Biology subjects

Chaudhari, N.

Publications and source records attributed to Chaudhari, N..

8 recordsLinked to original sources

bioRxiv2026

Dual Recognition Drives Site-Directed G-Quadruplex Stabilization: Exploring Oligonucleotide Design in G4 Ligand-Oligonucleotide Conjugates

G-quadruplex (G4) DNA structures are increasingly recognized for their roles in key cellular processes, including transcriptional regulation and genome stability, making them attractive therapeutic targets. Selective recognition of individual G4s remains challenging due to the high structural similarity among human G4 motifs. The G4 Ligand-conjugated Oligonucleotide strategy addresses this need by combining the G4-binding capabilities of small-molecule G4-ligands with the sequence specificity of an oligonucleotide complementary to the flanking region of the target G4. Here, we systematically explore how the oligonucleotide component governs G4 binding and stabilization by varying its length, backbone composition, and sequence complementarity. This revealed that efficient G4 recognition depends on a strong interdependence between hybridization and G4-ligand binding, such that both elements cooperatively reinforce complex stability and site specificity. Central mismatches disrupt this dual recognition and reduce selectivity. While longer oligonucleotides hybridize more slowly, they form more stable complexes and show stronger G4 stabilization in thermal melting and polymerase stop assays. Replacing the DNA oligonucleotide with peptide nucleic acid enhances binding strength, thermal stability, and metabolic stability, but selective G4 stabilization is achieved only upon ligand conjugation. Together, these results show how rational oligonucleotide design enables selective and potent recognition of G4 structures using GL-Os.

molecular biology↗

bioRxiv2026

Redox-dependent dimerization of PolDIP2 and a conserved ApaG-domain motif required for CHCHD2 interaction

PolDIP2 is a multifunctional mitochondrial protein implicated in redox regulation, mitochondrial proteostasis, and diverse mtDNA-associated processes, yet the principles underlying its regulation remain unclear. Crystallographic analysis revealed that PolDIP2 forms a redox-dependent disulfide-linked homodimer via a conserved Cys143 residue within its N-terminal YccV-like domain, and cellular and in vitro assays confirmed that this residue is essential for dimer formation. Oxidative stress enhanced dimerization of endogenous and ectopically expressed PolDIP2, and dimers were detected exclusively within mitochondria, requiring proper mitochondrial import. WT and C143A PolDIP2 overexpression produced similarly modest effects on mtDNA replication in cells, suggesting that dimerization has limited impact on mtDNA-associated processes. Proteomic analysis and biochemical validation identified both previously known and not yet characterized mitochondrial interactors of PolDIP2, and highlighted CHCHD2 as a specific binding partner. A conserved glycine-rich motif in the C-terminal ApaG/DUF525-like domain proved essential for this interaction, and disruption of the motif enhanced Cys143-dependent dimerization while abolishing CHCHD2 association, which preferentially occurs with monomeric PolDIP2. These findings define redox-controlled dimerization and a conserved ApaG-domain motif as key structural features shaping PolDIP2s interaction state within mitochondria and provide a basis for exploring its roles in redox-sensitive mitochondrial pathways.

cell biology↗

bioRxiv2025

Phytochemical Content and Antimicrobial Activity of Aloe Vera extract of Marathwada Region, India

Aloe vera (Aloe barbadensis) is widely recognized for its therapeutic properties due to its rich phytochemical composition, including proteins, carbohydrates, and steroids. The study aimed to evaluate the efficiency of solvents such as ethanol and methanol for extracting bioactive compounds and to analyse the phytochemical contents of Aloe vera extracts using various biochemical assays. The dinitro salicylic acid test (DNSA) quantified reducing sugars with ethanol extracts yielding 870 mg/ml compared to 450 mg/ml for methanol extracts. The Biuret test for proteins revealed concentrations of 13.8 mg/ml in ethanol extracts and 13.03 mg/ml in methanol extracts. The Barfoeds test indicated carbohydrate concentrations of 960 mg/ml in ethanol extracts. A qualitative test for steroids confirmed their presence in both solvents, with ethanol showing a more intense reaction, suggesting a higher concentration of steroidal compounds. The results establish ethanol as a more efficient solvent for extracting phytochemicals from Aloe vera. Antimicrobial activity test against E. coli demonstrated superior inhibition zones for ethanol extract, highlighting their potential as natural antibacterial agents. The research indicates the significance of solvent selection in optimizing the therapeutic utility of Aloe vera. It provides a foundation for further exploration into its bioactive compounds and mode of action.

plant biology↗

bioRxiv2023

G4-Ligand Conjugated Oligonucleotides Mediate Selective Binding and Stabilization of Individual G4 DNA Structures

G-quadruplex (G4) DNA structures are prevalent secondary DNA structures implicated in fundamental cellular functions such as replication and transcription. Furthermore, G4 structures are directly correlated to human diseases such as cancer and have been highlighted as promising therapeutic targets for their ability to regulate disease-causing genes, e.g., oncogenes. Small molecules that bind and stabilize these structures are thus valuable from a therapeutic perspective and helpful in studying the biological functions of G4 structures. However, there are hundreds of thousands of G4 DNA motifs in the human genome, and a longstanding problem in the field is how to achieve specificity amongst these different G4 structures. Here, we have developed a strategy to selectively target an individual G4 DNA structure. The strategy is based on a ligand that binds and stabilizes G4s without selectivity, conjugated to a guide oligonucleotide, that specifically directs the G4 Ligand conjugated Oligo (GL-O) to the single target G4 structure. By employing various biophysical and biochemical techniques, we show that the developed method enables the targeting of a unique, specific G4 structure without impacting other off-target G4 formations. Considering the vast amounts of G4s in the human genome, this represents a promising strategy to study the presence and functions of individual G4s but may also hold potential as a future therapeutic modality.

biochemistry↗

bioRxiv2023

Differential contribution of nitrifying prokaryotes to nitrification in groundwater

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX amoA genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

microbiology↗

bioRxiv2021

AAV-PHP.S-mediated delivery of reporters to cranial ganglion sensory neurons

Because of their ease of use and low risk containment, Adeno-Associated Virus vectors are indispensable tools for much of neuroscience. Yet AAVs have been used relatively little to study the identities and connectivity of peripheral sensory neurons because methods to selectively target particular receptive fields or neuron types have been limited. The introduction of the AAV-PHP.S capsid with selective tropism for peripheral neurons (Chan et al., 2017) offered a solution, which we further elaborate here. We demonstrate using AAV-PHP.S with GFP or mScarlet reporters, that all cranial sensory ganglia, i.e. for cranial nerves V, VII, IX and X, are targeted. Pseudounipolar neurons of both somatic and visceral origin, but not satellite glia, are efficiently transduced rapidly and express the gene of interest within 1 week of injection. Fluorescent reporter proteins are transported into the central and peripheral axons of these sensory neurons, permitting visualization of terminals at high resolution, and/or in intact, cleared brain using light sheet microscopy. By combining a Cre-dependent reporter with the AAV-PHP.S capsid, we confirmed expression in a cell-type dependent manner for both anatomical and targeted functional analyses. The AAV-PHP.S capsid will be a powerful tool for mapping the receptive fields and circuits of molecular subtypes of many somatosensory, gustatory and visceral sensory neurons. SIGNIFICANCE STATEMENTAAV vectors have become an essential tool for visualizing, manipulating, and recoding from neurons of the central nervous system. However, the technology is not widely used for peripheral neurons because of several technical limitations. The AAV-PHP.S synthetic capsid, which targets peripheral neurons, was recently introduced (Chan et al., 2017). Here, we establish key parameters for using this virus, including which cells are transduced, the timing of expression in central and peripheral terminals, distant from neuronal somata, and the effectiveness of Cre-dependent constructs for cell type selective expression. This permits the use of AAV for constructing detailed anatomic and functional maps of the projections of molecular subtypes of peripheral sensory neurons.

neuroscience↗

bioRxiv2019

Mouse trigeminal neurons respond to kokumi substances

1.Using in vivo confocal Ca2+ imaging, we investigated whether oral application of kokumi substances elicits responses in trigeminal somatosensory ganglion neurons of the mouse. Our results show that 100 M {gamma}EVG ({gamma}-Glu-Val-Gly), a potent kokumi stimulus, evokes responses in a very small fraction (0.6 %) of neurons in area V3 (oral sensory field) of the trigeminal ganglion. By comparison, cooled artificial saliva elicited thermal-evoked responses in >7 % of V3 trigeminal ganglion neurons. {gamma}EVG-evoked responses were small and quite variable, with latencies ranging from 2 to over 200 sec. Co-application of the calcium sensing receptor (CaSR) inhibitor NPS-2143 significantly decreased {gamma}EVG-evoked activity. Furthermore, we show that 4 additional kokumi substances evoked responses in mouse trigeminal ganglion neurons. All neurons responding to kokumi compounds were small cells, with mean diameters below 20 m. In summary, our data show that certain physiological and pharmacological properties of responses to kokumi compounds can be recorded from sensory neurons in the trigeminal ganglion of living mice. Thus, sensory neurons in the somatosensory trigeminal ganglia may transmit signals from the oral cavity to the central nervous system to generate the texture perceptions that are part of the enigmatic sensations evoked by kokumi substances.

neuroscience↗

bioRxiv2018

Oral thermosensing by murine trigeminal neurons:modulation by capsaicin, menthol, and mustard oil

When consumed with foods, mint, mustard and chili peppers generate pronounced oral thermosensations. Here we recorded responses in mouse trigeminal ganglion neurons to investigate interactions between thermal sensing and the active ingredients of these plants -- menthol, allyl isothiocyanate (AITC), and capsaicin, respectively -- at concentrations found in foods and commercial hygiene products. We carried out in vivo confocal calcium imaging of trigeminal ganglia in which neurons express GCaMP3 or GCAMP6s and recorded their responses to oral stimulation with thermal and the above chemesthetic stimuli. In the V3 (oral sensory) region of the ganglion, thermoreceptive neurons accounted for [~]10% of imaged neurons. We categorized them into 3 distinct classes: cool-responsive and warm-responsive thermosensors, and nociceptors (responsive only to temperatures [≥]43-45{degrees}). Menthol, AITC, and capsaicin also elicited robust calcium responses that differed markedly in their latencies and durations. Most of the neurons that responded to these chemesthetic stimuli were also thermosensitive. Capsaicin and AITC increased the numbers of warm-responding neurons and shifted the nociceptor threshold to lower temperatures. Menthol attenuated the responses in all classes of thermoreceptors. Our data show that while individual neurons may respond to a narrow temperature range (or even bimodally), taken collectively, the population is able to report on graded changes of temperature. Our findings also substantiate an explanation for the thermal sensations experienced when one consumes pungent spices or mint.\n\nKey points summaryO_LIOrosensory thermal trigeminal afferent neurons respond to cool, warm, and nociceptive hot temperatures with the majority activated in the cool range.\nC_LIO_LIMany of these thermosensitive trigeminal orosensory afferent neurons also respond to capsaicin, menthol and/or mustard oil (allyl isothiocyanate, AITC) at concentrations found in foods and spices.\nC_LIO_LIThere is significant but incomplete overlap between afferent trigeminal neurons that respond to heat and to the above chemesthetic compounds.\nC_LIO_LICapsaicin sensitizes warm trigeminal thermoreceptors and orosensory nociceptors; menthol attenuates cool thermoresponses.\nC_LI

neuroscience↗