Biology subjects

Ravi, R.

Publications and source records attributed to Ravi, R..

11 recordsLinked to original sources

bioRxiv2026

CSF glucosylsphingosine is a central readout of GCase impairment across genetic and sporadic Parkinson’s disease

Parkinsons disease (PD) risk converges on lysosomal biology, including reduced activity of glucocerebrosidase (GCase), encoded by GBA1. Glucosylsphingosine (GlcSph), a toxic deacylated glycosphingolipid and established target engagement biomarker in Gaucher disease, is difficult to quantify in cerebrospinal fluid (CSF) because of low abundance and isomeric interference. We optimized and qualified targeted LC-MS/MS assays for GlcSph in CSF and plasma and measured GlcSph and GCase activity (4-MU assay) in participants from the Parkinsons Progression Markers Initiative (PPMI), including GBA1 and LRRK2 mutation carriers with and without PD, sporadic PD, and healthy controls. Group level analyses showed higher levels of CSF and plasma GlcSph in GBA1 heterozygous variant carriers independent of disease status, [~]120% (p<0.0001) and [~]61% (p<0.0001), respectively, with CSF elevations reflecting allelic dosage and, to a lesser degree, variant severity. Notably, elevated CSF GlcSph was observed not only in carriers of pathogenic GBA1 mutations but also in individuals harboring common GBA1 risk variants. CSF GlcSph was also elevated by [~]30% in sporadic PD (p=0.002) and by [~]40% LRRK2 mutation carriers (p=0.0003), indicating shared central GCase pathway perturbation across PD subtypes. CSF and plasma GlcSph levels showed poor concordance across groups with the exception of the GBA-PD group, supporting the hypothesis that central and peripheral GCase pathway dysfunction arise through distinct biological mechanisms. Together, these findings establish CSF GlcSph as a sensitive biomarker of central GCase pathway impairment and may support its use as a pharmacodynamic and target engagement biomarker for therapeutics targeting GCase in PD. More broadly, CSF GlcSph may enable identification of biologically defined GCase-pathway dysfunction beyond genetically defined GBA1-associated PD, with potential implications for patient stratification in future disease-modifying trials.

Molecular Biology↗

bioRxiv2025

An acyltransferase protects Caenorhabditis elegans from thiol reductive stress through an autoinhibitory hypoxia response pathway

Cellular redox homeostasis depends on a finely tuned balance between oxidizing and reducing conditions, and disturbances in this balance lead to oxidative or reductive stress. While oxidative stress and its pathological outcomes are well studied, the molecular mechanisms underlying cellular responses to reductive stress remain poorly understood. Using Caenorhabditis elegans as a model, we investigate thiol reductive stress induced by dithiothreitol (DTT) and uncover a critical protective role for the hypoxia response pathway. We identify RHY-1, a membrane-associated acyltransferase and known negative regulator of the hypoxia-inducible factor HIF-1, as essential for survival under thiol reductive stress. Notably, rhy-1 is a direct transcriptional target of HIF-1, and overexpression of rhy-1 fully rescues the sensitivity of hif-1 loss-of-function mutants to DTT. We demonstrate that RHY-1 functions in an autoinhibitory feedback loop, where elevated RHY-1 levels suppress activation of the hypoxia response pathway even during reductive stress. Together, our findings establish RHY-1 as both a regulatory and effector component of the hypoxia response pathway that mediates cellular protection against thiol reductive stress.

physiology↗

bioRxiv2025

Micro RNA mediated enhanced growth in Solanum lycopersicum during cadmium hormesis

Hormesis refers to the adaptive mechanism of organisms in response to environmental challenges where a lower dose of a toxic compound induce an improvement in functionality and overall development and a higher dose endangers even the existence of the organism. The recent developments in hormetic studies are of paramount importance in plant research as they help in risk assessment of environmental contaminants, protect the vegetation against pollution, and improve crop productivity. As one of the most toxic contaminants, cadmium is considered to have detrimental effects on the growth and development of plants. However, recent studies have revealed the beneficial effects of cadmium in plants at low levels of exposure however the exact mechanism behind this phenomenon is poorly deciphered. In this study, we have focused on observing the response of tomato seedlings under different concentrations of cadmium. The morphological, biochemical, and histochemical characterization of these seedlings under low cadmium exposure has confirmed their hormetic effects. The differential gene expression by transcriptomic profiling in low cadmium showed that, apart from genes involved in oxidoreductase activity, and signaling, several lncRNAs, also differentially expressed. The lncRNAs are known to regulate gene expression on the chromatin level and post-transcriptional regulation. First time we are reporting the expression of lncRNAs in hormesis as important factor for enhanced growth. In-silico analysis revealed the functions of lncRNAs, involving the prediction of cis-targets, mi-RNA precursors, and their targets. Two miRNAs; sly-MIR396a and sly-MIR1063g were seen to have a direct role in improving the growth of plants treated with low cadmium provided an insight into the molecular mechanisms of their role in cadmium hormesis. These findings provided important understanding of the molecular basis of the hormetic phenomenon which can pave a path for generating crops with improved agronomic characteristics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/663119v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@8de5b0org.highwire.dtl.DTLVardef@1e2ad13org.highwire.dtl.DTLVardef@d0f7e2org.highwire.dtl.DTLVardef@14238b3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILow cadmium exposure on Solanum lycopersicum seedlings showed more promising outcomes in terms of growth and development. C_LIO_LIThe plants exposed to 1{micro}M Cd treatment continued to exhibit superior growth responses despite removing the cadmium from the media after 5 days of treatment. C_LIO_LIThe GO analysis of Differentially Expressed Genes (DEGs) suggested several lncRNAs differentially expressed in 1 {micro}M Cd condition. C_LIO_LIDifferentially expressed LncRNAs Solyc01g006780.4 and Solyc12g019150.1 generated the miRNAs, sly-MIR396a and sly-MIR1063g respectively. C_LIO_LIUpregulation of sly-MIR396a and sly-MIR1063g resulted in the downregulation of GRF12 and NET4B-like proteins respectively leading to increased growth of tomato plants. C_LI

plant biology↗

bioRxiv2025

Iron-deplete diet enhances Caenorhabditis elegans lifespan via oxidative stress response pathways

Gut microbes play a crucial role in modulating host lifespan. However, the microbial factors that influence host longevity and their mechanisms of action remain poorly understood. Using the expression of Caenorhabditis elegans FAT-7, a stearoyl-CoA 9-desaturase, as a proxy for lifespan modulation, we conduct a genome-wide bacterial mutant screen and identify 26 Escherichia coli mutants that enhance host lifespan. Transcriptomic and biochemical analyses reveal that these mutant diets induce oxidative stress and activate the mitochondrial unfolded protein response (UPRmt). Antioxidant supplementation abolishes lifespan extension, confirming that oxidative stress drives these effects. The extension of lifespan requires the oxidative stress response regulators SKN-1, SEK-1, and HLH-30. Mechanistically, these effects are linked to reduced iron availability, as iron supplementation restores FAT-7 expression, suppresses UPRmt activation, and abolishes lifespan extension. Iron chelation mimics the pro-longevity effects of the mutant diets, highlighting dietary iron as a key modulator of aging. Our findings reveal a bacterial-host metabolic axis that links oxidative stress, iron homeostasis, and longevity in C. elegans.

physiology↗

bioRxiv2024

Alterations in Lysosomal, Glial and Neurodegenerative Biomarkers in Patients with Sporadic and Genetic Forms of Frontotemporal Dementia

BackgroundFrontotemporal dementia (FTD) is the most common cause of early-onset dementia with 10-20% of cases caused by mutations in one of three genes: GRN, C9orf72, or MAPT. To effectively develop therapeutics for FTD, the identification and characterization of biomarkers to understand disease pathogenesis and evaluate the impact of specific therapeutic strategies on the target biology as well as the underlying disease pathology are essential. Moreover, tracking the longitudinal changes of these biomarkers throughout disease progression is crucial to discern their correlation with clinical manifestations for potential prognostic usage. MethodsWe conducted a comprehensive investigation of biomarkers indicative of lysosomal biology, glial cell activation, synaptic and neuronal health in cerebrospinal fluid (CSF) and plasma from non-carrier controls, sporadic FTD (symptomatic non-carriers) and symptomatic carriers of mutations in GRN, C9orf72, or MAPT, as well as asymptomatic GRN mutation carriers. We also assessed the longitudinal changes of biomarkers in GRN mutation carriers. Furthermore, we examined biomarker levels in disease impacted brain regions including middle temporal gyrus (MTG) and superior frontal gyrus (SFG) and disease-unaffected inferior occipital gyrus (IOG) from sporadic FTD and symptomatic GRN carriers. ResultsWe confirmed glucosylsphingosine (GlcSph), a lysosomal biomarker regulated by progranulin, was elevated in the plasma from GRN mutation carriers, both symptomatic and asymptomatic. GlcSph and other lysosomal biomarkers such as ganglioside GM2 and globoside GB3 were increased in the disease affected SFG and MTG regions from sporadic FTD and symptomatic GRN mutation carriers, but not in the IOG, compared to the same brain regions from controls. The glial biomarkers GFAP in plasma and YKL40 in CSF were elevated in asymptomatic GRN carriers, and all symptomatic groups, except the symptomatic C9orf72 mutation group. YKL40 was also increased in SFG and MTG regions from sporadic FTD and symptomatic GRN mutation carriers. Neuronal injury and degeneration biomarkers NfL in CSF and plasma, and UCHL1 in CSF were elevated in patients with all forms of FTD. Synaptic biomarkers NPTXR, NPTX1/2, and VGF were reduced in CSF from patients with all forms of FTD, with the most pronounced reductions observed in symptomatic MAPT mutation carriers. Furthermore, we demonstrated plasma NfL was significantly positively correlated with disease severity as measured by CDR+NACC FTLD{square}SB in genetic forms of FTD and CSF NPTXR was significantly negatively correlated with CDR+NACC FTLD{square}SB in symptomatic GRN and MAPT mutation carriers. ConclusionsIn conclusion, our comprehensive investigation replicated alterations in biofluid biomarkers indicative of lysosomal function, glial activation, synaptic and neuronal health across sporadic and genetic forms of FTD and unveiled novel insights into the dysregulation of these biomarkers within brain tissues from patients with GRN mutations. The observed correlations between biomarkers and disease severity open promising avenues for prognostic applications and for indicators of drug efficacy in clinical trials. Our data also implicated a complicated relationship between biofluid and tissue biomarker changes and future investigations should delve into the mechanistic underpinnings of these biomarkers, which will serve as a foundation for the development of targeted therapeutics for FTD.

neuroscience↗

bioRxiv2023

Thiol reductive stress activates the hypoxia response pathway

Owing to their capability to disrupt the oxidative protein folding environment in the endoplasmic reticulum (ER), thiol antioxidants such as dithiothreitol (DTT) are used as ER-specific stressors. We recently showed that thiol antioxidants modulate the methionine-homocysteine cycle by upregulating an S-adenosylmethionine-dependent methyltransferase, rips-1, in Caenorhabditis elegans. However, the changes in cellular physiology induced by thiol stress that modulate the methionine-homocysteine cycle remain uncharacterized. Here, using forward genetic screens in C. elegans, we discover that thiol stress enhances rips-1 expression via the hypoxia response pathway. We demonstrate that thiol stress activates the hypoxia response pathway. The activation of the hypoxia response pathway by thiol stress is conserved in human cells. The hypoxia response pathway enhances thiol toxicity via rips-1 expression and confers protection against thiol toxicity via rips-1-independent mechanisms. Finally, we show that DTT might activate the hypoxia response pathway by producing hydrogen sulfide. Our studies reveal an intriguing interaction between thiol-mediated reductive stress and the hypoxia response pathway and challenge the current model that thiol antioxidant DTT disrupts only the ER milieu in the cell.

molecular biology↗

bioRxiv2022

Inactivation of B. cereus Spores in Whole Milk and Almond Milk by Novel Serpentine Path Coiled Tube UV-C System

A novel continuous thin-film (1.59 mm) serpentine path coiled tube (SPCT) UV system operating at 254 nm wavelength was designed and compared with flow field distribution of whole milk with helical path coiled tube (HPCT) UV system using computational fluid dynamics. The results revealed efficient velocity magnitude distribution at serpentine bend geometric locations of the SPCT UV system. Further in this study, we evaluated B. cereus Spores inactivation in whole milk (WM) and almond milk (AM) using the developed SPCT UV system. Experimental data showed that > 4 log reduction of spores was achieved after six and ten passes of WM and AM at a flow rate of 70 and 162 mL/min, respectively. The biodosimetry method was used to verify the delivered reduction equivalent fluence (REF) and reported as 33 {+/-} 0.73 and 36.5 {+/-} 1.9 mJ/cm2. We noticed no significant effect on lipid oxidation and volatiles profile (p > 0.05) up to delivered REF of 60 mJ/cm2. This study demonstrated that high levels of inactivation of B. cereus spores could be feasible with minimal impact on product quality by UV-C processing of dairy and non-dairy opaque scattering fluids.

microbiology↗

bioRxiv2022

Pilot scale study on UV-C inactivation of bacterial endospores and virus particles in whole milk: evaluation of system efficiency and product quality

UV-C processing of whole milk (WM) using a designed pilot scale Dean flow system was conducted at flow rates (11.88, 23.77, and 47.55 gph), Reynolds number ranges from 2890-11562 and the Dean number (at curved region) calculated as (648-2595) to inactivate bacterial endospores and virus particles. Biodosimetry studies were conducted to quantify the reduction equivalent fluence at selected experimental conditions. Results revealed that the fluence distribution improved as flow rate increases, attributed to increase in Dean effects and turbulence intensity. Microbial inactivation studies conducted at 47.55 gph showed 0.91 {+/-} 0.15 and 2.14 {+/-} 0.19 log reduction/ pass for B. cereus endospores and T1UV phage. Linear inactivation trend was observed against number of passes which clearly demonstrates equivalent fluence delivery during each pass. Lipid peroxidation value and volatiles profile did not change significantly at UV fluence of 60 mJ/cm2. Lower EEO value signifies the higher electrical efficiency of the system.

microbiology↗

bioRxiv2020

Production and analysis of a mammalian septin hetero-octamer complex

The septins are filament-forming proteins found in diverse eukaryotes from fungi to vertebrates, with roles in cytokinesis, shaping of membranes and modifying cytoskeletal organization. These GTPases assemble into rod-shaped soluble hetero-hexamers and hetero-octamers in mammals, which polymerize into filaments and higher order structures. While the cell biology and pathobiology of septins are advancing rapidly, mechanistic study of the mammalian septins is limited by a lack of recombinant hetero-octamer materials. We describe here the production and characterization of a recombinant mammalian septin hetero-octamer of defined stoichiometry, the SEPT2/SEPT6/SEPT7/SEPT3 complex. Using a fluorescent protein fusion to the complex, we observed filaments assembled from this complex. In addition, we used this novel tool to resolve recent questions regarding the organization of the soluble septin complex. Biochemical characterization of a SEPT3 truncation that disrupts SEPT3-SEPT3 interactions is consistent with SEPT3 occupying a central position in the complex while the SEPT2 subunits are at the ends of the rod-shaped octameric complexes. Consistent with SEPT2 being on the complex ends, we find that our purified SEPT2/SEPT6/SEPT7/SEPT3 hetero-octamer copolymerizes into mixed filaments with separately purified SEPT2/SEPT6/SEPT7 hetero-hexamer. We expect this new recombinant production approach to lay essential groundwork for future studies into mammalian septin mechanism and function.

biochemistry↗

bioRxiv2020

Impact of glycan positioning on HIV-1 Env glycan shield density, function, and antibody recognition

N-glycans, which represent >50% mass of the HIV-1 envelope (Env) trimer, play important roles for virus-cell entry and immune evasion. How each glycan unit interacts to shape the Env protein-sugar complex and affects Env function is not well understood. Here, high-resolution glycomics analysis of two Env variants from the same donor, with differing functional characteristics and N-glycosylation-site composition, revealed that changes to key N-glycosylation-site not only affected the Env structure at distant locations, but also had a ripple effect on Env-wide glycan processing, virus infectivity, and antibody recognition and virus neutralization. Specifically, the N262 glycan, although not located in the CD4-binding site, controlled Env binding to the CD4 receptor, affected the recognition of Env by several glycan-dependent broadly neutralizing antibodies, and altered heterogeneity of glycosylation at several sites, with N156, N160, and N448 displaying limited glycan processing. Molecular dynamic simulations visualized how specific oligosaccharide positions can move to compensate for loss of a glycan. This study demonstrates how changes in individual glycan units can alter molecular dynamics and processing of the Env-glycan shield and, consequently, Env function.

microbiology↗

bioRxiv2020

Chemical composition and larvicidal activity against Aedes mosquitoes of flower extracts from Clitoria Ternatea

BackgroundMosquito is a human health tread nowadays, the major health problems caused by them are malaria, dengue fever, yellow fever, zika as well as several other outbreaks. The major problem in controlling dengue vectors are the resistant problems. Different classes of insecticides used for public have raised the concern of resistant problem with mosquitoes and environmental pollution. Thus, alternative chemical compounds search is necessary to be searched for overcoming the resistance problem of using pesticides in vectors and the chemical free environment respectively. Thus, to solve these problems, purpose of this study is to identify the larvicidal mechanism, metabolite, antioxidant, chemical compounds and its structure from C. ternatea flower and to test its efficacies against early 4th instar larvae of Ae. aegypti and Ae albopictus. MethodsClitoria ternatea flowers were collected from the Garden of the Faculty of Medicine in International Quest University, Ipoh, Perak and used for crude extraction. Then, the metabolite test, antioxidant test, chromatography techniques were conducted to identify chemical composition of extracts and their chemical structures were identified using GCMS-QP2010 Ultra (Shimadzu). Next, following WHO procedures for larval bioassays, the extracts were used to evaluate against early 4th instar larvae of Aedes mosquito vectors. ResultsThe larvicidal activity of Clitoria ternatea flowers extracts evidently affected the early 4th instar larvae of Aedes mosquito vectors. The highest larvicidal activity was observed against early 4th instar larvae of Ae. aegypti with the LC50 and LC95 values of 1056 and 2491 mg/L, respectively. Meanwhile larvae bioassay test for Ae.albopictus recorded with the LC50 and LC95 values of 1425 and 2753 mg/L. Moreover, the results for non target organism test on Guppy fish, Poecilia reticulate showed no mortalities with flower extracts at 2500 mg/L and posses no toxic effects on fish. In this study, total of 16 chemical compounds and 6 chemical compounds have been reported to posses direct effects on insecticidal, larvicidal and pupicidal effects. Namely 6 chemicals used for insecticidal properties were Glycerin, 2-Hydroxy-gamma-butyrolactone, Neophytadiene, n-Hexadecanoic acid, cis-Vaccenic acid, and Octadecanoic acid with total of 28.7%. Clitoria ternatea flower extracts also showed different types of phenols such as anthocyanin, flavonoid and tannin. ConclusionsOur findings showed that crude extract of Clitoria ternatea flower bioactive molecules to be effective and may be developed as biolarvicides for Aedes mosquito vector control. Furthermore, this study also provided a baseline understanding for future research work on the field applications of Clitoria ternatea flower extracts which could be tested for its long term effects on other non target organisms, including human health.

biochemistry↗