Biology subjects

Gupta, P. K.

Publications and source records attributed to Gupta, P. K..

9 recordsLinked to original sources

bioRxiv2026

MSMEG_1353 is a critical determinant of metabolic and cell envelope homeostasis in mycobacteria

The mycobacterial cell envelope is central to antibiotic resistance and stress adaptation, maintained by a network of essential proteins. Owing to their evolutionary divergence from other model organisms, mycobacteria encode numerous genus-specific genes that remain functionally uncharacterized, including the network of these essential genes. Here, we define MSMEG_1353 as a previously uncharacterized, essential ATP binding protein that plays a role in mycobacterial metabolism and cell envelope integrity. Conditional depletion of MSMEG_1353 resulted in severe growth attenuation, and the loss of characteristic mycobacterial cording. Further, the knockdown strain exhibited altered cell envelope permeability and an unusual antibiotic susceptibility profile, marked by isoniazid resistance accompanied with hypersensitivity to vancomycin. Functional analysis revealed pronounced membrane depolarisation and severe envelope defects, including distortion of outer membrane layers. Concomitantly, integrated transcriptomic and metabolomic profiling demonstrated widespread suppression of carbon metabolism accompanied by cofactor imbalance and redox perturbation, indicating a global metabolic rerouting upon MSMEG_1353 depletion. At the level of cell envelope composition, the lipid profiles indicate depletion of phthiocerol dimycocerosate (PDIM), trehalose polyphleate (TPP), and elevated levels of mycolic acid in the knockdown strain. Further, localisation studies revealed that MSMEG_1353 forms discrete clusters along the cell, with preferential enrichment at the old pole. Collectively, our findings establish MSMEG_1353 as a critical determinant of metabolic homeostasis and envelope permeability in Mycobacterium smegmatis, linking central carbon metabolism, and adaptive cell envelope remodeling.

microbiology↗

bioRxiv2026

Formulation Development of Topical Inserts Containing Doxycycline and Doxycycline Combined with Tenofovir Alafenamide and Elvitegravir for the Prevention of Sexually Transmitted Infections

PurposeDespite advances in oral and injectable HIV prevention options and oral prophylaxis for sexually transmitted infections (STIs) of bacterial origin, there remains a critical need for effective on-demand topical (vaginal/rectal) products for pre- and post-exposure prophylaxis (PrEP and PEP). To fill this gap, we have developed single and first-in-kind multi-active topical inserts for bacterial STIs and HIV/STIs prevention. MethodsWe have formulated two different inserts, one containing doxycycline (DOX) at 10, 50, and 100mg doses for bacterial STI prevention, and a multipurpose prevention product (TED insert) that combines DOX (10mg) with the antiretrovirals tenofovir alafenamide (TAF; 20mg) and elvitegravir (EVG; 16mg) to target both bacterial STIs and HIV. ResultsInserts were manufactured through a simple, cost-effective process. Drug loading was within 95-105% of the labeled amount, confirming a robust manufacturing process. In vitro, they disintegrated within 10min with >95% drug release within 60min. The dissolution behavior of DOX inserts showed surface erosion but was affected by medium volume and drug amount. The inserts met key physicochemical targets: hardness (5-8kg), friability (<1%), moisture content (<2%), and osmolality (<550mOsm/kg). Based on 6-month storage stability, DOX inserts maintained their physicochemical properties, suggesting a shelf life of >2years. Preliminary 1-month stability of TED inserts under accelerated conditions showed preservation of their physicochemical properties. ConclusionThis study represents the first formulation development report on topical inserts containing DOX alone or in combination with antiretrovirals. Both inserts offer a novel, on-demand topical STI prevention option that supports flexible PrEP/PEP use by both women and men.

bioengineering↗

bioRxiv2025

Widespread cortical representations of innate behaviors in the mouse

Across cortex, a substantial component of observed neuronal activity can be explained by movement. Voluntary movements elicit cortical activity that contain elements related to both motor planning and sensory activity. However, automatic movements that do not require conscious processing, for example grooming or drinking, are to a large extent controlled by subcortical systems such as the brainstem. While the cortex may not be required to generate these automatic behaviors, it is unclear whether cortical activity represents the movements associated with them. In this work, we use a simple procedure to stimulate stereotyped grooming behaviors in the head-fixed mouse while measuring neuronal function across the dorsal cortex. We find specific cortical representations of grooming both at a mesoscale network-level and single-cell resolution. Mesoscale cortical activation was most prominent at the onset of grooming episodes, and declined to baseline levels despite continuous engagement in the behavior. Further stratification of grooming component movements revealed that more directed and unilateral grooming movements had greater cortical associated responses than more stereotyped bilateral movements. These findings help to frame the impact of forms of automatic movements on large scale cortical ensembles and suggest they engage specific and transient cellular and regional cortical ensembles.

neuroscience↗

bioRxiv2025

Isolation of a nanobody specific to the PstS-1 protein and evaluation of its immunoreactivity with structural components of Mycobacterium tuberculosis granuloma

M. tuberculosis (Mtb) causes infectious granulomatous disease tuberculosis (TB). Within TB granuloma, foci of Mtb secreted antigens anchored on the surface of either bacilli or host cells may serve as targetable biomarkers for antibody based molecular imaging of TB. Nanobody is better suited over conventional antibody or its fragment derivatives for molecular imaging due to its quick localization in target tissue and rapid clearance from off-target organs. Here, we report the production of a high affinity nanobody against PstS-1 protein of Mtb which helps bacilli in phosphate uptake as well as host cell adhesion. C8 nanobody was isolated from a phage display library displaying nanobodies which was constructed from a camel immunized with secretory proteins of Mtb. C8 Nb was characterized in vitro and in vivo for its immunoreactivity against PstS-1 protein. Ability of C8 Nb to bind PstS-1 protein present on the surface of Mtb bacilli or adhered on macrophages and its localization around BCG cells injected intramuscularly in mice demonstrate its potential in the development of molecular imaging for tuberculosis.

microbiology↗

bioRxiv2025

Monoclonal antibody to Filarial serpin Wb123 impedes the urokinase plasminogen activator receptor-mediated Alternative activation of macrophages

Macrophages play a multifaceted role in mounting an immune response against pathogens through phagocytosis, antigen presentation and cytokine production. Activated macrophages are critical for the initiation, maintenance, and resolution of inflammation. They can either be classically activated (Th1 response), which promotes inflammation or alternatively activated (Th2 response), which resolves inflammation. The alternate activation of macrophages, along with diminished T cell response, is thought to be an important immune evasion strategy employed by the filarial parasites. However, the mechanism behind filaria-induced alternate activation remains unclear. In this study, by using in-silico approach we identified filarial serpins which are highly expressed in the infective L3 larval stages. We characterized the filarial serine protease inhibitor, Wb123 and established its role in alternate activation. We observed that Wb123 impairs nitric oxide (NO) and reactive oxygen species (ROS) expression, which plays a crucial role in mounting a strong immune response. Surprisingly, we also observed elevated IL6 expression and phosphorylation of STAT3, indicating IL-6-dependent alternate activation. Our findings indicate that the urokinase plasminogen activator receptor (uPAR) is essential for Wb123-induced alternate activation. Furthermore, we demonstrated that the monoclonal antibody MAbG8 impedes the Wb123-induced alternate activation, as shown by reduced CD163 expression along with increased ROS and uPA expression in response to lipopolysaccharide (LPS) and interferon-gamma (IFN-{gamma}). Overall, our study identifies the filarial serpin Wb123 and highlights its potent role in alternative activation. This interaction reveals, for the first time a mechanism exploited by filarial parasites to evade a strong pro-inflammatory immune response.

cell biology↗

bioRxiv2024

Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy

Increasingly, experiments designed to provide practical perturbations to circuits or behavior are required for hypothesis testing in various disciplines ranging from motor learning to recovery after injury. We present the implementation and efficacy of an open-source closed-loop neurofeedback (CLNF) and closed-loop movement feedback (CLMF) system. In CLNF, we measure mm-scale cortical mesoscale activity with GCaMP6s and provide graded auditory feedback (within [~]63 ms) based on changes in dorsal-cortical activation within regions of interest (ROI) and with a specified rule. Single or dual ROIs (ROI1, ROI2) on the dorsal cortical map were selected as targets. Both motor and sensory regions supported closed-loop training in male and female mice. Mice modulated activity in rule-specific target cortical ROIs to get increasing rewards over days (RM ANOVA p=2.83e-5) and adapted to changes in ROI rules (RM ANOVA p=8.3e-10, Table 4 for different rule changes). In CLMF, feedback (within [~]67 ms) was based on tracking a specified body movement, and rewards were generated when the behavior reached a threshold. For movement training, the group that received graded auditory feedback performed significantly better (RM-ANOVA p=9.6e-7) than a control group (RM-ANOVA p=0.49) within four training days. Additionally, mice can learn a change in task rule from left forelimb to right forelimb within a day, after a brief performance drop on day 5. Offline analysis of neural data and behavioral tracking revealed changes in the overall distribution of Ca2+ fluorescence values in CLNF and body-part speed values in CLMF experiments. Increased CLMF performance was accompanied by a decrease in task latency and cortical {Delta}F/F0 amplitude during the task, indicating lower cortical activation as the task gets more familiar.

neuroscience↗

bioRxiv2023

PMTPred: Machine Learning Based Prediction of Protein Methyltransferases using the Composition of k-spaced Amino Acid Pairs

Protein methyltransferases (PMTs) are a group of enzymes that help to catalyze the transfer of a methyl group to its substrates. These enzymes play an important role in epigenetic regulation and are able to methylate various substrates with DNA, RNA, protein, and smallmolecule secondary metabolites. Dysregulation of methyltransferases is involved in different types of human cancers. However, in light of the well-recognized significance of PMTs, it becomes crucial to have reliable and fast methods for identifying these proteins. In the present work, we propose a machine-learning-based method for the identification of PMTs. Various sequence-based features were calculated and prediction models were develped using different machine-learning methods. A ten-fold cross-validation technique was used for model training. The SVM-based CKSAAP model gave the best prediction and achieved the highest accuracy of 87.94% with balance sensitivity (88.8%) and specificity (87.11%) with MCC of 0.759 and AUROC of 0.945. Also, SVM performed better than the compared deep learning algorithms for the prediction of PMTs. Finally, the best model was implemented in standalone software of PMTPred to facilitate the prediction of PMTs. The PMTPred achieved 86.50% prediction accuracy with 82.33% sensitivity, 90.67% specificity and ROC value 0.939 on the blind dataset. The standalone software of PMTPred is freely available for download at https://github.com/ArvindYadav7/PMTPred for research and academic use.

bioinformatics↗

bioRxiv2017

A Web-resource for Nutrient Use Efficiency related Genes, QTLs, and microRNA in important cereals and model plants

Cereals are the key contributors to global food security. Genes involved in uptake (transport), assimilation and utilization of macro- and micro-nutrients are responsible for their content in grain and straw. Although many cereal genomic databases are available, currently there is no cohesive web-resource of manually curated nutrient use efficiency (NtUE) related genes and QTLs, etc. In this study, we present a web-resource containing information on NtUE related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops [wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare)], two alien species (Triticum urartu and Aegilops tauschii) related to wheat, and two model species including Brachypodium distachyon and Arabidopsis thaliana. Gene annotations integrated in the current web-resource were collected from the existing databases and the available literature. The primary goal of developing this web-resource is to provide descriptions of the NtUE related genes and their functional annotation. MicroRNA targeting some of the NtUE related genes and the quantitative trait loci (QTLs) for NtUE related traits are also included. The available information in the web-resource should help the users to readily search the desired information.\n\nWeb-resource URLhttp://bioclues.org/NtUE/

bioinformatics↗

bioRxiv2017

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

Simple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

bioinformatics↗