIAn. coluzzii coeloconic sensilla primarily detect amines and acids.
C_LI


title: Management of altered metabolic activity in Drosophila model of Huntington's disease by curcumin

abstract: Huntingtons disease (HD) is a devastating polyglutamine (polyQ) disorder characterized by extensive neurodegeneration and metabolic abnormalities at systemic, cellular and intracellular levels. Metabolic alterations in HD manifest as abnormal body weight, dysregulated biomolecule levels, impaired adipocyte functions and defective energy state which exacerbate disease progression and pose acute threat to the health of challenged individuals in form of insulin resistance, cardiovascular disease and energy crisis. To colossally mitigate disease symptoms, we tested the efficacy of curcumin in Drosophila model of HD. Curcumin is bioactive component of turmeric (Curcuma longa Linn), well-known for its ability to modulate metabolic activities. We found that curcumin effectively managed abnormal body weight, dysregulated lipid content and carbohydrate level in HD flies. In addition, curcumin administration lowered elevated reactive-oxygen-species (ROS) levels in adult adipose tissue of diseased flies, and improved survival and locomotor function in HD flies at advanced disease stage. Altogether, these findings clearly suggest that curcumin efficiently attenuates metabolic derangements in HD flies and can prove beneficial in alleviating the complexities associated with HD. Phytochemicals like curcumin that can regulate multiple targets in complex diseases like HD, with least side-effects and maximum benefits, provide a better hope for the treatment of terminally-ill HD patients.


title: Gut regulates brain synaptic assembly through neuroendocrine signaling pathway

abstract: The gut-brain axis plays an essential role in regulating neural development in response to environmental stimuli, such as microbes or nutrients. Defects in gut-brain communication can lead to various neurological disorders. However, it remains unknown whether gut plays any intrinsic role in regulating neuronal development. Through a genetic screen in C. elegans, we uncovered that an intrinsic Wnt-endocrine pathway in gut regulates synaptic development and neuronal activity in brain. Specifically, the Wnt signaling upregulates the expression of the neuropeptide NLP-40 in the gut, which then facilitates presynaptic assembly through the neuronal expressed GPCR AEX-2 receptor during development. The NLP-40 acts most likely through modulating neuronal activity and promoting synaptic protein trafficking. Therefore, this study reveals a novel role of gut in synaptic development in the brain.


title: Chemogenetic activation of nigrostriatal dopamine neurons in freely moving common marmosets

abstract: To interrogate particular neuronal pathways in non-human primates under natural and stress-free conditions, we applied designer receptors exclusively activated by designer drugs (DREADDs) technology to common marmosets. We injected adeno-associated virus vectors expressing the excitatory DREADD hM3Dq into the unilateral substantia nigra in three marmosets. Using multi-tracer positron emission tomography imaging, we detected DREADD expression in vivo, which was confirmed in nigrostriatal dopamine neurons by immunohisto-chemistry, and assessed activation of the substantia nigra and dopamine release following agonist administration. The marmosets rotated in a contralateral direction relative to the activated side 30-90 min after consuming food containing the highly potent DREADD agonist deschloroclozapine (DCZ), but not on the following days without DCZ. These results indicate that non-invasive and reversible DREADD manipulation will extend the utility of marmoset as a primate model for linking neuronal activity and natural behavior in various contexts.


title: Antisense therapy in a new rat model of Alexander disease reverses GFAP pathology, white matter deficits, and motor impairment.

abstract: Alexander disease (AxD) is a devastating leukodystrophy caused by gain of function mutations in GFAP, and the only available treatments are supportive. Recent advances in antisense oligonucleotide (ASO) therapy have demonstrated that transcript targeting can be a successful strategy for human neurodegenerative diseases amenable to this approach. We have previously used mouse models of AxD to show that Gfap-targeted ASO suppresses protein accumulation and reverses pathology; however, the mice have a mild phenotype with no apparent leukodystrophy or overt clinical features and are therefore limited for assessing functional outcomes. In this report we introduce a new rat model of AxD that exhibits hallmark pathology with GFAP aggregation in the form of Rosenthal fibers, widespread astrogliosis, and white matter deficits. These animals develop normally during the first postnatal weeks but fail to thrive after weaning and develop severe motor deficits as they mature, with approximately 15 % dying of unknown cause between 6 to 12 weeks of age. In this model, a single treatment with Gfap-targeted ASO provides long lasting suppression, reverses GFAP pathology, and depending on age of treatment, prevents or mitigates white matter deficits and motor impairment. This is the first report of an animal model of AxD with myelin pathology and motor impairment, recapitulating prominent features of the human disease. We use this model to show that ASO therapy has the potential to not only prevent but also reverse many aspects of disease.


title: Dysregulation of PAX5 causes uncommitted B cell development and tumorigenesis in mice

abstract:
PAX5 is the master transcription factor controlling B cell identity. In humans, mutations in PAX5 account for 30% of B cell acute lymphoblastic leukemia (B-ALL) cases. Investigating the causal effects of PAX5 mutations has however been difficult due to the premature lethality of Pax5-/- mice. Here we describe a novel mouse strain with a premature STOP mutation in Pax5 (Y351*) that produces a truncated protein and reduction in protein function, yet still allows for some B cell development to occur. A population of uncommitted and multipotent CD19+B220- B cells develops in the bone marrow of homozygous mice leading to the development of B-ALL. We show that the tumors frequently acquire secondary mutations in Jak3, and Ptpn11 highlighting key pathways interacting with PAX5 during malignant transformation. Analysis of the PAX5Y351* mice provide insight not only into the functional consequence of reduced PAX5 activity on B cell development and identity, but also provides an avenue in which to study PAX5-driven B-ALL in mice.

One Sentence SummaryReduction in PAX5 function in mice induces the development of uncommitted B cells that have multipotent and malignant potential.

category: immunology


title: Functional inactivation of pulmonary MAIT cells following 5-OP-RU treatment of non-human primates

abstract: Targeting MAIT cells holds promise for the treatment of different diseases and infections. We previously showed that treatment of Mycobacterium tuberculosis infected mice with 5-OP-RU, a major antigen for MAIT cells, expands MAIT cells and enhances bacterial control. Here we treated M. tuberculosis infected rhesus macaques with 5-OP-RU intratracheally but found no clinical or microbiological benefit in M. tuberculosis infected macaques. In fact, after 5-OP-RU treatment MAIT cells did not expand, but rather upregulated PD-1 and lost the ability to produce multiple cytokines, a phenotype resembling T cell exhaustion. Furthermore, we show that vaccination of uninfected macaques with 5-OP-RU+CpG instillation into the lungs also drives MAIT cell dysfunction, and PD-1 blockade during vaccination partly prevents the loss of MAIT cell function without facilitating their expansion. Thus, in rhesus macaques MAIT cells are prone to the loss of effector functions rather than expansion after TCR stimulation in vivo, representing a significant barrier to therapeutically targeting these cells.


title: Quantitative analysis and genome-scale modeling of human CD4+ T-cell differentiation reveals subset-specific regulation of glycosphingolipid pathways

abstract: T-cells are sentinels of adaptive cell-mediated immune responses. T-cell activation, proliferation and differentiation involves metabolic reprogramming involving the interplay of genes, proteins and metabolites. Here, we aim to understand the metabolic pathways involved in the activation and functional differentiation of human CD4+ T-cell subsets (Th1, Th2, Th17 and iTregs). We combined genome-scale metabolic modeling, gene expression data, targeted and non-targeted lipidomics experiments, together with in vitro gene knockdown experiments and showed that human CD4+ T-cells undergo specific metabolic changes during activation and functional differentiation. In addition, we identified and confirmed the importance of ceramide and glycosphingolipid synthesis pathways in Th17 differentiation and effector functions. Finally, through in vitro gene knockdown experiments, we substantiated the requirement of serine palmitoyl transferase (SPT), a de novo sphingolipid pathway in the expression of proinflammatory cytokine (IL17A and IL17F) by Th17 cells. Our findings may provide a comprehensive resource for identifying CD4+ T-cell-specific targets for their selective manipulation under disease conditions, particularly, diseases characterized by an imbalance of Treg / Th17 cells. Our data also suggest a role for elevated levels of ceramides in conditions comorbid with these diseases, e.g., obesity and insulin resistance.


abstract:
Plasma cells and their secreted antibodies play a central role in the long-term protection against chronic viral infection. However, due to experimental limitations, a comprehensive description of linked genotypic, phenotypic, and antibody repertoire features of plasma cells (gene expression, clonal frequency, virus specificity, and affinity) has been challenging to obtain. To address this, we performed single-cell transcriptome and antibody repertoire sequencing of the murine bone marrow plasma cell population following chronic lymphocytic choriomeningitis virus infection. Our single-cell sequencing approach recovered full-length and paired heavy and light chain sequence information for thousands of plasma cells and enabled us to perform recombinant antibody expression and specificity screening. Antibody repertoire analysis revealed that, relative to protein immunization, chronic infection led to increased levels of clonal expansion, class-switching, and somatic variants. Furthermore, antibodies from the highly expanded and class-switched (IgG) plasma cells were found to be specific for multiple viral antigens and a subset of clones exhibited cross-reactivity to non-viral- and auto-antigens. Integrating single-cell transcriptome data with antibody specificity suggested that plasma cell transcriptional phenotype was correlated to viral antigen specificity. Our findings demonstrate that chronic viral infection can induce and sustain plasma cell clonal expansion, combined with significant somatic hypermutation, and can generate cross-reactive antibodies.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/428852v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@9d0852org.highwire.dtl.DTLVardef@18d46fcorg.highwire.dtl.DTLVardef@2f7f80org.highwire.dtl.DTLVardef@5be3fd_HPS_FORMAT_FIGEXP  M_FIG Graphical abstract.Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies.

C_FIG


title: A Mycobacterium tuberculosis effector targets mitochondrion, controls energy metabolism and limits cytochrome c exit.

abstract: Host metabolism reprogramming is a key feature of Mycobacterium tuberculosis (Mtb) infection that enables the survival of this pathogen within phagocytic cells and modulates the immune response facilitating the spread of the tuberculosis disease. Here, we demonstrate that a previously uncharacterized secreted protein from Mtb, Rv1813c manipulates the host metabolism by targeting mitochondria. When expressed in eukaryotic cells, the protein is delivered to the mitochondrial intermembrane space and enhances host ATP production by boosting the oxidative phosphorylation metabolic pathway. Furthermore, Rv1813c appears to differentially modulate the host cell response to oxidative stress. Expression of Rv1813 in host cells inhibits the release of cytochrome c from mitochondria, an early apoptotic event, in response to short-term oxidative stress. However, Rv1813c expressing cells showed increased sensitivity to prolonged stress. This study reveals a novel class of mitochondria targeting effectors from Mtb and opens new research directions on host metabolic reprogramming and apoptosis control.

category: microbiology


title: Chemical defense and tonic immobility in early life stages of the Harlequin cabbage bug, Murgantia histrionica (Heteroptera: Pentatomidae)

abstract: Antipredation strategies are important for the survival and fitness of animals, especially in more vulnerable life stages. In insects, eggs and early juvenile stages are often either immobile or unable to rapidly flee and hide when facing predators. Understanding what alternative antipredation strategies they use, but also how those change over development time, is required to fully appreciate how species have adapted to biotic threats. Murgantia histrionica is a stink bug, conspicuously colored from egg to adult, known to sequester defensive glucosinolates from its cruciferous hosts as adults. We sought to assess whether this chemical defense is also present in its eggs and early nymphal instars and quantified how it fluctuates among life stages. In parallel, we looked at an alternative antipredation strategy, described for the first time in this species: tonic immobility. Our results show that the eggs are significantly more chemically defended than the first two mobile life stages, but not than the third instar. Tonic immobility is also favored by hatchlings, but less so by subsequent instars. We argue the case that over development time, tonic immobility is a useful defensive strategy until adequate chemical protection is achieved over an extended feeding period.

category: ecology