Atul Kumar Upadhyay

Thapar University · Department of biotechnology

Being one of the major food crops, rice faces enormous yield loss every year due to water scarcity all over the world. To investigate the positive impact of CPPU (N-(2-chloro-4-pyridyl)-N′-phenylurea), a phenylurea cytokinin, on rice plants during drought stress; we planted Oryza sativa ssp. Indica cv. Pathumthani1 under controlled conditions. The...

The phenomenon termed ”3D-domain swapping” occurs when two or more identical protein subunits relocate their secondary structure components, like strands or helices, to generate a different tertiary structure. This results in the creation of new protein-protein interactions and the formation of higher-order structures. This paper proposed an unsupe...

Colletotrichum falcatum is one of the devastating fungal pathogens of sugarcane, accountable for the red rot pandemic in India. Sucrose, being main assimilatory product of sugarcane, has been accredited for its crucial roles as signaling molecule, and association with biotic responses against pathogens. This is the first study to investigate the ef...

It has been proven that computational approaches can be used to find endpoints that can help with a cosmetic safety assessment. Thousands of mice, guinea pigs, rats, and rabbits die each year due to torturous experiments. This paradigm shift has enabled the highest number of regulations of chemical safety assessments while also mandating the use of...

Prostate cancer is the second most dangerous cancer type worldwide. While various treatment options are present i.e. agonists and antagonists, their utilization leads to adverse effects and due to this resistance developing, ultimately the outcome is remission. So, to overcome this issue, we have undertaken an in-silico investigation to identify pr...

Aldo-keto reductase 1C3 (AKR1C3) is a monomeric enzyme expressed in steroidogenic tissues such asthe testis, prostate, uterus, and breast. Overexpression of this AKR1C3 is associated with vast cancerssuch as breast, colon, colorectal, endometrial, prostate, and acute myeloid leukaemia. Regarding thetreatment of castration-resistant prostate cancer,...

Background: Prostate cancer (PCa) is the second most frequent kind of cancer in males globally after Lung Cancer. In clinical practice, medicines that act as antagonists/partial agonists of hormone receptors against prostate tissue are employed in PCa treatment. Cyproterone acetate, Flutamide, and Bicalutamide are prominent medications that induce...

Background: Lung cancer is the most commonly diagnosed cancer globally. There are numerous agonists and antagonistic treatment interventions available for therapy. However, all of them possess different detrimental consequences in addition to resistance and remission in sufferers. Medicinal plants have traditionally been employed to treat a wide ra...

Mushrooms are considered as one of the healthiest food due to presence of high quality and quantity of fiber, protein, and vitamins. Hence, mushrooms are highly consumed and have a great demand in the food and pharmaceutical industry. However, the consumption of mushroom leads to allergic reactions in certain individuals. Food allergy is mainly a T...

InBix-2022 International Conference on Frontiers in Nutrition, Medical Genomics, and Drug Discovery Organized by: Dept. of Biotechnology and Bioinformatics, School of Biotechnology and Pharmaceutical sciences, Vignan University and Bioclues.org

Inbix-2022 International Conference on Frontiers in Nutrition, Medical Genomics, and Drug Discovery Organized by: Dept. of Biotechnology and Bioinformatics, School of Biotechnology and Pharmaceutical sciences, Vignan University and Bioclues.org

Approximately, 10% of the world population is facing the challenge of food allergy in direct or indirect way. In this study, a genome-wide identification and annotation of the novel putative allergen from almond is performed. Initially, the whole proteome of almond (31,000 proteins) was scanned by Allergenonline, a publically available database of...

Background Candida tropicalis causes tropical invasive fungal infections, with a high mortality. This fungus has been found to be resistant to antifungal classes such as azoles, echinocandins, and polyenes in several studies. As a result, it is vital to identify novel approaches to prevent and treat C. tropicalis infections. In this study, an in si...

Purpose The food allergen protein profilin is responsible for oral epithelial remodelling and hypersensitive reactions in atopic individuals. Profilins are regarded as panallergens due to their IgE cross-reactivity. Methods The present study reports a bioinformatic pipeline including multiple sequence alignment, homology modelling, molecular dynam...

Cancer is a leading cause of death globally, with about 19.3 million new cases reported each year. Current therapies for cancer management include-chemotherapy, radiotherapy, and surgery. However, they are loaded with side effects and tend to cause toxicity in the patient's body posttreatment, ultimately hindering the response towards the treatment...

Approximately, 10% of the world population is facing the challenge of food allergy in direct or indirect way. In this study, a genome-wide identification and annotation of the novel putative allergen from Almond is performed. Initially, the whole proteome of Almond (31,000 proteins) was scanned by Allergenonline, a publically available database of...

Aryl hydrocarbon receptor (AhR) is a ligand-activated cytosolic transcription factor. Once activated AhR stimulates the pathways that are directly or indirectly linked to inflammation and breast cancer. Exogenous agonists of AhR including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzopyrene are found to be carcinogenic in nature. Breast cance...

Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected 235.6 million people worldwide. In the present study, RNA-dependent RNA polymerase (RdRp) (PDB Id: 6M71) of SARS-CoV-2, an essential enzyme needed for subgenomic replication and amplification of RNA, was selected. Similar to other RdRps, it...

Profilin protein is present ubiquitously in all forms of life and is allied with allergic responses among atopic individuals. In addition to this, profilins from various food sources are also associated with IgE cross-reactivity and are thus classified as pan-allergens. The present study unravels the physicochemical basis of differential amino acid...

Orthohantavirus, a zoonotic virus responsible for causing human cardio-pulmonary disease, is proven to be a fatal disease. Due to the paucity of regimens to cure the disease and efficient management to eradicate this deadly virus, there is a constant need to expand in-silico approaches belonging to immunology domain to formulate best feasible pepti...

We all must have had experience of food allergy causing severe problems to human health. Food allergy is an immunological set of reactions resulting from adverse responses to foods, which may cause severe symptoms such as anaphylaxis and gastrointestinal disorders. Food allergy is triggered by immunoglobulin E (IgE) immune response against the alle...

Nutritional value of the crops refers to the amount of protein, carbohydrate, lipid, fibre, minerals and vitamins present in the crop’s consumable part. The nutritional value varies among the crops depending upon the numerous factors such as variety and the genetic makeup of the crop and conditions in which the crop has been raised namely soil cond...

COVID-19 has emerged as a rapidly escalating serious global health issue, affecting every section of population in a detrimental way. Present situation invigorated researchers to look for potent targets, development as well as repurposing of conventional therapeutic drugs. NSP12, a RNA polymerase, is key player in viral RNA replication and, hence,...

The current pandemic has been declared as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO) on January 30, 2020. The causative agent of the COVID-19 is Sub-Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) that causes lung severe disease, is an enveloped RNA virus. The bats being the main zoonotic...

This book illustrates the importance and significance of bioinformatics in the field of agriculture. It first introduces the basic concepts of bioinformatics, such as homologous sequence and gene function analyses, determination of protein structures, and discusses machine learning applications for an in-depth understanding of the desired genes and...

A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways, MethodsX (2020), doi: https://doi.

Genomics is the study of complete genetic material of an organism. It would not be an exaggeration to say that we are at the peak of genomics era as with the advent of high-throughput sequencing technologies we have an enormous amount of genomic data coming every day. Genomics assisted breeding (GAB) is becoming increasingly popular in the field of...

Plant phenolics have been found to influence both plant biological processes and human health as a dietary component. Plants produce an enormous number of phenolic secondary metabolites which are involved in interaction with the environment, for their reproductive strategy and for their defence mechanisms. These include developmental signals, such...

Cancer is a complex disease, involving multiple defects at the levels of DNA, RNA, protein, metabolites and more. The emerging field of omics Sujata Maurya, Vaishali Chandel, Sibi Raj et al. 276 technologies shows promise in elucidating the biology of cancer at the level of genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipido...

Many biotic and abiotic factors affect agriculture production worldwide. Bio-fertilisers of microbial origin can be a good option for sustaining productivity with more environment-friendly and integrated nutrient management approach. They have been advanced to use the naturally occurring nutrient mobility mechanisms, which promotes soil fertility a...

Fungi belong to eukaryotic group of microorganisms and they are found in almost all type of ecosystem. Some of the common examples of fungi is molds, yeasts and mushrooms. Fungal secondary metabolites are different categories of compounds produce by the organisms of this kingdom. Secondary metabolites are compounds, which are produced as bi-product...

Computational biology

Trichoderma harzianum is widely used as a biocontrol agent for phytopathogens. In the present study, we surmise, it can be used to control human opportunistic pathogens. Extraction with fungus mycelium was performed with the Soxhlet method. The inhibitory concentration was tested on Candida sps, including multidrug-resistant C. auris strain and gra...

Zika fever is a disease caused by Zika virus which is a mosquito-borne flavivirus and infection is through the bite of mosquito from the Aedes genus. Other mode of transmission of Zika fever is blood transfusion, which is thoroughly investigated. Prominent symptoms of Zika virus fever are mild fever, skin rash, conjunctivitis, muscle and joint pain...

In this paper, we present the data acquired during transcriptome analysis of the plant Moringa oleifera [1] from five different tissues (root, stem, leaf, flower and seed) by RNA sequencing. A total of 271 million reads were assembled with an N50 of 2094bp. The combined transcriptome was assessed for transcript abundance across five tissues. The pr...

Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published...

Background: Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Amb...

Aging of the skin is a gradual process, which is associated with changes in the appearance, characteristics, and function of the skin. Skin aging occurs through genetic, lifestyle, dietary, and environmental factors. Within the skin the production of collagen and elastin slows down, dead skin cells do not shed quickly, and the turnover of new skin...

Niosomes a novel trend in drug delivery in which medication is encapsulated in a vesicle and the vesicle made up of bilayer of non-ionic surface active agents and then it is named as niosomes. However niosomes are structurally similar to liposomes in having a bilayer, and the materials used to prepare niosomes make them more stable. After preparing...

In this study, we show that NAC-like transcription factor (TF) has 90% sequence similarity with cDNA of the OsNac5 gene present in the NCBI database. Phylogenetic analysis of the NAC gene family was performed with inclusion of the highly diverse C-terminal sequences. We report that this gene is also found to be orthologous to Glycine max NAC8, NAC2...

Computational approaches to high-throughput data are gaining importance because of explosion of sequences in the post-genomic era. This explosion of sequence data creates a huge gap among the domains of sequence structure and function, since the experimental techniques to determine the structure and function are very expensive, time taking, and lab...

The large diversity present in ecosystem has tremendous potential in the microbial bioprospecting. Microbial bioprospecting is a branch of science, which deals with the identification of suitable microorganisms, biological compounds, or gene sequences which can be used for useful compounds for human welfare. Computational approach to biology is one...

Fungi are large group of organism with tremendous diversity and economical importance. Application of bioinformatics approaches to understand the development and growth of organisms has a great scope. Bioinformatics is one of the rapidly emerging branches of science, which helps in understanding biological systems by using computer softwares and to...

A variety of microorganisms generate highly potent surface-active bio-molecules, biosurfactants, which vary in their chemical properties and molecular size. The present study aimed to investigate the bioremediation potential of Kocuria rosea VB1 (GenBank ID.: KY608093.1) and Arthrobacter luteolus VB2 (GenBank ID.: KY608094.1) in industrial polluted...

Bacillus thuringiensis (Bt)is a bacterium present in soil having bio pesticidal activity. A special class of protein known as d-endotoxins is responsible for this unique and useful activity. Deltaendotoxins are made up of three domains having specific functions. Domain I at N-terminal of dendotoxin is comprised of six helices. Domain II is made of...

Current world energy demand is based on fossil fuels, which will vanish in coming decades. Renewable energy especially biofuels has attracted great interest as solutions to the current energy problem. Among available biofuel resources, bioethanol seems to be an efficient alternative. Saccharomyces cerevisiae a well-established organism for bioethan...

The phenomenon of protein domain swapping is interesting and acquires importance, since in some cases, it is implicated in neurodegenerative and other diseases. Predictive algorithms, that can attribute a chance of a protein to get engaged in domain swapping, will be of biomedical value. In such domain swapped structures, 'hinge regions' are key li...

With the advent of Next Generation Sequencing (NGS) there is huge amount of genome-transcriptome sequence data available in public domain from all most all the kingdom of life such as microbe, plant and animal. To make any meaning from this data, we need to analyse these sequences for the presence of the genes and other regulatory elements in these...

Present study aimed to analyze the genetic diversity among nine cotton genotypes using the molecular markers viz., RAPD, ISSR and SSR marker. A total of 25 RAPD, 22 ISSR and 16 SSR primers were used, which produced 171, 209 and 33 amplicons, respectively. The number of polymorphic amplicons was found to be 156 (RAPD), 142 (ISSR) and 24 (SSR) accoun...

Primary hypertension or essential hypertension is associated with high blood pressure. However, there is no known secondary prognosis for essential hypertension. Previous studies have shown that high blood pressure is linked to genetic factors and to the sedentary lifestyle. Recently, the interaction between angiotensin-converting enzyme (ACE) and...

Wheat is a staple food for most of the world. With the growing population there is a tremendous pressure to increase the productivity of food crops. Wheat being most used food crop must be investigated thoroughly. Leaf senescence is the final stage of growth and development. Delaying the leaf senescence by few days has shown an increase in producti...

Enhancers are DNA sequences containing multiple transcription factor binding sites, could be present upstream, downstream or within the gene. They are meant to enhance the expression of their target genes. Major features of enhancers are: clusters of transcription factor binding sites, evolutionary conserved non-coding DNA sequence and biochemical...

3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies et...

Predicted 3D-domain swapped sequences of human proteome. (TXT)

Prediction results on known cases of domain swapping from 3DSwap as validation. (DOC)

Examples of challenging cases for hinge prediction, experimentally identified hinges are marked in blue color (A: Central loop swapping (PDB: 1IXX), B and C: Intertwined dimmers (PDB: 1A64), D: Missing regions (PDB: 2ZEJ), E: Very small hinges (PDB: 5CRO) and F: Elaborate interface (2PJW)) (TIF)

Description of Gene Ontology terms prevalent in human domain swap predicted sequences. (DOC)

Predicted 3D-domain swapped human entries with Pfam domain family associations. (TXT)

Reviewed UniProt sequences of human proteome used as input to prediction models. (TXT)

Available three-dimensional structures of proteins suggest that proteins can engage in limited extent of aggregation through a peculiar form of ’hand-shake’ strategy that is defined as ’domain swapping’. Few proteins also form unlimited aggregation through domain swapping leading to diseases and hence this phenomenon acquires biomedical importance....

Cissus quadrangularis is a medicinal plant belonging to the family Vitaceae and is commonly found in the tropical regions of India, Ceylon, East Africa, Malaysia and Thailand. It is referred to as Veldt Grape and it is a traditional medicine for joint and bone health and shows promise in promoting bone growth rates. The whole plant is used in oral...

3D-Domain swapping is a process whereby two or more identical protein molecules associate to form dimers or higher order oligomers by exchanging identical structural elements, such that native intramolecular interactions are replaced by their intermolecular counterparts. These proteins, which undergo domain swapping, have acquired much attention ow...

Background: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-...

Available three-dimensional structures of proteins suggest that proteins can engage in limited extent of aggregation through a peculiar form of ‘hand-shake’ strategy that is defined as ‘domain swapping’. Few proteins also form unlimited aggregation through domain swapping leading to diseases and hence this phenomenon acquires biomedical importance....

Several G BPs are sub-jected to C-terminal isoprenylation. In the case of human GBP1 the CaaX motif serves as a signal for farnesylation, which is neces-sary for the recruitment to cellular membranes. In addition to that, our research revealed that the lipid modification changes the nucle-otide binding and GTP hydrolysis activity of hG BP1. Both fa...

Protein domain families are usually classified on the basis of similarity of amino acid sequences. Selection of a single representative sequence for each family provides targets for structure determination or modeling and also enables fast sequence searches to associate new members to a family. Such a selection could be challenging since some of th...

Background Genome sequencing has emerged recently as a technology that can be used to address questions regarding the clonal evolution of cancers. This has the potential to be translated into practical applications in a clinical setting. We have undertaken a case study by carrying out whole exome sequencing of a patient with CML since its clinical...

Background: Genome sequencing has emerged recently as a technology that can be used to address questions regarding the clonal evolution of cancers such as CML and has potential to be translated into practical applications in a clini- cal setting. In order to lay the foundation for exploring the possible use of such technologies in a lower resource...

Chronic Myeloid Leukaemia (CML) is a resultant of the 9∶22 translocation event leading to the constitutive kinase activity of BCR-ABL. Imatinib is the drug used as the first line therapy in CML. We report a longitudinal case study for a CML patient under treatment with imatinib. The bone marrow aspirate of this CML patient was used for exome sequen...

Chronic Myeloid Leukaemia (CML) is a resultant of the 9:22 translocation event leading to the constitutive kinase activity of BCR-ABL. Imatinib is the drug used as the first line therapy in CML. We report a longitudinal case study for a CML patient under treatment with imatinib. The bone marrow aspirate of this CML patient was used for exome sequen...

The phenomenon of protein domain swapping, observed originally amongst a handful of protein examples, is acquiring attention not only due to statistically significant number of examples, but their relevance in neurodegenerative and other diseases. We describe an algorithm which could automatically detect 'hinge regions' in 87% of domain swapped exa...

The phenomenon of protein domain swapping, observed originally amongst a handful of protein examples, is acquiring attention not only due to statistically significant number of examples, but their relevance in neurodegenerative and other diseases. We describe an algorithm which could automatically detect 'hinge regions' in 87% of domain swapped exa...

In the present study, an attempt was made to create random mutations in cry1Ac and cry2 genes from Bacillus thuriengiensis to analyze the effect of altered nucleotides on the toxicity to a chosen insect. The mutated cry1Ac was analyzed for its effect on toxicity by expressing in yeast also. The results obtained are summarized here: Both the native...