Biology subjects

Rao, M.

Publications and source records attributed to Rao, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Sex differences and immune correlates of Long COVID development, persistence, and resolution

Sex differences have been observed in acute COVID-19 and Long COVID (LC) outcomes, with greater disease severity and mortality during acute infection in males and a greater proportion of females developing LC. We hypothesized that sex-specific immune dysregulation contributes to the pathogenesis of LC. To investigate the immunologic underpinnings of LC development and persistence, we used single-cell transcriptomics, single-cell proteomics, and plasma proteomics on blood samples obtained during acute SARS-CoV-2 infection and at 3 and 12 months post-infection in a cohort of 45 patients who either developed LC or recovered. Several sex-specific immune pathways were associated with LC. Specifically, males who would develop LC at 3 months had widespread increases in TGF-{beta} signaling during acute infection in proliferating NK cells. Females who would develop LC demonstrated increased expression of XIST, an RNA gene implicated in autoimmunity, and increased IL1 signaling in monocytes at 12 months post infection. Several immune features of LC were also conserved across sexes. Both males and females with LC had reduced co-stimulatory signaling from monocytes and broad upregulation of NF-{kappa}B transcription factors. In both sexes, those with persistent LC demonstrated increased LAG3, a marker of T cell exhaustion, reduced ETS1 transcription factor expression across lymphocyte subsets, and elevated intracellular IL-4 levels in T cell subsets, suggesting that ETS1 alterations may drive an aberrantly elevated Th2-like response in LC. Altogether, this study describes multiple innate and adaptive immune correlates of LC, some of which differ by sex, and offers insights toward the pursuit of tailored therapeutics. One Sentence SummaryThis multi-omic analysis of Long COVID reveals sex differences and immune correlates of Long COVID development, persistence, and resolution.

immunology↗

bioRxiv2024

Observation of Higher-Order Assemblies Controlled by Protein One-dimensional Movement

RIG-I-like receptors (RLRs) detect cytosolic viral RNAs and initiate innate immune response. MDA5 is an RLR that recognizes viral long double-stranded RNA (dsRNA). The central helicase and C-terminal domains of MDA5 form a ring-like clamp around dsRNA, and its activation requires the oligomerization of N-terminal caspase activation and recruitment domains (CARDs). Another RLR, LGP2, lacks CARDs but plays essential roles in MDA5 signaling. However, the mechanisms underlying MDA5 CARDs assembly and the collaborative mechanics between MDA5 and LGP2 remain largely unresolved. Here we found the MDA5 ring-like clamp operates as an ATP-hydrolysis-driven motor, with the self-assembly of its CARDs strictly suppressed by the protein one-dimensional (1D) translocation along dsRNA. LGP2 recognizes a mobile MDA5 and inhibits the motors movement, thereby allowing MDA5 CARDs to assemble into oligomers that can further interact with downstream components. These findings highlight how RLR sensors orchestrate higher-order assemblies through 1D movement to direct immune response.

biophysics↗

bioRxiv2024

mTOR inhibition in Q175 Huntington's disease model mice facilitates neuronal autophagy and mutant huntingtin clearance

Huntingtons disease (HD) is caused by expansion of the polyglutamine stretch in huntingtin protein (HTT) resulting in hallmark aggresomes/inclusion bodies (IBs) composed of mutant huntingtin protein (mHTT) and its fragments. Stimulating autophagy to enhance mHTT clearance is considered a potential therapeutic strategy for HD. Our recent evaluation of the autophagic-lysosomal pathway (ALP) in human HD brain reveals upregulated lysosomal biogenesis and relatively normal autophagy flux in early Vonsattel grade brains, but impaired autolysosome clearance in late grade brains, suggesting that autophagy stimulation could have therapeutic benefits as an earlier clinical intervention. Here, we tested this hypothesis by crossing the Q175 HD knock-in model with our autophagy reporter mouse TRGL (Thy-1-RFP-GFP-LC3) to investigate in vivo neuronal ALP dynamics. In the Q175 and/or TRGL/Q175 mice, mHTT was detected in autophagic vacuoles and also exhibited a high level of colocalization with autophagy receptors p62/SQSTM1 and ubiquitin in the IBs. Compared to the robust lysosomal pathology in late-stage human HD striatum, ALP alterations in Q175 models are also late-onset but milder that included a lowered phospho-p70S6K level, lysosome depletion and autolysosome elevation including more poorly acidified autolysosomes and larger-sized lipofuscin granules, reflecting impaired autophagic flux. Administration of a mTOR inhibitor to 6-mo-old TRGL/Q175 normalized lysosome number, ameliorated aggresome pathology while reducing mHTT-, p62- and ubiquitin-immunoreactivities, suggesting the beneficial potential of autophagy modulation at early stages of disease progression.

pathology↗

bioRxiv2024

Enteric glia regulate Paneth cell secretion and intestinal microbial ecology

Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions [1]. To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express PLP1 in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1+ cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1+ glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.

neuroscience↗

bioRxiv2024

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions in a single tissue slice, and aligning or integrating multiple tissue slices originating from diverse sources for essential downstream analyses remain challenging. Numerous clustering, alignment, and integration methods have been specifically designed for ST data by leveraging its spatial information. The absence of benchmark studies complicates the selection of methods and future method development. Here we systematically benchmark a variety of state-of-the-art algorithms with a wide range of real and simulated datasets of varying sizes, technologies, species, and complexity. Different experimental metrics and analyses, like adjusted rand index (ARI), uniform manifold approximation and projection (UMAP) visualization, layer-wise and spot-to-spot alignment accuracy, spatial coherence score (SCS), and 3D reconstruction, are meticulously designed to assess method performance as well as data quality. We analyze the strengths and weaknesses of each method using diverse quantitative and qualitative metrics. This analysis leads to a comprehensive recommendation that covers multiple aspects for users. The code used for evaluation is available on GitHub. Additionally, we provide jupyter notebook tutorials and documentation to facilitate the reproduction of all benchmarking results and to support the study of new methods and new datasets (https://benchmarkst-reproducibility.readthedocs.io/en/latest/).

bioinformatics↗

bioRxiv2024

MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning

Recent advancements in spatial transcriptomics (ST) have underscored the importance of integrating data from multiple ST slices for joint analysis. A major challenge remains generating interpretable joint embeddings that preserve geometric information for downstream analyses. Here we introduce MaskGraphene, a graph neural network that combines self-supervised and self-contrastive training to integrate gene expression and spatial location into joint embeddings. By employing clusterwise alignment and a graph attention autoencoder with masked self-supervised and triplet loss optimizations, MaskGraphene effectively preserves geometric structures while achieving batch correction. In benchmarks against seven state-of-the-art methods, MaskGraphene consistently demonstrated superior alignment accuracy and geometric fidelity across diverse ST datasets. Its interpretable embeddings significantly enhanced downstream applications, including domain identification, spatial trajectory reconstruction, biomarker discovery, and the creation of topographical maps of brain slices. Notably, MaskGraphene successfully recovered layer-wise brain structures with near-perfect accuracy. MaskGraphene provides a powerful and versatile framework for advancing ST data integration and analysis, unlocking valuable biological insights.

bioinformatics↗

bioRxiv2024

Evaluating the likelihood for areas important for conservation to be recognized as Other Effective area-based Conservation Measures

Other effective area-based conservation measures (OECMs) have expanded area-based conservation to recognize sites that deliver effective biodiversity outcomes even if not managed for conservation. Yet our ability to identify sites likely to qualify as OECMs remains limited. To address this gap, we established and tested a set of indicators to judge whether sites meet the essential criteria to be considered OECMs, evaluating a large, global sample of 173 important conservation areas: 81 potential OECMs and 92 nearby protected areas. We found that most potential OECMs were largely in good condition with the potential to achieve conservation outcomes, but none currently met all the OECM criteria. Formally designated protected areas in our dataset performed better but the majority also failed the criteria. With so many important conservation areas unable to deliver effective conservation outcomes, our findings raise important questions about how to ensure area-based conservation promotes positive and sustained outcomes for biodiversity.

ecology↗

bioRxiv2024

Development and optimization of a diluted whole blood ELISpot assay to test immune function

BackgroundSepsis remains a leading cause of death worldwide with no proven immunomodulatory therapies. Stratifying Patient Immune Endotypes in Sepsis ( SPIES) is a prospective, multicenter observational study testing the utility of ELISpot as a functional bioassay specifically measuring cytokine-producing cells after stimulation to identify the immunosuppressed endotype, predict clinical outcomes in septic patients, and test potential immune stimulants for clinical development. Most ELISpot protocols call for the isolation of PBMC prior to their inclusion in the assay. In contrast, we developed a diluted whole blood (DWB) ELISpot protocol that has been validated across multiple laboratories. MethodsHeparinized whole blood was collected from healthy donors and septic patients and tested under different stimulation conditions to evaluate the impact of blood dilution, stimulant concentration, blood storage, and length of stimulation on ex vivo IFN{gamma} and TNF production as measured by ELISpot. ResultsWe demonstrate a dynamic range of whole blood dilutions that give a robust ex vivo cytokine response to stimuli. Additionally, a wide range of stimulant concentrations can be utilized to induce cytokine production. Further modifications demonstrate anticoagulated whole blood can be stored up to 24 hours at room temperature without losing significant functionality. Finally, we show ex vivo stimulation can be as brief as 4 hours allowing for a substantial decrease in processing time. ConclusionsThe data demonstrate the feasibility of using ELISpot to measure the functional capacity of cells within DWB under a variety of stimulation conditions to inform clinicians on the extent of immune dysregulation in septic patients.

immunology↗

bioRxiv2024

MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets

In order to illustrate the epigenetic heterogeneity, versatile tools of single-cell ChIP-seq (scChIP-seq) are necessary to meet the convenience and accuracy. Here, we develop MobiChIP, a compatible ChIP-seq library construction method based current sequencing platform with single cell level. As a novel capture strategy, MobiChIP is efficient to capture the fragments from tagmented nuclei of numerous species and execute the mixing of samples from different tissues or species. Especially, this strategy enables the flexible sequencing manipulation and sufficient nucleosome amplification without customized sequencing primers. MobiChIP reveals the landscape of chromatin regulation regions with active(H3K27ac) and repressive(H3K27me3) histone modification markers in peripheral blood mononuclear cells (PBMCs), and accurately unveiled the epigenetic repression of hox gene cluster in PBMCs than ATAC-seq. Meanwhile, we complete the bioinformatics pipeline to integrates the scChIP-seq data and scRNA-seq to illustrate the cellular epigenetic and genetic heterogeneity. One-Sentence SummaryA high-throughput single-cell ChIP-seq based droplet reveals the integration of scRNA-seq data and scChIP-seq data.

molecular biology↗

bioRxiv2023

Temporal Changes in Innate and Adaptive Immunity During Sepsis as Determined by ELISpot

BackgroundThe inability to evaluate host immunity in a rapid quantitative manner in patients with sepsis has severely hampered development of novel immune therapies. The ELISpot assay is a functional bioassay that measures the number of cytokine-secreting cells and the relative amount of cytokine produced at the single-cell level. A key advantage of ELISpot is its excellent dynamic range enabling a more precise quantifiable assessment of host immunity. Herein, we tested the hypothesis on whether the ELISpot assay can detect dynamic changes in both innate and adaptive immunity as they often occur during sepsis. We also tested whether ELISpot could detect the effect of immune drug therapies to modulate innate and adaptive immunity. MethodsMice were made septic using sublethal cecal ligation and puncture (CLP). Blood and spleens were harvested serially and ex vivo IFN-{gamma} and TNF- production were compared by ELISpot and ELISA. The capability of ELISpot to detect changes in innate and adaptive immunity due to in vivo immune therapy with dexamethasone, IL-7, and arginine was also evaluated. ResultsELISpot confirmed a decreased innate and adaptive immunity responsiveness during sepsis progression. More importantly, ELISpot was also able to detect changes in adaptive and innate immunity in response to immune-modulatory reagents, for example dexamethasone, arginine, and IL-7 in a readily quantifiable manner, as predicted by the reagents known mechanisms of action. ELISpot and ELISA results tended to parallel one another although some differences were noted. ConclusionELISpot offers a unique capability to assess the functional status of both adaptive and innate immunity over time. The results presented herein demonstrate that ELISpot can also be used to detect and follow the in vivo effects of drugs to ameliorate sepsis-induced immune dysfunction. This capability would be a major advance in guiding new immune therapies in sepsis.

immunology↗

bioRxiv2023

A survey of Rare Disease awareness among healthcare professionals and researchers in India

Rare diseases (RDs) are diseases that occur infrequently and affect a small fraction of the population. Although these diseases individually affect small number of people, together they affect 400 million people globally at any given time. In India, where resources are scarce, healthcare infrastructure and policy framework are focused on mitigating diseases that affect many people. Further, the level of RD awareness among healthcare professionals, researchers, and general public is considerably low. As a result, many cases of RDs remain unreported, undiagnosed, and untreated. To frame policies regarding RDs, it is crucial to understand the current level of RD awareness among healthcare professional and researchers, as they are key stakeholders in diagnosis, treatment, policy making, and drug development. We conducted an exploratory survey to understand the current level of RD awareness among healthcare professionals and researchers based on identification of an RD, time for diagnosis, treatment options, and relationship with family history and geographic location. We noted that our respondents have considerably low level of RD awareness. They correctly identified the importance of family history but failed to realize the association with geographic location. After presenting the survey findings, we have made recommendation to improve RD awareness in India. Our findings will be helpful to design awareness campaigns and frame relevant policies.

scientific communication and education↗

bioRxiv2022

Probing the genetic code and impacts of mistranslation using tRNAAla anticodon variants

Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single-or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C rich anticodons resulted in larger growth deficits than A/U rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.

molecular biology↗

bioRxiv2022

A novel fluorobenzothiazole RBx 10080758 as a dual inhibitor against bacterial GyraseB (GyrB) and Topoisomerase IV (parE) of Gram-positive pathogens causing skin and respiratory infections

Development of a novel inhibitor targeting Gyrase B and Topoisomerase IV offers a potential opportunity to combat the drug resistance. In the present study, we extensively investigated the efficacy of RBx 10080758, a novel fluorobenzothiazole, against skin and respiratory infections caused by Staphylococci and Streptococci in in vitro and in vivo models. RBx 10080758 showed a potent IC50 of 0.06 M against Gyrase and Topoisomerase IV and also exhibited a strong whole cell in vitro activity with MIC ranges of 0.015-0.06, 0.015-0.03, 0.008-0.03, 0.008-0.03, 0.008-0.0.06, 0.015-0.06 g/ml against Staphylococcus. aureus, Streptococcus pneumoniae, Coagulase negative Staphylococci, Streptococcus viridans, Streptococcus pyogenes and Enterococcus, respectively. As expected from the novel class of molecule, it retains potent even against linezolid and vancomycin resistant strains. Interesting, in mouse systemic infection 10 mg/kg, IV dose protected 100% mice from lethal infections. In rat thigh infection model with MRSA WCUH29 at 45 mg/kg exhibited >3-log10 cfu reduction in thigh muscles. RBx 10080758 displayed potent in vitro and in vivo activity against a panel of MDR Gram-positive bacteria. As a novel chemical class, the fluorobenzothiazoles have the potential to become clinically viable antibiotics, to address the drug resistance problem by its unique dual targeting mechanism of action.

microbiology↗

bioRxiv2022

Protein as evolvable functionally-constrained amorphous matter

We explore current ideas around the representation of a protein as an amorphous material, in turn represented by an abstract graph [G] with edges weighted by elastic stiffnesses. By embedding this graph in physical space, we can map every graph to a spectrum of conformational fluctuations and responses (as a result of say, ligand-binding). This sets up a "genotype-phenotype" map, which we use to evolve the amorphous material to select for fitness. Using this, we study the emergence of allosteric interaction, hinge joint, crack formation and a slide bolt in functional proteins such as Adenylate kinase, HSP90, Calmodulin and GPCR proteins. We find that these emergent features are associated with specific geometries and mode spectra of floppy or liquid-like regions. Our analysis provides insight into understanding the architectural demands on a protein that enable a prescribed function and its stability to mutations.

biophysics↗

bioRxiv2022

Optimal reliability, robustness and control of nucleus centering in fission yeast is contingent on nonequilibrium force patterning

Cells, such as fission yeast, center their division apparatus to ensure symmetric cell division, a challenging task when the governing dynamics is stochastic. Here we show that the spindle pole body (SPB) positioning, which defines the division septum, is controlled by the patterning of nonequilibrium polymerization forces of microtubule (MT) bundles. We define two cellular objectives, reliability, the mean SPB position relative to the geometric center, and robustness, the variance of the SPB position, which are sensitive to genetic perturbations that change cell length, MT-bundle number/orientation and MT dynamics. We show that the optimal control of reliability and robustness required to minimize septum positioning error is achieved by the wild-type (WT). A stochastic model for the MT-based nucleus centering, with parameters measured directly or estimated using Bayesian inference, recapitulates WT optimality. We use this to perform a sensitivity analysis of the parameters that control nuclear centering.

cell biology↗

bioRxiv2022

Quantitative analysis of three-dimensional cell organisation and concentration profiles within curved epithelial tissues

Organogenesis involves folding of flat epithelial tissues into three-dimensional (3D) shapes. Quantitative analysis in 3D of the concentration gradients of biochemical and mechano-chemical cues that shape the tissue has remained a challenge, due to the complex tissue geometries. Towards addressing this, we present a methodology that transforms the cartesian images acquired by high-resolution confocal microscopy of curved tissues into a laminar organisation from the outer-most tissue surface. We further detail a data-based intensity correction method to account for the intensity variations that arise as a consequence of the global geometry. Applying our approach to the dome-shaped Drosophila wing disc, we quantitatively estimate the concentration profiles of different biochemical signals, including the Wingless morphogen gradient. The laminar data-organisation method also enabled visualisation of apical and basal layers facilitating an accurate 3D reconstruction of cell shapes within the pseudostratified epithelium. We find that the columnar disc proper cells have irregular 3D shapes and undergo frequent apico-basal cell intercalations, concomitantly leading to cell neighbour exchanges along the apico-basal axis. The workflow of image processing described here may be employed to quantify 3D concentration gradients and 3D cellular organisation in any layered curved tissue, provided a marker describing the reference surface manifold is available.

developmental biology↗

bioRxiv2022

RET Signaling Persists in the Adult Intestine and Stimulates Motility by Limiting PYY Release from Enteroendocrine Cells

Background & AimsRET receptor tyrosine kinase is necessary for enteric nervous system (ENS) development. Loss-of-function RET mutations cause Hirschsprung disease (HSCR), in which infants are born with aganglionic bowel. Despite surgical correction, HSCR patients often experience chronic defecatory dysfunction and enterocolitis, suggesting that RET is important after development. To test this hypothesis, we determined the location of postnatal RET and its significance in gastrointestinal (GI) motility. MethodsRetCFP/+ mice and human transcriptional profiling data were studied to identify the enteric neuronal and epithelial cells that express RET. To determine whether RET signaling in these cells regulates adult gut motility in vivo, genetic and pharmacologic approaches were used to disrupt RET in either all RET-expressing cells, a major subset of enteric neurons, or intestinal epithelial cells. ResultsDistinct subsets of enteric neurons and enteroendocrine cells expressed RET in the adult intestine. RET disruption in the intestinal epithelium, rather than in enteric neurons, slowed GI motility selectively in adult male mice. This effect was phenocopied by RET kinase inhibition. Most RET+ epithelial cells were either enterochromaffin cells that release serotonin (5-HT) or L-cells that release peptide YY (PYY), both of which can alter motility. RET kinase inhibition exaggerated PYY release in a nutrient-dependent manner without altering 5-HT secretion. PYY receptor blockade fully rescued dysmotility in mice lacking epithelial RET. ConclusionRET signaling normally limits nutrient-dependent PYY release from L-cells and this activity is necessary for normal intestinal motility in male mice. These effects could contribute to post-operative dysmotility in HSCR, which predominantly affects males, and uncovers a mechanism that could be targeted to treat post-prandial GI dysfunction. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/488514v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@4c8e83org.highwire.dtl.DTLVardef@204d13org.highwire.dtl.DTLVardef@a429d8org.highwire.dtl.DTLVardef@1b75265_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling

The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered GPI-anchored proteins (GPI-APs) form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drive the creation of active emulsions, mesoscale liquid ordered (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid-phase segregation. To test these ideas we use spatial imaging of homo-FRET combined with local membrane order and demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions, and exhibit significant lipid order, consistent with predictions of the active composite model.

cell biology↗