title: Goitered Gazelle's (Gazella Subgutturosa) Habitat Desirability Modeling by Using Maximum Entropy (Maxent) Method

abstract: The models predicting the spatial distribution of species can simulate the suitability of species habitats on different spatial scales, based on species records and site characteristics to gain insight into ecological or evolutionary drivers or to help predict habitat suitability across large scales. Species distribution models (SDMs) based on presence-absence or presence-only data use widely in biogeography to characterize the ecological niche of species and to predict the geographical distribution of their habitat. Although presence-absence data is generally of higher quality, it is also less common than presence-only data because it requires more rigorous planning to visit a set of pre-determined sites. Among the algorithms available, one of the most widely used methods of developing SDMs is the Maximum Entropy (MaxEnt) method. The MaxEnt uses entropy to generalize specific observations of presence-only data and does not require or even incorporate points where the species is absent within the theoretical framework. The purpose of this study is to predict the suitable habitat for Goitered gazelle (Gazella subgutturosa) in the Samelghan plain in northeastern Iran. The results showed that the variables of the Mediterranean climate classes, slope 0-5% class and semi-dense pastures with type Acantholimon-Astragalus are more important than other environmental variables used in modeling. The area under curve (AUC), Receiver Operating Characteristic (ROC), and the classification threshold shows model performance. Based on the ROC (AUC=0.99) results in this study, it was found that Maxents performance was very good. Desirability habitat was classified based on the threshold value (0.0277) and the ROC, which approx 11% of the area, predicted suitable habitat for Goitered gazelle.

category: ecology


title: Inactivation of Nphp2 in renal epithelial cells drives infantile nephronophthisis like phenotypes in mouse

abstract:
BackgroundNephronophthisis (NPHP) is a ciliopathy characterized by renal fibrosis and cyst formation, and accounts for a significant portion of end stage renal disease in children and young adults. Currently no targeted therapy is available for this disease. NPHP2 is one of the 25 NPHP genes identified to date. In mouse, global knockout of Nphp2 leads to renal fibrosis and cysts. However, the precise contribution of different cell types and the relationship between epithelial cysts and interstitial fibrosis remains undefined.

MethodsHere, we generated cell-type specific knockout mouse models of Nphp2 and characterized kidney morphology and phenotype. We additionally investigated the impact of removing cilia via deletion of the cilia biogenesis gene Ift88 on phenotype severity in Nphp2 mutants.

ResultsEpithelial specific knockout of Nphp2 in Nphp2flox/flox; Ksp-Cre mutant mice resulted in renal cyst formation and severe fibrosis, while Nphp2flox/flox; Foxd1-Cre mice, where Nphp2 is deleted in stromal cells, displayed no observable phenotypes. Further, myofibroblast activation occurred early during disease progression and preceded detectable cyst formation in the Nphp2flox/flox; Ksp-Cre kidney. Moreover, concomitant removal of cilia partially suppressed the phenotypes of the Nphp2flox/flox; Ksp-Cre mutant kidney, supporting a significant role of cilia in Nphp2 function in vivo.

ConclusionsOur results highlight the critical role of renal epithelial cilia and epithelial-stromal communication in NPHP.

Significance statementNephronophthisis (NPHP) is a ciliopathy characterized by interstitial fibrosis and epithelial cysts in the kidney. A significant portion of end stage renal disease occurring before age 30 results from NPHP. However, the molecular etiology of NPHP remains to be elucidated. By generating and analyzing tissue specific knockout mouse models of Nphp2/Inversin, authors pinpoint defective epithelial cells as the driver for both epithelial cysts and interstitial fibrosis. Moreover, the profibrotic response is triggered before cyst formation in the epithelial-specific Nphp2 knockout model. Mechanistically, authors provide evidence that Nphp2 may function to inhibit a cilia-dependent pro-fibrotic and pro-cystic pathway.

category: genetics


title: Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry

abstract: The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations particularly in the S receptor-binding domain (S-RBD) that significantly improve transmissibility and evasion of neutralizing antibodies. But exactly how the mutations in the Omicron variant enhance viral escape from immunological protection remains to be understood. The S-RBD remains the principal target for neutralizing antibodies and therapeutics, thus new structural insights into the Omicron S-RBD and characterization of the post-translational glycosylation changes can inform rational design of vaccines and therapeutics. Here we report the molecular variations and O-glycoform changes of the Omicron S-RBD variant as compared to wild-type (WA1/2020) and Delta (B.1.617.2) variants using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings reveal high resolution detail of Omicron O-glycoforms and their utilization to provide direct molecular evidence of proteoform alterations in the Omicron variant which could shed light on how this variant escapes immunological protection.

category: biochemistry


title: Chemometrics-based evaluation on effect of sonication, contact time and solvent-to-solid ratio on total phenolics and flavonoids, fatty acids and antibacterial potency of Carica papaya seed against S. enteritidis, B. cereus, V. vulnificus and P. mirabilis

abstract: This study was aimed on extraction optimization of antibacterial agent from Carica papaya seed against S. enteritidis, B. cereus, V. vulnificus and P. mirabilis as affected by sonication-assisted extraction (SAE), contact time (CT) and solid-to-solvent ratio (SSR). The principal component analysis (PCA) and individual evaluation approaches identified that no SAE, 8 CT and 1:10 SSR was the best treatment with the highest antibacterial potency. The PCA identified no SAE, 8 CT, and 1:5 SSR as the second-beat treatment. The yield, total phenolic compound (TPC), C18:1n9t and C16:1 fatty acids (FAs) in no SAE, 8 CT and 1:10 SSR treatment inhibited the growth of B. cereus, V. vulnificus and P. mirabilis while C21:0 and C15:0 in 30 min SAE, 8 CT and 1:2 SSR inhibited the S. enteritidis growth. The yield, TPC, C18:1n9t and C16:1 FAs, and C6:0 and C24:1n9, C20:1, C4:0 and C20:0 FAs had antagonistic effects on B. cereus, V. vulnificus and P. mirabilis growths. The C21:0, C15:0, C6:0 and C13:0, and C23:0, C20:0 and C11:0 FAs had antagonistic effects on S. enteritidis growth. The PCA also denoted that the MIC50 and MIC0 had a higher variation than MIC; hence, the former variables were better to use in PCA.


title: Engineering Defensin α-helix to produce high-affinity SARS-CoV-2 Spike protein binding ligands.

abstract:
The binding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein to the Angiotensin-Converting Enzyme 2 (ACE2) receptor expressed on the host cells is a critical initial step for viral infection. This interaction is blocked through competitive inhibition by soluble ACE2 protein. Therefore, developing high-affinity and cost-effective ACE2 peptidomimetic ligands that disrupt this protein-protein interaction is a promising strategy for viral diagnostics and therapy. We employed human and plant defensins, a class of small and highly stable proteins, and engineered the amino acid residues on its conformationally constrained alpha-helices to mimic the critical residues on the ACE2 helix 1 that interacts with the Spike-protein. The engineered proteins were soluble and purified to homogeneity with high yield from a bacterial expression system. The proteins demonstrated exceptional thermostability, high-affinity binding to the Spike protein with dissociation constants in the low nanomolar range, and were used in a diagnostic assay that detected SARS-CoV-2 neutralizing antibodies. This work addresses the challenge of developing helical peptidomimetics by demonstrating that defensins provide promising scaffolds to engineer alpha-helices in a constrained form for designing high-affinity ligands.

Broad audience statementThe engineered proteins developed in this study are cost-effective and highly stable reagents for SARS-CoV-2 detection. These features may allow large-scale and cost-effective production of diagnostic tests to assist COVID-19 diagnostic and prevention.

category: bioengineering


title: Predicting Epitope Candidates for SARS-CoV-2

abstract: Epitopes are short amino acid sequences that define the antigen signature to which an antibody binds. In light of the current pandemic, epitope analysis and prediction is paramount to improving serological testing and developing vaccines. In this paper, we leverage known epitope sequences from SARS-CoV, SARS-CoV-2 and other Coronaviridae and use those known epitopes to identify additional antigen regions in 62k SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, discuss where epitopes are located on proteins, and how epitopes can be grouped into classes. We also discuss the mutation density of different regions on proteins using a big data approach. We find that there are many conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike Glycoprotein.

category: bioinformatics


title: Spatially Resolved and Highly Complexed Protein and RNA in situ Detection by Combining CODEX with RNAscope In Situ Hybridization

abstract: Highly multiplexed protein and RNA in situ concurrent detection on a single tissue section is highly desirable for both basic and applied biomedical research. CODEX is a new and powerful platform to visualize up to 60 protein biomarkers in situ and RNAscope in situ hybridization (RNAscope) is a novel RNA detection system with single-copy sensitivity and unprecedent specificity at a single cell level. Nevertheless, to our knowledge, the combination CODEX and RNAscope remained unreported until this study. Here we report a simple and reproducible combination of CODEX and RNAscope (Comb-CODEX-RNAscope). We also determined the cross-reactivities of CODEX anti-human antibodies to rhesus macaques, a widely used animal model of human disease.

category: pathology


title: Heparins enhance C1 esterase inhibitor activity: a promising remedy for acute hereditary angioedema

abstract:
RationaleHereditary angioedema (HAE) is a potentially life-threatening illness most commonly due to deficiency or dysfunction of C1-esterase inhibitor (C1-INH). While specific treatments are available to thwart acute exacerbations, they are extremely costly and some can be associated with rare but serious side effects. The heparins are long known to augment C1-INH activity and case reports / series have documented their efficacy in treating HAE.

Objectiveto determine if unfractionated heparin and two low-molecular weight heparins (enoxaparin and nadroparin) can augment C1-INH activity ex vivo in the sera of patients with HAE and in an in vitro biochemical assay.

MethodsC1-INH activity in the absence or presence of the heparin formulations were analyzed by two different methods. To measure C1-INH activity ex vivo, a commercially available assay was utilized with patient sera, excess amounts of C1s, and a substrate of C1s which, upon cleavage by C1s, produces a chromogenic product. To determine biochemically the C1-INH activity in vitro, a pharmacologic grade C1-INH, recombinant C1s (C1s-CCP12SP), and a peptide substrate of C1s were employed. Microscale thermophoresis was used to determine whether C1-INH binds to heparin.

Main resultsin patient sera, nadroparin was superior to enoxaparin and unfractionated heparin in augmenting C1-INH activity, followed by enoxaparin and then unfractionated heparin. In the in vitro biochemical assay, all three heparins augmented C1-INH-C1s binding linearly in a dose-dependent fashion. Microscale thermophoresis assay demonstrated that nadroparin binds to C1-INH, providing a mechanism by which heparin facilitates the interaction between C1-INH and the proteases known to produce bradykinin, the mediator of HAE.

Conclusionlow-molecular weight heparin augments C1-INH activity and should be studied as a potential treatment for acute HAE.

category: pharmacology and toxicology


title: Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects

abstract:
Environmental chemicals are commonly studied one at a time, and there is a need to advance our understanding of the effect of exposure to their combinations. Here we apply high-content microscopy imaging of cells stained with multiplexed dyes (Cell Painting) to profile the effects of Cetyltrimethylammonium bromide (CTAB), Bisphenol A (BPA), and Dibutyltin dilaurate (DBTDL) exposure on four human cell lines; both individually and in all combinations. We show that morphological features can be used with multivariate data analysis to discern between exposures from individual compounds, concentrations, and combinations. CTAB and DBTDL induced concentration-dependent morphological changes across the four cell lines, and BPA exacerbated morphological effects when combined with CTAB and DBTDL. Combined exposure to CTAB and BPA induced changes on the ER, Golgi apparatus, nucleoli and cytoplasmic RNA in one of the cell lines. Different responses between cell lines indicate that multiple cell types are needed when assessing combination effects. The rapid and relatively low-cost experiments combined with high information content makes Cell Painting an attractive methodology for future studies of combination effects. All data in the study is made publicly available on Figshare.

HighlightsO_LIAssessment of combination effects of BPA, CTAB and DBTDL on four human cell lines
C_LIO_LIMorphological profiling/Cell Painting captures dose and combination dependent effects
C_LIO_LIBPA exacerbated morphological effects when combined with CTAB and DBTDL.
C_LIO_LICell models of diverse origin are needed when profiling environmental chemicals
C_LI


title: Gi/o protein-coupled receptor inhibition of beta-cell electrical excitability and insulin secretion depends on Na+/K+ ATPase activation

abstract: Gi/o protein-coupled receptors (Gi/o-GPCRs) limit pancreatic islet insulin secretion by decreasing {beta}-cell Ca2+ entry, which is essential for maintenance of glucose homeostasis. However, the Gi/o-GPCR signaling mechanism that mediates inhibition of human islet hormone secretion has not been identified. Here we demonstrate that Gi/o-GPCRs cause hyperpolarization of the {beta}-cell membrane potential through activation of Na+/K+ ATPases (NKAs) in mouse and human islets. Stimulation of Gi/o-coupled somatostatin or 2-adrenergic receptors induced oscillations in {beta}-cell NKA activity, which resulted in islet Ca2+ fluctuations. Selective induction of {beta}-cell Gi/o signaling with a chemogenetic Gi/o-GPCR also activated NKAs and initiated islet Ca2+ oscillations, suggesting that {beta}-cell Gi/o-GPCRs tune pulsatile insulin secretion. Furthermore, intra-islet paracrine activation of {beta}-cell Gi/o-GPCR signaling and NKAs by {delta}-cell somatostatin secretion slowed Ca2+ oscillations, which decreased insulin secretion. Gi/o-GPCR-mediated oscillations in {beta}-cell membrane potential and Ca2+ were dependent on NKA phosphorylation by Src tyrosine kinases; an effect that was mimicked by stimulating islet insulin receptor tyrosine kinases. Whereas {beta}-cell NKA function was completely inhibited by cAMP-dependent PKA activation. Taken together, these data reveal that NKA-mediated hyperpolarization of {beta}-cell membrane potential serves as the primary and conserved mechanism for Gi/o-GPCR control of electrical excitability, Ca2+ handling, and insulin secretion.

category: physiology


title: Machine learning-assisted discovery of growth decision elements by relating bacterial population dynamics to environmental diversity

abstract: Microorganisms growing in their habitat constitute a complex system. How the individual constituents of the environment contribute to microbial growth remains largely unknown. The present study focused on the contribution of environmental constituents to population dynamics via a high-throughput assay and data-driven analysis of a wild-type Escherichia coli strain. A large dataset constituting a total of 12,828 bacterial growth curves with 966 medium combinations, which were composed of 44 pure chemical compounds, was acquired. Machine learning analysis of the big data relating the growth parameters to the medium combinations revealed that the decision-making components for bacterial growth were distinct among various growth phases, e.g., glucose, sulfate and serine for maximum growth, growth rate and growth delay, respectively. Further analyses and simulations indicated that branched-chain amino acids functioned as global coordinators for population dynamics, as well as, a survival strategy of risk diversification to prevent the bacterial population from undergoing extinction.

category: systems biology


title: Inferring cell motility in complex environments with incomplete tracking data

abstract:
Cell motility has important influence on cell interactions and functionality for various biological aspects. Deciphering these dynamics often relies on live-cell microscopy measurements, which partly have to deal with limitations that could impair a reliable quantification of their motility. Especially given complex environments and tissue structures, limited observation periods, cells moving in and out of focus and impaired calibration of observation axes often lead to loss of cell tracks and insufficient tracking of motility within several dimensions. However, a reliable quantification of cell motility dynamics is essential when aiming at extrapolating the observed dynamics in order to understand cell population dynamics at larger temporal and spatial scales using appropriate simulation environments.

To analyze how incomplete observations affect interpretation and parameterization of cell motility, we combined experimental observations with computational models. Studying individual cell dynamics within 3D collagen environments, we found that the gradual loss of cell tracks leads to an underestimation of several motility parameters with the effect dependent on the collagen density. By extending the automated fitting strategy FitMultiCell to account for cell track loss, we show that we are able to retrieve the actual cell dynamics and, thus, to reliably parameterize cell motility from such incomplete data. Applying our approach to the analysis of CD4+ T cells within 3D collagen environments that were infected with HIV-1, we could show that despite a considerable loss of cell tracks, the data still contained sufficient information to compare individual cell motilities by inferring and simulating their dynamics. Thereby, the analysis allowed us to disentangle the effect of HIV-1 infection and collagen density on individual cell motility. Our extended FitMultiCell-approach presented here provides a solution for the elimination of artifacts from cell track data analysis to robustly infer cell motility dynamics.


title: Digital twin reveals combinatorial code of non-linear computations in the mouse primary visual cortex

abstract: More than a dozen excitatory cell types have been identified in the mouse primary visual cortex (V1) based on transcriptomic, morphological and in vitro electrophysiological features. However, the functional landscape of excitatory neurons with respect to their responses to visual stimuli is currently unknown. Here, we combined large-scale two-photon imaging and deep learning neural predictive models to study the functional organization of mouse V1 using digital twins. Digital twins enable exhaustive in silico functional characterization providing a bar code summarizing the input-output function of each neuron. Clustering the bar codes revealed a continuum of function with around 30 modes. Each mode represented a group of neurons that exhibited a specific combination of stimulus selectivity and nonlinear response properties such as cross-orientation inhibition, size-contrast tuning and surround suppression. These non-linear properties were expressed independently spanning all possible combinations across the population. This combinatorial code provides the first large-scale, data-driven characterization of the functional organization of V1. This powerful approach based on digital twins is applicable to other brain areas and to complex non-linear systems beyond the brain.

category: neuroscience


title: InfoMuNet: Information-theory-based Functional Muscle Network Tracks Sensorimotor Integration Post-stroke

abstract: Sensory information is critical for motor coordination. However, understanding sensorimotor integration is complicated, especially in individuals with nervous system impairment. This research presents a novel functional biomarker, based on a nonlinear network graph of muscle connectivity, called InfoMuNet, to quantify the role of sensory information in motor performance. Thirty-two individuals with post-stroke hemiparesis performed a grasp-and-lift task while muscle activities were measured using eight surface electromyography (sEMG) sensors. Subjects performed the task with their affected hand before and after exposure to the sensory stimulation elicited by performing the task with the less-affected hand. For the first time, this work shows that InfoMuNet robustly quantifies functional muscle connectivity improvements in the affected hand after exposure of the less-affected side to sensory information. >90% of the subjects conformed with the improvement resulting from this sensory exposure. InfoMuNet also shows high sensitivity to tactile, kinesthetic, and visual input alterations at the subject level, highlighting the potential use in precision rehabilitation interventions.


title: Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2

abstract: Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to the poor stability, most current mRNA delivery platforms need to be stored at -20 {degrees}C or -70 {degrees}C. Here we present lyophilized thermostable mRNA loaded lipid nanoparticles, which could be stored at room temperature with long-term stability. We demonstrate the applicability of lyophilization techniques to different mRNA sequences and lipid components. Three lyophilized vaccines targeting wild-type, Delta and Omicron SARS-CoV-2 variant were prepared and demonstrated to be able induce high-level of IgG titer and neutralization response. In the Delta challenge in vivo experiment, the lyophilized mRNA vaccine successfully protected the mice from infection and clear the virus. This lyophilization platform could significantly improve the accessibility of mRNA vaccine or therapeutics, particularly in remote regions.

category: immunology


title: Lyophilized mRNA-lipid nanoparticle vaccines with long-term stability and high antigenicity against SARS-CoV-2


title: Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors

abstract:
Severe coronavirus disease 2019 (COVID-19) is characterized by systemic inflammation and can result in protracted symptoms. Robust systemic inflammation may trigger persistent changes in hematopoietic cells and innate immune memory through epigenetic mechanisms. We reveal that rare circulating hematopoietic stem and progenitor cells (HSPC), enriched from human blood, match the diversity of HSPC in bone marrow, enabling investigation of hematopoiesis and HSPC epigenomics. Following COVID-19, HSPC retain epigenomic alterations that are conveyed, through differentiation, to progeny innate immune cells. Epigenomic changes vary with disease severity, persist for months to a year, and are associated with increased myeloid cell differentiation and inflammatory or antiviral programs. Epigenetic reprogramming of HSPC may underly altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.

One Sentence SummaryTranscriptomic and epigenomic analysis of blood reveal sustained changes in hematopoiesis and innate immunity after COVID-19.

Graphical Abstract

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title: Dual Inhibition of Cathepsin L and 3CL-Pro by GC-376 Constrains SARS Cov2 Infection Including Omicron Variant

abstract:
Recurrent waves of SARS CoV2 infections remain a major global health concern. Emergence of highly infectious variants with reduced sensitivity to neutralization by vaccines and monoclonal antibodies (mAb) necessitates a deeper understanding of factors involved in SARS CoV2 infections and identification of drug candidates to halt infection. Here, we determined the primacy of endosomal protease cathepsin-L in mediating SARS CoV2 entry and screened a library of well-annotated bioactive compounds for potent cathepsin-L inhibitory activity. Whilst the potent cathepsin-L inhibitors were capable of inhibiting SARS CoV2 entry and cytopathic effect (CPE) in less susceptible cell lines such as human ACE2 expressing 293T cells, these drugs failed to inhibit SARS CoV2 in highly susceptible cell lines such as human TMPRSS2 or human-ACE2-TMPRSS2 overexpressing Vero E6 cells. Only drugs with dual inhibitory effect on both host cathepsin-L and virus 3CL-Protease enzymes such as Z-FA-FMK and GC-376 were capable of inhibiting prototypic (USA-WA1/2020, Lineage A) SARS CoV2 induced CPE in highly susceptible cell lines. Moreover, these drugs inhibited delta (Lineage-B.1.617.2) and omicron (Lineage-B.1.1.529) infection with equal potency showing that the newer mutations harbored in these variants did not affect the mechanism of action of these drugs such as cathepsin-L or 3CL-Pro inhibition. Moreover, our early evidence that 3CL-Pro inhibition can effectively inhibit omicron-induced CPE in highly susceptible cell lines suggests that the recently FDA-approved oral drug, a 3CL-Pro inhibitor which is a combination of nirmatrelvir/ritonavir (Paxlovid) could be effective against omicron variant which shows reduced sensitivity to vaccines and mAb.

ImportanceWe report that cathepsin-L and 3CL-Pro as major targets for designing antivirals against SARS CoV2. Dual inhibition of cathepsin-L and 3CL-Pro by GC-376 renders it effective in inhibiting SARS CoV2-induced cytopathic effect in highly susceptible cell lines. Moreover, this candidate drug is equally effective against prototypic SARS CoV2 lineage A and emerging variants such as delta and omicron which show reduced sensitivity to vaccines and monoclonal antibodies. Given the recent wave of SARS CoV2 omicron variant infection around the world, and 3CL-Pro inhibitor nirmatrelvir is one of the components of the FDA-approved Paxlovid, our findings are timely, important and should be of broad interest.

category: microbiology


title: Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants

abstract:
Genetic variation of SARS-CoV-2 has resulted in the emergence and rapid spread of multiple variants throughout the pandemic, of which Omicron is currently the predominant variant circulating worldwide. SARS-CoV-2 variants of concern or interest (VOC/VOI) have evidence of increased viral transmission, disease severity, or decreased effectiveness of vaccines and neutralizing antibodies. Remdesivir (RDV, VEKLURY(R)) is a nucleoside analog prodrug and the first FDA-approved antiviral treatment of COVID-19. Here we present a comprehensive antiviral activity assessment of RDV and its parent nucleoside, GS-441524, against 10 current and former SARS-CoV-2 VOC/VOI clinical isolates by nucleoprotein ELISA and plaque reduction assay.

Delta and Omicron variants remained susceptible to RDV and GS-441524, with EC50 values 0.31 to 0.62-fold of those observed against the ancestral WA1 isolate. All other tested variants exhibited EC50 values ranging from 0.15 to 2.3-fold of the observed EC50 values against WA1. Analysis of nearly 6 million publicly available variant isolate sequences confirmed that Nsp12, the RNA-dependent RNA polymerase (RdRp) target of RDV and GS-441524, is highly conserved across variants with only 2 prevalent changes (P323L and G671S). Using recombinant viruses, both RDV and GS-441524 retained potency against all viruses containing frequent variant substitutions or their combination. Taken together, these results highlight the conserved nature of SARS-CoV-2 Nsp12 and provide evidence of sustained SARS-CoV-2 antiviral activity of RDV and GS-441524 across the tested variants. The observed pan-variant activity of RDV supports its continued use for the treatment of COVID-19 regardless of the SARS-CoV-2 variant.


title: Sexual transmission of Anopheles gambiae densovirus (AgDNV) leads to disseminated infection in mated females

abstract:
BackgroundAnopheles gambiae densovirus (AgDNV) is an insect-specific, single-stranded DNA virus that infects An. gambiae, the major mosquito species responsible for transmitting malaria parasites throughout Sub-Saharan Africa. AgDNV is a benign virus that is very specific to its mosquito host and therefore has potential to serve as a vector control tool via paratransgenesis (genetic modification of mosquito symbionts) to limit transmission of human pathogens. Prior to being engineered into a control tool, the natural transmission dynamics of AgDNV between An. gambiae mosquitoes needs to be fully understood. Additionally, improved knowledge of AgDNV infection in male mosquitoes is needed. In this study, we examine the tissue tropism of AgDNV in the male reproductive tract and investigate both venereal and vertical transmission dynamics of the virus.

MethodsAn. gambiae adult males were infected with AgDNV via micro-injection and reproductive tissues collected and assayed for AgDNV using qPCR. Next, uninfected females were introduced to AgDNV-infected or control males and, after several nights of mating, both the spermatheca and female carcass were assessed for venereally transmitted AgDNV. Finally, F1s from this cross were collected and assayed to quantify vertical transmission of the virus.

ResultsAgDNV infected the reproductive tract of male mosquitoes, including the testes and male accessory glands (MAGs), without affecting mating rates. AgDNV-infected males venereally transmitted virus to females, and these venereally-infected females developed disseminated infection throughout the body. However, AgDNV was not vertically transmitted to F1s resulting from this cross.

ConclusionsInfected male releases could be an effective strategy to introduce AgDNV-based paratransgenic tools into naive populations of An. gambiae females.


title: SARS-CoV-2 Nsp1 N-terminal and linker regions as a platform for host translational shutoff

abstract: In the early stages of SARS-CoV-2 infection, non-structural protein 1 (Nsp1) inhibits the innate immune response by inserting its C-terminal helices into the mRNA entry channel of the ribosome and promoting mRNA degradation. Nevertheless, the mechanism by which Nsp1 achieves host translational shutoff while allowing for viral protein synthesis remains elusive. We set out to characterize the interactome of full-length Nsp1 and its topology by crosslinking mass spectrometry in order to investigate the role of the N-terminal domain and linker regions in host translational shutoff. We find that these regions are in contact with 40S proteins lining the mRNA entry channel and detect a novel interaction with the G subunit of the eIF3 complex. The crosslink-derived distance restraints allowed us to derive an integrative model of full-length Nsp1 on the 40S subunit, reporting on the dynamic interface between Nsp1, the ribosome and the eIF3 complex. The significance of the Nsp1-eIF3G interaction is supported by further evidence that Nsp1 predominantly binds to 40-43S complexes. Our results point towards a mechanism by which Nsp1 is preferentially recruited to canonical initiation complexes, leading to selective inhibition of host-translating ribosomes and subsequent mRNA degradation.

category: molecular biology


title: The rise and fall of SARS-CoV-2 variants and the emergence of competing Omicron lineages

abstract:
In late December of 2019, high throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we analyze a subset (n=83,204) of all publicly available SARS-CoV-2 genomes (n=~5.6 million) that were randomly selected, but equally distributed over the course of the pandemic. We plot the emergence and extinction of new variants of concern (VOCs) over time and show how this corresponds to the ongoing accumulation of mutations in SARS-CoV-2 genomes and individual proteins. While the accumulation of mutations generally follows a linear regression, non-synonymous mutations are significantly greater in Omicron viruses than in previous variants-especially in the spike and nucleoproteins-and these differences are more pronounced in a recently identified sub-lineage (BA.2) of Omicron.

ImportanceOmicron is the fifth SARS-CoV-2 variant to be designated a Variant of Concern (VOC) by the World Health Organization (WHO). Here we provide a retrospective analysis of SARS-CoV-2 variants and explain how the Omicron variant is distinct. Our work shows that the spike and nucleoproteins have accumulated the most mutations in Omicron variants, but that the accessory proteins of SARS-CoV-2 sequences are changing most rapidly relative to their size. Collectively, this "Observation" provides a concise overview of SARS-CoV-2 evolution, reveals mutational differences between two Omicron lineages, and highlights changes in the SARS-CoV-2 proteome that have been under reported.

category: evolutionary biology


title: Cell delivery peptides for small interfering RNAs targeting SARS-CoV-2 new variants through a bioinformatics and deep learning design

abstract: Nucleic acid technologies with designed delivery systems have surged as one the most promising therapies of the future, due to their contribution in combating SARS-CoV-2 severe disease. Nevertheless, the emergence of new variants of concern still represents a real threat in the years to come. It is here that the use of small interfering RNA sequences to inhibit gene expression and, thus, protein synthesis, may complement the already developed vaccines, with faster design and production. Here, we have designed new sequences targeting COVID-19 variants and other related viral diseases through bioinformatics, while also addressing the limited number of delivery peptides by a deep learning approach. Two sequences databases were produced, from which 62 were able to target the virus mRNA, and ten displayed properties present in delivery peptides, which we compared to the broad use TAT delivery peptide.


title: Preclinical establishment of a divalent vaccine against SARS-CoV-2

abstract: First-generation vaccines against SARS-CoV-2 have been administered to more than 60% of the population in developed countries. However, the monovalent vaccines currently available in Europe do not confer adequate and durable immune protection. To satisfy the need for a novel vaccine, we engineered a divalent gene construct consisting of the receptor binding domain (RBD, 300-685 aa) of the spike protein and the immunodominant region of the nucleocapsid (100-300 aa). This fusion protein was cloned into a pET-30a plasmid and expressed either in Escherichia coli or in a recombinant baculovirus in insect cells. Following purification via its His-tag, the fusion protein was mixed with adjuvant, and administered to mice in a prime-booster-mode. Upon testing for IgG antibody response against nucleocapsid and RBD, a titer of 10-4 - 10-5 was demonstrated 14 days after the first booster injection in 72% of the animals, which could be increased to 100% by a second booster. Notably, comparable IgG responses were detected against the delta, gamma and omicron variants of the RBD region. Durability testing revealed the presence of IgG beyond 90 days. In addition, granzyme A and perforin mRNA expression (cytolytic effector cell molecules) was increased in cytotoxic lymphocytes isolated from peripheral blood. Ex vivo stimulation of T-cells by nucleocapsid and RBD peptides showed antigen-specific upregulation of CD44 in vaccinated mice among their CD4+ and CD8+ T-cells. No side-effect was documented in the central nervous system, be it either endothelial inflammation or neuronal damage. Cumulatively, the combined induction of B-cell and T-cell response by a bivalent protein-based vaccine directed against two structural SARS-CoV-2 proteins represents a proof-of-principle approach alternative to existing mRNA vaccination strategies, which could confer long-lasting immunity against all known viral strains.


title: Crest maturation at the cardiomyocyte surface contributes to a new late postnatal development stage that controls the diastolic function of the adult heart

abstract:
RATIONALEIn addition to its typical rod-shape, the mammalian adult cardiomyocyte (CM) harbors a unique lateral membrane surface architecture with periodic crests, relying on the presence of subsarcolemmal mitochondria (SSM) the role of which is still unknown.

OBJECTIVETo investigate the development and functional role of CM crests during the postnatal period.

METHODS AND RESULTSElectron/confocal microscopy and western-blot of left ventricular tissues from rat hearts indicated a late CM surface crest maturation, between postnatal day 20 (P20) and P60, as shown by substantial SSM swelling and increased claudin-5 cell surface expression. The P20-P60 postnatal stage also correlates with an ultimate maturation of the T-Tubules and the intercalated disk. At the cellular level, we identified an atypical CM hypertrophy characterized by an increase in long- and short-axes without myofibril addition and with sarcomere lateral stretching, indicative of lateral stretch-based CM hypertrophy. We confirmed the P20-P60 hypertrophy at the organ level by echocardiography but also demonstrated a transcriptomic program after P20 targeting all the cardiac cell populations. At the functional level, using Doppler echocardiography, we found that the P20-P60 period is specifically dedicated to the improvement of relaxation. Mechanistically, using CM-specific knock-out mice, we identified ephrin-B1 as a determinant of CM crest maturation after P20 controlling lateral CM stretch-hypertrophy and relaxation. Interestingly, while young adult Efnb1CMspe-/- mice essentially show a relaxation impairment with exercise intolerance, they progressively switch toward heart failure with 100% KO mice dying after 13 months.

CONCLUSIONSThis study highlights a new late P20-P60 postnatal developmental stage of the heart in rodents during which the CM surface crests mature through an ephrin-B1-dependant mechanism and regulate the diastolic function. Moreover, we demonstrate for the first time that the CM crest architecture is cardioprotective.

category: cell biology


title: Prox1 dynamically regulates downstream targets and chromatin accessibility during venous to lymphatic endothelial cell transdifferentiation in the embryo

abstract: During development, lymphatic vasculature forms as a second, distinct vascular network derived from blood vessels. Transdifferentiation of venous into lymphatic endothelial cells (LECs) is the first step in this process. Specification, transdifferentiation and maintenance of LEC fate requires the transcription factor Prox1 but downstream mechanisms and markers remain to be described in full. We present a single cell transcriptomic atlas of lymphangiogenesis in zebrafish revealing new markers and hallmarks of LEC differentiation. We further profile single cell transcriptomic and chromatin accessibility changes in Prox1 mutants. This work reveals dynamic, multifaceted roles for Prox1 that include blocking blood vascular and hematopoietic fate and up-regulating essential factors for lymphatic development. We reveal that Prox1 controls chromatin state and evidence for Prox1-independent regulation of early LEC differentiation. This work thus provides new insights and a detailed resource for further understanding an enigmatic developmental process that is central in pathological lymphangiogenesis in disease.

category: developmental biology


title: Causes, temporal trends and the effects of urbanisation on admissions of wild raptors to rehabilitation centres in England and Wales

abstract: Data from wildlife rehabilitation centres can provide on-the-ground records of causes of raptor morbidity and mortality, allowing threat patterns to be explored throughout time and space. We provide an overview of native raptor admissions to four wildlife rehabilitation centres (WRCs) in England and Wales, quantifying the main causes of morbidity and mortality, trends over time and whether certain causes were more common in more urbanised areas between 2001-2019. Throughout the study period 14 raptor species were admitted totalling 3305 admission records. The Common Buzzard (Buteo buteo; 31%) and Tawny Owl (Strix aluco; 29%) were most numerous. Relative to the proportion of breeding individuals in Britain & Ireland, Peregrine Falcons (Falco peregrinus), Little Owls (Athene noctua) and Western Barn Owls (Tyto alba) were over-represented in the admissions data by 103%, 73% and 69%, respectively. Contrastingly Northern Long-eared Owls (Asio otus), Western Marsh Harriers (Circus aeruginosus) and Merlin (Falco columbarius) were under-represented by 187%, 163% and 126%, respectively. Across all species, vehicle collisions were the most frequent anthropogenic admission cause (22%) and orphaned young birds (10%) were most frequent natural admission cause. Mortality rate was highest for infection/parasite admissions (90%), whereas orphaned birds experienced lowest mortality rates (16%). For one WRC, there was a notable decline in admissions over the study period. Red Kite (Milvus milvus) admissions increased over time, whereas Common Buzzard and Common Kestrel admissions declined. There were significant declines in the relative proportion of persecution and metabolic admissions, and an increase in orphaned young birds. Urban areas were positively associated with persecution, building collisions and unknown trauma admissions, whereas vehicle collisions were associated with more rural areas. Many threats persist for raptors in England and Wales, however, have not changed substantially over the past two decades. Threats associated with urban areas, such as building collisions, may increase over time in line with human population growth and subsequent urban expansion.


title: Hebbian and homeostatic plasticity mechanisms are segregated in sub-types of layer 5 neuron in the visual cortex

abstract:
Cortical layer 5 contains two major types of projection neuron known as IB (intrinsic bursting) cells that project sub-cortically and RS (regular spiking) cells that project between cortical areas. We studied the plasticity properties of RS and IB cells in the visual cortex during the critical period for ocular dominance plasticity in mice. RS neurons exhibited synaptic depression in response to both dark exposure (DE) and monocular deprivation (MD), and their homeostatic recovery from depression was dependent on TNF. In contrast, IB cells demonstrated opposite responses to DE and MD, potentiating to DE and depressing to MD. IB cells potentiation depended on CaMKII-autophosphorylation and not TNF. IB cells showed mature synaptic properties at the start of the critical period while RS cells matured during the critical period. Together with observations in somatosensory cortex, these results suggest that differences in RS and IB plasticity mechanisms are a general cortical property.

Significance StatementThe neocortex contains cells that project to different locations in the brain. In this study we show that neurons projecting to different target locations exhibit different synaptic plasticity mechanisms. Cortically projecting cells show synaptic depression and homeostatic up-regulation, subcortically projecting cells show classical Hebbian potentiation. This is important because it implies that the way a cortical neuron responds to experience and encodes information depends on the neuronal subcircuits in which it is embedded. We show that ignoring this distinction leads to erroneous conclusions regarding plasticity time-course and significance. These findings constitute an important step toward understanding how learning and memory is organized within subcircuits in the cerebral cortex.


title: Omission responses in field potentials but not spikes in rat auditory cortex

abstract: Non-invasive recordings of gross neural activity in humans often show responses to omitted stimuli in steady trains of identical stimuli. This has been taken as evidence for the neural coding of prediction or prediction error. However, evidence for such omission responses from invasive recordings of cellular-scale responses in animal models is scarce. Here, we sought to characterise omission responses using extracellular recordings in the auditory cortex of anaesthetised rats. We profiled omission responses across local field potentials (LFP), analogue multiunit activity (AMUA), and single/multi-unit spiking activity, using stimuli that were fixed-rate trains of acoustic noise bursts where 5% of bursts were randomly omitted. Significant omission responses were observed in LFP and AMUA signals, but not in spiking activity. These omission responses had a lower amplitude and longer latency than burst-evoked sensory responses, and omission response amplitude increased as a function of the number of preceding bursts. Contrary to theories of neural entrainment, rhythmic stimulus presentation did not increase low-frequency phase-locking of neural activity specific to the stimulus presentation rate. Together, our findings show that omission responses are observed in LFP and AMUA signals, with laminar specificity, but are not observed in spiking activity, and do not show evidence for low-frequency phase locking. This has implications for models of cortical processing that require many neurons to encode prediction error in their spike output, and may have some consistency with representation of error in dendrites electrotonically distant from the soma.


title: Phosphorylation by casein kinase 2 ensures ER-phagy receptor TEX264 binding to ATG8 proteins

abstract: Selective autophagy cargos are recruited to autophagosomes primarily by interacting with autophagosomal ATG8 family proteins via the LC3-interacting region (LIR). The upstream sequence of most LIRs contains negatively charged residues such as Asp, Glu, and phosphorylated Ser and Thr. However, the significance of LIR phosphorylation (compared with having acidic amino acids) and the structural basis of phosphorylated LIR-ATG8 binding are not entirely understood. Here, we show that the serine residues upstream of the core LIR of the endoplasmic reticulum (ER)-phagy receptor TEX264 are phosphorylated by casein kinase 2, which is critical for its interaction with ATG8s, autophagosomal localization, and ER-phagy. Structural analysis showed that phosphorylation of these serine residues increased binding affinity by producing multiple hydrogen bonds with ATG8s that cannot be mimicked by acidic residues. This binding mode is different from those of other ER-phagy receptors that utilize a downstream helix, which is absent from TEX264, to increase affinity. These results suggest that phosphorylation of the LIR is critically important for strong LIR-ATG8 interactions, even in the absence of auxiliary interactions.


title: MOSPD2 a new endoplasmic reticulum-lipid droplet tether functioning in LD homeostasis

abstract: Membrane contact sites between organelles are organized by protein bridges. Among the components of these contacts, the VAP family comprises endoplasmic reticulum (ER)-anchored proteins, such as MOSPD2, functioning as major ER-organelle tethers. MOSPD2 distinguishes itself from the other members of the VAP family by the presence of a CRAL-TRIO domain. In this study, we show that MOSPD2 forms ER-LD contacts thanks to its CRAL-TRIO domain. MOSPD2 ensures the attachment of the ER to LDs through a direct protein-membrane interaction involving an amphipathic helix that has an affinity for lipid packing defects present at the surface of LDs. Remarkably, the absence of MOSPD2 markedly disturbs the assembly of lipid droplets. These data show that MOSPD2, in addition to being a general ER receptor for inter-organelle contacts, possesses an additional tethering activity and is specifically implicated in the biology of LDs via its CRAL-TRIO domain.


title: Timely Schwann cell division during migration drives peripheral myelination in vivo via Laminin/cAMP pathway

abstract: Schwann cells (SC) migrate along peripheral axons and divide intensively to generate the right number of cells prior to axonal ensheathment; however, little is known regarding the temporal and molecular control of their division, particularly during migration, and its impact on myelination. We report that Sil, a spindle pole protein associated with autosomal recessive primary microcephaly (MCPH), is required for temporal mitotic exit of SC. In sil-deficient cassiopeia (csp-/-) mutants, SC fail to radially sort and myelinate peripheral axons. Elevation of cAMP, but not Rac1 activity in csp-/- restores myelin ensheathment. Most importantly, we show a significant decrease in Laminin expression within csp-/- posterior lateral line nerve and that forcing Laminin2 expression in csp-/- fully restores SC ability to myelinate. We also discovered that SC have a restricted time window during which they have to divide, while migrating, in order to trigger myelination. Thus, we unravel a novel and essential role for timely SC division during migration in mediating Laminin expression to orchestrate radial sorting and peripheral myelination in vivo.


title: Glioblastoma exosomes influence glial cell hyaluronic acid deposition to promote invasiveness

abstract: A deeper understanding of the mechanisms invoked by glioblastoma (GBM) to infiltrate the brain is needed to develop approaches to contain the disease and reduce recurrence. Here we report that GBM cells which have acquired a p53 mutation (p53273H) with established pro-invasive gain-of-function release exosomes/extracellular vesicles (EVs) containing a sialomucin, podocalyxin (PODXL), which encourages other brain cells, such as astrocytes to deposit extracellular matrix (ECM) with increased levels of hyaluronic acid (HA). This HA-rich ECM, in turn, promotes invasiveness of the GBM cells. Consistently, CRISPR-mediated deletion of PODXL opposes infiltration of GBM in vivo. This study offers a mechanistic basis for the particularly poor prognosis of GBM which are driven by the p53273H mutant, and how these tumours influence the wider brain ECM microenvironment through which glioma cells invade.

category: cancer biology


title: A single cell atlas of the cycling murine ovary

abstract: The estrous cycle is regulated by rhythmic endocrine interactions of the nervous and reproductive systems, which coordinate the hormonal and ovulatory functions of the ovary. Folliculogenesis and follicle progression require the orchestrated response of a variety of cell types to allow the maturation of the follicle and its sequela, ovulation, corpus luteum (CL) formation, and ovulatory wound repair. Little is known about the cell state dynamics of the ovary during the estrous cycle, and the paracrine factors that help coordinate this process. Herein we used single-cell RNA sequencing to evaluate the transcriptome of > 34,000 cells of the adult mouse ovary and describe the transcriptional changes that occur across the normal estrous cycle and other reproductive states to build a comprehensive dynamic atlas of murine ovarian cell types and states.


title: Tropical land use alters functional diversity of soil food webs and leads to monopolization of the detrital energy channel

abstract: Agricultural expansion is among the main threats to biodiversity and functions of tropical ecosystems. Conversion of rainforest into plantations erodes biodiversity with little-explored consequences for food-web structure and energetics of belowground communities, and associated ecosystem functions and services. We used a unique combination of approaches in stable isotope analysis and food web energetics to analyze in a comprehensive way consequences of the conversion of rainforest into plantations on the structure of and channeling of energy through soil animal food webs in Sumatra, Indonesia. Across the 23 animal groups studied, the channeling of energy shifted towards freshly-fixed plant carbon in plantations, indicating fast energy channeling as opposed to slow energy channeling in rainforests. Earthworms as major detritivores stayed unchanged in their trophic niche and monopolized the detrital pathway in plantations. Functional diversity metrics of soil food webs reflected the reduced amount of litter, tree density and species richness in plantations, providing guidelines how to improve the complexity of the structure of and channeling of energy through soil food webs. Our results highlight the strong restructuring of soil food webs with the conversion of rainforest into plantations threatening soil functioning and ecosystem stability in the long term.

category: ecology


title: Chronic Intermittent Hypobaric Hypoxia Prevents Contrast-Induced Acute Kidney Injury By Modulating The HIF-1α Signaling Pathway

abstract: The aim of this study was to explore the role of CIHH in preventing contrast-induced acute kidney injury (CI-AKI) in rats and its mechanism. Rats mean arterial pressure, heart rate, serum creatinine and blood urea nitrogen levels were measured. The kidney tissue pathological changes, superoxide dismutase (SOD) activity, malondialdehyde (MDA) levels, hypoxia inducible factor-1, Bcl-2/adenovirus E1B-19kDa-interacting protein3 (BNIP3) , cysteiny aspartate specific protease3(caspase3) and poly(ADP-ribose) polymerase (PARP) expression levels were testing. The results showed that CIHH prevented CI-AKI group mean arterial pressure, heart rate, serum creatinine and blood urea nitrogen levels were reduced, kidney tissue SOD activity was increased, MDA levels was reduced, HIF-1,BNIP3,caspase3 and PARP levels were increased than the CI-AKI group. This study indicates that CIHH pretreatment may have a protective effect on contrast-induced early kidney injury by activating the HIF-1/BNIP3 signaling pathway to regulate mitochondrial autophagy and enhance cellular anti-apoptotic and renal antioxidant capacity, for the first time.


title: Orchestration of Chlorophyll and Carotenoid Biosynthesis by ORANGE Family Proteins in Plant

abstract: Chlorophyll and carotenoid are essential photosynthetic pigments. Plants must spatiotemporally coordinate the needs of chlorophyll and carotenoid for optimal photosynthesis and plant fitness in response to diverse environmental and developmental cues. However, how these two biosynthesis pathways are orchestrated remains largely unknown. Here, we report that the highly conserved ORANGE (OR) family proteins are the common regulators of both pathways via posttranslationally regulating the first committed enzyme in each pathway. We demonstrate that OR family proteins physically interact with magnesium chelatase subunit I (CHLI) in addition to phytoene synthase (PSY) and concurrently regulate CHLI and PSY protein stability and activity. We show that loss of OR genes hinders both chlorophyll and carotenoid biosynthesis, limits light-harvesting complex assembly, and impairs thylakoid grana stacking in chloroplast. OR overexpression safeguards photosynthetic pigment biosynthesis and enhances thermotolerance in both Arabidopsis and tomato plants. Our findings establish a conserved mechanism of green plant to coordinate chlorophyll and carotenoid biosynthesis and provide a potential genetic target to generate climate-resilient crops.

category: plant biology


title: Novel AlphasynucleinPAN in human Mesenchymal Stem Cells-derived neurons masks SNCA140 and creates dissociation of deleterious SNCA98 in astrocytoma stem cells

abstract: This manuscript has been withdrawn by the authors as it was submitted and made public without the full consent of all the authors. If you have any questions, please contact the corresponding author.


title: Allometric scaling of a superposition eye optimises sensitivity and acuity in large and small hawkmoths

abstract: Animals vary widely in body size across and within species. This has consequences in large and small individuals for the function of organs and body parts. How these scale in relation to body size reveals evolutionary investment strategies, often resulting in trade-offs between functions. Eyes exemplify these trade-offs, as they are limited by their absolute size in two key performance features: sensitivity and spatial acuity. Previous studies of the 3D structure of apposition compound eyes, which are ideal models for allometric studies due to their size polymorphism, revealed that allometric scaling improves both local resolution and visual sensitivity in larger bumblebees (Taylor et al., 2019). Here, we build on the established methods and results to investigate allometric scaling in superposition compound eyes - the second prominent eye type in insects - for the first time. Our research highlights a surprising strategy to cope with the challenge of trading off sensitivity and spatial resolution in small eyes, as we show that the eyes of the hummingbird hawkmoth retain an optimal balance of these performance measures across all body sizes.


title: In situ cell-surface conformation of the TCR-CD3 signaling complex

abstract: T cells play a vital role in adaptive immune responses to infections, inflammation and cancer and are dysregulated in autoimmunity. Antigen recognition by T cells - a key step in adaptive immune responses - is performed by the T cell receptor (TCR)-CD3 complex. The extracellular molecular organization of the individual CD3 subunits (CD3{delta}{varepsilon} and CD3 {gamma}{varepsilon}) around the {beta}TCR is critical for T cell signaling. Here, we incorporated unnatural amino acid (UAA) photo-crosslinkers at specific mouse TCR, TCR{beta}, CD3{delta} and CD3{gamma} sites, based on previous mutagenesis, NMR spectroscopy and cryo-EM evidence, and crosslinking allowing us to identify nearby interacting CD3 or TCR subunits on the mammalian cell surface. Using this approach, we show that CD3{gamma} and CD3{varepsilon}, belonging to CD3{gamma}{varepsilon} heterodimer crosslinks to C{beta} FG loop and C{beta} G strand, respectively and CD3{delta} crosslinks to C{beta} CC loop and C DE loop. Together with computational docking, we identify that in in situ cell-surface conformation, the CD3 subunits exists in CD3{varepsilon}-CD3{gamma}-CD3{varepsilon}-CD3{delta} arrangement around the {beta} TCR. This unconventional technique, which uses the native mammalian cell surface microenvironment, includes the plasma membrane and excludes random, artificial crosslinks, captures a dynamic, biologically relevant, cell-surface conformation of the TCR-CD3 complex, which is compatible with the reported static cryo-EM structures overall CD3 subunits arrangement, but with key differences at the TCR-CD3 interface, which may be critical for experiments in T cell model systems.


title: Tongue immune compartment analysis reveals spatial macrophage heterogeneity

abstract: The tongue is a unique muscular organ situated in the oral cavity where it is involved in taste sensation, mastication and articulation. As a barrier organ, which is constantly exposed to environmental pathogens, the tongue is expected to host an immune cell network ensuring local immune defence. However, the composition and the transcriptional landscape of the tongue immune system are currently not completely defined. Here we characterised the tissue-resident immune compartment of the murine tongue during development, health and disease, combining single cell RNA-sequencing with in situ immunophenotyping. We identified distinct local immune cell populations and described two specific subsets of tongue-resident macrophages occupying discrete anatomical niches. Cx3cr1+ macrophages were located specifically in the highly innervated lamina propria beneath the tongue epidermis and at times in close proximity to fungiform papillae. Folr2+ macrophages were detected in deeper muscular tissue. The two macrophage subsets originate from a common proliferative precursor during early postnatal development and responded differently to systemic LPS in vivo. Our description of the under-investigated tongue immune system sets a starting point to facilitate research on tongue immune-physiology and pathology including cancer and taste disorders.


title: Targeting NAAA counters dopamine neuron loss and symptom progression in mouse models of Parkinson's disease

abstract: The lysosomal cysteine hydrolase N-acylethanolamine acid amidase (NAAA) deactivates the lipidderived mediator palmitoylethanolamide (PEA), an endogenous PPAR- agonist that is critically involved in the control of inflammation and nociception. In this study, we asked whether NAAA-regulated PEA signaling might contribute to the pathogenesis of Parkinsons disease (PD), a neurodegenerative disorder characterized by progressive loss of nigrostriatal dopamine neurons. Analyses of postmortem brain cortex and premortem blood-derived exosomes found elevated levels of NAAA expression in persons with PD compared to age-matched controls. Furthermore, in vitro experiments showed that the dopaminergic neurotoxins, 6-hydroxydopamine (6-OHDA) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), enhanced NAAA expression and lowered PEA content in human SH-SY5Y cells. A similar effect was observed in dopamine neurons and, subsequently, in microglia following 6-OHDA injection in mice. Importantly, deletion of the Naaa gene or pharmacological inhibition of NAAA activity markedly attenuated both dopamine neuron death and parkinsonian symptoms in mice treated with 6-OHDA or MPTP. The results identify NAAA-regulated PEA signaling as a control node for dopaminergic neuron survival and a potential target for therapeutic intervention in PD.


title: Characterization of alkaloids and metabolic intermediates from Dendrobium officinale induced by methyl jasmonate

abstract: JA signaling plays a pivotal role in plant stress responses and secondary metabolism. Many studies have demonstrated that jasmonates effectively induce the expressions of alkaloid biosynthesis genes in various plants, which rendered to the accumulation of alkaloid to counteract stresses. Despite the multiple roles of JAs in the regulation of plant growth and different stresses, less studied involved in the regulatory role of JA in Dendrobium officinale. Here, a strategy for the rapid identification of alkaloid and precursors of D. officinale was established based on a solid-phase extraction-high performance liquid chromatography-linear ion trap- Orbitrap tandem mass spectrometry (SPE-HPLC-LTQ-Orbitrap) method. The potential compounds were tentatively identified by aligning the accurate molecular weight with the METLIN and Dictionary of Natural Products databases. The chemical structures and main characteristic fragments of the potential compounds were further confirmed by retrieving the multistage mass spectra from the MassBank and METLIN databases.The Mass Frontier software was used to speculate the fragmentation pathway of the identified compounds. As a result, seven alkaloids were separated and identified from D. officinale, which were mainly classified into five types (tropane alkaloids, tetrahydroisoquinoline alkaloids, quinolizidine alkaloids, piperidine alkaloids and spermidine alkaloids). Besides the alkaloids, forty-nine chemical substances, including guanidines, nucleotides, dipeptides, sphingolipids and nitrogen-containing glucosides, were concurrently identified in the experiment. Taken together, this study revealed the composition of chemicals currently found in D. officinale, which could provide the scientific method for the identification of alkaloids in other Dendrobium plants.


title: Binding Interactions between RBD of Spike-Protein and Human ACE2 in Omicron variant

abstract:
Emergence of new SARS-CoV-2 Omicron VOC (OV) has exacerbated the COVID-19 pandemic due to a large number of mutations in the spike-protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strain. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly due predominantly to strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.

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category: biochemistry


title: Molecular Dynamics Simulations Studies On The Effects Of Mutations On The Binding Affinities Between SARS-CoV-2 Spike RBD And Human ACE2

abstract: CONSPECTUSThe SARS-CoV-2 viruses had made a great impact on humankind and the world economy. Phylogenetic analysis revealed the newly identified B.1.617.1 and B.1.617.2 lineages possessed with few key mutations predominantly circulating. The signature mutations possessed by these lineages are situated in the RBD motif of S protein. Reports revealed variants L452R, T478K, and E484Q harbours in enhancement with hACE2 binding while P681R situated in furin cleavage site resulting in better transmissibility. To gain a deeper understanding of the impact of these variants (L452R, T478K and E484Q) binding with hACE2, structural dynamics at the interface between S-RBD protein and hACE2 were studied. We performed our dynamics studies with both single mutant complex (L452R, T478K and E484Q) and in the combination of triple mutants (L452R + T478K + E484Q) at 100ns in contrast with the wild type. Interfacial docking interactions and Molecular Mechanics approach exhibited that the spike mutants -L452R, T478K and E484Q harbour with higher binding affinity on hACE2 in contrast with its native spike protein. The presence of interfacial residue, intermolecular contacts such as hydrogen bonding, salt bridge and non-hydrogen bonded interactions might be the reason for its higher binding affinity. Hence the findings from our study unravelled plausible mechanism for the increase in affinities of mutants to hACE2 thus leading to higher transmissibility and infection of emerging variants. Further, the conformational alterations in the course of dynamics at the RBD motif led to enhancement of hACE2 binding and immune escape. These results suggest that the structural changes introduced by these variants enhance the binding affinities of the S protein with the hACE2 that could form the basis to further aid in designing therapeutics that could inhibit at the interface of S protein and hACE2 receptor.


title: Omicron (BA.1) and Sub-Variants (BA.1, BA.2 and BA.3) of SARS-CoV-2 Spike Infectivity and Pathogenicity: A Comparative Sequence and Structural-based Computational Assessment

abstract: The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread throughout the world. We used computational tools to assess the spike infectivity, transmission, and pathogenicity of Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) in this study. BA.1 has 39 mutations, BA.1.1 has 40 mutations, BA.2 has 31 mutations, and BA.3 has 34 mutations, with 21 shared mutations between all. We observed 11 common mutations in Omicrons receptor-binding domain and sub-variants. In pathogenicity analysis, the Y505H, N786K, T95I, N211I, N856K, and V213R mutations in omicron and sub-variants are predicted to be deleterious. Due to the major effect of the mutations characterising, in the receptor-binding domain (RBD), we found that Omicron and sub-variants had a higher positive electrostatic surface potential. This could increase interaction between RBD and electronegative human angiotensin-converting enzyme 2 (hACE2). Omicron and sub-variants had a higher affinity for hACE2 and the potential for increased transmission when compared to the wild type. Among Omicron sub-lineages, BA.2 and BA.3 have a higher transmission potential than BA.1 and BA.1.1. We predicted that mutated residues in BA.1.1 (K478), BA.2 (R400, R490, R495), and BA.3 (R397 and H499) formation of new salt bridges and hydrogen bonds. Omicron and sub-variant mutations at Receptor-binding Motif (RBM) residues such as Q493R, N501Y, Q498, T478K, and Y505H all contribute significantly to binding affinity with human ACE2. Interactions with Omicron variant mutations at residues 493, 496, 498, and 501 seem to restore ACE2 binding effectiveness lost due to other mutations like K417N and Y505H.


title: An efficient and cost-effective method for directed mutagenesis at multiple dispersed sites - a case study with Omicron Spike DNA

abstract:
Site directed mutagenesis is an invaluable technique which enables the elucidation of the contribution of specific residues to protein structure and function. The simultaneous introduction of mutations at a large number of sites (>10), singly and in multiple combinations is often necessary to fully understand the functional contributions. We report a simple, efficient, time and cost effective method to achieve this using commonly available molecular biology reagents and protocols, as an alternative to gene synthesis. We demonstrate this method using the Omicron Spike DNA construct as an example, and create a construct bearing 37 mutations (as compared to wild-type Spike DNA), as well as four other constructs bearing subsets of the full spectrum of mutations. We believe that this method can be an excellent alternative to gene synthesis, especially when three or more variants are required.

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title: Increased prevalence of a frontoparietal brain state at rest is associated with better motor recovery in individuals with pontine stroke affecting dominant-hand corticospinal tract

abstract: Strokes cause lesions that damage brain tissue, disrupt normal brain activity patterns and can lead to impairments in motor function. Although modulation of cortical activity is central to stimulation-based rehabilitative therapies, aberrant and adaptive patterns of brain activity after stroke have not yet been fully characterized. Here, we apply a brain dynamics analysis approach to study longitudinal brain activity patterns in individuals with ischemic pontine stroke. We first found 4 commonly occurring brain states largely characterized by high amplitude activations in the visual, frontoparietal, default mode, and motor networks. Stroke subjects spent less time in the frontoparietal state compared to controls. For individuals with dominant-hand CST damage, more time spent in the frontoparietal state from 1 week to 3-6 months post-stroke was associated with better motor recovery over the same time period, an association which was independent of baseline impairment. Furthermore, the amount of time spent in brain states was linked empirically to functional connectivity. This work suggests that when the dominant-hand CST is compromised in stroke, resting state configurations may include increased activation of the frontoparietal network, which may facilitate compensatory neural pathways that support recovery of motor function when traditional motor circuits of the dominant-hemisphere are compromised.


title: Increased prevalence of a frontoparietal brain state is associated with better motor recovery in individuals with pontine stroke affecting dominant-hand corticospinal tract


title: Predicting Math Ability using Working Memory, Number Sense, and Neurophysiology in Children and Adults

abstract: Previous work has shown relations between domain-general processes, domain-specific processes, and mathematical ability. However, the underlying neurophysiological effects of mathematical ability are less clear. Recent evidence highlighted the potential role of beta oscillations in mathematical ability. Here we investigate whether domain-general (working memory) and domain-specific (number sense) mediate the relation between resting-state beta oscillations and mathematical ability, and how this may differ as a function of development (children vs. adults). We compared a traditional analysis method normally used in EEG studies with a more recently developed parameterization method that separates periodic from aperiodic activity. Regardless of methods chosen, we found no support for mediation of working memory and number sense, neither for children nor for adults. However, we found subtle differences between the methods. Additionally, we showed that the traditional EEG analysis method conflates periodic activity with aperiodic activity, and the latter is strongly related to mathematical ability and this relation differs between children and adults. At the cognitive level, our findings do not support previous suggestions of a mediation of working memory and number sense. At the neurophysiological level our findings suggest that aperiodic, rather than periodic, activity is linked to mathematical ability as a function of development.


title: Genetic and microbial diversity of the invasive mosquito vector species Culex tritaeniorhynchus across its extensive inter-continental geographic range

abstract:
Culex (Cx.) tritaeniorhynchus is a mosquito species with an extensive and expanding inter-continental geographic distribution, currently reported in over 50 countries, across Asia, Africa, the Middle East, Europe and now Australia. It is an important vector of medical and veterinary concern, capable of transmitting multiple arboviruses which cause significant morbidity and mortality in human and animal populations. In regions endemic for Japanese encephalitis virus (JEV) in Asia, Cx. tritaeniorhynchus is considered the major vector and this species has also been shown to contribute to the transmission of several other significant zoonotic arboviruses, including Rift Valley fever virus and West Nile virus.

Significant variation in vectorial capacity can occur between different vector populations. Obtaining knowledge of a species from across its geographic range is crucial to understanding its significance for pathogen transmission across diverse environments and localities. Vectorial capacity can be influenced by factors including the mosquito genetic background, composition of the microbiota associated with the mosquito and the co-infection of human or animal pathogens. In addition to enhancing information on vector surveillance and potential risks for pathogen transmission, determining the genetic and microbial diversity of distinct populations of a vector species is also critical for the development and application of effective control strategies.

In this study, multiple geographically dispersed populations of Cx. tritaeniorhynchus from countries within Europe, Africa, Eurasia and Asia were sampled. Molecular analysis demonstrated a high level of genetic and microbial diversity within and between populations, including genetic divergence in the mosquito CO1 gene, as well as diverse microbiomes identified by 16S rRNA gene amplicon sequencing. Evidence for the detection of the endosymbiotic bacteria Wolbachia in some populations was confirmed using Wolbachia-specific PCR detection and sequencing of Wolbachia MLST genes; in addition to PCR-based detection of insect-specific viruses. Laboratory vector competence showed Cx. tritaeniorhynchus from a Greek population are likely to be competent vectors of JEV. This study expands understanding of the diversity of Cx. tritaeniorhynchus across its inter-continental range, highlights the need for a greater focus on this invasive vector species and helps to inform potential future directions for development of vector control strategies.

category: genetics


title: Profiling of the most reliable mutations from sequenced SARS-CoV-2 genomes scattered in Uzbekistan

abstract: Due to rapid mutations in the coronavirus genome over time and re-emergence of multiple novel variants of concerns (VOC), there is a continuous need for a periodic genome sequencing of SARS-CoV-2 genotypes of particular region. This is for on-time development of diagnostics, monitoring and therapeutic tools against virus in the global pandemics condition. Toward this goal, we have generated 18 high-quality whole-genome sequence data from 32 SARS-CoV-2 genotypes of PCR-positive COVID-19 patients, sampled from the Tashkent region of Uzbekistan. The nucleotide polymorphisms in the sequenced sample genomes were determined, including nonsynonymous (missense) and synonymous mutations in coding regions of coronavirus genome. Phylogenetic analysis grouped fourteen whole genome sample sequences (1, 2, 4, 5, 8, 10-15, 17, 32) into the G clade (or GR sub-clade) and four whole genome sample sequences (3, 6, 25, 27) into the S clade. A total of 128 mutations were identified, consisting of 45 shared and 83 unique mutations. Collectively, nucleotide changes represented one unique frameshift mutation, four upstream region mutations, six downstream region mutations, 50 synonymous mutations, and 67 missense mutations. The sequence data, presented herein, is the first coronavirus genomic sequence data from the Republic of Uzbekistan, which should contribute to enrich the global coronavirus sequence database, helping in future comparative studies. More importantly, the sequenced genomic data of coronavirus genotypes of this study should be useful for comparisons, diagnostics, monitoring, and therapeutics of COVID-19 disease in local and regional levels.

category: genomics


title: PP1 inhibitor-2 promotes PP1γ positive regulation of synaptic transmission

abstract: Inhibitor-2 (I-2) is a prototypic inhibitor of protein phosphatase-1 (PP1), a major serine-threonine phosphatase that regulates synaptic plasticity and learning and memory. Although I-2 is a potent inhibitor of PP1 in vitro, our previous work has elucidated that, in vivo, I-2 may act as a positive regulator of PP1. Here we show that I-2 and PP1{gamma}, but not PP1, positively regulate synaptic transmission in hippocampal neurons. Moreover, we demonstrated that I-2 enhances PP1{gamma} interaction with its major synaptic scaffold, neurabin, by Forster resonance energy transfer (FRET)/Fluorescence lifetime imaging microscopy (FLIM) studies, while having a limited effect on PP1 autoinhibitory phosphorylation. Furthermore, our study indicates that the effect of I-2 on PP1 activity in vivo is dictated by I-2 threonine-72 phosphorylation. Our work thus demonstrates a molecular mechanism by which I-2 positively regulates PP1 function in synaptic transmission.


title: Duration reproduction under memory pressure: Modeling the roles of visual memory load in duration encoding and reproduction

abstract: Duration estimates are often biased by the sampled statistical context, yielding the classical central-tendency effect, i.e., short durations are over- and long duration underestimated. Most studies of the central-tendency bias have primarily focused on the integration of the sensory measure and the prior information, without considering any cognitive limits. Here, we investigated the impact of cognitive (visual working-memory) load on duration estimation in the duration encoding and reproduction stages. In four experiments, observers had to perform a dual, attention-sharing task: reproducing a given duration (primary) and memorizing a variable set of color patches (secondary). We found an increase in memory load (i.e., set size) during the duration-encoding stage to increase the central-tendency bias, while shortening the reproduced duration in general; in contrast, increasing the load during the reproduction stage prolonged the reproduced duration, without influencing the central tendency. By integrating an attentional-sharing account into a hierarchical Bayesian model, we were able to predict both the general over- and underestimation and the central-tendency effects observed in all four experiments. The model suggests that memory pressure during the encoding stage increases the sensory noise, which elevates the central-tendency effect. In contrast, memory pressure during the reproduction stage only influences the monitoring of elapsed time, leading to a general duration over-reproduction without impacting the central tendency.


title: Non-invasive stimulation with Temporal Interference: Optimization of the electric field deep in the brain with the use of a genetic algorithm

abstract:
ObjectiveSince the introduction of transcranial temporal interference stimulation (tTIS), there has been an ever-growing interest in this novel method, as it theoretically allows non-invasive stimulation of deep brain target regions. To date, attempts have been made to optimize the electrode montages and injected current to achieve personalized area targeting using two electrode pairs. Most of these methods use exhaustive search to find the best match, but faster and, at the same time, reliable solutions are required. In this study, the aforementioned stimulation settings were optimized using a genetic algorithm.

MethodsSimulations were performed on head models from the Population Head Model (PHM) repository. First, each model was fitted with an electrode array based on the 10-10 international EEG electrode placement system. Following electrode placement, the models were meshed and solved for all single-pair electrode combinations using an electrode on the left mastoid as a reference (ground). At the optimization stage, different electrode pairs and injection currents were tested using a genetic algorithm to obtain the optimal combination for each model.

ResultsGreater focality was achieved with optimization, specifically for the right hippocampus (region of interest), with a significant decrease in the surrounding electric field intensity. In the non-optimized case, the brain volumes stimulated above 0.2V/m were 99.9% in the region of interest (ROI), and 76.4% in the rest of the gray matter. In contrast, the stimulated volumes were 91.4% and 29.6% for the best optimization case. Additionally, the maximum electric field intensity inside the region of interest was consistently higher than that outside the ROI for all optimized cases.

SignificanceGiven that the accomplishment of a globally optimal solution requires a brute-force approach, the use of a genetic algorithm can significantly decrease the optimization time and provide usable results. Although the method is promising and the indications are becoming more robust, such that optimal solutions can be achieved at the individual level, there are limitations on what can be achieved using only two electrode pairs.


title: Aging and white matter microstructure and macrostructure: a longitudinal multi-site diffusion MRI study of 1,184 participants

abstract: Quantifying the microstructural and macrostructural geometrical features of the human brains connections is necessary for understanding normal aging and disease. Here, we examine brain white matter diffusion magnetic resonance imaging data from one cross-sectional and two longitudinal datasets totaling in 1184 subjects and 2236 sessions of people aged 50-97 years. Data was drawn from well-established cohorts, including the Baltimore Longitudinal Study of Aging dataset, Cambridge Centre for Ageing Neuroscience dataset, and the Vanderbilt Memory & Aging Project. Quantifying 4 microstructural features and, for the first time, 11 macrostructure-based features of volume, area, and length across 120 white matter pathways, we apply linear mixed effect modeling to investigate changes in pathway-specific features over time, and document large age associations within white matter. Conventional diffusion tensor microstructure indices are the most age-sensitive measures, with positive age associations for diffusivities and negative age associations with anisotropies, with similar patterns observed across all pathways. Similarly, pathway shape measures also change with age, with negative age associations for most length, surface area, and volume-based features. A particularly novel finding of this study is that while trends were homogeneous throughout the brain for microstructure features, macrostructural features demonstrated heterogeneity across pathways, whereby several projection, thalamic, and commissural tracts exhibited more decline with age compared to association and limbic tracts. The findings from this large-scale study provide a comprehensive overview of the age-related decline in white matter and demonstrate that macrostructural features may be more sensitive to heterogeneous white matter decline. Therefore, leveraging macrostructural features may be useful for studying aging and could have widespread implications for a variety of neurodegenerative disorders.


title: Operational tolerance is early acquired and long maintained in 50% liver allograft transplantation

abstract: Lifelong anti-rejection therapy is mandatory to weaken the host immune system and maintain the graft functions after organ transplantation, its toxicities and side-effects incidentally elicit mortalities and morbidities. Operational tolerance is a long immunosuppression-free state in which the allograft functions well and no immunological rejections occur, and no operational tolerance is clinically in use. Here we introduce that operational tolerance, based on hypertrophy to hyperplasia switch upon liver regeneration, is early achieved and maintained well in half-size liver allograft transplantation through host bone marrow stem cells repopulation and 9-day immunosuppression. Compared with whole and partial rat liver transplantations as the controls, longer-term survivals (over 430 days) were observed in the tolerant hosts (p= 0.001), the allografts functioned well and no acute or chronic rejections were confirmed by histology examinations. Further study revealed that the allograft was reinstituted by host-derived stem cells marked with CD34, which migrated, repopulated and differentiated after mobilization. However donor-specific hyporesponse was not achieved through skin transplantation, indicating no adaptive immune activity occurrence. Our protocol is characteristic of targeting the allografts and almost no immunological intervention, offering a novel avenue to operational tolerance induction which is of highly clinical relevance.


title: RNA polymerase redistribution and increased gene dosage support growth in E. coli strains with a minimal number of ribosomal RNA operons

abstract: Bacterial transcription by RNA polymerase (RNAP) is spatially organised. RNAPs transcribing highly expressed genes locate in the nucleoid periphery, and form clusters in rich media, with several studies linking RNAP clustering and transcription of ribosomal RNA (rrn). However, the nature of RNAP clusters and their association with rrn transcription remains unclear. Here we address these questions by using single-molecule tracking to monitor the subcellular distribution of mobile and immobile RNAP in strains with a heavily reduced number of chromosomal rrn operons ({Delta}rrn strains). Strikingly, we find that the fraction of chromosome-associated RNAP (which is mainly engaged in transcription) is robust to deleting 5 or 6 of the 7 chromosomal rrn operons. Spatial analysis in{Delta} rrn strains showed substantial RNAP redistribution during moderate growth, with clustering increasing at the cell end-caps, where the remaining rrn operons reside. These results support a model where RNAPs in{Delta} rrn strains relocate to copies of the remaining rrn operons. We also show that{Delta} rrn strains experience increased rrn gene dosage in rich media, minimising growth defects due to rrn deletions. Our study further links RNAP clusters and rrn transcription, and offers insight on how bacteria maintain growth in the presence of only 1-2 rrn operons.


title: Clostridia isolated from helminth-colonized humans promote hatching of Trichuris muris

abstract: Soil transmitted intestinal worms known as helminths colonize over 1.5 billion people worldwide. Although helminth colonization has been associated with altered composition of the gut microbiota, such as increases in Clostridia, individual species have not been isolated and characterized. Here, we isolated and sequenced the genome of 13 Clostridia from the Orang Asli, an indigenous population in Malaysia with high prevalence of helminth infections. Metagenomic analysis of 650 fecal samples from urban and rural Malaysians revealed higher prevalence and abundance of these isolates compared to individuals in the United States, with Peptostreptococcaceae family members displaying a specific association with helminth colonization. Remarkably, Peptostreptococcaceae isolated from the Orang Asli displayed superior capacity to induce hatching of eggs from the murine helminth Trichuris muris. These findings support a model in which helminths select for gut colonization of microbes that in turn support their life cycle by promoting egg hatching.


title: DISSECTING LIGHT SENSING AND METABOLIC PATHWAYS ON THE MILLIMETER SCALE IN HIGH-ALTITUDE MODERN STROMATOLITES

abstract: Modern non-lithifying stromatolites (STs) on the shore of the volcanic lake Socompa in the Puna are affected by several extreme conditions. Although STs were proposed as ecologic models for understanding stress response and resilience in microbial ecosystems constituting a window into the past, our knowledge of ST function is still nascent. The present study assesses for the first time light utilization and functional metabolic stratification of STs on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. Our results demonstrated that Bacteroidetes and Cyanobacteria play major roles as ST builders and primary producers to sustain a diverse community of heterotrophs. STs manifest a high occurrence of genes for the synthesis of UV-protecting pigments, the cryptochrome-photolyase family (CPF), and rhodopsins in the surface layers. Three different ecologic niches involving the use of light in energy production were defined. Calvin-Benson and Wood-Ljungdahl pathways were proposed as the main mechanisms for carbon fixation. Several genes account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the ST described previously. Finally, our study points to STs as ideal modern analogues of ancient STs.


title: Photolabile curcumin with physically and molecularly produced light for attenuating of neurotoxicity of amyloid beta species

abstract: Over the past decades, classical drug development approaches for Alzheimers disease have yielded limited success, and this futileness has prompted scientists to seek non-classical approaches. In this report, we demonstrated that, with irradiation of LED light or with molecularly generated light (dubbed as "molecular light") from chemiluminescence probe ADLumin-4, photolabile CRANAD-147 could cause changes of properties, structures (sequences) and neurotoxicity of amyloid beta (A{beta}) species in vitro. We further demonstrated that, with the assistance from molecular chemiluminescence imaging, the combination of CRANAD-147/LED or CRANAD-147/ADLumin-4 (molecular light) could slow down the accumulation of A{beta}s in transgenic 5xFAD mice in vivo. Due to the unlimited capacity of tissue penetration of molecular light in vivo, phototherapy with the combination of photolabile A{beta} ligand and molecular light has great potential as an alternative approach for AD drug discovery.


title: CaSee: A lightning transfer-learning model directly used to discriminate cancer/normal cells from scRNA-seq

abstract: Single-cell RNA sequencing (scRNA-seq) is one of the most efficient technologies for human tumor research. However, data analysis is still faced with some technical challenges, especially the difficulty in efficiently and accurately discriminate cancer/normal cells in the scRNA-seq expression matrix. In this study, we developed a cancer/normal cell discrimination pipeline called pan-cancer seeker (CaSee) devoted to scRNA-seq expression matrix, which is based on the traditional high-quality pan-cancer bulk sequencing data using transfer learning. It is compatible with mainstream sequencings technology platforms, 10x Genomics Chromium, Smart-seq2, and Microwell-seq. Here, CaSee pipeline exhibited excellent performance in the multicenter data evaluation of 11 retrospective cohorts and one independent dataset, with an average discrimination accuracy of 96.69%. In general, the development of a deep-learning based, pan-cancer cell discrimination model, CaSee, to distinguish cancer cells from normal cells will be compelling to researchers working in the genomics, cancer, and single-cell fields.

category: bioinformatics


title: polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies

abstract: Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) Continuous Long Reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.


title: MIAMI: Mutual Information-based Analysis of Multiplex Imaging data

abstract:
MotivationStudying the interaction or co-expression of the proteins or markers in the tumor microenvironment (TME) of cancer subjects can be crucial in the assessment of risks, such as death or recurrence. In the conventional approach, the cells need to be declared positive or negative for a marker based on its intensity. For multiple markers, manual thresholds are required for each marker, which can become cumbersome. The performance of the subsequent analysis relies heavily on this step and thus suffers from subjectivity and lack of robustness.

ResultsWe present a new method where different marker intensities are viewed as dependent random variables, and the mutual information (MI) between them is considered to be a metric of co-expression. Estimation of the joint density, as required in the traditional form of MI, becomes increasingly challenging as the number of markers increases. We consider an alternative formulation of MI which is conceptually similar but has an efficient estimation technique for which we develop a new generalization. With the proposed method, we analyze a lung cancer dataset and a triple-negative breast cancer dataset finding the co-expression of the markers, HLA-DR and CK and the co-expression of markers, HLA-DR, CD45RO, HLA-Class-1, H3K27me3 and H3K9ac to be associated with survival in the two datasets respectively. We also demonstrate the robustness of our method through different simulation studies.

AvailabilityThe associated R package can be found here, https://github.com/sealx017/MIAMI.

Contactsouvik.seal@cuanschutz.edu

Supplementary informationThe supplementary material is attached.