Vishal Acharya

• PhD
• Principal Scientist at Institute of Himalayan Bioresource Technology

NACHT NTPases and AP-ATPases belongs to STAND (signal transduction ATPases with numerous domain) P-loop NTPase class, which are known to be involved in defense signaling pathways and apoptosis regulation. The AP-ATPases (also known as NB-ARC) and NACHT NTPases are widely spread throughout all kingdoms of life except in plants, where only AP-ATPases...

Systems-biology inspired identification of drug targets and machine learning-based screening of small molecules which modulate their activity have the potential to revolutionize modern drug discovery by complementing conventional methods. To utilize the effectiveness of such pipelines, we first analyzed the dysregulated gene pairs between control a...

Background Oral squamous cell carcinoma (OSCC) is associated with substantial mortality and morbidity but, OSCC can be difficult to detect at its earliest stage due to its molecular complexity and clinical behavior. Therefore, identification of key gene signatures at an early stage will be highly helpful. Methods The aim of this study was to iden...

Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 N...

Variations are mostly due to nonsynonymous single nucleotide polymorphisms (nsSNPs), some of which are associated with certain diseases. Phenotypic effects of a large number of nsSNPs have not been characterized. Although several methods have been developed to predict the effects of nsSNPs as "disease" or "neutral," there is still a need for develo...

A prevalent pathobiont, Candida albicans, accounts for approximately 70% of fungal infections worldwide owing to its virulence traits that culminate in devastating fatalities within healthcare facilities. Protein–protein interactions (PPIs) between Homo sapiens and C. albicans play a pivotal role in infection and disease progression. Additionally,...

Aims: Geophytic plants have evolved to develop underground storage organs (USO) in the active growing season to withstand harsh environments as well as to coordinate growth and reproduction when conditions are favourable. Saffron is an autumn flowering geophyte and an expensive spice crop restricted to certain geographical locations in the world. S...

Virtual screening (VS) is an integral and ever-evolving domain of the drug discovery framework. The VS is traditionally classified into ligand-based (LB) and structure-based (SB) approaches. Machine intelligence or artificial intelligence has wide applications in the drug discovery domain to reduce time and resource consumption. In combination with...

Potato (Solanum tuberosum L.) is a modified stem and important food crop rich in starch, proteins, antioxidants, and vitamins. Potato is consumed globally; however, being a temperate region crop, it is negatively affected by temperature rise. Histone methylation dynamically regulates plant growth and development in response to environmental stresse...

Ophiocordyceps is a species-rich genus in the order Hypocreales (Sordariomycetes, Ascomycota) depicting a fascinating relationship between microbes and insects. In the present study, a new species, Ophiocordyceps indica sp. nov., is discovered infecting lepidopteran larvae from tree line locations (2,202–2,653 m AMSL) of the Kullu District, Himacha...

Effector proteins are highly diverse, often lacking similarity in their protein sequences, making it challenging to determine their biological function. Using AlphaFold2 (AF2), Seong and Krasileva recently found that effector structures, but not sequences, share commonality. This helps further understanding of effector evolution across fungal speci...

Indian Himalayan metagenome database (IHM-DB) is a web-based database consisting of information on metagenomic datasets from various databases and publications that are specifically reported from the Indian Himalayan Region (IHR). The online interface allows users to view or download the dataset-specific information for the respective states, categ...

Investigating network behavior from host-pathogen interactions is challenging. Here, we present the deep-learning-based protocol to construct an immune-related gene network and list the genes involved in the defense response of host to specific biotic stress. The protocol includes the steps to pre-process the interaction pairs and expression profil...

The human immunodeficiency virus (HIV) connects to the cluster of differentiation (CD4) and any of the entry co-receptors (CCR5 and CXCR4); followed by unloading the viral genome, reverse transcriptase, and integrase enzymes within the host cell. The co-receptors facilitate the entry of virus and vital enzymes, leading to replication and pre-matura...

Virtual screening (VS) aids in prioritizing unknown bio-interactions between compounds and protein targets for empirical drug discovery. In standard VS exercise, roughly 10% of top-ranked molecules exhibit activity when examined in biochemical assays, which accounts for many false positive hits, making it an arduous task. Attempts for conquering fa...

Rice, apart from abiotic stress, is prone to attack from multiple pathogens. Predominately, the two rice pathogens, bacterial Xanthomonas oryzae (Xoo) and hemibiotrophic fungus, Magnaporthe oryzae, are extensively well explored for more than last decade. However, due to lack of holistic study, we design a deep learning-based rice network model (DLN...

Rhodiola imbricata (Crassulaceae) is a traditional trans-Himalayan endangered medicinal herb with immense therapeutic applications. Over the years, over-exploitation, un-managed harvesting, and lack of captive cultivation procedures led to the huge market gap. Therefore, plant tissue culture and RNA-Seq-based molecular bioprospection of key regulat...

Rice, apart from abiotic stress, is prone to attack from multiple pathogens. Predominately, the two rice pathogens, bacterial Xanthomonas oryzae (Xoo) and hemibiotrophic fungus, Magnaporthe oryzae, is extensively well explored for more than last decade. However, due to lack of holistic study, we design deep learning based rice network model (DLNet)...

Amplification of oxidative stress can be utilized as a strategy to attenuate cancer progression by instigating apoptosis. However, the duration of positive response to such therapies is limited, as cancer cells eventually develop resistance. The underlying molecular mechanisms of cancer cells to escape apoptosis under high oxidative stress is unkno...

Ethnopharmacological relevance Swertia purpurascens Wall belongs to a well-known genus in traditional systems of medicine worldwide. In folklore, it is used to treat various ailments, including hepatic disorders, as an alternative to the endangered species Swertia chirayita. However, the therapeutic potential of Swertia purpurascens Wall against he...

Background Adventitious root formation is considered a major developmental step during the propagation of difficult to root plants, especially in horticultural crops. Recently, adventitious roots induced through plant tissue culture methods have also been used for production of phytochemicals such as flavonoids, anthocyanins and anthraquinones. It...

Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) is a critically endangered medicinal herb of immense importance due to its pharmaceutical bioactive compound, especially sipeimine, used for the treatment of chronic respiratory disorders. However, the industrial demand for sipeimine solely depends on its endangered natural habi...

Ethnopharmacological relevance There is growing inclination towards developing bioactive molecule-based strategies for the management of allergic airway inflammation associated respiratory diseases. Vitex negundo Linn., also known as Nirgundi, is one such medicinal plant enriched with phytochemicals and used for inflammatory and respiratory disorde...

Objective Sudden unexpected death in epilepsy (SUDEP) is a major outcome of cardiac dysfunction in patients with epilepsy. In continuation of our previous work, the present study was envisaged to explore the key regulators responsible for cardiac damage associated with chronic seizures using whole transcriptome and proteome analysis in a rat model...

Arthrobacter is a dominant aerobic bacterium under the class Actinobacteria, known for its nutritionally versatile nature and wide prevalence in stressful environments. In the current study representative two strains of Arthrobacter, ERGS1:01 and ERGS4:06, with efficient survivability under high altitude stress conditions were selected for comparat...

Bacterial lipases with activity spanning over a broad temperature and substrate range have several industrial applications. An efficient enzyme-producing bacterium Chryseobacterium polytrichastri ERMR1:04, previously reported from Sikkim Himalaya, was explored for purification and characterization of cold-adapted lipase. Optimum lipase production w...

A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus...

Metabolomics, an extended branch deals with targeted metabolite analysis, takes transcriptome and proteome analysis in consideration to solve complex biological puzzles. Improved insight in the metabolomics has generated huge complex of data that makes room for improved in silico methodologies to reveal the basic biological mechanism from the gener...

Nitrate is the main source of inorganic nitrogen for plants, which also act as signaling molecule. Present study was aimed to understand nitrate regulatory mechanism in Brassica juncea cultivars, with contrasting nitrogen-use-efficiency (NUE) viz. Pusa Bold (PB, high-NUE) and Pusa Jai Kisan (PJK, low-NUE), employing RNA-seq approach. A total of 403...

Pseudomonas frederiksbergensis ERDD5:01 is a psychrotrophic bacteria isolated from the glacial stream flowing from East Rathong glacier in Sikkim Himalaya. The strain showed survivability at high altitude stress conditions like freezing, frequent freeze-thaw cycles, and UV-C radiations. The complete genome of 5,746,824 bp circular chromosome and a...

STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, th...

Bread wheat is one of the major staple foods of worldwide population and iron plays a significant role in growth and development of the plant. In this report, we are presenting the genome wide identification of iron-binding proteins in bread wheat. The wheat genome derived putative proteome was screened for identification of iron-binding sequence m...

List of protein sequence accession number used for phylogenetic analyses in the report from different species. (XLS)

Blast hits of corresponding protein sequences of early green plant lineages. (XLS)

List of NACHT NTPases used for phylogenetic analysis in Fig 6. (XLS)

The MADS-box transcription factors play essential roles in various processes of plant growth and development. In the present study, phylogenetic analysis of 142 apple MADS-box proteins with that of other dicotyledonous species identified six putative Dormancy-Associated MADS-box (DAM) and four putative Flowering Locus C-like (FLC-like) proteins. In...

Copper is a vital micronutrient for plant growth and development, but in high concentration it leads to the oxidative damage thereby initiating biosynthesis of jasmonic acid (JA). The JA signalling is mediated by various transcription factors (TFs) such as JAZ and MYC2. JAZ TFs are the negative regulators of JA signalling which are degraded in pres...

Rice is an important staple cereal crop grown world-wide and is among the highly consumed food commodity. The various diseases in rice cost for an average of 37% reduction in the yield globally. Rice-blast fungus (Magnaporthe) is the most common phyto-pathogenic fungi responsible for substantial loss in production. The mechanism by which pathogens...

The advancement in genome sequencing of early green plant lineages provides valuable data to unveil the phenomenon behind the origin and evolution of genes in the modern flowering plants. Recent findings shows the importance of apoptotic machinery in plant growth and development which were previously known to be absent. Therefore, we employed a gen...

Rauvolfia serpentina has been known to produce therapeutically important indole alkaloids used in treatment of various diseases. Despite its medicinal importance, complete understanding of its secondary metabolism is challenging due to complex interplay among various transcription factors (TFs) and genes. However, weighted co-expression analysis of...

Enzymes are known to be denatured upon boiling, although Cu, Zn superoxide dismutase of Potentilla atrosanguinea (Pot-SOD) retains significant catalytic activity even after autoclaving (heating at 121°C at a pressure of 1.1 kg per square cm for 20 min). The polypeptide backbone of Pot-SOD consists of 152 amino acids with a central core spanning His...

The availability of complete genome sequences from unicellular to multicellular organisms are advantageous to study the evolution of functional systems, unique to eukaryotes. One of the unique capability of eukaryotes is to defend themselves from pathogen infection where apoptosis related domain play an important role. These domain containing prote...

Complex systems are often organized in the form of networks. The last decade has seen numerous breakthroughs in the network theory, which have been implicated in every aspect of biological sciences. In this chapter, we review contributions of the network analysis for understanding cellular organization in system biology era using protein-protein in...

NAC [no apical meristem (NAM), Arabidopsis thaliana transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins belong to one of the largest plant-specific transcription factor (TF) families and play important roles in plant development processes, response to biotic and abiotic cues and hormone signalling. Our genome-wide an...

The present work was conducted to understand the basis of adaptation in Caragana jubata in its niche environment at high altitude cold desert of Himalaya. Molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (LT), a major cue operative at high altitude. Importantly, these ge...

Supplementary information

Hypohidrotic/anhidrotic ectodermal dysplasia (HED) is a rare Mendelian disorder affecting ectodermal tissues. The disease is primarily caused by inactivation of any one of three genes, namely ectodysplasin A1 (EDA-A1), which encodes a ligand belonging to the tumour necrosis factor (TNF) superfamily; ectodysplasin A receptor (EDAR), encoding the EDA...

Familial Hypertrophic Cardiomyopathy (FHC) is an autosomal dominant disorder affecting the cardiac muscle and exhibits varied clinical symptoms because of genetic heterogeneity. Several disease causing genes have been identified and most code for sarcomere proteins. In the current study, we have carried out clinical and molecular analysis of FHC pa...

Background: Hypohidrotic/anhydrotic ectodermal dysplasia (HED) is a rare mendelian disorder affecting ectodermal tissues. The disease is primarily caused by inactivation of any one of three genes viz. Ectodysplasin A1 (EDA-A1) which encodes a ligand belonging to the Tumor Necrosis Factor (TNF) super family; Ectodysplasin A receptor (EDAR) encoding...

The HNH Database is a collection and sequence-based classification of HNH domain proteins. The database contains about 1913 HNH domain containing proteins, and is classified into 10 subsets based on the sequence pattern. Each of these subsets has unique signature sequences. We have shown a correlation between the subset combination and their domain...