Biology subjects

Ojha, S.

Publications and source records attributed to Ojha, S..

11 recordsLinked to original sources

bioRxiv2026

Distinct phases of immune system programming during ART-suppressed immunodeficiency virus infection

People living with HIV (PLWH) on suppressive antiretroviral therapy (ART) can face non-AIDS complications, partially driven by chronic immune activation. To define immune perturbations during ART-suppressed viral infection, we performed longitudinal single-cell transcriptomic and plasma proteomic analysis of rhesus macaques infected with SIVmac239M and ART-treated for 70 weeks. We identified broad, bi-phasic immune changes. Acute infection involves an interferon-driven signature, correlated with viral replication, that largely resolves with viral control. Cell-associated virus correlated with interferon-stimulated genes in most tissues; however, this was blunted in gut-associated lymph nodes, a feature that may contribute to reservoir persistence. Separate alterations manifest 54-66 weeks-post-infection, after 40 weeks of viral suppression, including broad TGF-{beta} and NF-kB signaling and discrete bursts of inflammatory monocytes, largely restricted to bone marrow. These data highlight the biphasic remodeling of long-term ART-suppressed HIV, identifying specific tissues and cell populations with dysregulation, with implications for the treatment of PLWH.

immunology↗

bioRxiv2025

Combining a rhesus cytomegalovirus/SIV vaccine with neutralizing antibody to protect against SIV challenge in rhesus macaques

A vaccine is widely regarded as necessary for the control of the HIV pandemic and eventual eradication of AIDS. Neutralizing antibodies and MHC-E-restricted CD8+ T cells have both been shown capable of vaccine protection against the simian counterpart of HIV, SIV, in rhesus macaques. Here we provide preliminary evidence that combining these orthogonal antiviral mechanisms can provide increased protection against SIV challenge such that replication arrest observed following vaccination with a rhesus cytomegalovirus (RhCMV/SIV)-based vaccine was enhanced in the presence of passively administered incompletely protective levels of neutralizing antibody. The report invites studies involving larger cohorts of macaques and alternate routes of providing neutralizing antibody.

immunology↗

bioRxiv2024

Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

Accumulation of extracellular matrix (ECM) in liver fibrosis is associated with changes in protein abundance and composition depending upon etiology of the underlying liver disease. Current efforts to unravel etiology-specific mechanisms and pharmacological targets rely on several models of experimental fibrosis. Here, we characterize and compare dynamics of hepatic proteome remodeling during fibrosis development and spontaneous healing in experimental models of hepatotoxic (carbon tetrachloride (CCl4) intoxication) and cholestatic (3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) feeding) injury. Using detergent-based tissue extraction and mass spectrometry, we identified compartment-specific changes in the liver proteome with detailed attention to ECM composition and changes in protein solubility. Our analysis revealed distinct time-resolved CCl4 and DDC signatures, with identified signaling pathways suggesting limited healing and a potential for carcinogenesis associated with cholestasis. Correlation of protein abundance profiles with fibrous deposits revealed extracellular chaperone clusterin with implicated role in fibrosis resolution. Dynamics of clusterin expression was validated in the context of human liver fibrosis. Atomic force microscopy of fibrotic livers complemented proteomics with profiles of disease-associated changes in local liver tissue mechanics. This study determined compartment-specific proteomic landscapes of liver fibrosis and delineated etiology-specific ECM components, providing thus a foundation for future antifibrotic therapies.

pathology↗

bioRxiv2023

Uncertainty Quantification in Acoustic Impedance ofAtlantic Salmon Fish Scale using Scanning AcousticMicroscopy

Scanning Acoustic Microscopy (SAM) emerges as a versatile label-free imaging technology with broad applications in biomedical imaging, non-destructive testing, and material research. This article presents a framework for the estimation of stochastic impedance through SAM, with a particular focus on its application to the salmon fish scale. The framework leverages uncertain reflectance, marking its pioneering application to uncertainty quantification in the acoustic impedance of fish scales through acoustic responses. The study uses maximal overlap discrete wavelet transform, to decompose acoustic responses effectively and is further processed to predict the acoustic impedance. To establish the effectiveness of the proposed framework, well-known materials like a pair of target medium (polyvinylidene fluoride) and reference medium (polyimide) are employed for impedance characterization. Results demonstrate over 90%accuracy in PVDF impedance estimation, validating the framework. A stochastic impedance map, using Kriging with a Gaussian variogram, offers insights into the complex biomechanics of a fishs scale.

biophysics↗

bioRxiv2023

Spatial mapping of acoustic impedance of shrimp scale using multiple overlap discrete wavelet transform (moDWT)

There are lots of challenges associated with conventional optical observation of biological tissues, where specimens are typically sliced and stained for better contrast. In contrast, Scanning Acoustic Microscopy (SAM) is a versatile label-free imaging technology widely applied in various domains, including biomedical imaging, non-destructive testing, and material research. It excels in offering precise visualization of both surface and subsurface structures, providing valuable insights through visual inspection and quantitative analysis. Acknowledging the SAM, this paper presents acoustic impedance microscopy of the shrimp scale in a novel manner. The proposed technique aims to image the local distribution of cross-sectional acoustic impedance in biological tissue, which is a parameter closely related to sound speed and potentially valuable for tissue characterization. The study leverages advanced signal processing techniques, maximal overlap discrete wavelet transform (moDWT), to decompose acoustic responses effectively. The moDWT, with its ability to handle signals of various lengths without constraints, is highlighted as a promising approach. To determine shrimp scale impedance, we first establish the accuracy of the proposed algorithm using PVDF as the target and polyimide as reference material. The results indicate an algorithm accuracy exceeding 90%. An impedance map is generated through Gaussian process regression (GPR), which predicts the impedance over the complete domain, addressing spatial variations in biological specimens. The resulting acoustic impedance maps provide in-depth insights into the functional framework and advance our understanding of shrimp biomechanics.

biophysics↗

bioRxiv2023

Natural Product Screen Identifies Asiatic Acid Targeting Mutant p53

Mutations in p53 are common in different cancer types and are reported to protect cancer via different mechanisms. R175H, R248Q, and R273H are the hotspot mutations of p53 and are suggested to increase aerobic glycolysis in cancer cells. Cancer cells rely mostly upon aerobic glycolysis, so it will be interesting to target these three p53 mutants for designing alternative cancer therapy. The class of compounds studied for their potential to target energy metabolism of cancer cells is called mitocans. The current study is an approach to explore if these selected 3 mutants of p53 may act as suitable target(s) for natural mitocans. Hereby, we selected 60 phytocompounds altogether from Andrographis paniculata and Centella asiatica and docked against all three p53 mutants, using Autodock vina. 11 compounds were sorted based on their binding energies and drug-like properties, and toxicity levels prediction showed asiatic acid to be the most significant. As asiatic acid was observed to significantly bind with R248Q only, R248Q-Asiatic acid was identified for molecular dynamics simulation using GROMACS which showed significant interactions. In conclusion, mutant R248Q was observed to be the best target for asiatic acid, though additional in-vitro experiments are important to validate the findings of this study.

cancer biology↗

bioRxiv2020

Non-apoptotic function of caspase-3 in morphogenesis of epithelial tubes of Drosophila renal system

Cells trigger apoptosis to eliminate themselves from the system, when tissue needs to be sculptured or they detect any abnormality within them, thus preventing irreparable damage to the host. Drosophila Malpighian tubules express apoptotic proteins, without succumbing to cell death. Here we present evidence to show apoptosis independent role of executioner caspase, Drice, for precise architecture and function of Malpighian tubules. Drice is required for precise cytoskeleton organization and convergent extension, failing which the morphology, size, cellular number and arrangement gets affected. Acquisition of star shape of stellate cells in adult Malpighian tubules requires Drice. We demonstrate that Drice regulates expression of Rho1GTPase and localization of polarity proteins. Our study shows a probable mechanism by which Drice governs tubulogenesis via Rho1GTPase mediated coordinated organization of actin cytoskeleton and membrane stablisation. Furthermore, defective morphology of tubules leads to abnormal osmoregulation and excretory functions. Collectively our findings suggest a possible non-apoptotic function of caspase-3 in the fine tuning of cell mobility during tubule development and our results will add to the growing understanding of diverse roles of caspases during its evolution in metazoans.

developmental biology↗

bioRxiv2020

A Novel Stress Response Pathway Regulates Ribosome Biogenesis

Production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and, when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but represents an independent stress-response pathway that we term Ribosome Biogenesis Stress Response (RiBiSR). Failure to coordinately regulate ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils a novel stress response pathway that aims at conserving energy, preserving the nucleolus, and prevents further stress by regulation of rRNA processing.

biochemistry↗

bioRxiv2020

Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as "Crosslinking and Immunoprecipitation" (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs incorporated into cellular RNA has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP). Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA, and for the isolation of crosslinked RNA. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

microbiology↗

bioRxiv2020

Dual-level autoregulation of the E. coli DeaD RNA helicase via mRNA stability and Rho-dependent transcription termination

DEAD-box proteins (DBPs) are RNA remodeling factors associated with RNA helicase activity that are found in nearly all organisms. Despite extensive studies on the mechanisms used by DBPs to regulate RNA function, very little is known about how DBPs themselves are regulated. In this work, we have analyzed the expression and regulation of DeaD/CsdA, the largest of the DBPs in Escherichia coli (E. coli). We show that deaD transcription initiates 838 nts upstream of the start of the coding region. We have also found that DeaD is autoregulated through a negative feedback mechanism that operates both at the level of mRNA stability and Rho-dependent transcription termination, and this regulation is dependent upon the 5 untranslated region (5 UTR). These findings suggest that DeaD might be regulating the conformation of its own mRNA through its RNA helicase activity to facilitate ribonuclease and Rho access to its 5UTR.

microbiology↗

bioRxiv2019

Development of PAR-CLIP to analyze RNA-protein interactions in prokaryotes

The ability to identify RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as "Crosslinking and Immunoprecipitation" (CLIP) has revolutionized the genome-wide discovery of RNA targets. Among the different versions of CLIP developed, the incorporation of photoactivable nucleoside analogs into cellular RNA has proven to be especially valuable, allowing for high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP). Although PAR-CLIP has become an established technique for use in eukaryotes, it has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we first investigated whether 4-thiouridine (4SU), a photoactivable nucleoside, can be incorporated into E. coli RNA. After determining 4SU incorporation into RNA, we developed suitable conditions for crosslinking of proteins in E. coli cells and for the isolation of crosslinked RNA. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA) - messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq. Based on our results, PAR-CLIP represents an improved method to identify the RNAs recognized by RNA-BPs in prokaryotes.

microbiology↗