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Biology subjects

Verma, S. K.

Publications and source records attributed to Verma, S. K..

10 recordsLinked to original sources

Network-enabled drug repurposing identifies lithium to promote cardiomyocyte proliferation

The adult mammalian heart has minimal regenerative capacity, limited in part by endogenous cardiomyocyte (CM) renewal. Although CM proliferation is a promising target in both congenital and adult heart disease, no current therapies specifically target this process. Progress has been hindered by the complexity of CM proliferation signaling networks, which may require systems-level approaches. The overall goal of this study was to leverage systems modeling to identify FDA approved drugs that have the potential to be repurposed towards CM proliferation. To achieve this goal, we developed a computational drug repurposing framework that integrates drug-target interaction data with a previously developed logic-based network model of CM proliferation signaling. Using this framework, we identified 81 drugs that directly target nodes within the CM proliferation network, corresponding to 32 unique drug-target interactions. Virtual screening predicted 5 unique drug-target interactions that increase CM proliferation and 14 that decrease CM proliferation outputs. Lithium, a GSK3{beta} inhibitor widely prescribed for bipolar disorder, was predicted and experimentally validated to promote CM proliferation through a Cyclin D/CDK4 pathway. In vivo, treatment of pregnant mice with lithium increased DNA synthesis in the CMs of their embryos. A retrospective analysis of the FDA Adverse Events Reporting System confirmed that relative to other mood stabilizers, in utero exposure to lithium was associated with an increased incidence of congenital heart defects, in males but not females. Together, this work provides a computational-experimental framework for repurposing FDA-approved drugs to modulate CM proliferation, which highlights therapeutic potential of lithium for adult CM regeneration but congenital risks to developing embryos.

systems biology↗

A combined Eulerian-Lagrangian and thin film approximation model to investigate the disease-specific drug delivery efficacy on realistic lung geometry and breathing profiles

This work presents a computational approach to investigate antiviral aerosol deposition in anatomically realistic human airways under various physiological inhalation conditions. Antiviral drugs are represented as fine liquid droplets that form a thin coating on airway surfaces, primarily targeting early infection sites. The suggested method combines an Eulerian-Lagrangian discrete phase model (DPM) to track droplet motion and an Eulerian wall film (EWF) model to mimic the evolution of deposited liquid films. This combination effectively addresses the shortcomings of previous studies that employed DPM exclusively, which ignored the post-deposition redistribution dynamics of liquid drugs on airway surfaces. Furthermore, the effects of the distressed breathing of patients with chronic obstructive pulmonary disease (COPD) are compared with both idealized and physiologically realistic breathing patterns in healthy individuals. The study assesses airflow parameters, film thickness, deposition efficiency, and surface area coverage for aerosol particles from 1 to 10 {micro}m. Results reveal that distressed breathing patterns of COPD patients significantly alter the deposition preferences between the upper (~5.28%) and lower lobes (~2.52%) compared to the equivalent ideal and realistic healthy inhalations. Moreover, the distressed breathing also limits the drug penetration into deeper generations, as the highest surface coverage is observed at the carinal region rather than the usual left lower lobe (LLL) found in ideal and realistic healthy breathing cases. Such deposition contrasts highlight the importance of optimizing inhalation therapy and device designs for individuals with obstructive airway diseases.

bioengineering↗

Bridging fungal resistance and plant growth through constitutive overexpression of Thchit42 gene in Pelargonium graveolens

Pelargonium graveolens essential oil possesses significant attributes, known for perfumery and aromatherapy. However, optimal yield and propagation are predominantly hindered by biotic stress. All biotechnological approaches have yet to prove effective in addressing fungal resistance. The current study developed transgenic geranium bridging molecular mechanism of fungal resistance and plant growth by introducing cassette 35S::Thchit42. Furthermore, 120 independently putative transformed explants were regenerated on kanamycin fortified medium. Primarily transgenic lines were demonstrated peak pathogenicity and antifungal activity against formidable Colletotrichum gloeosporioides and Fusarium oxysporum. Additionally, phenotypic analysis revealed [~]2fold increase in leaf size and [~]2.1fold enhanced oil content. To elucidate the molecular mechanisms for genotypic cause, De novo transcriptional profiles were analyzed to indicate that the auxin-regulated longifolia gene is accountable for augmentation in leaf size, and ZF RICESLEEPER attributes growth upregulation. Collectively, data provides valuable insights into unravelling the mechanism of Thchit42-mediated crosstalk between morphological and chemical alteration in transgenic plants. This knowledge might create novel opportunities to cultivate fungal-resistant geranium throughout all seasons to fulfil demand.

plant biology↗

An associative transcriptomics study on rice bean (Vigna umbellata) provides new insights into genetic basis and candidate genes governing flowering, maturity and seed weight

Rice bean is an underrated legume with significant potential to support food and nutritional security worldwide, being a rich source of proteins, minerals, and essential fatty acids. Therefore, we considered three pivotal production traits of rice bean; flowering, maturity and seed weight, to identify associated candidate genes. One-hundred diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank were considered for phenotypic data collection and genotyping by transcriptome sequencing approach. Association analysis involving various GWAS models was conducted to identify significant marker-trait associations. The results revealed association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The annotation of associated transcripts unraveled the functional genes related to the considered traits. Among the significant candidate genes identified, HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A were found associated with flowering. Further, associations of WRKY1 and DEAD-box-RH27 with seed weight, PIF3 and pentatricopeptide-repeat-containing-gene with maturity & seed weight and aldo-keto-reductase with flowering & maturity have been revealed. The present investigation provides insights into the genetic mechanisms governing economically-essential traits like flowering, maturity and seed weight that can be potentially utilized for rice bean improvement. HighlightsThe present investigation is the first associative transcriptomics approach implemented on Vigna umbellata. Based on the marker-trait association analysis, candidate genes for flowering, maturity and seed weight traits are reported.

bioinformatics↗

Subcellular dynamics studies reveal how tissue-specific distribution patterns of iron are established in developing wheat grains

Understanding iron trafficking in plants is key to enhancing the nutritional quality of crops. Due to the difficulty of imaging iron in transit, little is known about iron translocation and distribution in developing seeds. A novel approach, combining 57Fe isotope labelling and NanoSIMS, was used to visualize iron translocation dynamics at the subcellular level in wheat grain, Triticum aestivum L. We were able to track the main route of iron from maternal tissues to the embryo through different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, as confirmed by histological staining and TEM-EDS. Virtually all iron was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Aleurone cells contained a new type of iron body, highly enriched in 57Fe, and most likely represents iron-nicotianamine being delivered to phytate globoids. Correlation with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification efforts.

plant biology↗

Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples

The ongoing spread of pandemic coronavirus disease (COVID-19) is caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). In the lack of specific drugs or vaccines for SARS-CoV-2, demands rapid diagnosis and management are crucial for controlling the outbreak in the community. Here we report the development of the first rapid-colorimetric assay capable of detecting SARS-CoV-2 in the human nasopharyngeal RNA sample in less than 30 minutes. We utilized a nanomaterial-based optical sensing platform to detect RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2, where the formation of oligo probe-target hybrid led to salt-induced aggregation and changes in gold-colloid color from pink to blue in visible range. Accordingly, we found a change in colloid color from pink to blue in assay containing nasopharyngeal RNA sample from the subject with clinically diagnosed COVID-19. The colloid retained pink color when the test includes samples from COVID-19 negative subjects or human papillomavirus (HPV) infected women. The results were validated using nasopharangeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has detection limit as little as 0.5 ng of SARS-CoV-2 RNA. Overall, the developed assay rapidly detects SARS-CoV-2 RNA in clinical samples in a cost-effective manner and would be useful in pandemic management by facilitating mass screening.

microbiology↗

RBFOX2 Is Critical For Maintaining Alternative Polyadenylation And Mitochondrial Health In Myoblasts

RBFOX2, which has a well-established role in alternative splicing, is linked to heart diseases. However, it is unclear whether RBFOX2 has other roles in RNA processing that can influence gene expression/function in muscle cells, contributing to disease pathology. Here, we employed both 3-end and nanopore cDNA sequencing to reveal a previously unrecognized role for RBFOX2 in maintaining alternative polyadenylation (APA) signatures in myoblasts. We found that RBFOX2-mediated APA modulates both mRNA levels and isoform expression of a collection of genes including contractile and mitochondrial genes. We identified the key muscle-specific contractile gene, Tropomyosin 1 and essential mitochondrial gene, Slc25a4 as APA targets of RBFOX2. Unexpectedly, depletion of RBFOX2 adversely affected mitochondrial health in myoblasts that is in part mediated by disrupted APA of mitochondrial gene Slc25a4. Mechanistically, we found that RBFOX2 regulation of Slc25a4 APA is mediated through consensus RBFOX2 binding motifs near the distal polyadenylation site enforcing the use of the proximal polyadenylation site. In sum, our results unveiled a new role for RBFOX2 in fine tuning expression levels of mitochondrial and contractile genes via APA in myoblasts relevant to heart diseases.

molecular biology↗

Delivering on the Vision of Bench to Bedside: A Rare Disease Funding Community Collaboration to Develop Effective Therapies for Neurofibromatosis Type 1 Tumors

The time from target identification to new drug approval is often measured in decades. This can be even more challenging for rare diseases. Indeed, 95% of rare diseases do not have a specific therapy approved. Coordinated efforts to support research along the drug development pipeline can provide long term and comprehensive support to enable scientific breakthroughs for rare diseases. However, this requires coordination across multiple stakeholders. The present article analyzes the funding efforts of four major federal and philanthropic organizations to accelerate the advancement of MEK inhibitors to human clinical trials for NF1-associated tumors.

scientific communication and education↗

Association of the types of alcoholic beverages and blood lipids in a local population in Jharkhand, India

Although light-to-moderate alcohol consumption is considered beneficial, alcohol in binge doses or high cumulative lifetime consumption leads to cardiovascular diseases, metabolic syndrome and structural damage to various organs. Alcohol is known to alter blood lipid concentrations; however, the association of the types of alcohol on the lipid profile has not been investigated extensively. A cross-sectional study involving male participants (n = 86) aged 20 to 60 from the Ranchi and Dhanbad zone of Jharkhand, India, was carried out to investigate the effects of cumulative lifetime consumption of Haria, a local rice-based fermented alcohol, Indian made foreign liquor (IMFL), and a combination of the two on the blood lipid profiles. Demographic characteristics, dietary intake and medical history were obtained from the participants by questionnaire, and lipid levels were determined by analysis of blood samples. The effect of Haria alone on the blood lipids was also investigated on the local female population (n = 31). After adjusting for demographic and dietary factors, IMFL and combination of IMFL and Haria consumption was associated with increased serum total cholesterol, triglyceride, and low density lipoprotein (LDL) cholesterol levels (P < 0.05) and decreased high density lipoprotein (HDL) cholesterol levels (P < 0.05). None of the blood lipids changed significantly in Haria consumers in both male and female groups. This study suggests that Haria, a popular alcoholic beverage of West Bengal and east-central India, is a relatively safe local alcoholic beverage and does not alter the lipid profile in consumers.

biochemistry↗

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle

Hammondia hammondi is the nearest relative of Toxoplasma gondii, but unlike T. gondii is obligately heteroxenous. We have compared H. hammondi and T. gondii development in vitro and identified multiple H. hammondi-specific growth states. Despite replicating slower than T. gondii, H. hammondi was resistant to pH-induced tissue cyst formation early after excystation. However, in the absence of stress H. hammondi spontaneously converted to a terminally differentiated tissue cyst stage while T. gondii did not. Cultured H. hammondi could infect new host cells for up to 8 days following excystation, and this period was exploited to generate stably transgenic H. hammondi. Coupled with RNAseq analyses, our data clearly show that H. hammondi zoites grow as stringently regulated life stages that are fundamentally distinct from T. gondii tachyzoites and bradyzoites.

microbiology↗