title: Discrimination of edge orientation by bumblebees

abstract: Simple feature detectors in the visual system, such as edge-detectors, are likely to underlie even the most complex visual processing, so understanding the limits of these systems is crucial for a fuller understanding of visual processing. We investigated the ability of bumblebees (Bombus terrestris) to discriminate between differently angled edges. In a multiple-choice, "meadow-like" scenario, bumblebees successfully discriminated between angled bars with 7{degrees} differences, significantly exceeding the previously reported performance of eastern honeybees (Apis cerana, limit: 15{degrees}). Neither the number of choices required to learn, nor the bees final discrimination performance were affected by the angular orientation of the training bars, indicating a uniform performance across the visual field. Previous work has found that, in dual-choice tests, eastern honeybees cannot reliably discriminate between angles with less than 25{degrees} difference, suggesting that performance in discrimination tasks is affected by the training regime, and doesnt simply reflect the perceptual limitations of the visual system. We used high resolution LCD monitors to investigate the limits of bumblebees angular resolution in dual-choice experiments. Bumblebee could still discriminate 7{degrees} angle differences under such conditions (exceeding the previously reported limit for Apis mellifera, of 10{degrees}, as well as that of A. cerana), eventually reaching similar levels of accuracy, but required longer learning periods than under multiple-choice conditions. Bumblebees show impressive abilities to discriminate between angled edges, performing better than two previously tested species of honeybee. This high performance may, in turn, support complex visual processing in the bumblebee brain.

category: animal behavior and cognition


title: Comparative study of the unbinding process of some HTLV-1 protease inhibitors using Unbiased Molecular Dynamics simulation

abstract: The HTLV-1 protease is one of the major antiviral targets to overwhelm this virus. Several research groups have been developing protease inhibitors over the years, but none has been successful. In this regard, the development of new HTLV-1 protease inhibitors based on fixing the defects of previous inhibitors will overcome the absence of curative treatment for this oncovirus. Thus, we decided to study the unbinding pathways of the most potent (compound 10, Ki = 15 nM) and one of the weakest (compound 9, Ki = 7900 nM) protease inhibitors, which are very structurally similar, with the PDB IDs: 4YDG, 4YDF, using the Supervised Molecular Dynamics (SuMD) method. In this project, we had various short and long-time-scale simulations, that in total, we could have 12 successful unbindings (a total of 14.8 s) for the two compounds in both mp forms. This comparative study measured all the essential factors simultaneously in two different inhibitors, which improved our results. This study revealed that Asp32 or Asp32' in the two forms of mp state similarly exert super power effects on maintaining both potent and weak inhibitors in the binding pocket of HTLV-1 protease. In parallel with the important impact of these two residues, in the potent inhibitors unbinding process, His66' was a great supporter, that was absent in the weak inhibitors unbinding pathway. In contrast, in the weak inhibitors unbinding process, Trp98/Trp98' by pi-pi stacking interactions were unfavorable for the stability of the inhibitor in the binding site. In our opinion, these results will assist in designing more potent and effective inhibitors for the HTLV-1 protease.

category: bioinformatics


title: The voltage-gated Cav Ca2+ channel subunit α2δ-4 is required for locomotor behavior and sensorimotor gating in mice

abstract: Voltage-gated Cav Ca2+ channels are critical for the development and mature function of the nervous system. Variants in the CACNA2D4 gene encoding the 2{delta}-4 auxiliary subunit of these channels are associated with neuropsychiatric and neurodevelopmental disorders. 2{delta}-4 is prominently expressed in the retina and is crucial for vision, but extra-retinal functions of 2{delta}-4 have not been investigated. Here, we sought to fill this gap by analyzing the behavioral phenotypes of 2{delta}-4 knockout (KO) mice. 2{delta}-4 KO mice (both males and females) exhibited significant impairments in prepulse inhibition that were unlikely to result from the modestly elevated auditory brainstem response thresholds. Whereas 2{delta}-4 KO mice of both sexes were hyperactive in various assays, only females showed impaired motor learning/coordination in the rotarod assay. Female but not male 2{delta}-4 KO mice exhibited anxiolytic and anti-depressive behaviors in the elevated plus maze and tail suspension tests, respectively. Our results reveal an unexpected role for 2{delta}-4 in cognitive and motor function and identify 2{delta}-4 KO mice as a novel model for studying the pathophysiology associated with CACNA2D4 variants.

category: neuroscience


title: The Streptococcus agalactiae R3 surface protein is encoded by sar5

abstract: Streptococcus agalactiae (a group B streptococcus; GBS) is an important human pathogen causing pneumonia, sepsis and meningitis in neonates, as well as infections in pregnant women, immunocompromised individuals, and the elderly. For the future control of GBS-inflicted disease, GBS surface exposed proteins are particularly relevant as they may act as antigens for vaccine development and/or as serosubtype markers in epidemiological settings. Even so, the genes encoding some of the surface proteins established as serosubtype markers by antibody-based methods are still unknown. Here, we identify sar5 as the gene encoding the R3 surface protein, a serosubtype marker of hitherto unknown genetic origin.

category: microbiology


title: A quantitative analysis of the similarities and differences of the HIV/FIV gag genome

abstract: 1.Among viruses, human immunodeficiency virus (HIV) presents the greatest challenge to humans. Here, we retrieved genome sequences from NCBI and were then run through LALIGN bioinformatics software to compute the E value, bit score, Waterman eggert score, and percent identity, which are four important indicators of how similar the sequences are. These 4 values are 3.1 x 10^-9,51.9, 241 and 55.4%.Bases 1600 to 1990 in HIV and bases 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genomes are rather similar, it is unlikely that this similarity is due to random chance; therefore, there are a noticeable number of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term, it will provide new insights into the differences observed in previous studies or even facilitate the development of an effective HIV treatment.


title: Task-specific neural processes underlying conflict resolution during cognitive control

abstract: Cognitive control involves flexibly combining multiple sensory inputs with task-dependent goals during decision making. Several tasks have been proposed to examine cognitive control, including Stroop, Eriksen-Flanker, and the Multi-source interference task. Because these tasks have been studied independently, it remains unclear whether the neural signatures of cognitive control reflect abstract control mechanisms or specific combinations of sensory and behavioral aspects of each task. To address this question, here we recorded invasive neurophysiological signals from 16 subjects and directly compared the three tasks against each other. Neural activity patterns in the theta and high-gamma frequency bands differed between incongruent and congruent conditions, revealing strong modulation by conflicting task demands. These neural signals were specific to each task, generalizing within a task but not across tasks. These results highlight the complex interplay between sensory inputs, motor outputs, and task demands and argue against a universal and abstract representation of conflict.


title: Criticality and network structure drive emergent oscillations in a stochastic whole-brain model

abstract: Understanding the relation between the structure of brain networks and its functions is a fundamental open question. Simple models of neural activity based on real anatomical networks have proven effective in describing features of whole-brain spontaneous activity when tuned at their critical point. In this work, we show that indeed structural networks are a crucial ingredient in the emergence of synchronized oscillations in a whole-brain stochastic model at criticality. We study such model in the mean-field limit, providing an analytical understanding of the associated first-order phase transition, arising from the presence of a bistable region in the parameters space. Then, we derive the power spectrum in the linear noise approximation and we show that, in the mean-field limit, no global oscillations emerge. Finally, by adding back an underlying brain network structure with homeostatic normalization, we numerically show how the bi-stability region is disrupted and concomitantly a synchronized phase with maximal dynamic range is observed. Hence, both the structure of brain networks and criticality are fundamental in driving the collective coordinated responses and maximal sensitivity of whole-brain stochastic models.


title: Brainwide input-output architecture of paraventricular oxytocin and vasopressin neurons

abstract: Oxytocin and vasopressin are pleiotropic neuropeptides with well-established roles in the regulation of social behavior and homeostatic functions. Their structural similarity and conserved functions in vertebrate social behavior suggest that neurohypophyseal peptides may represent a single integrative neuromodulatory system, yet both peptides subserve sexually dimorphic functions at the behavioral level. The extent to which central oxytocin and vasopressin systems share similar circuit architecture has not been previously studied. Sex differences in the central circuitry of the oxytocin and vasopressin systems may underlie sex-variant behaviors, but it is currently unknown whether the synaptic inputs or outputs of each neuropeptidergic system vary across males and females. To close this gap, we generated quantitative anterograde and retrograde maps of the paraventricular oxytocin and vasopressin systems in mice. We observed that both oxytocinergic and vasopressinergic neurons share highly similar synaptic inputs that are sex-conserved. Projection patterns differed across systems and showed sex differences, more pronounced in the vasopressin neurons. Together our data represent the first comparative study of oxytocin and vasopressin input-output architecture highlighting how these neurohypopheseal peptides can play complementary and overlapping roles that are sex-dependent.


title: A hippocampal-hypothalamic circuit essential for anxiety-related behavioral avoidance

abstract: Anxiety over perceived threats triggers avoidance behavior, but the underlying neural circuit mechanism remains poorly understood. Taking hints from the deep connection between anxiety and predator defense, we examined the role of the anterior hypothalamic nucleus (AHN), a critical node in the predator defense network, in anxiety-related behaviors. By recording Ca2+ transients in behaving mice, we found that activity of AHN GABAergic (AHNVgat+) neurons showed individually stable increases when animals approached unfamiliar objects in an open field (OF) or explored the open arm of an elevated plus-maze (EPM). Moreover, AHNVgat+ neuron activity foreshadowed behavioral retreats and correlated with object and open-arm avoidance. Crucially, exploration-triggered optogenetic inhibition of AHNVgat+ neurons dramatically reduced avoidance behaviors. Furthermore, retrograde viral tracing identified the ventral subiculum (vSub) of the hippocampal formation as a significant input to AHNVgat+ neurons in driving avoidance behaviors. Thus, the activity of the hippocampal-hypothalamic pathway promotes idiosyncratic anxiety-related behavioral avoidance.


title: Collateral cleavage of 28s rRNA by RfxCas13d causes death of mice

abstract: The CRISPR-Cas13 system is an RNA-guided RNA-targeting system, and has been widely used in transcriptome engineering with potentially important clinical applications. However, it is still controversial whether Cas13 exhibits collateral activity in mammalian cells. Here, we found that knocking down gene expression using RfxCas13d in the adult brain neurons caused death of mice, which was not resulted from the loss of target gene function or off-target effects. Mechanistically, we showed that RfxCas13d exhibited collateral activity in mammalian cells, which is positively correlated with the abundance of target RNA. The collateral activity of RfxCas13d could cleave 28s rRNA into two fragments, leading to translation attenuation and activation of the ZAK-JNK/p38-immediate early gene (IEG) pathway. These results provide new mechanistic insights into the collateral activity of RfxCas13d and warn that the biosafety of CRISPR-Cas13 system needs further evaluation before applying it to clinical treatments.

category: bioengineering


title: Quantitative Models of Lipid Transfer and Membrane Contact Formation

abstract: Lipid transfer proteins (LTPs) transfer lipids between different organelles, and thus play key roles in lipid homeostasis and organelle dynamics. The lipid transfer often occurs at the membrane contact sites (MCS) where two membranes are held within 10-30 nm. While most LTPs act as a shuttle to transfer lipids, recent experiments reveal a new category of eukaryotic LTPs that may serve as a bridge to transport lipids in bulk at MCSs. However, the molecular mechanisms underlying lipid transfer and MCS formation are not well understood. Here, we first review two recent studies of extended synaptotagmin (E-Syt)-mediated membrane binding and lipid transfer using novel approaches. Then we describe mathematical models to quantify the kinetics of lipid transfer by shuttle LTPs based on a lipid exchange mechanism. We find that simple lipid mixing among membranes of similar composition and/or lipid partitioning among membranes of distinct composition can explain lipid transfer against a concentration gradient widely observed for LTPs. We predict that selective transport of lipids, but not membrane proteins, by bridge LTPs leads to osmotic membrane tension by analogy to the osmotic pressure across a semipermeable membrane. A gradient of such tension and the conventional membrane tension may drive bulk lipid flow through bridge LTPs at a speed consistent with the fast membrane expansion observed in vivo. Finally, we discuss the implications of membrane tension and lipid transfer in organelle biogenesis. Overall, the quantitative models may help clarify the mechanisms of LTP-mediated MCS formation and lipid transfer.

category: biophysics


title: Light activation of Orange Carotenoid Protein reveals initial C8'-C7' double bond trans/cis photoisomerization

abstract: Orange Carotenoid protein (OCP) is the only known photoreceptor which uses carotenoid for its activation1,2. It is found exclusively in cyanobacteria, where it functions to control light-harvesting of the photosynthetic machinery. However, the photochemical reactions and structural dynamics of this unique photosensing process are not yet resolved. We present time-resolved crystal structures at second-to-minute delays under bright illumination, capturing the early photoproduct and structures of the subsequent reaction intermediates. The first stable photoproduct shows carotenoid trans/cis isomerization at the C7-C8double bond and structural changes in the N-terminal domain with minute timescale kinetics. These are followed by a thermally-driven cis/trans isomerization that recovers to the dark state carotenoid configuration. Structural changes propagate to the C-terminal domain, resulting, at later time, in the H-bond rupture of the carotenoid keto group with protein residues. The isomerization and its transient nature are confirmed in OCP crystals and solution by FTIR and UV/Vis spectroscopy. This study reveals the isomerization of the carotenoid and subsequent thermal structural reactions as the basis of OCP photoreception. Understanding and potentially controlling the OCP dynamics offers the prospect of novel applications in biomass engineering3 as well as in optogenetics and bioimaging.


title: Light activation of Orange Carotenoid Protein reveals initial C8'-C7' double bond trans/cis isomerization


title: Mucosal associated invariant T cells are altered in patients with Hidradenitis Suppurativa and contribute to the inflammatory milieu

abstract: Mucosal Associated Invariant T cells are a population of "innate" T cells, which express the invariant T cell receptor (TCR)  chain V 7.2-J 33 and are capable of robust rapid cytokine secretion, producing a milieu of cytokines including IFN-{gamma} and IL-17. MAIT cells have been reported in multiple human tissues including the gut, periphery and skin. On-going research has highlighted their involvement in numerous inflammatory diseases ranging from rheumatoid arthritis and obesity to psoriasis. Hidradenitis Suppurativa (H.S) is a chronic inflammatory disease of the hair follicles, resulting in painful lesions of apocrine-bearing skin. Several inflammatory cytokines have been implicated in the pathogenesis of H.S including IL-17. The role of MAIT cells in H.S is currently unknown. In this study we show for the first time, that MAIT cells are altered in the peripheral blood of patients with H.S, with reduced frequencies and an IL-17 cytokine bias. We show that CCL20 expression is elevated in lesions of patients with H.S, and MAIT cells can actively traffic towards lesions via CCL20. We show that MAIT cells can accumulate in the lesions from patients with H.S. when compared to adjacent skin, with an IL-17 bias. We show that elevated IL-17, can be linked to the activation of dermal fibroblasts, promoting the expression of chemotactic signals including CCL20 and CXCL1. Finally, we show that targeting the IL-17A transcription factor RORyt robustly reduces IL-17 production by MAIT cells from patients with H.S. Collectively our data details IL-17 producing MAIT cells as a novel player in the pathogenesis of H.S and highlights the potential of RORyt inhibition as a novel therapeutic strategy.

category: immunology


title: Catch bond models explain how force amplifies TCR signaling and antigen discrimination

abstract: Central to T cell biology, the TCR integrates forces in its triggering process upon interaction with pMHC. Phenotypically, forces elicit TCR catch-slip bonds with strong pMHCs but slip-only bonds with weak pMHCs. While such correlation is generally observed, the quantitative bond pattern and degree of "catchiness" vary. We developed two models based on the structure, elastic properties, and force-induced conformational changes of the TCR-pMHC-I/II complexes to derive from their bond characteristics more intrinsic parameters that underlie structural mechanisms, predict T cell signaling, and discriminate antigens. Applying the models to all published 48 datasets of 11 TCRs and their mutants interacting with corresponding pMHCs revealed the ability for structural and physical parameters to quantitatively integrate and classify a broad range of bond behaviors and biological activities. The extensive comparisons between theory and experiment allowed us to validate the models and identify specific conformational changes that control bond profiles, thereby providing structural insights into the inner workings of the TCR mechanosensing machinery and explaining why and how force amplifies TCR signaling and antigen discrimination.


title: Sparse and Skew Hashing of K-Mers

abstract:
MotivationA dictionary of k-mers is a data structure that stores a set of n distinct k-mers and supports membership queries. This data structure is at the hearth of many important tasks in computational biology. High-throughput sequencing of DNA can produce very large k-mer sets, in the size of billions of strings - in such cases, the memory consumption and query efficiency of the data structure is a concrete challenge.

ResultsTo tackle this problem, we describe a compressed and associative dictionary for k-mers, that is: a data structure where strings are represented in compact form and each of them is associated to a unique integer identifier in the range [0, n). We show that some statistical properties of k-mer minimizers can be exploited by minimal perfect hashing to substantially improve the space/time trade-off of the dictionary compared to the best-known solutions.

AvailabilityThe C++ implementation of the dictionary is available at https://github.com/jermp/sshash.

Contactgiulio.ermanno.pibiri@isti.cnr.it


title: Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

abstract: Clusters of genetically similar infections suggest rapid transmission and may indicate priorities for public health action or reveal underlying epidemiological processes. However, clusters often require user-defined thresholds and are sensitive to non-epidemiological factors, such as non-random sampling. Consequently the ideal threshold for public health applications varies substantially across settings. Here, we show a method which selects optimal thresholds for phylogenetic (subset tree) clustering based on population. We evaluated this method on HIV-1 pol datasets (n = 14,221 sequences) from four sites in USA (Tennessee, Seattle), Canada (Northern Alberta) and China (Beijing). Clusters were defined by tips descending from an ancestral node (with a minimum bootstrap support of 95%) through a series of branches, each with a length below a given threshold. Next, we used pplacer to graft new cases to the fixed tree by maximum likelihood. We evaluated the effect of varying branch-length thresholds on cluster growth as a count outcome by fitting two Poisson regression models: a null model that predicts growth from cluster size, and an alternative model that includes mean collection date as an additional covariate. The alternative model was favoured by AIC across most thresholds, with optimal (greatest difference in AIC) thresholds ranging 0.007-0.013 across sites. The range of optimal thresholds was more variable when re-sampling 80% of the data by location (IQR 0.008 - 0.016, n = 100 replicates). Our results use prospective phylogenetic cluster growth and suggest that there is more variation in effective thresholds for public health than those typically used in clustering studies.


title: Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models

abstract: Whole genome sequencing (WGS) of circulating tumour DNA (ctDNA) is now a clinically important biomarker for predicting therapy response, disease burden and disease progression. However, the translation of ctDNA monitoring into vital pre-clinical PDX models has not been possible owing to low circulating blood volumes in small rodents. Here, we describe the longitudinal detection and monitoring of ctDNA from minute volumes of blood in PDX mice. We developed a xenograft Tumour Fraction (xTF) metric using shallow WGS of dried blood spots (DBS), and demonstrate its application to quantify disease burden, monitor treatment response and predict disease outcome in a pre-clinical study of PDX mice. Further, we show how our DBS-based ctDNA assay can be used to detect gene-specific copy number changes and examine the copy number landscape over time. Use of sequential DBS ctDNA assays will transform future trial designs in both mice and patients.

category: cancer biology


title: Differential remodelling in small and large murine airways revealed by novel whole lung airway analysis.

abstract: Airway remodelling occurs in chronic asthma leading to increased airway smooth muscle (ASM) mass and extra-cellular matrix (ECM) deposition. Whilst extensively studied in murine airways; studies report only selected larger airways at one time point meaning the spatial distribution and resolution of remodelling are poorly understood. Here we use a new method allowing comprehensive assessment of the spatial and temporal changes in ASM, ECM and epithelium in large numbers of murine airways after allergen challenge. Using image processing to analyse 20-50 airways from a whole lung section revealed increases in ASM and ECM after allergen challenge were greater in small and large rather than intermediate airways. ASM predominantly accumulated adjacent to the basement membrane whereas ECM was distributed across the airway wall. Epithelial hyperplasia was most marked in small and intermediate airways. Post challenge, ASM changes resolved over seven days whereas ECM and epithelial changes persisted. The new method suggests large and small airways remodel differently and the long-term consequences of airway inflammation may depend more on ECM and epithelial changes than ASM. The method reduces the number of animals needed, reveals important spatial differences in remodelling and could set new analysis standards for murine asthma models.

category: physiology


title: Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction

abstract: Pathobionts employ unique metabolic adaptation mechanisms to maximize their growth in disease conditions. Adherent-invasive Escherichia coli (AIEC), a pathobiont enriched in the gut mucosa of patients with inflammatory bowel disease (IBD), utilizes diet-derived L-serine to adapt to the inflamed gut. Therefore, the restriction of dietary L-serine starves AIEC and limits its fitness advantage. Here, we find that AIEC can overcome this nutrient limitation by switching the nutrient source from the diet to the host cells in the presence of mucolytic bacteria. During diet-derived L-serine restriction, the mucolytic symbiont Akkermansia muciniphila promotes the encroachment of AIEC to the epithelial niche by degrading the mucus layer. In the epithelial niche, AIEC acquires L-serine from the colonic epithelium and thus proliferates. Our work suggests that the indirect metabolic network between pathobionts and commensal symbionts enables pathobionts to overcome nutritional restriction and thrive in the gut.


title: The secreted metabolome of HeLa cells under effect of Crotamine, a cell-penetrating peptide from a rattlesnake using NMR-based metabolomics analyses

abstract: Sequestering and reprogramming of cellular metabolism represents one of the principal hallmarks several cells. Antimicrobial peptides have been shown to exhibit selective anticancer activities. In this study, the secreted metabolome of HeLa cells under action of the antimicrobial peptide Crotamine was evaluated. Although, Crotamine has been shown to be selective for highly proliferating cells and is able to extend the in vivo lifespan. The present study using a cell line of cervical cancer, HeLa cells provide insights into how Crotamine acts in cell metabolism. NMR spectroscopy was used to identify and quantify relative metabolite levels, which are associated with Crotamine uptake. Statistical analysis reveals that Crotamine dramatically affects metabolites related to glycolysis, metabolism and biosynthesis of amino acids and pyruvate metabolism. The developed machine learning model is found to be robust by ROC curve analysis, suggesting that the metabolic state of HeLa cells treated with Crotamine is different from the control samples. To account for metabolite levels, it is suggested that Crotamine would have to act on glycolysis, which, in turn, affects several other metabolic pathways, such as, glutathione metabolism, TCA cycle and pyruvate metabolism. The observed metabolic changes shed light into the mode of Crotamine function.

category: cell biology


title: Dietary butyrate treatment enhances healthy metabolites by longitudinal untargeted metabolomic analysis in amyotrophic lateral sclerosis mice

abstract:
Microbial metabolites affect the neuron system and muscle cell functions. Amyotrophic Lateral Sclerosis (ALS) is a multifactorial neuromuscular disease. Our previous study has demonstrated elevated intestinal inflammation and dysfunctional microbiome in ALS patients and an ALS mouse model (human-SOD1G93A transgenic mice). However, the metabolites in ALS progression are unknown. Using an unbiased global metabolomic measurement and targeted measurement, we investigated the longitudinal changes of fecal metabolites in the SOD1G93A mice over the course of 13 weeks. We compared the changes of metabolites and inflammatory response in age-matched WT and SOD1G93A mice treated with bacterial product butyrate. We found changes in carbohydrate levels, amino acid metabolism, and formation of gamma-glutamyl amino acids. Shifts in several microbially-contributed catabolites of aromatic amino acids agree with butyrate-induced changes in composition of gut microbiome. Declines in gamma-glutamyl amino acids in feces may stem from differential expression of GGT in response to butyrate administration. Due to signaling nature of amino acid-derived metabolites, these changes indicate changes in inflammation (e.g. histamine) and contribute to differences in systemic levels of neurotransmitters (e.g. GABA, glutamate). Butyrate treatment was able to restore some of the healthy metabolites in ALS mice. Moreover, microglia in the spinal cord were measured by the IBA1 staining. Butyrate treatment significantly suppressed the IBA1 level in the SOD1G93A mice. The serum IL-17 and LPS were significantly reduced in the butyrate treated SOD1G93A mice. We have demonstrated an inter-organ communications link among metabolites, inflammation, and ALS progression, suggesting the potential to use metabolites as ALS hallmarks and for treatment.

Graphic Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/476456v1_ufig1.gif" ALT="Figure 1">
View larger version (31K):
org.highwire.dtl.DTLVardef@16d3e4dorg.highwire.dtl.DTLVardef@1155c05org.highwire.dtl.DTLVardef@14c6155org.highwire.dtl.DTLVardef@18a30d6_HPS_FORMAT_FIGEXP  M_FIG We compared the changes of metabolites and inflammatory response in age-matched WT and SOD1G93A mice treated with bacterial product butyrate. Butyrate treatment was able to restore some of the healthy metabolites in ALS mice. Due to signaling nature of amino acid-derived metabolites, these changes indicate changes in inflammation and contribute to differences in systemic levels of neurotransmitters (e.g. GABA, glutamate). Moreover, butyrate treatment significantly suppressed the microglia IBA1 level and aggregated SOD1G93A in the SOD1G93A mice. The inflammatory cytokine, e.g serum IL-17, was significantly reduced in the butyrate treated SOD1G93A mice. We have demonstrated an inter-organ communications link among metabolites, inflammation, and ALS progression, suggesting the potential to use metabolites as ALS hallmarks and for treatment.

C_FIG


title: Occurrence Of Avian Reovirus And Picobirnavirus In Wild Birds In An Environmental Protection Area In The Amazon Biome, Para, Brazil

abstract: Wild birds have great prominence on transmission of diseases to humans, mainly due to their ease of access to human population, raising concerns about the potential impact of that proximity in context of the One Health. Studies referring to circulation of avian reovirus (ARV) and picobirnavirus (PBV) in wild birds are limited, in addition to reinforcing the development of researches that describe the prevalence, characterize the variants and evaluate the potential impact of these infections on the wild ecosystem and public health. The present study reports the occurrence of ARV and PBV in wild birds collected from an environmental protection area in the Amazon biome. RT-PCR analysis showed ARV infection prevalence in 0.6% (1/155) and PBV infection in 1.29% (2/155) on the samples. ARV strain isolated in this study demonstrated more phylogenetically related to other ARVs previously circulating in poultry in the same region. The two PBV strains obtained belong to genogroup I, and showed phylogenetically related to other PBV isolated from different animal species in different geographic regions. This study is a pioneer in the detection of ARV in wild birds in Brazil and presents a report of the first occurrence of PBV in wild birds of Guira guira specie. Additional studies in wild birds are required to increase the epidemiology, origin, evolution and emergence of new viruses that may provoke problems in the context of One Health.


title: Rapid and repeatable genome evolution across three hybrid ant populations

abstract: Hybridization is frequent in the wild but it is unclear whether admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation in less than 50 generations in three hybrid Formica aquilonia x F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened repeatedly in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.

category: evolutionary biology


title: Strategies of invertebrate osmoregulation: an evolutionary blueprint for transmuting into fresh water from the sea

abstract: Early marine invertebrates like the Branchiopoda began their sojourn into dilute media some 500 million years ago in the Middle Cambrian. Others like the Mollusca, Annelida and many crustacean taxa have followed, accompanying major marine transgressions and regressions, shifting landmasses, orogenies and glaciations. In adapting to these events and new habitats such invertebrates acquired novel physiological abilities that attenuate the ion loss and water gain that constitute severe challenges to life in dilute media. Among these taxon-specific adaptations, selected from the subcellular to organismal levels of organization, are reduced body permeability and surface (S) to volume (V) ratios, lowered osmotic gradients, increased surface areas of interface epithelia, relocation of membrane proteins in ion-transporting cells and augmented transport enzyme abundance, activity and affinity. We examine adaptations in taxa that have penetrated into fresh water, revealing diversified modifications, a consequence of distinct body plans, morpho-physiological resources and occupation routes. Contingent on life history and reproductive strategy, numerous patterns of osmotic regulation have emerged, including intracellular isosmotic regulation in weak hyper-regulators and well-developed anisosmotic extracellular regulation in strong hyper-regulators, likely reflecting inertial adaptations to early life in an estuarine environment. Our analyses show that across sixty-four freshwater invertebrate species from six phyla/classes, hemolymph osmolalities decrease logarithmically with increasing S: V ratios. The arthropods have the highest osmolalities, from 300 to 650 mOsmoles/kg H2O in the Decapoda with 220 to 320 mOsmoles/kg H2O in the Insecta; osmolalities in the Annelida range from 150 to 200 mOsmoles/kg H2O, the Mollusca showing the lowest osmolalities at 40 to 120 mOsmoles/kg H2O. Overall, osmolalities reach a cut-off at {approx}200 mOsmoles/kg H2O, independently of increasing S: V ratio. The ability of species with small S: V ratios to maintain large osmotic gradients is mirrored in their putatively higher Na+/K+-ATPase activities that drive ion uptake processes. Selection pressures on these morpho-physiological characteristics have led to differential osmoregulatory abilities, rendering possible the conquest of fresh water while retaining some tolerance of the ancestral medium.


title: Topological supramolecular network enabled highly conductive and stretchable organic bioelectronics

abstract: Intrinsically stretchable bioelectronic devices based on soft and conducting organic materials have been regarded as the ideal interface for seamless and biocompatible integration with the human body. However, the grand challenge remains for the conducting polymer to possess both high mechanical ductility and good electrical conduction at cellular level feature sizes. This longstanding material limitation in organic bioelectronics has impeded the full exploitation of its unique benefits. Here, we introduce a new molecular engineering strategy based on rationally designed topological supramolecular networks, which allows effective decoupling of competing effects from multiple molecular building blocks to meet complex requirements. We achieve two orders of magnitude improvement in the conductivity under 100% strain in physiological environment, along with the capability for direct photopatterning down to 2 m. These unprecedented capabilities allow us to realize previously inaccessible bioelectronic applications including high-resolution monitoring of  soft and malleable creatures, e.g., octopus, and localized neuromodulation down to single nucleus precision for controlling organ-specific activities through delicate tissues, e.g., brainstem.


title: Wireless closed-loop smart bandage for chronic wound management and accelerated tissue regeneration

abstract: Chronic non-healing wounds represent a major source of morbidity for patients and a significant economic burden. Current wound care treatments are generally passive and are unable to adapt to changes in the wound environment in real time. By integrating multimodal sensors and adding stimulators in a bandage, real-time physiological monitoring is possible and provides an opportunity for active intervention into the complex wound environment. Here, we develop a battery-free flexible bioelectronic system consisting of wirelessly powered, closed-loop sensing and stimulation circuits with tissue-interfacing tough conducting hydrogel electrodes for robust signal transduction, on-demand adhesion, and detachment. Using multiple pre-clinical models, we demonstrate the capability of our wound care system to continuously monitor skin impedance and temperature, to trigger directional electrical stimulation. The accelerated wound closure was confirmed to be due to the activation of pro-regenerative genes linked to accelerated wound closure, increased neovascularization, and enhanced dermal recovery.


title: Yeast biopanning for detecting antibody binding to site-specific phosphorylations in tau

abstract: The detection of phosphorylated tau (p-tau) levels in clinical samples is of extreme importance for the detection of Alzheimers Disease (AD) as well as other neurodegenerative diseases. Recent reports show that detecting low levels of p-tau in plasma can be used as a reliable biomarker for detecting AD prior to the onset of memory loss. The ability to detect such low levels of p-tau is dependent on antibodies specific to the post translationally modified protein. However, the need for reliable phospho-site specific antibodies persists due to a lack of approaches for identifying monoclonal antibodies and characterizing non-specific binding. Here, we report a novel approach using the principles of yeast biopanning to create a robust platform that uses synthetic peptides as target antigens. Using peptides as antigens enables screening antibodies against defined post-translational modification sites, particularly for targeting intrinsically disordered proteins such as the human tau protein. To readily assess yeast binding and distinguish non-specific binding, we developed bi-directional expression vectors that allow antibody fragment surface display and intracellular fluorescent protein expression. We show that our platform can specifically and robustly detect a specific site within the p-tau target peptide when compared against non-phosphorylated controls. By improving biopanning parameters, we enabled phospho-specific capture of yeast cells displaying single-chain variable region fragments (scFvs) against p-tau with a wide range of affinities (KD = 0.2 to 60 nM). These results demonstrate that yeast biopanning can robustly capture yeast cells based on phospho-site specific antibody binding, opening doors for facile identification of high-quality monoclonal antibodies.


title: Data-driven extraction of human kinase-substrate relationships from omics datasets

abstract: Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as celll division and differentiation. To date, a large portion of identified phosphosites are not known to be targeted by any kinase. At the same time around 30% of kinases have no known target. This knowledge gap stresses the need to make large scale, data-driven computational predictions. In this paper, we have created a machine learning-based model to derive a probabilistic kinase-substrate network from omics datasets. We show that our methodology displays improved performance compared to other state of the art kinase-substrate predictions, and provides predictions for more kinases than most of them. Importantly, it better captures new experimentally-identified kinase-substrate relationships. It can therefore allow the improved prioritisation of kinase-substrate pairs for illuminating the dark human cell signalling space.


title: 3D MRI atlases of congenital aortic arch anomalies and normal fetal heart: application to automated multi-label segmentation

abstract:
Background3D image-domain reconstruction of black blood contrast T2w SSTSE fetal MRI datasets using slice-to-volume registration methods showed to provide high-resolution 3D images of the heart with superior visualisation of fetal aortic arch anomalies [1]. However, there is a lack of formalisation of the MRI appearance of fetal cardiovascular anatomy and standardisation of vessel segmentation protocols.

MethodsIn this work, we present the first set of 3D fetal MRI atlases defining normal and abnormal fetal aortic arch anatomy created from 3D reconstructed images from 87 subjects scanned between 29-34 weeks of gestation with postnatally confirmed outcomes. We also implement and evaluate atlas-guided registration and deep learning (UNETR) methods for automated 3D multi-label fetal heart vessel segmentation.

ResultsWe created four atlases representing the average anatomy of the normal fetal heart, coarctation of the aorta, right aortic arch and suspected double aortic arch. Inspection of atlases confirmed the expected pronounced differences in the anatomy of the aortic arch. The results of the multi-label heart vessel UNETR segmentation showed 100% per-vessel detection rate for both normal and abnormal aortic arch anatomy.

ConclusionsThis work introduces the first set of 3D black blood T2w MRI atlases of the normal and abnormal fetal cardiovascular anatomy along with detailed segmentation of the major cardiovascular structures. We also demonstrated the feasibility of using deep learning for multi-label vessel segmentation.


title: Spatially resolved single-cell deconvolution of bulk RNA-seq using Bulk2Space

abstract: Uncovering the tissue molecular architecture at single-cell resolution could help better understand the biological and pathological processes in organisms. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing molecular heterogeneity and spatial patterns of single cells. Herein, we introduce Bulk2Space (https://github.com/ZJUFanLab/bulk2space), a deep learning framework-based spatial deconvolution algorithm that can simultaneously reveal the spatial and cellular heterogeneity of bulk RNA-seq data. The use of bulk transcriptomics to validate Bulk2Space revealed, in particular, the spatial variance of immune cells in different tumor regions, the molecular and spatial heterogeneity of tissues during inflammation-induced tumorigenesis, and spatial patterns of novel genes in different cell types. Moreover, Bulk2Space further annotated cell types that cannot be identified by original methods when it was used to spatially deconvolve the bulk data derived from our in-house developed sequencing approach Spatial-seq. Bulk2Space is distributed via an open-source Python software package.


title: Hidden multiplicity in the analysis of variance (ANOVA): multiple contrast tests as an alternative

abstract: In bio-medical studies, the p-values of the F-tests in ANOVA are usually interpreted independently as measures of the significance of the associated factors. This hidden multiplicity effect increases the false positive rate. Therefore, Cramer et al. (2016) proposed the Bonferroni adjustment of the p-values to control for familywise error rate for the experiment. Here, instead of using F-tests, it is alternatively suggested to use multiple contrast tests vs. total mean and to perform multiplicity adjustment by object merging in the interplay between the R-packages emmeans and multcomp. This new approach, denotes as multipleANOM, allows not only to interpret global factor effects but also local effects between factor levels as adjusted p-values or simultaneous confidence intervals for selected effect measures in generalized linear models. R-code is provided by means of selected data examples.


title: A new method for the sampling and preservation of placental specimens in low-resource settings for histology and analysis of nucleic acids

abstract: Collection, preservation, and shipment of histological specimens in low-resource settings is challenging. We present a novel method that achieved excellent preservation of placental specimens from rural Mali by using formalin fixation, ethanol dehydration, and long-term storage in a solar-powered freezer. Sample preservation success was 92%, permitting evaluation of current and past malaria infection, anemia, placental maturity, and inflammation. Using RNAscope(R) hybridization we were able to visualize cell-specific gene expression patterns in the formalin-fixed paraffin-embedded (FFPE) specimens. Additionally, our method entailed mirrored sampling from the two cut faces of a cotyledon, one for the FFPE workflows and the other for storage in RNAlater and RNA-seq.

category: pathology


title: A new method for the sampling and preservation of placental specimens in low-resource settings for the identification of P. falciparum and analysis of nucleic acids


title: Cell morphological profiling enables high-throughput screening for PROteolysis TArgeting Chimera (PROTAC) phenotypic signature

abstract:
PROTACs (PROteolysis TArgeting Chimeras) use the ubiquitin-proteasome system to degrade a protein of interest for therapeutic benefit. Advances in targeted protein degradation technology have been remarkable with several molecules moving into clinical studies. However, robust routes to assess and better understand the safety risks of PROTACs need to be identified, which is an essential step towards delivering efficacious and safe compounds to patients. In this work, we used Cell Painting, an unbiased high content imaging method, to identify phenotypic signatures of PROTACs. Chemical clustering and model prediction allowed the identification of a mitotoxicity signature that could not be expected by screening the individual PROTAC components. The data highlighted the benefit of unbiased phenotypic methods for identifying toxic signatures and the potential to impact drug design.

HighlightsO_LIMorphological profiling detects various PROTACs phenotypic signatures
C_LIO_LIPhenotypic signatures can be attributed to diverse biological responses
C_LIO_LIChemical clustering from phenotypic signatures separates on drug selection
C_LIO_LITrained in-silico machine learning models to predict PROTACs mitochondrial toxicity
C_LI

category: pharmacology and toxicology


title: Analog of the Hutchinson equation in biophysical neurodynamics: from the Morris-Lecar model to a delay differential equation

abstract: Starting with the classical biophysical Morris-Lecar model of neuronal excitability, we introduce a functional analog of the Hutchinson equation initially obtained for population dynamics with delayed negative feedback. It is shown that the resulting equation with a fixed time delay qualitatively reproduces the dynamics of the original model upon direct current stimulation, preserving both the initial type of neuronal excitability and biophysically realistic spike shape within a wide range of the delay values. If the delay becomes very small (2 ms or less), the simplified delay-based model exhibits a distinct transition from the 1st to the 2nd excitability type.


title: Multiplexed imaging mass cytometry reveals distincttumor-immune microenvironments linked to immunotherapyresponses in melanoma

abstract: Single-cell technologies have enabled extensive analysis of complex immune composition, phenotype and interactions within tumor, which is crucial in understanding the mechanisms behind cancer progression and treatment resistance. Unfortunately, the knowledge on cell phenotypes and their spatial interactions at present has only limited utilization in guiding pathological stratification on patients based on their immune microenvironments for better clinical decisions. Here we used imaging mass cytometry (IMC) to simultaneously quantify 35 proteins in a spatially resolved manner on tumor tissues from melanoma patients receiving anti-programmed cell death-1 (anti-PD-1) therapy. Unbiased single-cell analysis revealed highly dynamic tumor-immune microenvironments that are characterized with variable tumor and immune cell phenotypes and their organizations across and within melanomas, and identified distinct archetypes of melanoma microenvironments that are associated with benefit from anti-PD-1 therapy based on high-dimensional multicellular features. Our results demonstrate the utility of multiplex proteomic imaging technologies in studying complex molecular events in a spatially resolved manner for the development of new strategies for patient stratification and treatment outcome prediction.


title: Dual Specificity Phosphatase 7 Drives the Formation of Cardiac Mesoderm in Mouse Embryonic Stem Cells

abstract: Dual specificity phosphatase 7 (DUSP7) is a protein belonging to a broad group of phosphatases that 14 can dephosphorylate phosphoserine/phosphothreonine as well as phosphotyrosine residues within the 15 same substrate. DUSP7 has been linked to the negative regulation of mitogen activated protein kinases 16 (MAPK), and in particular to the regulation of extracellular signal-regulated kinases 1 and 2 (ERK1/2). 17 MAPKs play an important role in embryonic development, where their duration, magnitude, and 18 spatiotemporal activity must be strictly controlled by other proteins, among others by DUSPs. In this 19 study, we focused on the effect of DUSP7 depletion on the in vitro differentiation of mouse embryonic 20 stem (ES) cells. We showed that even though DUSP7 knock-out ES cells do retain some of their basic 21 characteristics, when it comes to differentiation, they preferentially differentiate towards neural cells, 22 while the formation of early cardiac mesoderm is repressed. Therefore, our data indicate that DUSP7 23 is necessary for the correct formation of neuroectoderm and cardiac mesoderm during the in vitro 24 differentiation of ES cells.


title: Entamoeba histolytica EHD1 is involved in mitosome-endosome contact

abstract: Inter-organellar crosstalk is often mediated by membrane contact sites (MCSs), which are zones where participating membranes come within a proximity of 30 nm. MCSs have been found in organelles including the endoplasmic reticulum, Golgi bodies, endosomes, and mitochondria. Despite its seeming ubiquity, reports of MCS involving mitochondrion-related organelles (MROs) present in a few anaerobic parasitic protozoa remain lacking. Entamoeba histolytica, the etiological agent of amoebiasis, possesses an MRO called mitosome. We previously discovered several Entamoeba-specific transmembrane mitosomal proteins (ETMPs) from in silico and cell biological analyses. One of them, ETMP1 (EHI_175060), was predicted to have one transmembrane domain and two coiled-coil regions, and was demonstrated to be mitosome membrane-integrated based on carbonate fractionation and immunoelectron microscopy (IEM) data. Immunoprecipitation analysis detected a candidate interacting partner, EH-domain containing protein (EHD1, EHI_105270). We expressed HA-tagged EHD1 in E. histolytica and subsequent immunofluorescence and IEM data indicated an unprecedented MCS between the mitosome and the endosome. Live imaging of GFP-EHD1 expressing strain demonstrated that EHD1 is involved in early endosome formation, and is observed in MCS between endosomes of various sizes. In vitro assay using recombinant His-EHD1 demonstrated ATPase activity. MCSs are involved in lipid transfer, ion homeostasis, and organelle dynamics. The serendipitous discovery of the ETMP1 interacting partner EHD1, led to the observation of the mitosome-endosome contact site in E. histolytica. It opened a new view of how the relic mitochondria of Entamoeba may likewise be involved in organelle crosstalk, a conserved feature of mitochondria and other organelles in general.


title: On the Edge: Identifying priority areas for conservation of Fishing Cat, a threatened wetland felid, amidst rapidly altering freshwater landscapes

abstract:
O_LIFreshwater ecosystems have been most severely impacted in the Anthropocene with 27% of its species threatened with extinction. Fishing Cat is a globally threatened South and South-east Asian wetland felid that is also a highly rated Evolutionarily Distinct and Globally Endangered (EDGE) species, i.e., it is a global priority for conservation and research. Being an understudied species, knowledge gaps exist on its basic ecology, such as distribution and niche.
C_LIO_LITo address this, ensemble species distribution modeling (ESDM) was used to clarify doubts on its potential distribution and niche. To provide a relatable current context, loss of suitable habitat to urbanization (2010-2020) was estimated by analyzing range-wide survey data with environmental and anthropogenic variables (night-time lights and land surface temperature as proxies for urbanization).
C_LIO_LIWetlands (18.36%) and elevation (17.15%) are the most important variables determining the ecological niche of Fishing Cat. It was predicted to be mainly restricted to low-elevation (<111 m) wetlands in river basins of South and South-east Asia. An estimated 23.74% suitable habitat was lost to urbanization.
C_LIO_LIIncrementally building on the ESDM outputs, high priority movement corridors and landscape conservation units were identified.
C_LIO_LISouth Asia holds the core of the global Fishing Cat population with two very important regions - Ganges Brahmaputra Basin and Indus Basin - sharing transboundary areas with highly suitable habitat and many priority conservation units. The former is strategic to maintaining connectivity between South and South-east Asian Fishing Cat populations while isolation effects in the latter need investigation. Coastal wetlands of South-east Asia, though severely impacted, are crucial for the felids persistence.
C_LIO_LIMore than 90% of Fishing Cats potential range lies outside the protected area network. Here, the felid can be adopted as a flagship species to conserve rapidly degrading low- elevation wetlands within a socio-ecological framework by involving multiple stakeholders.
C_LI

category: ecology


title: Engineering Rotating Apical-Out Airway Organoid for Assessing Respiratory Cilia Motility

abstract: Motile cilia project from the airway apical surface and directly interface with inhaled external environment. Due to cilias nanoscale dimension and high beating frequency, quantitative assessment of their motility remains a sophisticated task. Here we described a robust approach for reproducible engineering of apical-out airway organoid (AOAO) of defined size. Propelled by exterior-facing cilia beating, the mature AOAO exhibited stable rotational motion when surrounded by Matrigel. We developed a computational framework leveraging computer vision algorithms to quantify AOAO rotation and validated its correlation with direct measurement of cilia motility. We further established the feasibility of using AOAO rotation to recapitulate and measure defective cilia motility caused by chemotherapy-induced toxicity and by CCDC39 mutations in cells from primary ciliary dyskinesia patient. We expect our rotating AOAO model and the associated computational pipeline to offer a generalizable framework to expediate modeling of and therapeutic development for genetic and environmental ciliopathies.


title: MERIT: controlling Monte-Carlo error rate in large-scale Monte-Carlo hypothesis testing

abstract: The use of Monte-Carlo (MC) p-values when testing the significance of a large number of hypotheses is now commonplace. In large-scale hypothesis testing, we will typically encounter at least some p-values near the threshold of significance, which require a larger number of MC replicates than p-values that are far from the threshold. As a result, the list of detections can vary when different MC replicates are used, resulting in lack of reproducibility. The method of Gandy and Hahn (GH) (2014; 2016; 2017) is the only method that has directly addressed this problem, defining a Monte-Carlo error rate (MCER) to be the probability that any decisions on accepting or rejecting a hypothesis based on MC p-values are different from decisions based on ideal p-values, and then making decisions that control the MCER. Unfortunately, GH is frequently very conservative, often making no rejections at all and leaving a large number of hypotheses "undecided". In this article, we propose MERIT, a method for large-scale MC hypothesis testing that also controls the MCER but is more statistically efficient than the GH method. Through extensive simulation studies, we demonstrated that MERIT controlled the MCER and substantially improved the sensitivity and specificity of detections compared to GH. We also illustrated our method by an analysis of gene expression data from a prostate cancer study.


title: scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data

abstract:
SummaryThe number of cells measured in single-cell transcriptomic data has grown fast in recent years. For such large-scale data, subsampling is a powerful and often necessary tool for exploratory data analysis. However, the easiest random subsampling is not ideal from the perspective of preserving rare cell types. Therefore, diversity-preserving subsampling is required for fast exploration of cell types in a large-scale dataset. Here we propose scSampler, an algorithm for fast diversity-preserving subsampling of single-cell transcriptomic data. Using simulated and real data, we show that scSampler consistently outperforms existing subsam-pling methods in terms of both the computational time and the Hausdorff distance between the full and subsampled datasets.

AvailabilityscSampler is implemented in Python and is published under the MIT source license. It can be installed by pip install scsampler and used with the Scanpy pipline. The code is available on GitHub: https://github.com/SONGDONGYUAN1994/scsampler.

Contactlinwang@gwu.edu; jli@stat.ucla.edu


title: NIMAA: an R/CRAN package to accomplish NomInal data Mining AnAlysis

abstract:
SummaryNominal data is data that has been "labeled" and can be designated into a number of non-overlapping unordered groups. The analysis of this type of data is often trivial because it is not feasible to conduct extensive numerical methods on this type of data. Graphs or networks, on the other hand, are comprised of sets of nodes and edges that can also be considered as nominal variables. By integrating graph theory and data mining approaches, we offer the R package NIMAA to define a nominal data-mining pipeline to explore more information. Using nominal variables in a dataset, NIMAA provides functions for constructing weighted and unweighted bipartite graphs, analysing the similarity of labels in nominal variables, clustering labels or categories to super-labels, validating clustering results, predicting bipartite edges by missing weight imputation, and providing a variety of visualization tools. Here, we also indicated the application of nominal data mining in a biological dataset with well-riched nominal variables.

AvailabilityNIMAAs official release and the beta update are available on CRAN and Github, respectively. URLs: https://CRAN.R-project.org/package=NIMAA and https://github.com/jafarilab/NIMAA

Contactmohieddin.jafari@helsinki.fi; jing.tang@helisnki.fi

ContributionsMJ conceived the study and developed the models, MJ and CC adopted and implemented the methods, MM improved the methods, JT provided the funding, MJ, CC, MM and JT wrote the paper.


title: Single-sequence protein structure prediction using supervised transformer protein language models

abstract: It remains challenging for single-sequence protein structure prediction with AlphaFold2 and other deep learning methods. In this work, we introduce trRosettaX-Single, a novel algorithm for singlesequence protein structure prediction. It is built on sequence embedding from s-ESM-1b, a supervised transformer protein language model optimized from the pre-trained model ESM-1b. The sequence embedding is fed into a multi-scale network with knowledge distillation to predict inter-residue 2D geometry, including distance and orientations. The predicted 2D geometry is then used to reconstruct 3D structure models based on energy minimization. Benchmark tests show that trRosettaX-Single outperforms AlphaFold2 and RoseTTAFold on natural proteins. For instance, with single-sequence input, trRosettaX-Single generates structure models with an average TM-score ~0.5 on 77 CASP14 domains, significantly higher than AlphaFold2 (0.35) and RoseTTAFold (0.34). Further test on 101 human-designed proteins indicates that trRosettaX-Single works very well, with accuracy (average TM-score 0.77) approaching AlphaFold2 and higher than RoseTTAFold, but using much less computing resource. On 2000 designed proteins from network hallucination, trRosettaX-Single generates structure models highly consistent to the hallucinated ones. These data suggest that trRosettaX-Single may find immediate applications in de novo protein design and related studies. trRosettaX-Single is available through the trRosetta server at: http://yanglab.nankai.edu.cn/trRosetta/.


title: MutSigCVsyn: Identification of Thirty Synonymous Cancer Drivers

abstract: Synonymous mutations, which change only the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations can act as cancer drivers has been explored in several recent studies. However, none of these studies control for all three levels (patient, histology, and gene) of mutational heterogeneity that are known to affect the accurate identification of non-synonymous cancer drivers. Here, we create an algorithm, MutSigCVsyn, an adaptation of MutSigCV, to identify synonymous cancer drivers based on a novel non-coding background model that takes into account the mutational heterogeneity across these levels. Examining 2,572 PCAWG cancer whole-genome sequences, MutSigCVsyn identifies 30 novel synonymous drivers that include mutations in promising candidates like BCL-2. By bringing the best practices in non-synonymous driver identification to the analysis of synonymous drivers, these are promising candidates for future experimental study.


title: Differential Impact of Doxorubicin Dose on Cell Death and Autophagy Pathways during Acute Cardiotoxicity.

abstract: Doxorubicin (DOX) is an effective anthracycline used in chemotherapeutic regimens for a variety of haematological and solid tumors. However, its utility remains limited by its well-described, but poorly understood cardiotoxicity. Despite numerous studies describing various forms of regulated cell death and their involvement in DOX-mediated cardiotoxicity, the predominate form of cell death remains unclear. Part of this inconsistency lies in a lack of standardization of in vivo and in vitro model design. To this end, the objective of this study was to characterize acute low- and high-dose DOX exposure on cardiac structure and function in C57BL/6N mice, and evaluate regulated cell death pathways and autophagy both in vivo and in cardiomyocyte culture models. Acute low-dose DOX had little impact on cardiac structure or function; however, acute high-dose DOX elicited substantial cardiac necrosis resulting in diminished cardiac mass and volume, with a corresponding reduced cardiac output, and without impacting ejection fraction or fibrosis. Low-dose DOX consistently activated caspase-signaling with evidence of mitochondrial permeability transition. However, acute high-dose DOX had only modest impact on common necrotic signaling pathways, but instead led to an inhibition in autophagic flux. Intriguingly, when autophagy was inhibited in cultured cardiomyoblasts, DOX-induced necrosis was enhanced. Collectively, these observations implicate inhibition of autophagy flux as an important component of the acute necrotic response to DOX, but also suggest that acute high-dose DOX exposure does not recapitulate the disease phenotype observed in human cardiotoxicity.


title: Second Climate Survey of Biomedical PhD Students in the Time of Covid

abstract: In July 2021, sixteen months into the Covid-19 pandemic, the institutional climate for PhD training in the School of Medicine was assessed for a second time. This survey of graduate students occurred 1 year after initial surveys of graduate students and training faculty in July 2020. The 2021 survey was completed by 99 PhD students in 11 PhD-granting programs. To allow comparisons between years, most of the 2021 questions were repeated with only minor edits. A few items were added to assess impacts of school-wide town hall meetings, a new PhD career club program, and enlarged mental health services. Several themes emerged. Students remain extremely concerned about the pandemics impact upon their training and long-term career prospects. They worry specifically about pandemic related reductions in research productivity and networking opportunities. Many students successfully adapted to laboratory research under pandemic restrictions but suffer from the continuing lack of social interaction even after in-person work hours increased. Symptoms of anxiety and/or depression persist amongst 46% of the students, as compared to 51% in 2020. Nearly 80% of students continue to report strong satisfaction with mentoring relationships with their dissertation advisors, but to lesser extents with programs (66%), departments or centers (71%), the School of Medicine (32%) and the University (49%). Students (26%) express interest in the Ombuds office that was announced in late 2021. Some students wrote that the medical school could do a better job in embracing diversity and inclusion and in mentor training, and many stated that town hall meetings do not serve them well. Coping mechanisms shared by some students demonstrate impressive resilience. These results present a mixed picture. While aspects of biomedical PhD training have begun to recover as the pandemic continues, long-term consequences of the disruption raise challenges that must be addressed by efforts to restore and improve the learning environment required for 21st century research education.

category: scientific communication and education


title: Differential UBE2H-CTLH E2-E3 ubiquitylation modules regulate erythroid maturation

abstract: The development of haematopoietic stem cells into mature erythrocytes - erythropoiesis - is a controlled process characterized by cellular reorganisation and drastic reshaping of the proteome landscape. Failure of ordered erythropoiesis is associated with anaemias and haematological malignancies. Although the ubiquitin (UB) system is a known crucial post-translational regulator in erythropoiesis, how the erythrocyte is reshaped by the UB system is poorly understood. By measuring the proteomic landscape of in vitro human erythropoiesis models, we found dynamic differential expression of subunits of the CTLH E3 ubiquitin ligase complex that formed distinct maturation stage-dependent assemblies of structurally homologous RANBP9-and RANBP10-CTLH complexes. Moreover, protein abundance of CTLHs cognate E2-conjugating enzyme UBE2H increased during terminal differentiation, which depended on catalytically active CTLH E3 complexes. CRISPR-Cas9 mediated inactivation of all CTLH E3 assemblies by targeting the catalytic subunit MAEA, or UBE2H, triggered spontaneous and accelerated maturation of erythroid progenitor cells including increased heme and haemoglobin synthesis. Thus, the orderly progression of human erythropoiesis is controlled by the assembly of distinct UBE2H-CTLH modules functioning at different developmental stages.


title: The Idiopathic Pulmonary Fibrosis-associated single nucleotide polymorphism rs35705950 is transcribed in a MUC5B PromoterAssociated Long Non-Coding RNA(AC061979.1)

abstract: LncRNAs are involved in regulatory processes in the human genome, including gene expression. The rs35705950 SNP, previously associated with IPF, overlaps the recently annotated lncRNA AC061979.1, a 1,712 nucleotide transcript located within the MUC5B promoter at chromosome 11p15.5. To document the expression pattern of the transcript, we processed 3.9 TBases of publicly available RNA-SEQ data across 27 independent studies involving lung airway epithelial cells. Epithelial lung cells showed expression of this putative pancRNA. The findings were independently validated in cell lines and primary cells. The rs35705950 is found within a conserved region (from fish to primates) within the expressed sequence indicating functional importance. These results implicate the rs35705950-containing AC061979.1 pancRNA as a novel component of the MUC5B expression control minicircuitry.


title: Avobenzone, Guaiazulene and Tioxolone identified as potent autophagy inducers in a high-throughput image based screen for autophagy flux

abstract: Autophagy is a conserved intracellular degradation pathway that is essential for maintaining cellular homeostasis. Given its critical role in several disease conditions, recent studies are focussed on identifying drugs/small molecules with autophagy modulating capacity for potential clinical applications. Here, we describe the development and characterisation of a quantitative image-based high content screening platform for autophagy flux measurements using the human melanoma A375 cell line that stably expresses the GFP-LC3-RFP probe. The GFP-LC3 is incorporated into autophagosomes, while RFP serves an internal control. The GFP/RFP fluorescence intensity ratio gives an accurate indication of autophagy induction (low ratio) vs blockage of autophagy flux (high ratio), and was validated with the autophagy inducer Torin1 and inhibitor Bafilomycin A1. This assay was used to screen the Spectrum collection library comprising of 2560 compounds, to identify autophagy modulators. In addition to known autophagy effectors, several novel autophagy inducers and inhibitors were identified in our study. Further three FDA approved drugs that are widely used in skin-care products: Avobenzone, Guaiazulene and Tioxolone, were validated as potent autophagy inducers that function in an mTOR independent manner.


title: Capturing the signalling dynamics of the MAPK-AKT-mTOR pathway in a single targeted phosphoproteomics assay

abstract:
The MAPK-AKT-mTOR protein network integrates extra- and intracellular signals to determine cellular fate, regulating pivotal biological processes such as cell growth and metabolism. Due to this crucial role, pathway dysregulation has been implicated in multiple diseases, such as metabolic disorders and cancer. The MAPK-AKT-mTOR pathway consists of dozens of proteins and signal transduction is primarily driven by protein phosphorylation. Here, we present a targeted phosphoproteomics assay to study the phosphorylation dynamics of the MAPK-AKT-mTOR pathway in detail with high sensitivity and in a high throughput manner. By using a multi-protease approach, we increased the pathway coverage with phosphosites that were previously inaccessible. This novel approach yields the most comprehensive method for the detailed study of mTOR signalling to date (covering 150 phosphopeptides on more than 70 phosphoproteins), which can be applied to in vitro and in vivo systems and has the sensitivity to be compatible with small sample amounts. We demonstrate the feasibility of this assay to monitor the plasticity of MAPK-AKT-mTOR phosphorylation dynamics in response to cellular stimuli with high temporal resolution and amino acid residue specificity. We found highly dynamic phosphorylation events upon treatment with growth factors, revealing the sequential nature of phosphosites in this signalling pathway. Furthermore, starvation of glucose and amino acids showed upregulation of AKT-targets PRAS40T246 and FOXO3T32, highlighting the role of AKT in cellular response to starvation. These findings illustrate the potential of this assay to obtain new biological insight when monitoring dynamics of functional phosphosites.

HighlightsO_LIRobust targeted MS assay to study the phosphorylation dynamics of the MAPK-AKT-mTOR network
C_LIO_LIExtended pathway coverage by application of multiple proteases for protein digestion
C_LIO_LIHighly sensitive, high throughput and readily applicable assay for in vivo and in vitro systems
C_LIO_LIPhosphorylation patterns of MAPK-AKT-mTOR network are highly dynamic and change upon stimulation with growth factors, amino acids and glucose
C_LI

MotivationThe MAPK-AKT-mTOR protein network integrates extra- and intracellular signals to determine cellular fate, regulating pivotal biological processes such as cell growth and metabolism. Due to this crucial role, pathway dysregulation has been implicated in multiple diseases, such as metabolic disorders and cancer. Our understanding of the complex regulation of this intricate signalling network is incomplete and is hampered by the lack of analytical methods to study its phosphorylation dynamics in detail. In this study, we present a targeted phosphoproteomics assay to monitor the phosphorylation events of the MAPK-AKT-mTOR pathway with amino acid residue specificity and in a high throughput manner. We increased the pathway coverage with phosphosites that were previously inaccessible by the use of multiple proteases for protein digestion. This novel approach yields the most comprehensive method for the detailed study of MAPK-AKT-mTOR signalling to date, which can be applied to in vitro and in vivo human samples and has the sensitivity to be compatible with small amounts of starting material.

Graphical abstract

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title: Cell viability assessment associated with a contact of gas bubbles produced by femtosecond laser breakdown in cell culture media

abstract: High intensity near infrared femtosecond laser is a promising tool for three-dimensional processing of biological materials. During the processing of cells and tissues, long lasting gas bubbles randomly appeared around the laser focal point, however physicochemical and mechanical effects of the gas bubbles has not been emphasized. This paper presents characteristic behaviors of the gas gabbles and their contact effects on cell viability. High-speed imaging of the gas bubble formation with various additives in physiological medium confirms that the gas bubble consists of dissolved air, and amphipathic proteins stabilize the bubble surface. This surface protective layer reduces interactions of gas bubbles and cell membranes. Consequently, the gas bubble contact does not cause critical effects on cell viability. On the other hands, burst of gas bubbles stimulated by an impact of femtosecond laser induced cavitation can lead to liquid jet flow that might cause serious mechanical damages on cells. These results provide insights for the parameter of biological tissue processing with intense fs laser pulses.


title: Immunokinetic Model for COVID-19 Patients

abstract:
In this paper, we develop a fractional-order differential model for the dynamics of immune responses to SARS-CoV-2 viral load in one host. In the model, a fractional-order derivative is incorporated to represent the effects of temporal long-run memory on immune cells and tissues for any age group of patients. The population of cytotoxic T-cells (CD8+), natural killer (NK) cells and infected viruses are unknown in this model. Some interesting sufficient conditions that ensure the asymptotic stability of the steady states are obtained.

This model indicates some complex phenomena in COVID-19 such as "immune exhaustion" and "Long COVID". Sensitivity analysis is also investigated for model parameters to determine the parameters that are effective in determining of the long COVID duration, disease control and future treatment as well as vaccine design. The model is verified with clinical and experimental data of 5 patients with COVID-19.


title: RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis

abstract:
An important component of efforts to manage the ongoing COVID19 pandemic is the Rapid Assessment of how natural selection contributes to the emergence and proliferation of potentially dangerous SARS-CoV-2 lineages and CLades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations.

AvailabilityRASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl. Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl.

ContactDr. Sergei L Kosakovsky Pond (spond@temple.edu).

Supplementary informationN/A


title: Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

abstract:
Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing (scDNAseq) data, such as SCI{Phi} and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these methods are not scalable to the extensive genomic breadth of single-cell whole-genome (scWGS) and whole-exome sequencing (scWES) data.

Here we report on a new scalable method, Phylovar, which extends the phylogeny-guided variant calling approach to sequencing datasets containing millions of loci. Through benchmarking on simulated datasets under different settings, we show that, Phylovar outperforms SCI{Phi} in terms of running time while being more accurate than Monovar (which is not phylogeny-aware) in terms of SNV detection. Furthermore, we applied Phylovar to two real biological datasets: an scWES triple-negative breast cancer data consisting of 32 cells and 3375 loci as well as an scWGS data of neuron cells from a normal human brain containing 16 cells and approximately 2.5 million loci. For the cancer data, Phylovar detected somatic SNVs with high or moderate functional impact that were also supported by bulk sequencing dataset and for the neuron dataset, Phylovar identified 5745 SNVs with non-synonymous effects some of which were associated with neurodegenerative diseases. We implemented Phylovar and made it publicly available at https://github.com/mae6/Phylovar.git.


title: Bayesian stroke modeling details sex biases in the white matter substrates of aphasia

abstract: Ischemic cerebrovascular events often lead to aphasia. Previous work provided hints that such strokes may affect women and men in distinct ways. Women tend to suffer strokes with more disabling language impairment, even if the lesion size is comparable to men. In 1,401 patients, we isolated data-led representations of anatomical lesion patterns and hand-tailored a Bayesian analytical solution to carefully model the degree of sex divergence in predicting language outcomes [~]3 months after stroke. We located lesion-outcome effects in the left-dominant language network that highlight the ventral pathway as a core lesion focus across different tests of language performance. We provide newly detailed evidence for sex-specific brain-behavior associations in the domain-general networks associated with cortico-subcortical pathways, with unique contributions of the fornix in women and cingular fiber bundles in men. Our collective findings suggest diverging white matter substrates in how stroke causes language deficits in women and men. Clinically acknowledging such sex disparities has the potential to improve personalized treatment for stroke patients worldwide.


title: Evolutionary conservation of A/T-ending codons reflects co-regulation of expression and complex formation.

abstract:
BackgroundIn a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias that plays an important role in determining expression levels. However, the importance of codon bias to facilitate the simultaneous turnover of thousands of protein-coding transcripts to bring about phenotypic changes in cellular programs such as development, has not yet been investigated in detail.

ResultsHere, we discover that genes with A/T-ending codon preferences are expressed coordinately and display a high codon conservation in mammals. This feature is not observed in genes enriched in G/C-ending codons. A paradigmatic case of this phenomenon is KRAS, from the RAS family, an A/T-rich gene with a high codon conservation (95%) in comparison to HRAS (76%). Also, we find that genes with similar codon composition are more likely to be part of the same protein complex, and that genes with A/T-ending codons are more prone to form protein complexes than those rich in G/C. The codon preferences of genes with A/T-ending codons are conserved among vertebrates. We propose that codon conservation, a feature of expression-coordinated transcripts, is linked to the high expression variation and coordination of tRNA isoacceptors reading A/T-ending codons.

ConclusionsOur data indicate that cells exploit A/T-ending codons to generate coordinated, fine-tuned changes of protein-coding transcripts. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.


title: YAP restricts renal inflammation and mitigates kidney damage in nephronothisis related kidney disease.

abstract:
Nephronophthisis (NPH) is an orphan recessive kidney disease mostly caused by mutations in NPHP1 and 20 other genes encoding proteins that localize to primary cilia. To date the pathways linking altered primary cilia function to progressive kidney scarring in NPH remain poorly defined and therapeutic options allowing NPH patients to escape end-stage kidney disease are lacking.

Distinct proteins mutated in NPH interact with components of the Hippo pathway, an important regulator of cell fate. YAP (Yes-associated protein) overactivation has been shown to induce renal scarring while YAP inhibition showed protective effect in kidney diseases unrelated to NPH. Yet, the therapeutic potential of YAP inhibition in NPH has not been formerly assessed.

Here we studied the impact of both genetic and pharmacologic YAP inhibition on the NPH-like phenotype caused by a bi-allelic mutation of Lkb1, a ciliary kinase interacting with NPHP1. Contrary to non NPH renal disease, our results reveal an unexpected protective role of YAP in Lkb1 mutant kidneys. Indeed, YAP genetic disruption drastically increase kidney disease burden in Lkb1 deficient mice, while pharmacologic inhibition of YAP failed to improve their phenotype.

Collectively these results suggest that YAP inhibition is not a valid therapeutic strategy in NPH and suggest that LKB1 and YAP are parallel negative regulators of a yet uncharacterized pathway detrimental for kidney health.


title: Supporting per-locus substitution rates improves the accuracy of species networks and avoids spurious reticulations

abstract:
The development of statistical methods to infer species phylogenies with reticulation (species networks) has led to many discoveries of gene flow between distinct species. However, because the dimensionality of species networks is not fixed, these methods may compensate for kinds of model misspecification, such as assuming a single substitution rate for all genomic loci, by increasing the number of dimensions beyond the true value. The popular full Bayesian species network method MCMC_SEQ has previously made this assumption, so we have added support for the proven Dirichlet model for per-locus rates to enhance its accuracy and avoid spurious results. We studied the effects of this model using simulation and an empirical dataset from Heliconius butterflies.

We found that assuming a single substitution rate applies to all loci leads to the inference of spurious reticulation in simulated and empirical datasets when a full Bayesian method is used, however, the summary method InferNetwork_ML is robust to per-locus variation in substitution rates when set to ignore gene tree branch lengths. Our implementation of the model resolves this misspecification and successfully converges to the true species networks. It also infers far more accurate gene trees than assuming a single rate, or independent inference of gene trees.

Our implementation of the Dirichlet per-locus rates model is now available in PhyloNet, a software package for phylogenetic inference, open source on GitHub https://github.com/NakhlehLab/PhyloNet.


title: Genome-wide identification of preferentially located motifs in gene-proximal regions provides new insights into cis-regulatory sequences in plants

abstract: The identification of cis-regulatory elements controlling gene expression is an arduous challenge that is being actively explored to discover the key genetic factors responsible for traits of agronomic interest. In this regard, in silico predictive methods have the advantage of being of high-resolution and independent of experimental conditions. Here, we expanded the preferentially located motif (PLM) detection method to comprehensively analyze the gene-proximal regions of Arabidopsis thaliana and Zea mays. We identified three groups of PLMs in each region for each species and highlighted conserved PLMs in both species, particularly in the 3-proximal region. Moreover, we showed that PLMs occurred at both transcription factor and microRNA binding sites in each group with specific positional distributions for each region. Although the majority of PLMs were unassigned PLMs, it is noteworthy that some were supported by MNase-defined cistrome occupancy analysis. Enrichment analysis also revealed that unassigned PLMs provide functional predictions distinct from those inferred by the other PLMs. Using PLMs that occured at transcription factor binding sites, we inferred the regulatory network of a poorly characterized Z. mays-specific gene family, paving the way for further characterization of its individual members.

category: genomics


title: Mapping the developing human immune system across organs

abstract:
Recent advances in single cell genomics technologies have facilitated studies on the developing immune system at unprecedented scale and resolution. However, these studies have focused on one or a few organs and were thus limited in understanding the developing immune system as a distributed network across tissues. Here, we profiled prenatal haematopoietic organs, lymphoid organs and non-lymphoid tissues using a combination of single-cell RNA sequencing, paired antigen-receptor sequencing and spatial transcriptomics to reconstruct the developing human immune system. Our analysis revealed the acquisition of immune effector transcriptome profiles in macrophages, mast cells and NK cells from the second trimester, and the transcriptomic changes accompanying the late-stage maturation of developing monocytes and T cells that extended from their organ of origin to peripheral tissues. We uncovered system-wide blood and immune cell development beyond the conventional primary haematopoietic organs. We further identified, extensively characterised and functionally validated the human prenatal B1 cells. Finally, we provide evidence for thymocyte-thymocyte selection origin for {beta}TCR- expressing unconventional T cells based on TCR gene usage and an in vitro artificial thymic organoid culture model. Our comprehensive atlas of the developing human immune system provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine and disease understanding.

One-Sentence SummaryBy performing a comprehensive single-cell RNA sequencing atlas of human developing immune system together with antigen-receptor sequencing and spatial transcriptomics, we explored the cross-gestation and cross-organ variability in immune cells, discovered system-wide blood and immune cell development, identified, characterised and functionally validated the properties of human prenatal B1 cells and the origin of unconventional T cells.


title: Central tolerance is impaired in the middle-aged thymic environment

abstract: One of the earliest hallmarks of immune aging is thymus involution, which not only reduces the number of newly generated and exported T cells, but also alters the composition and organization of the thymic microenvironment. Thymic T-cell export continues into adulthood, yet the impact of thymic involution on the quality of newly generated T-cell clones is not well established. Notably, the number and proportion of medullary thymic epithelial cells (mTECs) and expression of tissue restricted antigens (TRAs) decline with age, suggesting the involuting thymus may not promote efficient central tolerance. Here, we demonstrate that the middle-aged thymic environment does not support rapid motility of medullary thymocytes, potentially diminishing their ability to scan antigen presenting cells that display the diverse self-antigens that induce central tolerance. Consistent with this possibility, thymic slice assays reveal that the middle-aged thymic environment does not support efficient negative selection or regulatory T cell (Treg) induction of thymocytes responsive to either TRAs or ubiquitous self-antigens. This decline in central tolerance is not universal, but instead impacts lower-avidity self-antigens that are either presented at low levels or bind to TCRs with moderate affinities. Additionally, the decline in thymic tolerance by middle-age is accompanied by both a reduction in mTECs and hematopoietic antigen presenting cell subsets that cooperate to drive central tolerance. Thus, age-associated changes in the thymic environment result in impaired central tolerance against moderate avidity self-antigens, potentially resulting in export of increasingly autoreactive naive T cells, with a deficit of Treg counterparts by middle age.


title: Chronic hyperglycemia drives alterations in macrophage effector function in pulmonary tuberculosis

abstract:
BackgroundThe rising prevalence of Diabetes mellitus (DM) in high TB endemic countries has the potential to adversely affect sustainability of TB control since DM can lead to alterations in both innate and adaptive immune response constituting as a risk factor for development of active tuberculosis (TB). The impact of hyperglycemia on TB specific innate immune response in terms of macrophage functions remains poorly addressed.

Material and methodsMacrophage effector functions in diabetic and non-diabetic individuals with and without PTB infection as well as non-diabetic-uninfected controls (fifty individuals in each group) were assessed. Phagocytic capacity against BCG and surface expression of PRRs (CD11b, CD14, CD206, MARCO and TLR2) were measured via flow cytometry. Effector molecules (ROS and NO) were assessed via DCFDA and Griess reaction respectively.

ResultsA systematic dysregulation in phagocytic capacity with concurrent alterations in expression pattern of key PRRs (CD11b, MARCO and CD206) and effector molecules (ROS and NO) was observed in diabetic individuals with PTB. These altered macrophage functions were positively correlated with increase in disease severity in diabetic individuals.

ConclusionOur results highlight several key patterns of immune dysregulation against M.Tb under hyperglycemic conditions. A significant reduction in macrophage effector functions in infected diabetic individuals which further correlated with increase in disease severity reveals a negative impact of hyperglycemia with aetiology and pathological progression of TB.


title: Obesity associated with attenuated tissue immune cell responses in COVID-19

abstract: Obesity is common and associated with more severe COVID-19, proposed to be in part related to an adipokine-driven pro-inflammatory state. Here we analysed single cell transcriptomes from bronchiolar lavage in three adult cohorts, comparing obese (Ob, body mass index (BMI) >30m2) and non-obese (N-Ob, BMI <30m2). Surprisingly, we found that Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN), IFN{gamma} and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Analysis of peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFN{gamma} response genes, as well as decreased serum IFN, in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFN and IFN{gamma} response genes. Altogether, these findings show blunted tissue immune responses in Ob COVID-19 patients, with clinical implications.


abstract:
Backgroud & AimsCurrently, the COVID-19 pandemic, caused by SARS-CoV-2 infection, represents a serious public health problem worldwide. Although it has been shown that ACE2 serves as the main receptor for SARS-CoV-2 entry into host cells, studies have shown that ACE2 is expressed at extremely low levels in various tissues, especially in some organs where virus particles have been found, such as the heart and liver. Therefore, these organs potentially express additional SARS-CoV-2 receptors that have not yet been discovered.

Methods & ResultsHere, by a genome-wide CRISPR-Cas9 activation library screening, we found that ASGR1 promoted SARS-CoV-2 infection of 293T cells. In Huh-7 and HepG2 cell lines, simultaneous knock out of ACE2 and ASGR1 prevented SARS-CoV-2 pseudovirus infection. In the immortalized THLE-2 hepatocyte cell line and primary liver parenchymal cells, both of which hardly express ACE2, SARS-CoV-2 could successfully establish an infection. After treatment with ASGR1 antibody, the infection rate significantly reduced. This suggests that SARS-CoV-2 infects liver cells mainly through an ASGR1-dependent mechanism. Finally, we also found that the soluble ASGR1 could not only prevent the SARS-CoV-2 pseudovirus, which binds to the ASGR1 receptors, from infecting host liver cells, but also had a protective effect on those expressing ACE2, indicating that administration of soluble ASGR1 protein may represent a new treatment approach.

ConclusionsColletively, these findings indicate that ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of liver cells.

Lay SummaryWe show that ASGR1 is a candidate receptor for SARS-CoV-2 to infect liver cells.


title: Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages

abstract: Recent research has underscored the immense diversity and key biogeochemical roles of large DNA viruses in the ocean. Although they are important constituents of marine ecosystems, it is often difficult to detect these viruses due to their large size and complex genomes. This is true for "jumbo" bacteriophages, which have genome sizes >200 kbp and large capsids reaching up to 0.45 m in diameter. In this study, we sought to assess the genomic diversity and distribution of these bacteriophages in the ocean by developing a bioinformatic pipeline to generate and validate jumbo phage genomes from metagenomes. We recover 85 marine jumbo phages that ranged in size from 201-498 kilobases, and we examine their genetic similarities and biogeography together with a reference database of marine jumbo phage genomes. By analyzing Tara Oceans metagenomic data we show that jumbo phages are less common in <0.22 m size fractions but are widespread in larger fractions, consistent with their large size. Our network-based analysis of gene sharing patterns reveals that jumbo bacteriophage belong to five genome clusters that are typified by diverse replication strategies, genomic repertoires, and potential host ranges. Our analysis of jumbo phage distributions in the ocean reveals that depth is a major factor shaping their biogeography, with some phage genome clusters exhibiting higher relative abundance in either surface or mesopelagic waters, respectively. Taken together, our findings demonstrate that jumbo phages are widespread community members in the ocean with complex genomic repertoires and ecological impacts that warrant further targeted investigation.