Papers by Muktesh Chandra
Industrial Crops and Products, Dec 1, 2021
Abstract Medicinal and aromatic plants (MAPs) possess phytoremediation potential owing to antioxi... more Abstract Medicinal and aromatic plants (MAPs) possess phytoremediation potential owing to antioxidants, secondary metabolites, and morphological features. Moringa oleifera, Pelargonium graveolens, Tagetes patula, and Calotropis gigantea are known for their phytoremediation properties in heavy metals polluted soil. These plants with phytoremediation properties due to antioxidants, specific secondary metabolites synthesis, and distinctive morphological characteristics ultimately become the ideal choice for effective remediation. The main aim of the current study is to provide a genetic evaluation using bioinformatics techniques, antioxidant compounds, metabolites, and their activity. Genomic and transcriptomic studies endorsed genes related to hyperaccumulation in these plant species having essential domains as catalase (CAT) and superoxide dismutase (SOD_Cu, SOD_Fe_C, and SOD_Fe_N). The phylogenetic study showed its close evolutionary relationship to other plant species. The accumulation of total photosynthetic pigments, carotenoids, non-enzymatic antioxidants, and enzymatic antioxidants determined spectrophotometrically, involved in stress tolerance and ROS homeostasis maintenance mechanisms. Tagetes leaves showed the highest proline, flavonoids, and phenolics content, while Moringa showed higher CAT, guaiacol peroxidase (G-POD), and glutathione peroxidase (GPX) activities. Results also revealed that plants accumulated more primary and secondary metabolites in young tissue to tackle pathogens, herbivores, attract pollinators, and in mature tissues to develop strong physiology. Total antioxidant activity, reducing power, and radical scavenging activities were observed. These MAPs have intriguing antioxidant characteristics and a phytochemical composition that might give scientific support for their stress tolerance and ROS management activities. The study establishes the groundwork for using MAPs as phytoremediators; further confirmatory research is required for their use in sustainable phytoremediation.
Molecular Biology Reports, Aug 28, 2020
Key message We performed a comparative transcriptome between two different concentrations of CGA ... more Key message We performed a comparative transcriptome between two different concentrations of CGA from leaves in E. ulmoides. The key genes in the biosynthesis of CGA were identified by differential expression analysis. Abstract Eucommia ulmoides Oliv. is native to China and famous for its extensive medicinal value, such as anti-fatigue, anti-aging, and enhanced immunity, etc. Chlorogenic acid (CGA) is the main medicinal ingredient of E. ulmoides. In E. ulmoides, the gene functions related to CGA biosynthesis are not fully understood. In this study, we conducted Illumina transcriptome sequencing and digital gene expression (DGE) for E. ulmoides with high content of CGA (H01, H02, and H03) and low content of CGA (L01, L02, and L03) to explore the potential genes involved in CGA biosynthesis. A total of 82,065 unigenes were generated. Of these unigenes, 28 were involved in CGA biosynthesis pathways and 116 regulated the CGA biosynthesis. Furthermore, by gene expression profiling and differential expression analysis, three functional genes including two PALs (c133625.graph_c5 and c133625.graph_c7), one 4CL (c139078.graph_c0), and three transcription factors (TFs), including one ERF2 (c139016.graph_c3) and two WRKY (c139022.graph_c3 and c139022.graph_c0) were different expressed, these genes may play key roles in CGA biosynthesis. This study will provide useful genomic resources for the investigation of CGA biosynthesis and genetic improvements of E. ulmoides.
Journal of Computational Chemistry, Jul 20, 2021
Since December 2019, coronavirus disease (COVID‐19) has claimed the lives of millions of people a... more Since December 2019, coronavirus disease (COVID‐19) has claimed the lives of millions of people across the globe. To date, no medicine is available for the responsible virus SARS‐CoV‐2. 3CLpro, that is, 3‐chymotrypsin‐like protease, the main protease (Mpro), has an important role in cleaving pp1a and pp1ab polyproteins. This Mpro serves as an important target in drug designing against COVID‐19. Herein, the study includes the investigation, screening, and identification of potent leads from (Withania sps.), against SARS‐CoV‐2, using virtual screening, molecular docking, and molecular dynamics (MD) simulations. Seventy‐three natural compounds from this important medicinal plant were screened. The Binding affinity was used to identify the most probable target to inhibit the Mpro, compounds 27‐hydroxywithanolide F (W32, −11.5 kcal/mol), withanolide A (W56, −11.4 kcal/mol), and withacoagulin H (W30, −11.1 kcal/mol) showed highest binding energy. Lipinski's rule, followed by drug‐likability and likeness screening, resulted in 36 molecules. Further, MD simulation of 50 ns predicted withacoagulin H possessing strong binding affinity and hydrogen‐bonding interactions with the active site. The binding free energy calculation showed the most negative energy of withacoagulin H (−63.463 KJ/mol) compared to other selected compounds. The study also compared the bonding energy of already reported repurposed and newly synthesized drugs. Further, absorption, distribution, metabolism, and excretion predictions were made to found a good balance of potency. Hence the following screened compounds from Withania sps. could serve as the potential leads for drug development against COVID‐19.
<p>The scale representing the relative signal intensity values is shown above. The differen... more <p>The scale representing the relative signal intensity values is shown above. The different stages of developing spikes are S1 (spike emergence); S2 (pollination stage); S3 (dough stage) and S4 (maturation).</p
<p>The different stages of developing spikes are S1 (spike emergence); S2 (pollination stag... more <p>The different stages of developing spikes are S1 (spike emergence); S2 (pollination stage); S3 (dough stage) and S4 (maturation).</p
<p>The number indicated on each cell represents the log2 calculated FPKM values. FPKM value... more <p>The number indicated on each cell represents the log2 calculated FPKM values. FPKM values smaller than 1 were not calculated due to negative logarithm and they were stated as in the original data.</p
<p>Multilevel consensus sequences for the MEME defined motifs of members of different calci... more <p>Multilevel consensus sequences for the MEME defined motifs of members of different calcium sensor genes.</p
<p>Neighbor-joining tree was created using MEGA6 software with 1000 bootstrap using ORF seq... more <p>Neighbor-joining tree was created using MEGA6 software with 1000 bootstrap using ORF sequences of rice and finger millet CaM and CaMLs, CBLs, CRKs, PEPRKs, CaMKs and CCaMK proteins. Eight groups were labelled as A, B, C, D, E, F, G and H.</p
<p>C Chloroplast, i.e. the sequence contains cTP, a chloroplast transit peptide;</p>&... more <p>C Chloroplast, i.e. the sequence contains cTP, a chloroplast transit peptide;</p><p>M Mitochondrion, i.e. the sequence contains mTP, a mitochondrial targeting peptide;</p><p>S Secretory pathway, i.e. the sequence contains SP, a signal peptide;</p><p>_ any other location.</p><p>List of domain, sub-cellular localization and instability index analysis of finger millet calcium sensor.</p
<p>List of Primers designed from highly expressed genes from transcriptome data of high Ca ... more <p>List of Primers designed from highly expressed genes from transcriptome data of high Ca containing genotype for qPCR analysis.</p
<p>Functional category of differentially expressed calcium sensor gene in finger millet.</p
Bioinformatics, 2022
Abstract The biological information is stored in the form of DNA, RNA, or proteins. These biomole... more Abstract The biological information is stored in the form of DNA, RNA, or proteins. These biomolecules are purported to be acquainted with a unique code of life. Bioinformatics and computational biology fields include essential operation as biological sequence alignment, which has important application in disease diagnosis, biomaterial engineering, genetic engineering, and drug discovery. The score is assigned for the similarity or correlation in alignment, either pairwise alignment or multiple sequence alignment. Based on that score, the degree of similarity is adjudicated and inferred that the sequences are related or distant. Algorithms, such as dynamic programming, greedy method, and genetic algorithms, make the alignment quick and accurate. With the advancement of sequencing techniques, the data size is increasing, researchers along with parallel processing and distributed file systems are using modern tools to ease the process of alignment. This chapter discusses the basics of sequence alignment, algorithms, and tools available for biological sequence alignment.
Industrial Crops and Products, 2021
Abstract Medicinal and aromatic plants (MAPs) possess phytoremediation potential owing to antioxi... more Abstract Medicinal and aromatic plants (MAPs) possess phytoremediation potential owing to antioxidants, secondary metabolites, and morphological features. Moringa oleifera, Pelargonium graveolens, Tagetes patula, and Calotropis gigantea are known for their phytoremediation properties in heavy metals polluted soil. These plants with phytoremediation properties due to antioxidants, specific secondary metabolites synthesis, and distinctive morphological characteristics ultimately become the ideal choice for effective remediation. The main aim of the current study is to provide a genetic evaluation using bioinformatics techniques, antioxidant compounds, metabolites, and their activity. Genomic and transcriptomic studies endorsed genes related to hyperaccumulation in these plant species having essential domains as catalase (CAT) and superoxide dismutase (SOD_Cu, SOD_Fe_C, and SOD_Fe_N). The phylogenetic study showed its close evolutionary relationship to other plant species. The accumulation of total photosynthetic pigments, carotenoids, non-enzymatic antioxidants, and enzymatic antioxidants determined spectrophotometrically, involved in stress tolerance and ROS homeostasis maintenance mechanisms. Tagetes leaves showed the highest proline, flavonoids, and phenolics content, while Moringa showed higher CAT, guaiacol peroxidase (G-POD), and glutathione peroxidase (GPX) activities. Results also revealed that plants accumulated more primary and secondary metabolites in young tissue to tackle pathogens, herbivores, attract pollinators, and in mature tissues to develop strong physiology. Total antioxidant activity, reducing power, and radical scavenging activities were observed. These MAPs have intriguing antioxidant characteristics and a phytochemical composition that might give scientific support for their stress tolerance and ROS management activities. The study establishes the groundwork for using MAPs as phytoremediators; further confirmatory research is required for their use in sustainable phytoremediation.
Journal of Computational Chemistry, 2021
Since December 2019, coronavirus disease (COVID‐19) has claimed the lives of millions of people a... more Since December 2019, coronavirus disease (COVID‐19) has claimed the lives of millions of people across the globe. To date, no medicine is available for the responsible virus SARS‐CoV‐2. 3CLpro, that is, 3‐chymotrypsin‐like protease, the main protease (Mpro), has an important role in cleaving pp1a and pp1ab polyproteins. This Mpro serves as an important target in drug designing against COVID‐19. Herein, the study includes the investigation, screening, and identification of potent leads from (Withania sps.), against SARS‐CoV‐2, using virtual screening, molecular docking, and molecular dynamics (MD) simulations. Seventy‐three natural compounds from this important medicinal plant were screened. The Binding affinity was used to identify the most probable target to inhibit the Mpro, compounds 27‐hydroxywithanolide F (W32, −11.5 kcal/mol), withanolide A (W56, −11.4 kcal/mol), and withacoagulin H (W30, −11.1 kcal/mol) showed highest binding energy. Lipinski's rule, followed by drug‐lika...
Canadian Journal of Biotechnology, 2017
Food Chemistry, 2019
Use of harmful chemicals and expensive maintenance of cold-storage conditions for controlling spr... more Use of harmful chemicals and expensive maintenance of cold-storage conditions for controlling sprouting are among the major problems in potato storage. Here, 20 essential oils (EOs) were tested for their sprouting-inhibiting and sprouting-inducing activities. Overall, treatments of lemon grass (LG) and clove (CL) oils could induce sprouting whereas palmarosa (PR) and ajwain (AZ) oils could inhibit sprouting of potato tubers at normal-room-temperature (25±2ºC) storage. Selected-EOs treatments affected sprouting by modulation of accumulation of reducing sugars, ethylene, and expression of genes involved in tuber-sprouting such as ARF, ARP, AIP and ERF. Surprisingly, 7-days AZ-treatments could inhibit sprouting for 30-days which was mediated via damaging apical meristem. However, LG-and CL-treated tubers could produce enhanced potato yield as well. Present work clearly demonstrates that selected-EOs can be used as a promising eco-friendly approach for inducing/inhibiting sprouting of potato tubers during potato storage and those enhancing sprouting can be used for enhancing productivity.
Protoplasma, 2019
Ocimum species commonly referred to as BTulsi^are well-known for their distinct medicinal and aro... more Ocimum species commonly referred to as BTulsi^are well-known for their distinct medicinal and aromatic properties. The characteristic aroma of Ocimum species and cultivars is attributed to their specific combination of volatile phytochemicals mainly belonging to terpenoid and/or phenylpropanoid classes in their essential oils. The essential oil constituents are synthesized and sequestered in specialized epidermal secretory structures called as glandular trichomes. In this comparative study, inter-and intraspecies diversity in structural attributes and profiles of expression of selected genes related to terpenoid and phenylpropanoid biosynthetic pathways have been investigated. This is performed to seek relationship of variations in the yield and phytochemical composition of the essential oils. Microscopic analysis of trichomes of O. basilicum, O. gratissimum, O. kilimandscharicum, and O. tenuiflorum (green and purple cultivars) revealed substantial variations in density, size, and relative proportions of peltate and capitate trichomes among them. The essential oil yield has been observed to be controlled by the population, dominance, and size of peltate and capitate glandular trichomes. The essential oil sequestration in leaf is controlled by the dominance of peltate glandular trichome size over its number and is also affected by the capitate glandular trichome size/number with variations in leaf area albeit at lower proportions. Comprehension and comparison of results of GC-MS analysis of essential oils showed that most of the Ocimum (O. basilicum, O. tenuiflorum, and O. gratissimum) species produce phenylpropanoids (eugenol, methyl chavicol) as major volatiles except O. kilimandscharicum, which is discrete in being monoterpenoid-rich species. Among the phenylpropanoid-enriched Ocimum (O. basilicum, O. gratissimum, O. tenuiflorum purple, O. tenuiflorum green) as well, terpenoids were important constituents in imparting characteristic aroma. Further, comparative abundance of transcripts of key genes Shiwani Maurya and Muktesh Chandra contributed equally to this work. Highlights • Inter-and intra-specific diversity in phytochemicals, trichome types, and abundance • Number and size of peltate trichomes are the key determinants of essential oil accumulation • Major Ocimum species are phenylpropanoid-rich, whereas O. kilimandscharicum is unique in monoterpenoids • Compositional diversity is governed by differential expression of key genes of biosynthetic pathway of phytochemical class
Scientific reports, Jan 7, 2018
Thymol, as a dietary monoterpene, is a phenol derivative of cymene, which is the major component ... more Thymol, as a dietary monoterpene, is a phenol derivative of cymene, which is the major component of the essential oil of Trachyspermum ammi (L.). It shows multiple biological activities: antifungal, antibacterial, antivirus and anti-inflammatory. T. ammi, commonly known as ajowan, belongs to Apiaceae and is an important medicinal seed spice. To identify the putative genes involved in thymol and other monoterpene biosynthesis, we provided transcriptomes of four inflorescence tissues of two ajowan ecotypes, containing different thymol yield. This study has detected the genes encoding enzymes for the go-between stages of the terpenoid biosynthesis pathways. A large number of unigenes, differentially expressed between four inflorescence tissues of two ajowan ecotypes, was revealed by a transcriptome analysis. Furthermore, differentially expressed unigenes encoding dehydrogenases, transcription factors, and cytochrome P450s, which might be associated with terpenoid diversity in T. ammi, ...
Scientific reports, Jan 23, 2018
Ocimum kilimandscharicum is unique in possessing terpenoids whereas other Ocimum species are reno... more Ocimum kilimandscharicum is unique in possessing terpenoids whereas other Ocimum species are renowned for phenylpropanoids as major constituents of essential oil. The key enzyme of MVA/terpenoid metabolic pathway viz 3-hydroxy-3-methylglutaryl Co-A reductase (OkHMGR) of 1.7-Kb ORF encoding ~60-kDa protein was cloned from O. kilimandscharicum and its kinetic characteristics revealed the availability of HMG-CoA as a control point of MVA-pathway. Transcript profiling of the OkHMGR elucidated tissue-specific functions of the gene in flower and leaf tissues in accumulation of terpenoidal essential oil. OkHMGR was differentially regulated in response to exposure to methyl-jasmonate, salicylic-acid, and stress conditions such-as salt and temperature stress, demonstrating its key role in managing signaling and stress-responses. To elucidate its functional role, OkHMGR was transiently over-expressed in homologous and heterologous plants such as O. sanctum, O. basilicum, O. gratissimum, Witha...
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Papers by Muktesh Chandra