title: Effects of diversifying the planting period of maize on herbivorous and their natural enemies

abstract:
Knowledge of the specific insect densities during crop development is necessary to perform appropriate measures for the control of insect pests and to minimize yield losses. In a previous study, both spatial and temporal approaches were adopted to analyse the influence of landscape structure and field variables on herbivore and predatory insects on maize. Both types of variables influenced insect abundance, but the highest effect was found with maize phenology. Given that the field planting date could modulate the influence produced by the structure of the landscape on herbivores and predatory insects, analyses of population dynamics must be performed at both the local and landscape levels. The anterior prompted us to study these aspects in the two common planting periods (early and late) in northern Spain. The present study tests the hypothesis that the period of maize planting could have a higher effect than phenology or interannual variation on the abundance of natural enemies and herbivores on maize. Our results showed that only the abundances of  other herbivore thrips and Syrphidae were significantly different between the two planting periods. Moreover, we found significant effects of planting period when we performed yearly analysis in 2015 for Coccinellidae and Chrysopidae and in 2016 and 2017 for Aeolothrips sp. Most of the taxa had abundance peaks in earlier growth stages, which are related to pollination (before or during), while only Stethorus punctillum and Syrphidae increased later in the season. Furthermore, Frankliniella occidentalis, aphids, Syrphidae and Coccinellidae registered higher abundances in fields sown in the late planting period than in the rest of the insect species. The results of the present study highlight the effects of sowing dates on insect dynamics in maize.

HighlightsO_LIHerbivorous and natural enemy abundance peaks in earlier growth stages.
C_LIO_LIAbundance of thrip and Syrphidae were different between the two planting periods.
C_LIO_LIAbundance of Coccinellidae, Chrysopidae and Aeolothrips sp. was different when performed yearly analysis.
C_LI


title: Resonant fluctuations of selection pressure exponentially accelerate fitness valley crossing

abstract: Two functional protein sequences can sometimes be separated by a fitness valley - a series of low or non-functional intermediate mutations that must be traversed to reach a more optimal or refined function. Time-varying selection pressure modulates evolutionary sampling of such valleys. Yet, how the amplitude and frequency of fluctuating selection influence the rate of protein evolution is poorly understood. Here, we derive a simple equation for the time-dependent probability of crossing a fitness valley as a function of evolutionary parameters: valley width, protein size, mutation rate, and selection pressure. The equation predicts that, under low selection pressure, the valley crossing rate is magnified by a factor that depends exponentially on valley width. However, after a characteristic time set by the evolutionary parameters, the rate rapidly decays. Thus, there is an optimal frequency of selection-pressure fluctuations that maximizes the rate of protein optimization. This result is reminiscent of the resonance frequency in mechanical systems. The equation unites empirical and theoretical results that were previously disconnected, and is consistent with time-dependent in vitro and clinical data. More generally, these results suggest that seasonal and climate oscillations could synchronously drive protein evolution at the resonant frequency across a range of organism hosts and timescales. This theory could also be applied to optimize de novo protein evolution in laboratory directed evolution using time-varying protocols.

category: evolutionary biology


title: The RNA binding protein Swm is critical for Drosophila melanogaster intestinalprogenitor cell maintenance

abstract: The regulation of stem cell survival, self-renewal, and differentiation is critical for the maintenance of tissue homeostasis. Although the involvement of signaling pathways and transcriptional control mechanisms in stem cell regulation have been extensively investigated, the role of post-transcriptional control is still poorly understood. Here we show that the nuclear activity of the RNA-binding protein Second Mitotic Wave Missing (Swm) is critical for Drosophila intestinal stem cells (ISCs) and their daughter cells, enteroblasts (EBs), to maintain their identity and function. Loss of swm in these intestinal progenitor cells leads ISCs and EBs to lose defined cell identities, fail to proliferate, and detach from the basement membrane, resulting in severe progenitor cell loss. swm loss further causes nuclear accumulation of poly(A)+ RNA in progenitor cells. Swm associates with transcripts involved in epithelial cell maintenance and adhesion, and the loss of swm, while not generally affecting the levels of these Swm-bound mRNAs, leads to elevated expression of proteins encoded by some of them, including the fly orthologs of Filamin and Talin. Taken together, this study indicates a role for Swm in adult stem cell maintenance, and raises the possibility that nuclear post-transcriptional gene regulation plays vital roles in controlling adult stem cell maintenance and function.

category: genetics


title: High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets

abstract: The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with beta cell proliferation. Recent studies have found that expression of circular species of ANRIL is linked to the regulation of cardiovascular phenotypes. Less is known about how the abundance of circular ANRIL may influence T2D phenotypes. Herein, we sequence circular RNA in pancreatic islets to characterize circular isoforms of ANRIL. We identify highly expressed circular ANRIL isoforms whose expression is correlated across dozens of individuals and characterize ANRIL splice sites that are commonly involved in back-splicing. We find that samples with the T2D risk allele in ANRIL exon 2 had higher ratios of circular to linear ANRIL compared to protective-allele carriers, and that higher circular:linear ANRIL was associated with decreased beta cell proliferation. Our study points to a combined involvement of both linear and circular ANRIL species in T2D phenotypes and opens the door for future studies of the molecular mechanisms by which ANRIL impacts cellular function in pancreatic islets.

category: genomics


title: Plasma and ovarian metabolomics responses to chronic stress in female mice

abstract:
BackgroundChronic stress may affect metabolism of amino acids, lipids, and other small molecule metabolites, but these alterations may differ depending on tissue evaluated. We examined metabolomic changes in plasma and ovarian tissue samples from female mice due to chronic stress exposure.

MethodsAt 12 weeks old, healthy, female, C57 black mice were randomly assigned to three weeks of chronic stress using daily restraint (2 hours/day; n=9) or normal care (n=10). Metabolomic profiling was conducted on plasma and ovarian tissues. Using the Wilcoxon Rank Test, Metabolite Set Enrichment Analysis, and Differential Network Analysis we identified metabolomic alterations occurring in response to restraint stress. All p-values were corrected for multiple testing using the false discovery rate approach.

ResultsIn plasma, individual lysophosphatidylcholines (positively) and the metabolite classes carnitines (positively), diacylglycerols and triacylglycerols (inversely) were associated with restraint stress (adjusted-ps<0.2). In contrast, diacylglycerols and triacylglycerols were increased while carnitines were decreased in ovarian tissue from stressed mice (adjusted-ps<0.2). However, several metabolites (cholesteryl esters, phosphatidylcholines/ phosphatidylethanolamines plasmalogens and multiple amino acids) were consistently inversely associated with restraint stress in plasma and ovarian tissue (adjusted-ps<0.2).

ConclusionWe identified differences in multiple lipid and amino acid metabolites in plasma and ovarian tissue of female mice after exposure to chronic stress. Some affected metabolites (primarily triacylglycerols and diacylglycerols) exhibited opposite associations with chronic stress in plasma (a marker of systemic influences) versus in ovarian tissue (representing local changes), suggesting research to understand the biological impact of chronic stress needs to consider both systemic and tissue-specific alterations.

category: animal behavior and cognition


title: Magnetic torque-driven living microrobots for enhanced tumor infiltration

abstract:
Bacterial microrobots combining self-propulsion and magnetic guidance are increasingly recognized as promising drug delivery vehicles for targeted cancer therapy. Thus far, control strategies have either relied on poorly scalable magnetic field gradients or employed directing magnetic fields with propulsive forces limited by the bacterial motor. Here, we present a magnetic torque-driven actuation scheme based on rotating magnetic fields to wirelessly control Magnetospirillum magneticum AMB-1 bearing versatile liposomal cargo. We observed a 4-fold increase in conjugate translocation across a model of the vascular endothelium and found that the primary mechanism driving this increased transport is torque-driven surface exploration at the cell interface. Using spheroids as a 3D tumor model, fluorescently labeled bacteria colonized their core regions with up to 21-fold higher signal in samples exposed to rotating magnetic fields. In addition to enhanced transport, we demonstrated the suitability of this magnetic stimulus for simultaneous actuation and inductive detection of AMB-1. Finally, we demonstrated that RMF significantly enhances AMB-1 tumor accumulation in vivo following systemic intravenous administration in mice. Our findings suggest that scalable magnetic torque-driven control strategies can be leveraged advantageously with biohybrid microrobots.

One-Sentence SummaryMagnetic torque-driven motion enhances infiltration of living microrobots across physiological barriers both in vitro and in vivo.

category: bioengineering


title: Tree House Explorer: A Novel Genome Browser for Phylogenomics

abstract: Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.

category: bioinformatics


title: Characterizing RNA-binding Ligands on Structures, Chemical Information, Binding Affinity and Drug-likeness

abstract:
Recent studies suggest RNAs playing essential roles in many cell activities and act as promising drug targets. However, limited development has been achieved in detecting RNA-ligand interactions. To guide the discovery of RNA-binding ligands, it is necessary to characterize them comprehensively. We established a database, RNALID that collects RNA-ligand interactions validated by low-throughput experiment. RNALID contains 358 RNA-ligand interactions. Comparing to other databases, 94.5% of ligands in RNALID are completely or partially novel collections, and 51.78% have novel two-dimensional (2D) structures. The ligand structure analysis indicated that multivalent ligands (MV), ligands binding with cellular mRNA (mRNA), ligands binding with RNA from virus (vRNA) and ligands binding with RNA containing repetitive sequence (rep RNA) are more structurally conserved in both 2D and 3D structures than other ligand types. Binding affinity analysis revealed that interactions between ligands and rep RNA were significantly stronger (two-tailed MW-U test P-value = 0.012) than the interactions between ligands and non-rep RNAs; the interactions between ligands and vRNA were significantly stronger (two-tailed MW-U test P-value = 0.012) than those between ligands and mRNA. Drug-likeness analysis indicated that small molecule (SM) ligands binding with non-rep RNA or vRNA may have higher probability to be drugs than other types of ligands. Comparing ligands in RNALID to FDA-approved drugs and ligands without bioactivity indicated that RNA-binding ligands are different from them in chemical properties, structural properties and drug-likeness. Thus, characterizing the RNA-ligand interactions in RNALID in multiple respects provides new insights into discovering and designing druggable ligands binding with RNA.

KEY POINTSO_LIWe established a database, RNALID, by collecting RNA-ligand interactions validated by low-throughput experiments, which contains 358 RNA-ligand interactions, and 94.5% of them are completely or partially novel collections.
C_LIO_LILigands in RNALID were divided into fourteen types, and were analyzed on chemical properties, spatial properties, binding affinity and drug-likeness. Small molecule (SM) ligands binding with non-repeat RNA or virus RNA were indicated having higher probability to be drugs than other types of ligands.
C_LIO_LILigands in RNALID were different from protein-binding ligands and ligands without bioactivity in chemical properties, structural properties and drug-likeness.
C_LI


title: Nm-Nano: Predicting 2'-O-methylation (Nm) Sites in Nanopore RNA Sequencing Data

abstract: Nm (2-O-methylation) is one of the most abundant modifications of mRNAs and non-coding RNAs occurring when a methyl group (-CH3) is added to the 2 hydroxyl (-OH) of the ribose moiety. This modification can appear on any nucleotide (base) regardless of the type of nitrogenous base, because each ribose sugar has a hydroxyl group and so 2-O-methyl ribose can occur on any base. Nm modification has a great contribution in many biological processes such as the normal functioning of tRNA, the protection of mRNA against degradation by DXO, and the biogenesis and specificity of rRNA. Recently, the single-molecule sequencing techniques for long reads of RNA sequences data offered by Oxford Nanopore technologies have enabled the direct detection of RNA modifications on the molecule that is being sequenced, but to our knowledge there was only one research attempt that applied this technology to predict the stoichiometry of Nm-modified sites in RNA sequence of yeast cells. To this end, in this paper, we extend this research direction by proposing a bio-computational framework, Nm-Nano for predicting Nm sites in Nanopore direct RNA sequencing reads of human cell lines. Nm-Nano framework integrates two supervised machine learning (ML) models for predicting Nm sites in Nanopore sequencing data, namely Xgboost and Random Forest (RF). Each model is trained with set of features that are extracted from the raw signal generated by the Oxford Nanopore MinION device, as well as the corresponding basecalled k-mer resulting from inferring the RNA sequence reads from the generated Nanopore signals. The results on two benchmark data sets generated from RNA Nanopore sequencing data of Hela and Hek293 cell lines show a great performance of Nm-Nano. In independent validation testing, Nm-Nano has been able to identify Nm sites with a high accuracy of 93% and 88% using Xgboost and RF models respectively by training each model with Hela benchmark dataset and testing it for identifying Nm sites on Hek293 benchmark dataset. Thus, Nm-Nano outperforms the Nm sites predictors existing in the literature (not relying on Nanopore technology) that were only limited to predict Nm sites on short reads of RNA sequences and unable to predict Nm sites on long RNA sequence reads. By deploying Nm-Nano to predict Nm sites in Hela cell line, it was revealed that a total of 196 genes was identified to have the most abundance of Nm modification among all other genes that have been modified by Nm in this cell line. Similarly, deploying Nm-Nano to predict Nm sites in Hek393 cell line revealed that a total of 196 genes line was identified to have the most abundance of Nm modification among all other genes that have been modified by Nm in this cell line. According to this, a significant enrichment of a wide range of functional processes like high confidences (adjusted p-val < 0.05) enriched ontologies that were more representative of Nm modification role in immune response and cellular homeostasis were revealed in Hela cell line, and "MHC class 1 protein complex", "mitotic spindle assembly", "response to glucocorticoid", and "nucleocytoplasmic transport" were revealed in Hek293 cell line. The source code of Nm-Nano can be freely accessed at https://github.com/Janga-Lab/Nm-Nano.


title: A global Anopheles gambiae gene co-expression network constructed from hundreds of experimental conditions with missing values

abstract: Gene co-expression networks can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarrays and RNA-sequencing, allow evaluating thousands of gene expression data simultaneously, but these methodologies provide results that cannot be directly compared. Thus, it is complex to analyze coexpression relations between genes, especially when there are missing values arising for experimental reasons. Networks are a helpful tool for studying gene co-expression, where nodes represent genes and edges represent co-expression of pairs of genes. In this paper, we propose a method for constructing a gene co-expression network for the Anopheles gambiae transcriptome from 257 unique studies obtained with different methodologies and experimental designs. We introduce the sliding threshold approach to select node pairs with high Pearson correlation coefficients. The robustness of the method was verified by comparing edge weight distributions under random removal of conditions. The properties of the constructed network are studied in this paper, including node degree distribution, coreness, and community structure. The network core is largely comprised of genes that encode components of the mitochondrial respiratory chain and the ribosome, while different communities are enriched for genes involved in distinct biological processes. This suggests that the overall network structure is driven to maximize the integration of essential cellular functions, possibly allowing the flexibility to add novel functions.


title: Trait variation between and within Andes and coastal mountain ranges in the iconic South American tree Araucaria araucana in Chile

abstract: As global commitments to restoration are underway, science is needed to support capacity to achieve meaningful gains for ecosystems and human communities. In Chile, identification and generation of appropriate plant material is a barrier to achieving major restoration goals under the Paris Climate Agreement. Understanding genetic differentiation among plant populations is needed to maximize restoration success. For Araucaria araucana, a highly threatened iconic South American tree, this information is greatly needed to guide restoration and conservation efforts because this species occurs across a strong climate gradient. We grew seedlings from 12 populations of A. araucana across its range in Chile in a common garden to assess regional (coastal versus Andes mountain ranges) and population variation in key plant traits and relate this variation to environmental variables. We demonstrate that A. araucana is differentiated within regions and populations across its range in Chile by a suite of traits, particularly branch number and length (showing plant architectural differences) and needle width (showing leaf investment differences). We show that this variation is at least partly explained by climate and soil variables, with the most variation explained by differences between regions in temperature annual range. Thus, we recommend that restoration efforts focus on conserving genetic variation among and within regions and their populations and preventing the translocations of genotypes between coastal and Andes populations.

category: plant biology


title: Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes

abstract: Photosystem I (PSI) contributes to light-conversion reactions; however, its oligomerization state is variable among photosynthetic organisms. Herein we present a 3.8-[A] resolution cryo-electron microscopic structure of tetrameric PSI isolated from a glaucophyte alga Cyanophora paradoxa. The PSI tetramer is organized in a dimer of dimers form with a C2 symmetry. Different from cyanobacterial PSI tetramer, two of the four monomers are rotated around 90{degrees}, resulting in a totally different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and energy transfer in the Cyanophora PSI tetramer, thus offering an attractive idea for the changes of PSI from prokaryotes to eukaryotes.


title: Visual search training benefits from the integrative effect of enhanced covert attention and optimized overt eye movements

abstract: Visual search in a complex environment requires efficient discrimination between target and distractors. Training serves as an effective approach to improve visual search performance when the target does not automatically pop out from the distractors. In the present study, we trained subjects on a conjunction visual search task and examined the training effects in behavior and eye movement from Experiments 1 to 4. The results showed that training improved behavioral performance and reduced the number of saccades and overall scanning time. Training also increased the search initiation time before the first saccade and the proportion of trials in which the subjects correctly identified the target without any saccade, but these effects were modulated by stimulus parameters. In Experiment 5, we replicated these training effects when eye movements and EEG signals were recorded simultaneously. The results revealed significant N2pc components after the stimulus onset (i.e., stimulus-locked) and before the first saccade (i.e., saccade-locked) when the search target was the trained one. These N2pc components can be considered as the neural signatures for the training-induced boost of covert attention to the trained target. The enhanced covert attention led to a beneficial tradeoff between search initiation time and the number of saccades as a small amount of increase in search initiation time could result in a larger reduction in scanning time. These findings suggest that the enhanced covert attention to target and optimized overt eye movements are coordinated together to facilitate visual search training.

category: neuroscience


title: Quality assessment of anatomical MRI images from Generative Adversarial Networks: human assessment and image quality metrics

abstract:
BackgroundGenerative Adversarial Networks (GANs) can synthesize brain images from image or noise input. So far, the gold standard for assessing the quality of the generated images has been human expert ratings. However, due to limitations of human assessment in terms of cost, scalability, and the limited sensitivity of the human eye to more subtle statistical relationships, a more automated approach towards evaluating GANs is required.

New methodWe investigated to what extent visual quality can be assessed using image quality metrics and we used group analysis and spatial independent components analysis to verify that the GAN reproduces multivariate statistical relationships found in real data. Reference human data was obtained by recruiting neuroimaging experts to assess real Magnetic Resonance (MR) images and images generated by a Wasserstein GAN. Image quality was manipulated by exporting images at different stages of GAN training. Results: Experts were sensitive to changes in image quality as evidenced by ratings and reaction times, and the generated images reproduced group effects (age, gender) and spatial correlations moderately well. We also surveyed a number of image quality metrics which consistently failed to fully reproduce human data. While the metrics Structural Similarity Index Measure (SSIM) and Naturalness Image Quality Evaluator (NIQE) showed good overall agreement with human assessment for lower-quality images (i.e. images from early stages of GAN training), only a Deep Quality Assessment (QA) model trained on human ratings was sensitive to the subtle differences between higher-quality images.

ConclusionsWe recommend a combination of group analyses, spatial correlation analyses, and both distortion metrics (SSIM, NIQE) and perceptual models (Deep QA) for a comprehensive evaluation and comparison of brain images produced by GANs.


title: Hippocampal Volume, Neurite Density and Trace Eye-Blink Conditioning in Young Children

abstract: The current study examined the relations between hippocampal structure (e.g., volume and neurite density) and performance on a trace eye blink conditioning (EBC) task in young children. Our first aim assessed whether individual differences in hippocampal volume were associated with trace EBC performance, using both percent Conditioned Responses (% CR) and CR onset latency or the average latency (ms) at which the child started their blink, as measures of hippocampal-dependent associative learning. Our second aim evaluated whether individual differences in hippocampal neurite density were associated with EBC performance using the same outcome measures. Typically developing 4- to 6-year-olds (N = 31; 14 girls; Mage = 5.67; SDage = 0.89) completed T1 and diffusion-weighted MRI scans and a 15-minute trace eyeblink conditioning task outside of the scanner. % CR and CR onset latency were computed across all tone-puff and tone-alone trials. While hippocampal volume was not associated with any of our EBC measures, greater hippocampal neurite density bilaterally, was associated with later CR onset. In other words, children with greater left and right hippocampal neurite density blinked closer to the US (i.e., air puff) than children with less hippocampal neurite density, indicating that structural changes in the hippocampus assisted in the accurate timing of conditioned responses.


title: Encoding of speech in convolutional layers and the brain stem based on language experience

abstract: Comparing artificial neural networks (ANNs) with outputs of neuroimaging techniques has recently seen substantial advances in (computer) vision and text-based language models. Here, we propose a framework to compare biological and artificial neural computations of spoken language representations and propose several new challenges to this paradigm. Using a technique proposed by Begu[s] and Zhou (2022), we can analyze encoding of any acoustic property in intermediate convolutional layers of an artificial neural network. The proposed technique is based on a similar principle that underlies EEG: averaging of neural (artificial or biological) activity across neurons in the time domain. This allows us to test similarities in speech encoding between the brain and artificial neural networks in a way that is more interpretable than the majority of existing proposals that focus on correlations and supervised models. We introduce fully unsupervised deep generative models (the Generative Adversarial Network architecture) trained on raw speech to the brain-and-ANN-comparison paradigm, which enable testing of both the production and perception principles in human speech. Our approach allows a direct comparison of responses to a phonetic property in the brain and in deep neural networks: we compare peak latency (i) in cABR relative to the stimulus in the brain stem and in (ii) intermediate convolutional layers relative to the input/output in deep convolutional networks. We also examine and compare the effect of prior language exposure on the peak latency in cABR and in intermediate convolutional layers. Specifically, peak latency in cABR responses to a [ba] syllable (with Voice Onset Time 10ms) differs significantly between English and Spanish speakers. We present results suggesting that peak latency in intermediate convolutional layers is also different in similar and interpretable ways between English-trained (TIMIT) and Spanish-trained (DIMEx) deep convolutional neural networks both in the production and perception networks. Substantial similarities in peak latency encoding between the human brain and intermediate convolutional networks thus emerge based on results from eight trained networks (including a replication experiment). The proposed technique can be used to compare encoding between the human brain and intermediate convolutional layers for any acoustic property and for other neuroimaging techniques.


title: S100A4 exerts robust mucosal adjuvant activity for co-administered antigens in mice

abstract: The lack of clinically applicable mucosal adjuvants is a major hurdle in designing effective mucosal vaccines. We hereby report that the calcium-binding protein S100A4, which regulates a wide range of biological functions, is a potent mucosal adjuvant in mice for co-administered antigens, including the SARS-CoV-2 spike protein, with comparable or even superior efficacy as cholera toxin but without causing any adverse reactions. Intranasal immunization with recombinant S100A4 elicited antigen-specific antibody and pulmonary cytotoxic T cell responses, and these responses were remarkably sustained for longer than six months. As a self-protein, S100A4 did not stimulate antibody responses against itself, a quality desired of adjuvants. S100A4 prolonged nasal residence of intranasally delivered antigens and promoted migration of antigen-presenting cells. S100A4-pulsed dendritic cells potently activated cognate T cells. Furthermore, S100A4 induced strong germinal center responses revealed by both microscopy and mass spectrometry, a novel technique for measuring germinal center activity. In conclusion, S100A4 may be a promising adjuvant in formulating mucosal vaccines, including vaccines against pathogens that infect via the respiratory tract, such as SARS-CoV-2.

category: immunology


title: BDSF is a degradation-prone quorum-sensing signal detected by the histidine kinase RpfC of Xanthomonas campestris pv. campestris

abstract:
Diffusible signal factors (DSFs) are medium-chain fatty acids that induce bacterial quorum sensing. Among these compounds, BDSF is a structural analog of DSF that is commonly detected in bacterial species (e.g., Xanthomonas, Pseudomonas, and Burkholderia). Additionally, BDSF contributes to the interkingdom communication regulating fungal life stage transitions. How BDSF is sensed in Xanthomonas spp. and the functional diversity between BDSF and DSF remain unclear. In this study, we generated genetic and biochemical evidence that BDSF is a low-active regulator of X. campestris pv. campestris quorum sensing, whereas trans-BDSF seems not a signaling compound. BDSF is detected by the sensor histidine kinase RpfC. Although BDSF has relatively low physiological activities, it binds to the RpfC sensor with a high affinity and activates RpfC autophosphorylation to a level that is similar to that induced by DSF in vitro. The inconsistency in the physiological and biochemical activities of BDSF is not due to RpfC- RpfG phosphorylation or RpfG hydrolase. Neither BDSF nor DSF controls the phosphotransferase and phosphatase activities of RpfC or the ability of RpfG hydrolase to degrade the bacterial second messenger cyclic di-GMP. We demonstrated that BDSF is prone to degradation by RpfB, a critical fatty acyl-CoA ligase involved in the turnover of DSF-family signals. rpfB mutations lead to substantial increases in BDSF-induced quorum sensing. Although DSF and BDSF are similarly detected by RpfC, our data suggest that their differential degradation in cells is the major factor responsible for the diversity in their physiological effects.

IMPORTANCEDiffusible signal factor (DSF) family are quorum-sensing signals employed by gram-negative bacteria. These signals are a group of cis-2-unsaturated fatty acids, such as DSF, BDSF, IDSF, CDSF, and SDSF. However, the functional divergence of various DSF signals remains unclear. The present study demonstrates that though BDSF is a low active quorum-sensing signal than that of DSF, it binds histidine kinase RpfC with a higher affinity and activates RpfC autophosphorylation to the similar level as DSF. Rather than regulation of enzymatic activities of RpfC and its cognate response regulator RpfG encoding a c-di-GMP hydrolase, BDSF is prone to degradation in bacterial cells by RpfB, which effectively avoided the inhibition of bacterial growth by accumulating high concentration of BDSF. Therefore, our study shed new light on the functional difference of quorum-sensing signals and revealed that bacteria balance quorum-sensing and growth by fine-turning concentration of signaling chemical.

category: microbiology


title: A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota

abstract: To address the emergence of antimicrobial-resistant pathogens in livestock, microbiome-based strategies are increasingly being sought to reduce antimicrobial use. Here, we describe the intranasal application of bacterial therapeutics (BTs) for mitigating bovine respiratory disease (BRD) and used structural equation modeling to investigate the causal networks after BT application. Beef cattle received i) an intranasal cocktail of previously characterized BT strains, ii) an injection of metaphylactic antimicrobial (tulathromycin), or iii) intranasal saline. Despite being transient colonizers, inoculated BT strains induced longitudinal modulation of the nasopharyngeal bacterial microbiota while showing no adverse effect on animal health. The BT-mediated changes in bacteria included reduced diversity and richness and strengthened cooperative and competitive interactions. In contrast, tulathromycin increased bacterial diversity and antibiotic resistance, and disrupted bacterial interactions. Overall, a single intranasal dose of BTs can modulate the bovine respiratory microbiota, highlighting that microbiome-based strategies have the potential in being utilized to mitigate BRD in feedlot cattle.


title: The 2009 pandemic H1N1 hemagglutinin stalk remained antigenically stable after circulating in humans for a decade

abstract:
An H1N1 influenza virus caused a pandemic in 2009 and descendants of this virus continue to circulate seasonally in humans. Upon infection with the 2009 H1N1 pandemic strain (pH1N1), many humans produced antibodies against epitopes in the hemagglutinin (HA) stalk. HA stalk-focused antibody responses were common among pH1N1-infected individuals because HA stalk epitopes were conserved between the pH1N1 strain and previously circulating H1N1 strains. Here, we completed a series of experiments to determine if the pH1N1 HA stalk has acquired substitutions since 2009 that prevent the binding of human antibodies. We identified several amino acid substitutions that have accrued in the pH1N1 HA stalk from 2009-2019. We completed enzyme-linked immunosorbent assays, absorption-based binding assays, and surface plasmon resonance experiments to determine if these substitutions affect antibody binding. Using sera collected from 230 humans (aged 21-80 years), we found that pH1N1 HA stalk substitutions that have emerged since 2009 do not affect antibody binding. Our data suggest that the HA stalk domain of pH1N1 viruses remained antigenically stable after circulating in humans for a decade.

ImportanceIn 2009, a new pandemic H1N1 (pH1N1) virus began circulating in humans. Many individuals mounted hemagglutinin (HA) stalk-focused antibody responses upon infection with the 2009 pH1N1, since the HA stalk of this virus was relatively conserved with other seasonal H1N1 strains. Here, we completed a series of studies to determine if the 2009 pH1N1 strain has undergone antigenic drift in the HA stalk domain over the past decade. We found that serum antibodies from 230 humans could not antigenically distinguish the 2009 and 2019 HA stalk. These data suggest that the HA stalk of pH1N1 has remained antigenically stable, despite the presence of high levels of HA stalk antibodies within the human population.


title: The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

abstract: Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance genes in human pathogens, including the particularly problematic group of ESKAPE pathogens, such as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), in the ESKAPE pathogens. We characterized over 1700 complete ESKAPE genomes and found that different MGE types are asymmetrically distributed across these pathogens. While some MGEs are capable of exchanging DNA beyond the genus (and phylum) barrier, horizontal gene transfer (HGT) is mainly restricted by phylum or genus. We further observed that most genes on MGEs have unknown functions and show intricate distribution patterns. Moreover, AMR genes and anti-CRISPRs are overrepresented in the ESKAPE mobilome. Our results also underscored species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we found that CRISPR targets vary according to MGE type: while plasmid CRISPRs almost exclusively target other plasmids, ICEs/IME CRISPRs preferentially target ICEs/IMEs and prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.


title: Hemato-vascular specification requires arnt1 and arnt2 genes in zebrafish embryos

abstract: During embryonic development, a subset of cells in the mesoderm germ layer are specified as hemato-vascular progenitor cells, which then differentiate into endothelial cells and hematopoietic stem and progenitor cells. In zebrafish, the transcription factor npas4l, also known as cloche, is required for the specification of hemato-vascular progenitor cells. However, it is unclear if npas4l is the sole factor at the top of the hemato-vascular specification cascade. Here we show that arnt1 and arnt2 genes are required for hemato-vascular specification. We found that arnt1;arnt2 double homozygous mutant zebrafish embryos (herein called arnt1/2 mutants), but not arnt1 or arnt2 single mutants, lack blood cells and most vascular endothelial cells. arnt1/2 mutants have reduced or absent expression of etv2 and tal1, the earliest known endothelial and hematopoietic transcription factor genes. npas4l and arnt genes are PAS domain-containing bHLH transcription factors that function as dimers. We found that Npas4l binds both Arnt1 and Arnt2 proteins in vitro, consistent with the idea that PAS domain-containing bHLH transcription factors act in a multimeric complex to regulate gene expression. Our results demonstrate that npas4l, arnt1 and arnt2 act together as master regulators of endothelial and hematopoietic cell fate. Our results also demonstrate that arnt1 and arnt2 act redundantly in a transcriptional complex containing npas4l, but do not act redundantly when interacting with another PAS domain-containing bHLH transcription factor, the aryl hydrocarbon receptor. Altogether, our data enhance our understanding of hemato-vascular specification and the function of PAS domain-containing bHLH transcription factors.

category: developmental biology


title: Hbxip (Lamtor5) is essential for embryogenesis and regulates embryonic stem cell differentiation through activating mTORC1

abstract: Hbxip, also named Lamtor5, has been well characterized as a transcriptional coactivator in various cancers. However, the role of Hbxip in normal development remains unexplored. Here, we demonstrated that homozygous knockout of Hbxip leads to embryonic lethality, with retarded growth around E7.5. Using Hbxip knockout embryonic stem cells (ESCs), we showed that depletion of Hbxip compromises the self-renewal of ESCs, with reduced expression of pluripotency genes, reduced cell proliferation, and decreased colony forming capacity. In addition, Hbxip-/- ESCs are defective in differentiation, particularly ectodermal and mesodermal differentiation. Consistently, Hbxip-/- epiblast fails to differentiate properly, indicated by sustained expression of Oct4 in E8.5 Hbxip-/- epiblast. Mechanistically, in ESCs, Hbxip interacts with other components of the Ragulator complex, which is required for mTORC1 activation by amino acids. Importantly, ESCs depleted of Ragulator subunits, Lamtor3 or Lamtor4, display differentiation defects similar to those of Hbxip-/- ESCs. Moreover, Hbxip-/-, p14-/-, and p18-/- mice, lacking subunits of the Ragulator complex, also share similar phenotypes, embryonic lethality and retarded growth around E7-8. Thus, we conclude that Hbxip plays a pivotal role in the development and differentiation of the epiblast, as well as the self-renewal and differentiation of ESCs, through activating mTORC1 signaling.


title: Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers

abstract: Nitrifying microorganisms, including ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrite-oxidizing bacteria, are the most abundant chemoautotrophs in the ocean and play an important role in the global carbon cycle by fixing dissolved inorganic carbon (DIC) into biomass. The release of organic compounds by these microbes is less well known but may represent an as-yet unaccounted source of dissolved organic carbon (DOC) available to heterotrophic marine food webs. Here, we provide measurements of cellular carbon and nitrogen quotas, DIC fixation yields and DOC release of ten phylogenetically diverse marine nitrifiers grown in multiple culture conditions. All investigated strains released DOC during growth, making up on average 5-15% of the fixed DIC. Neither substrate concentration nor temperature affected the proportion of fixed DIC released as DOC, but release rates varied between closely related species. Our results also indicate previous studies may have underestimated DIC fixation yields of marine nitrite oxidizers due to partial decoupling of nitrite oxidation from CO2 fixation, and due to lower observed yields in artificial compared to natural seawater medium. The results of this study provide values for biogeochemical models of the global carbon cycle, and help to further constrain the implications of nitrification-fueled chemoautotrophy for marine food-web functioning and the biological sequestration of carbon in the ocean.

category: ecology


title: randtip, a generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

abstract:
O_LIThe increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the worlds biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come.
C_LIO_LIThis prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms.
C_LIO_LIHere, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package  randtip, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information.
C_LIO_LIAlthough randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the  blind expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow.
C_LIO_LIPhylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.
C_LI


title: E.PAGE: A curated database and enrichment tool to predict modules associated with gene-environment interactions

abstract:
BackgroundThe purpose of this study was to manually and semi-automatically curate a database and develop an R package that will provide a comprehensive resource to uncover associations between biological processes and environmental factors in health and disease.

We followed a two-step process to achieve the objectives of this study. First, we conducted a systematic review of existing gene expression datasets to identify those with integrated genomic and environmental factors. This enabled us to curate a comprehensive genomic-environmental database for four key environmental factors (smoking, diet, infections and toxic chemicals) associated with various autoimmune and chronic conditions. Second, we developed a statistical analysis package that allows users to interrogate the relationships between differentially expressed genes and environmental factors under different disease conditions.

ResultsThe initial database search run on the Gene Expression Omnibus (GEO) and the Molecular Signature Database (MSigDB) retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 186 studies were selected. From those, 243 individual sets of genes, or "gene modules", were obtained. We then curated a database containing four environmental factors, namely cigarette smoking, diet, infections and toxic chemicals, along with a total of 25789 genes that had an association with one or more of these gene modules. In six case studies, the database and statistical analysis package were then tested with lists of differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes.

ConclusionsA novel curated database and software tool is provided as an R Package. Users can enter a list of genes to discover associated environmental factors under various disease conditions.


title: Systematic whole-genome sequencing reveals an unexpected diversity among actinomycetoma pathogens and provides insights into their antibacterial susceptibilities

abstract:
Mycetoma is a neglected tropical chronic granulomatous inflammatory disease of the skin and subcutaneous tissues. More than 70 species with a broad taxonomic diversity have been implicated as agents of mycetoma. Understanding the full range of causative organisms and their antibiotic sensitivity profiles are essential for the appropriate treatment of infections. The present study focuses on the analysis of full genome sequences and antibiotic resistance profiles of actinomycetoma strains from patients seen at the Mycetoma Research Centre in Sudan with a view to developing rapid diagnostic tests. Seventeen pathogenic isolates obtained by surgical biopsies were sequenced using MinION and Illumina methods, and their antibiotic resistance profiles determined. The results highlight an unexpected diversity of actinomycetoma causing pathogens, including three Streptomyces isolates assigned to species not previously associated with human actinomycetoma and one new Streptomyces species. Thus, current approaches for clinical and histopathological classification of mycetoma may need to be updated. The standard treatment for actinomycetoma is a combination of sulfamethoxazole/trimethoprim and amoxicillin/clavulanic acid. Most tested isolates were not susceptible to sulfamethoxazole/trimethoprim or to amoxicillin alone. However, the addition of the {beta}-lactamase inhibitor clavulanic acid to amoxicillin increased susceptibility, particularly for Streptomyces somaliensis and Streptomyces sudanensis. Actinomadura madurae isolates appear to be particularly resistant under laboratory conditions, suggesting that alternative agents, such as amikacin, should be considered for more effective treatment. The results obtained will inform future diagnostic methods for the identification of actinomycetoma and treatment.

Author SummaryMycetoma is a common health and medical problem that is endemic in many tropical and subtropical countries and has devastating effects on patients. The destructive nature of late-stage infection means that treatment often requires long term use of antibiotic therapy, massive surgical excisions and amputation. Several different bacterial species have been described as causing this disease but our understanding of the true diversity of mycetoma causing bacteria has been limited by a lack of molecular sequence data. We have now sequenced the genomes of 17 samples isolated from patients at the Mycetoma Research Centre in Sudan, revealing a diverse range of species associated with infection including one new Streptomyces species, and three species with no previous association with human mycetoma. Crucially, all isolates had a high level of resistance against the current first-line antibiotics used to treat actinomycetoma under laboratory conditions. This resistance was strongest in Actinomadura madurae, which was also the most frequently observed species isolated from patients in our study. We hope that these results will aid in the development of future rapid diagnostic tools and the improvement of treatment outcomes.


title: Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

abstract: Animal cell lines cultured for extended periods often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In Drosophila, many established cell lines also exhibit massive proliferation of transposable elements (TEs) relative to wild-type flies. To better understand the role of transposition during long-term animal somatic cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. Relative to comparable data from inbred whole flies, WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called "TELR" that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a [~]130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by somatic transposition in cell culture after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TE copies within the S2R+ genome, which revealed that proliferation of different TE families during cell line evolution in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are not amenable to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.


title: One-step pipetting of barcoded planar microparticles into compact monolayer assembling chip for efficient readout of multiplexed immunoassay

abstract: Barcoded planar microparticles have many qualities suitable for developing cost-efficient multiplexed immunoassays. But at the translational research level, there are a number of technical aspects yet remain to be addressed which includes robustness and efficiency of the assay readout process. Assay readout process involves automated barcode identification and signal intensity values from each planar microparticle. For this, each microparticle has to be correctly aligned for correct barcode readout while being, ideally, compactly assembled for maximum microparticle imaging efficiency. To simultaneously achieve such alignment and assembly of microparticles but in a straightforward manner, we designed a microfluidic microparticle assembling chip that only requires a single pipetting step. Our design utilizes capillary flow based guided particle assembly, which allows maximum microparticle-based immunoassay readout efficiency. With the aid of image processing algorithms, we obtained good multiplex immunoassay readout accuracy similar to conventional imaging platforms. Our approach is applicable to both soft elastomer materials (e.g. PDMS) and rigid materials (e.g. polystyrene), the latter of which is frequently used for injection molding based mass production. We anticipate our device could help developing facile and user-friendly platform technologies based on barcoded planar microparticles.


title: Clustering Deviation Index (CDI): A robust and accurate unsupervised measure for evaluating scRNA-seq data clustering

abstract: Single-cell RNA-sequencing (scRNA-seq) technology allows us to explore cellular heterogeneity in the transcriptome. Because most scRNA-seq data analyses begin with cell clustering, its accuracy considerably impacts the validity of downstream analyses. Although many clustering methods have been developed, few tools are available to evaluate the clustering "goodness-of-fit" to the scRNA-seq data. In this paper, we propose a new Clustering Deviation Index (CDI) that measures the deviation of any clustering label set from the observed single-cell data. We conduct in silico and experimental scRNA-seq studies to show that CDI can select the optimal clustering label set. Particularly, CDI also informs the optimal tuning parameters for any given clustering method and the correct number of cluster components.


title: Calculation of centralities in protein kinase A

abstract:
Topological analysis of amino acid networks is a common method that can help to understand the roles of individual residues. The most popular approach for network construction is to create a connection between residues if they interact. These interactions are usually weighted by absolute values of correlation coefficients or mutual information. Here we argue that connections in such networks have to reflect levels of cohesion within the protein instead of a simple fact of interaction between residues. If this is correct, an indiscriminate combination of correlation and anti-correlation, as well as the all-inclusive nature of the mutual information metrics, should be detrimental for the analysis. To test our hypothesis, we studied amino acid networks of the protein kinase A created by Local Spatial Pattern alignment, a method that can detect conserved patterns formed by C-C{beta} vectors. Our results showed that, in comparison with the traditional methods, this approach is more efficient in detecting functionally important residues. Out of four studied centrality metrics, Closeness centrality was the least efficient measure of residue importance. Eigenvector centrality proved to be ineffective as the spectral gap values of the networks were very low due to the bilobal structure of the kinase. We recommend using joint graphs of Betweenness centrality and Degree centrality to visualize different aspects of amino acid roles.

Author Summary

Protein structures can be viewed as networks of residues with some of them being a part of highly interconnected hubs and some being connectors between the hubs. Analysis of these networks can be helpful for understanding of possible roles of single amino acids. In this paper, we challenged existing methods for the creation of such networks. A traditional way is to connect residues if they can interact. We propose that residues should be connected only if they retain their mutual positions in space during molecular dynamic simulation, that is they move cohesively. We show that this approach improves the efficiency of the analysis indicating that a significant revision of the existing views on amino acid networks is necessary.


title: Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes

abstract: Rhabdomyosarcomas (RMS) are mesenchyme-derived tumors and the most common childhood soft tissue sarcomas. Treatment is intense, with a nevertheless poor prognosis for high-risk patients. Discovery of new therapies would benefit from additional preclinical models. Here we describe the generation of a collection of pediatric RMS tumor organoid (tumoroid) models comprising all major subtypes. For aggressive tumors, tumoroid models can often be established within four to eight weeks, indicating the feasibility of personalized drug screening. Molecular, genetic and histological characterization show that the models closely resemble the original tumors, with genetic stability over extended culture periods of up to six months. Importantly, drug screening reflects established sensitivities and the models can be modified by CRISPR/Cas9 with TP53 knockout in an embryonal RMS model resulting in replicative stress drug sensitivity. Tumors of mesenchymal origin can therefore be used to generate organoid models, relevant for a variety of preclinical and clinical research questions.

category: cancer biology


title: The SARS-CoV-2 infection in Thailand: analysis of spike variants complemented by protein structure insights

abstract: Thailand was the first country outside China to officially report COVID-19 cases. Despite the strict regulations for international arrivals, up until February 2021, Thailand had been hit by two major outbreaks. With a large number of SARS-CoV-2 sequences collected from patients, the effects of many genetic variations, especially those unique to Thai strains, are yet to be elucidated. In this study, we analysed 439,197 sequences of the SARS-CoV-2 spike protein collected from NCBI and GISAID databases. 595 sequences were from Thailand and contained 52 variants, of which 6 had not been observed outside Thailand (p.T51N, p.P57T, p.I68R, p.S205T, p.K278T, p.G832C). These variants were not predicted to be of concern. We demonstrate that the p.D614G, although already present during the first Thai outbreak, became the prevalent strain during the second outbreak, similarly to what was described in other countries. Moreover, we show that the most common variants detected in Thailand (p.A829T, p.S459F and p.S939F) do not appear to cause any major structural change to the spike trimer or the spike-ACE2 interaction. Among the variants identified in Thailand was p.N501T. This variant, which involves an asparagine critical for spike-ACE2 binding, was not predicted to increase SARS-CoV-2 binding, thus in contrast to the variant of global concern p.N501Y. In conclusion, novel variants identified in Thailand are unlikely to increase the fitness of SARS-CoV-2. The insights obtained from this study could aid SARS-CoV-2 variants prioritisations and help molecular biologists and virologists working on strain surveillance.


title: Reduced interferon antagonism but similar drug sensitivity in Omicron variant compared to Delta variant SARS-CoV-2 isolates

abstract: The SARS-CoV-2 Omicron variant is currently causing a large number of infections in many countries. A number of antiviral agents are approved or in clinical testing for the treatment of COVID-19. Despite the high number of mutations in the Omicron variant, we here show that Omicron isolates display similar sensitivity to eight of the most important anti-SARS-CoV-2 drugs and drug candidates (including remdesivir, molnupiravir, and PF-07321332, the active compound in paxlovid), which is of timely relevance for the treatment of the increasing number of Omicron patients. Most importantly, we also found that the Omicron variant displays a reduced capability of antagonising the host cell interferon response. This provides a potential mechanistic explanation for the clinically observed reduced pathogenicity of Omicron variant viruses compared to Delta variant viruses.


title: E3 ubiquitin ligase MARCHF5 controls BAK apoptotic activity independently of BH3-only proteins

abstract: Intrinsic apoptosis is principally governed by the BCL-2 family of proteins, but some non-BCL-2 proteins are also critical to control this process. To identify novel apoptosis regulators, we performed a genome-wide CRISPR-Cas9 library screen, and it identified the mitochondrial E3 ubiquitin ligase MARCHF5/MITOL/RNF153 as an important regulator of BAK apoptotic function. Deleting MARCHF5 in diverse cell lines dependent on BAK conferred profound resistance to BH3-mimetic drugs. The loss of MARCHF5 or its E3 ubiquitin ligase activity surprisingly drove BAK to adopt an activated conformation, with resistance to BH3-mimetics afforded by the formation of inhibitory complexes with pro-survival proteins MCL-1 and BCL-XL. Importantly, these changes to BAK conformation and pro-survival association occurred independently of BH3-only proteins and influence on pro-survival proteins. This study identifies a new mechanism by which MARCHF5 regulates apoptotic cell death and provides new insight into how cancer cells respond to BH3-mimetic drugs. These data also highlight the emerging role of ubiquitin signalling in apoptosis that may be exploited therapeutically.

category: cell biology


title: Fasting Induces a Highly Resilient Deep Quiescent State in Muscle Stem Cells via Ketone Body Signaling

abstract: Short-term fasting is beneficial for the regeneration of multiple tissue types. However, the effects of fasting on muscle regeneration are largely unknown. Here we report that fasting slows muscle repair both immediately after the conclusion of fasting as well as after multiple days of refeeding. We show that ketosis, either endogenously produced during fasting or a ketogenic diet, or exogenously administered, promotes a deep quiescent state in muscle stem cells (MuSCs). Although deep quiescent MuSCs are less poised to activate, slowing muscle regeneration, they have markedly improved survival when facing sources of cellular stress. Further, we show that ketone bodies, specifically {beta}-hydroxybutyrate, directly promote MuSC deep quiescence via a non-metabolic mechanism. We show that {beta}-hydroxybutyrate functions as an HDAC inhibitor within MuSCs leading to acetylation and activation of an HDAC1 target protein p53. Finally, we demonstrate that p53 activation contributes to the deep quiescence and enhanced resilience observed during fasting.


title: Specialized protrusions coordinate migratory border cell cluster cohesion via Scribble, Cdep, and Rac

abstract: Apicobasal polarity is a defining characteristic of epithelial cells and its disruption is a cancer hallmark. Distinct apical and basolateral protein modules antagonize each other to establish separate membrane domains. These modules interact with dozens of potential effector proteins. Here we describe polarity protein localization and function within a migrating epithelial cell cluster and identify a functionally significant effector protein. In Drosophila egg chambers, border cells delaminate from the follicular epithelium and migrate collectively. We report that the basolateral protein Scribble is required for border cell cluster cohesion and migration. The basolateral module localizes the Rac guanine nucleotide exchange factor Cdep to membranes, and Cdep knockdown phenocopies Scribble cluster cohesion defects. Remarkably, membrane targeting of Cdep is sufficient to partially suppress multiple Scribble phenotypes. We describe specialized basolateral protrusions that promote cluster cohesion. Scribble restricts these protrusions from encroaching onto the apical domain. Thus, a major function of the basolateral module is to localize Cdep, promoting specialized protrusions, cluster cohesion, and collective migration.


title: PLEKHA5 regulates mitotic progression by promoting APC/C localization to microtubules

abstract: The anaphase-promoting complex/cyclosome (APC/C) coordinates advancement through mitosis via temporally controlled polyubiquitination of effector proteins. Despite the long-appreciated spatial organization of key events in mitosis mediated largely by cytoskeletal networks, the spatial regulation of APC/C, the major mitotic E3 ligase, is poorly understood. Here, we describe a microtubule-resident protein, PLEKHA5, as an interactor of APC/C and spatial regulator of its activity in mitosis. PLEKHA5 knockdown delayed mitotic progression, causing accumulation of APC/C substrates dependent upon the PLEKHA5-APC/C interaction. To assess the spatial importance of this interaction, we developed microtubule-localized proximity biotinylation tools, which revealed that depletion of PLEKHA5 decreased the extent of APC/C association with the microtubule cytoskeleton. This decreased APC/C microtubule-localization in turn prevented efficient loading of APC/C with its co-activator CDC20, leading to defects in E3 ligase catalytic activity. We propose that PLEKHA5 functions as an adaptor of APC/C that promotes its subcellular localization to microtubules and facilitates its activation by CDC20, thus ensuring the timely turnover of key mitotic APC/C substrates and proper progression through mitosis.


title: Spatial regulation of the anaphase-promoting complex/cyclosome by a microtubule adaptor


title: Proximity labeling reveals spatial regulation of the anaphase-promoting complex/cyclosome by a microtubule adaptor


title: Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling

abstract: The heterogenous and dynamic constitution of the membrane fine-tunes signal transduction. In particular, the polyunsaturated fatty acid (PUFA) tails of phospholipids influence the biophysical properties of the membrane, production of second messengers, or membrane partitioning. Few evidence mostly originating from studies of rhodopsin suggest that PUFAs directly modulate the conformational dynamic of transmembrane proteins. However, whether such properties translate to other G protein-coupled receptors remains unclear. We focused on the dopamine D2 receptor (D2R), a main target of antipsychotics. Membrane enrichment in n-3, but not n-6, PUFAs potentiates ligand binding. Molecular dynamics simulations show that the D2R preferentially interacts with n-3 over n-6 PUFAs. Furthermore, even though this mildly affects signalling in heterologous systems, in vivo n-3 PUFA deficiency blunts the effects of D2R ligands. These results suggest that n-3 PUFAs act as allosteric modulators of the D2R and provide a putative mechanism for their potentiating effect on antipsychotic efficacy.


title: ZYG-9ch-TOG promotes the stability of acentrosomal poles via regulation of spindle microtubules in C. elegans oocyte meiosis

abstract: During mitosis, centrosomes serve as microtubule organizing centers that guide the formation of a bipolar spindle. However, oocytes of many species lack centrosomes; how meiotic spindles establish and maintain these acentrosomal poles remains poorly understood. Here, we show that the microtubule polymerase ZYG-9ch-TOG is required to maintain acentrosomal pole integrity in C. elegans oocyte meiosis; following acute depletion of ZYG-9 from pre-formed spindles, the poles split apart and an unstable multipolar structure forms. Depletion of TAC-1, a protein known to interact with ZYG-9 in mitosis, caused loss of proper ZYG-9 localization and similar spindle phenotypes, further demonstrating that ZYG-9 is required for pole integrity. However, depletion of ZYG-9 surprisingly did not affect the assembly or stability of monopolar spindles, suggesting that ZYG-9 is not required for acentrosomal pole structure per se. Moreover, fluorescence recovery after photobleaching (FRAP) revealed that ZYG-9 turns over rapidly at acentrosomal poles, displaying similar turnover dynamics to tubulin itself, suggesting that ZYG-9 does not play a static structural role at poles. Together, these data support a global role for ZYG-9 in regulating the stability of bipolar spindles and demonstrate that the maintenance of acentrosomal poles requires factors beyond those acting to organize the pole structure itself.


title: The Mitochondrial RNA Granule is Necessary for Parkinsonism-Associated Metal Toxicity

abstract:
Prolonged manganese exposure causes manganism, a neurodegenerative movement disorder. The identity of adaptive and non-adaptive cellular processes targeted by manganese remains mostly unexplored. Here we study mechanisms engaged by manganese in genetic cellular models known to increase susceptibility to manganese exposure, the plasma membrane manganese efflux transporter SLC30A10 and the mitochondrial Parkinsons gene PARK2. We found that SLC30A10 and PARK2 mutations as well as manganese exposure compromised the mitochondrial RNA granule as well as mitochondrial transcript processing. These RNA granule defects led to impaired assembly and function of the mitochondrial respiratory chain. Notably, cells that survived a cytotoxic manganese challenge had impaired RNA granule function, thus suggesting that this granule phenotype was adaptive. CRISPR gene editing of subunits of the mitochondrial RNA granule, FASTKD2 or DHX30, as well as pharmacological inhibition of mitochondrial transcription-translation, were protective rather than deleterious for survival of cells acutely exposed to manganese. Similarly, adult Drosophila mutants with defects in the mitochondrial RNA granule component scully were safeguarded from manganese-induced mortality. We conclude that the downregulation of the mitochondrial RNA granule function is a protective mechanism for acute metal toxicity.

Significance StatementMutations in the manganese efflux transporter SLC30A10 and the mitochondrial Parkinsons gene PARK2, cause neurodegeneration and increased susceptibility to toxic manganese exposure. Thus, molecular processes affected in both mutants could offer insight into fundamental mechanisms conferring susceptibility or resilience to environmental and genetic factors associated with neurodegeneration. Here we report that SLC30A10 and PARK2 mutations compromise an understudied structure, the mitochondrial RNA granule, which is required for processing polycistronic mitochondrial RNAs. Cells and Drosophila lacking mitochondrial RNA granule components were resistant to manganese exposure. We conclude that the downregulation of the mitochondrial RNA granule function is an adaptive mechanism for cells exposed to manganese.


title: The Mitochondrial RNA Granule Modulates Manganese-Dependent Cell Toxicity


title: The onset of whole-body regeneration in Botryllus schlosseri: morphological and molecular characterization

abstract:
Colonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body.

In this manuscript, we characterized the onset of WBR in Botryllus schlosseri, one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization, in vivo observations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR in B. schlosseri is initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis in B. schlosseri and allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.


title: Generation of Vascularized Brain Organoids to Study Neurovascular Interactions

abstract: The recently developed brain organoids have been used to recapitulate the processes of brain development and related diseases. However, the lack of vasculatures, which regulate neurogenesis, brain disorders, and aging process, limits the utility of brain organoids. In this study, we induced vessel and brain organoids respectively, and then fused two types of organoids together to obtain vascularized brain organoids. The fused brain organoids were engrafted with robust vascular network-like structures, and exhibited increased number of neural progenitors, in line with the possibility that vessels regulate neural development. Fusion organoids also contained functional blood-brain-barrier (BBB)-like structures, as well as microglial cells, a specific population of immune cells in the brain. The incorporated microglia responded actively to immune stimuli to the fused brain organoids. Thus, the fusion organoids established in this study allow modeling interactions between the neuronal and non-neuronal components in vitro, in particular the vasculature and microglia niche.


title: hPSC-Derived Enteric Ganglioids Model Human ENS Development and Function

abstract: The enteric nervous system (ENS) plays a central role in gut physiology and mediating the crosstalk between the gastrointestinal (GI) tract and other organs. The human ENS has remained elusive, highlighting the need for an in vitro modeling and mapping blueprint. Here we map out the developmental and functional features of the human ENS, by establishing robust and scalable 2D ENS cultures and 3D enteric ganglioids from human pluripotent stem cells (hPSCs). These models recapitulate the remarkable neuronal and glial diversity found in primary tissue and enable comprehensive molecular analyses that uncover functional and developmental relationships within these lineages. As a salient example of the power of this system, we performed in-depth characterization of enteric nitrergic neurons (NO neurons) which are implicated in a wide range of GI motility disorders. We conducted an unbiased screen and identified drug candidates that modulate the activity of NO neurons and demonstrated their potential in promoting motility in mouse colonic tissue ex vivo. We established a high-throughput strategy to define the developmental programs involved in NO neuron specification and discovered that PDGFR inhibition boosts the induction of NO neurons in enteric ganglioids. Transplantation of these ganglioids in the colon of NO neuron-deficient mice results in extensive tissue engraftment, providing a xenograft model for the study of human ENS in vivo and the development of cell-based therapies for neurodegenerative GI disorders. These studies provide a framework for deciphering fundamental features of the human ENS and designing effective strategies to treat enteric neuropathies.


title: mTORC2 loss in oligodendrocyte progenitor cells results in regional hypomyelination in the central nervous system

abstract:
In the central nervous system (CNS), oligodendrocyte progenitor cells (OPCs) differentiate into mature oligodendrocytes to generate myelin, which is essential for normal nervous system function. OPC differentiation is driven by signaling pathways such as mTOR (Mechanistic Target of Rapamycin), which functions in two distinct complexes: mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), containing Raptor or Rictor respectively. In the current studies, mTORC2 signaling was selectively deleted from OPCs in PDGFR-Cre X Rictorfl/fl mice. This study examined developmental myelination in male and female mice, comparing the impact of mTORC2 deletion in the corpus callosum and spinal cord. In both corpus callosum and spinal cord, Rictor loss in OPCs resulted in early reduction in myelin RNAs and some myelin proteins. However, these deficits rapidly recovered in spinal cord, where normal myelin abundance and thickness was noted at post-natal day 21 and 1.5 months. By contrast, the losses in corpus callosum resulted in severe hypomyelination, and increased unmyelinated axons. The current studies focus on uniquely altered signaling pathways following mTORC2 loss in developing oligodendrocytes. A major mTORC2 substrate is phospho-Akt-S473, which was significantly reduced throughout development in both corpus callosum and spinal cord at all ages measured, yet this had little impact in spinal cord. Loss of mTORC2 signaling resulted in decreased expression of actin regulators such as gelsolin in corpus callosum, but only minimal loss in spinal cord. The current study establishes a regionally-specific role for mTORC2 signaling in OPCs, particularly in the corpus callosum.

Significance StatementmTORC1 and mTORC2 signaling have differential impact on myelination in the central nervous system. Numerous studies identify a role for mTORC1, but deletion of Rictor (mTORC2 signaling) in late-stage oligodendrocytes had little impact on myelination in the CNS. However, the current studies establish that deletion of mTORC2 signaling from oligodendrocyte progenitor cells results in reduced myelination of brain axons. These studies also establish a regional impact of mTORC2, with little change in spinal cord in these conditional Rictor deletion mice. Importantly, in both, brain and spinal cord, mTORC2 downstream signaling targets were impacted by Rictor deletion. Yet, these signaling changes had little impact on myelination in spinal cord, while they resulted in long term alterations in myelination in brain.


title: The generation of a Nutm1 knock-in reporter mouse line for imaging post-meiotic spermatogenesis

abstract: Spermiogenesis, the post-meiotic stage of sperm development, is critical for normal male fertility. Many genetic defects and environmental assaults that affect spermiogenesis have been shown to be associated with male infertility. In addition, this later stage of spermatogenesis has been proposed to be an ideal target for male contraceptive development. The mouse is a widely used model for studying the mechanisms of spermatogenesis and spermiogenesis. However, due to the complexity and the asynchronous nature of spermatogenesis in adult testis, it is challenging to study molecular processes restricted to this specific developmental stage. It is also challenging to monitor the spermiogenesic activity in live mice, which is critical for screening for fertility-modulating interventions such as contraceptives. Here we reported the development of a Nutm1-T2A-luciferase 2(Luc2)-tandem Tomato(TdTomato) knock-in reporter mouse model that specifically labels post-meiotic spermatids. Homozygous reporter mice are healthy and fully fertile, demonstrating no interference with the normal functions of the Nutm1 gene by the reporter. We demonstrated the visualization of post-meiotic spermatids by fluorescent imaging of the TdTomato reporter in both live and fixed testis tissues. We also demonstrated bioluminescence imaging of Nutm1 expressing cells in live mice. The Nutm1-T2A-Luc2TdTomato reporter mouse can serve as a valuable tool for studying spermiogenesis.


title: The tetraspanin TSPAN5 regulates AMPARs exocytosis by interacting with the AP-4 complex

abstract: Intracellular trafficking of AMPA receptors is a tightly regulated process which involves several adaptor proteins, and is crucial for the activity of excitatory synapses in both basal conditions and during synaptic plasticity. We found that, in rat hippocampal neurons, an intracellular pool of the tetraspanin TSPAN5 specifically promotes exocytosis of newly synthesised GluA2-containing AMPA receptors without affecting their internalisation. TSPAN5 mediates this function by interacting with AP-4 and Stargazin and possibly using recycling endosomes as a delivery route. This work highlights TSPAN5 as a new adaptor regulating AMPA receptor trafficking. In addition, it provides a possible mechanism for the intellectual disability symptoms that occur in AP-4 deficiency syndrome.


title: Maternal cytokine response after SARS-CoV-2 infection during pregnancy

abstract:
ObjectiveDysregulation of the immune system during pregnancy is associated with adverse pregnancy outcomes. Recent studies report cytokine changes during the acute phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We examine whether there is a lasting association between SARS-CoV-2 infection during pregnancy and peripheral blood cytokine levels.

Study designWe conducted a case-control study at the Mount Sinai health system in NYC including 100 SARS-CoV-2 IgG antibody positive people matched to 100 SARS-CoV-2 IgG antibody negative people on age, race/ethnicity, parity, and insurance status. Blood samples were collected at a median gestational age of 34 weeks. Levels of 14 cytokines were measured.

ResultsIndividual cytokine levels and cytokine cluster Eigenvalues did not differ significantly between groups, indicating no persisting maternal cytokine changes after SARS-CoV-2 infection during pregnancy.

ConclusionOur findings suggest that the acute inflammatory response after SARS-CoV-2 infection may be restored to normal values during pregnancy.


title: A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron

abstract: Bispecific antibodies have emerged as a promising strategy for curtailing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape. This brief report highlights RBT-0813 (also known as TB493-04), a synthetic, humanized, receptor-binding domain (RBD)-targeted bispecific antibody that retains picomolar affinity to the Spike (S) trimers of all major variants of concern and neutralizes both SARS-CoV-2 Delta and Omicron in vitro.


title: Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2

abstract:
Inhibition of the protein kinase CSNK2 with any of 30 specific and selective inhibitors representing different chemotypes, blocked replication of pathogenic human and murine {beta}-coronaviruses. The potency of in-cell CSNK2A target engagement across the set of inhibitors correlated with antiviral activity and genetic knockdown confirmed the essential role of the CSNK2 holoenzyme in {beta}-coronavirus replication. Spike protein uptake was blocked by CSNK2A inhibition, indicating that antiviral activity was due in part to a suppression of viral entry. CSNK2A inhibition may be a viable target for development of new broad spectrum anti-{beta}-coronavirus drugs.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/474779v3_ufig1.gif" ALT="Figure 1">
View larger version (19K):
org.highwire.dtl.DTLVardef@5d2799org.highwire.dtl.DTLVardef@1d2de35org.highwire.dtl.DTLVardef@fa852eorg.highwire.dtl.DTLVardef@13da300_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Caveolae promote successful abscission by controlling intercellular bridge tension during cytokinesis

abstract:
During cytokinesis, the intercellular bridge (ICB) connecting the daughter cells experiences pulling forces, which delay abscission by preventing the assembly of the ESCRT scission machinery. Abscission is thus triggered by tension release, but how ICB tension is controlled is unknown. Here, we report that caveolae, which are known to control membrane tension upon mechanical stress in interphase cells, are located at the midbody, at the abscission site and at the ICB/cell interface in dividing cells. Functionally, the loss of caveolae delays ESCRT-III recruitment during cytokinesis and impairs abscission. This is the consequence of a 2-fold increase of ICB tension measured by laser ablation, associated with a local increase in myosin II activity at the ICB/cell interface. We thus propose that caveolae buffer membrane tension and limit contractibility at the ICB to promote ESCRT-III assembly and cytokinetic abscission. Altogether, this work reveals an unexpected connection between caveolae and the ESCRT machinery and the first role of caveolae in cell division.

TEASERCaveolae limit the tension in the intercellular bridge during cytokinesis to enable ESCRT-III assembly and successful abscission.


title: Structural and computational insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction

abstract: Since SARS-CoV-2 Omicron variant (B.1.1.529) was reported in November 2021, it has quickly spread to many countries and outcompeted the globally dominant Delta variant in several countries. The Omicron variant contains the largest number of mutations to date, with 32 mutations located at spike (S) glycoprotein, which raised great concern for its enhanced viral fitness and immune escape[1-4]. In this study, we reported the crystal structure of the receptor binding domain (RBD) of Omicron variant S glycoprotein bound to human ACE2 at a resolution of 2.6 [A]. Structural comparison, molecular dynamics simulation and binding free energy calculation collectively identified four key mutations (S477N, G496S, Q498R and N501Y) for the enhanced binding of ACE2 by the Omicron RBD compared to the WT RBD. Representative states of the WT and Omicron RBD-ACE2 systems were identified by Markov State Model, which provides a dynamic explanation for the enhanced binding of Omicron RBD. The effects of the mutations in the RBD for antibody recognition were analyzed, especially for the S371L/S373P/S375F substitutions significantly changing the local conformation of the residing loop to deactivate several class IV neutralizing antibodies.

category: biophysics


title: Structural basis of Omicron neutralization by affinity-matured public antibodies

abstract: The SARS-CoV-2 Omicron1 Variant of Concern (B.1.1.529) has spread rapidly in many countries. With a spike that is highly diverged from that of the pandemic founder, it escapes most available monoclonal antibody therapeutics2,3 and erodes vaccine protection4. A public class of IGHV3-53-using SARS-CoV-2 neutralizing antibodies5,6 typically fails to neutralize variants carrying mutations in the receptor-binding motif7-11, including Omicron. As antibodies from this class are likely elicited in most people following SARS-CoV-2 infection or vaccination, their subsequent affinity maturation is of particular interest. Here, we isolated IGHV3-53-using antibodies from an individual seven months after infection and identified several antibodies capable of broad and potent SARS-CoV-2 neutralization, extending to Omicron without loss of potency. By introducing select somatic hypermutations into a germline-reverted form of one such antibody, CAB-A17, we demonstrate the potential for commonly elicited antibodies to develop broad cross-neutralization through affinity maturation. Further, we resolved the structure of CAB-A17 Fab in complex with Omicron spike at an overall resolution of 2.6 [A] by cryo-electron microscopy and defined the structural basis for this breadth. Thus, public SARS-CoV-2 neutralizing antibodies can, without modified spike vaccines, mature to cross-neutralize exceptionally antigenically diverged SARS-CoV-2 variants.


title: Transglutaminase mediated asprosin oligomerization allows its tissue storage as fibers

abstract: Asprosin, the C-terminal furin cleavage product of profibrillin-1, was reported to act as a hormone that circulates at nanomolar levels and is recruited to the liver where it induces G protein-coupled activation of the cAMP-PKA pathway and stimulates rapid glucose release into the circulation. Although derived from profibrillin-1, a multidomain extracellular matrix glycoprotein with a ubiquitous distribution in connective tissues, little is known about the tissue distribution of asprosin. In the current view, asprosin is mainly produced by white adipose tissue from where it is released into the blood in monomeric form. Here, by employing newly generated specific asprosin antibodies we monitored the distribution pattern of asprosin in human and murine connective tissues such as placenta, and muscle. Thereby we detected the presence of asprosin positive extracellular fibers. Further, by screening established cell lines for asprosin synthesis we found that most cells derived from musculoskeletal tissues render asprosin into an oligomerized form. This oligomerization is facilitated by transglutaminase activity and requires an intact fibrillin fiber network for proper linear deposition. Our data suggest a new extracellular storage mechanism of asprosin in oligomerized form which may regulate its cellular bioavailability in tissues.

category: biochemistry


title: Improving disease resistance in plants by editing the epigenome

abstract:
Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas axonopodis pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. We directed methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display increased resistance to CBB while maintaining normal growth and development. This work establishes epigenome editing as a new strategy for crop improvement.

One-Sentence SummaryImproving disease resistance with epigenomic editing.


title: Exploring the rules of chimeric antigen receptor phenotypic output using combinatorial signaling motif libraries and machine learning

abstract:
Chimeric antigen receptor (CAR) costimulatory domains steer the phenotypic output of therapeutic T cells. In most cases these domains are derived from native immune receptors, composed of signaling motif combinations selected by evolution. To explore if non-natural combinations of signaling motifs could drive novel cell fates of interest, we constructed a library of CARs containing [~]2,300 synthetic costimulatory domains, built from combinations of 13 peptide signaling motifs. The library produced CARs driving diverse fate outputs, which were sensitive to motif combinations and configurations. Neural networks trained to decode the combinatorial grammar of CAR signaling motifs allowed extraction of key design rules. For example, the non-native combination of TRAF- and PLC{gamma}1-binding motifs was found to simultaneously enhance cytotoxicity and stemness, a clinically desirable phenotype associated with effective and durable tumor killing. The neural network accurately predicts that addition of PLC{gamma}1-binding motifs improves this phenotype when combined with TRAF-binding motifs, but not when combined with other immune signaling motifs (e.g. PI3K-or Grb2-binding motifs). This work shows how libraries built from the minimal building blocks of signaling, combined with machine learning, can efficiently guide engineering of receptors with desired phenotypes.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/474985v2_ufig1.gif" ALT="Figure 1">
View larger version (17K):
org.highwire.dtl.DTLVardef@8dbf97org.highwire.dtl.DTLVardef@1d8300org.highwire.dtl.DTLVardef@1838ba0org.highwire.dtl.DTLVardef@143d907_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: synthetic biology


title: Mosquito Olfactory Response Ensemble: a curated database of behavioral and electrophysiological responses enables pattern discovery

abstract: Many experimental studies have examined behavioral and electrophysiological responses of mosquitoes to odors. However, the differences across studies in data collection, processing, and reporting make it difficult to perform large-scale analyses combining data from multiple studies. Here we extract and standardize data for 12 mosquito species, along with Drosophila melanogaster for comparison, from over 170 studies and curate the Mosquito Olfactory Response Ensemble (MORE), publicly available at https://neuralsystems.github.io/MORE. We demonstrate the ability of MORE in generating biological insights by finding patterns across studies. Our analyses reveal that ORs are tuned to specific ranges of several physicochemical properties of odorants; the empty-neuron recording technique for measuring OR responses is more sensitive than the Xenopus oocyte technique; there are systematic differences in the behavioral preferences reported by different types of assays; and odorants tend to become less attractive or more aversive at higher concentrations.


title: Wnt5A supports antigen cross-presentation and CD8 T cell activation.

abstract: Antigen processing, cross-presentation, and antigen-specific CD8 T cell response form part and parcel of T cell-mediated immunity. Yet, lacunae remain in our understanding of antigen processing/presentation and CD8 T cell response. Given the association of Wnt5A signaling with immune homeostasis, we evaluated the utility of Wnt5A in antigen processing, cross-presentation, and CD8 T cell activation. Using mouse bone marrow-derived dendritic cells as antigen-presenting cells and ovalbumin as a model antigen we found that Wnt5A mediated regulation of actin and proteasome dynamics is inherently associated with antigen processing. A Wnt5A-Actin-Protasome axis also contributes to antigen cross-presentation and antigen responsive CD8 T cell expansion. In concurrence with these observations, we demonstrated impaired activation of ovalbumin-specific CD8 T cells in ovalbumin immunized Wnt5A heterozygous mice as illustrated by their poor CD8 T cell recall response to ovalbumin when compared to similarly immunized wild type cohorts. Our results suggest that Wnt5A signaling-directed antigen processing/presentation could be vital for generating CD8 T cell recall response to antigen, thus shedding light on a critical parameter of immunity.


title: GWAS and functional studies implicate a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis

abstract: The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis (GWAS) using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, for the first time, we identified a strong association between the mutations in the DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis (Msm) and Mtb. Results show that variant mutations abrogated the function of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. Notably, in an in vivo Guinea pig infection model, the MutY variant outcompeted the wild-type strain. Collectively, we show that novel variant mutations in the DNA repair genes abrogate their function and contribute to better survival under antibiotic/host stress conditions.