295 results on '"Tapan Kumar Mondal"'
Search Results
2. Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis
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Soni Chowrasia, Jyoti Nishad, Rekha Mahato, Kanti Kiran, Nitasana Rajkumari, Alok Kumar Panda, Hukam C. Rawal, Mandira Barman, and Tapan Kumar Mondal
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Genetics ,Plant Science ,General Medicine ,Agronomy and Crop Science - Published
- 2023
3. Fabrication of a New Coumarin Based Fluorescent 'turn-on' Probe for Distinct and Sequential Recognition of Al3+ and F− Along With Its Application in Live Cell Imaging
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Atanu Maji, Rahul Naskar, Debarpan Mitra, Saswati Gharami, Nabendu Murmu, and Tapan Kumar Mondal
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Clinical Psychology ,Sociology and Political Science ,Clinical Biochemistry ,Law ,Biochemistry ,Spectroscopy ,Social Sciences (miscellaneous) - Published
- 2023
4. Exploration of eQTLs regulating transcript for internode elongation under deep water treatment employing haplotype network in diverse deep water rice landraces of Assam, India
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Megha Rohilla, Nisha Singh, Jagtar Singh, Dhiren Chowdhury, and Tapan Kumar Mondal
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Plant Science ,Agronomy and Crop Science ,Biotechnology - Published
- 2023
5. Allantoin mediated regulation of miRNAs for short term salinity stress tolerance in Oryza sativa L. cv. IR-29
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Jyoti Nishad, Alok Kumar Panda, Soni Chowrasia, Chongtham Nirmala, and Tapan Kumar Mondal
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Plant Science ,Agronomy and Crop Science ,Biotechnology - Published
- 2022
6. A new 'turn-on' molecular switch for idiosyncratic detection of Al3+ ion along with its application in live cell imaging
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Amitav Biswas, Rahul Naskar, Debarpan Mitra, Akash Das, Saswati Gharami, Nabendu Murmu, and Tapan Kumar Mondal
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Materials Chemistry ,General Chemistry ,Catalysis - Abstract
A new highly sensitive, reversible, reusable and fluorogenic “turn-on” switch (HBTC) has been fabricated for the sole detection of Al3+.
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- 2022
7. A new chromone-based fluorescent probe for ratiometric detection of Pd2+
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Rahul Naskar, Saswati Gharami, Subrata Mandal, and Tapan Kumar Mondal
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Materials Chemistry ,General Chemistry ,Catalysis - Abstract
A new chromone-based fluorescent probe (HMPM) is developed for the selective detection of Pd2+.
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- 2022
8. A new ratiometric switch 'two-way' detects hydrazine and hypochlorite via a 'dye-release' mechanism with a PBMC bioimaging study
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Sangita Das, Lakshman Patra, Partha Pratim Das, Kakali Ghoshal, Saswati Gharami, James W. Walton, Maitree Bhattacharyya, and Tapan Kumar Mondal
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General Physics and Astronomy ,Physical and Theoretical Chemistry - Abstract
A new ratiometric fluorescent probe (E)-2-(benzo[d]thiazol-2-yl)-3-(8-methoxyquinolin-2-yl)acrylonitrile (HQCN) was synthesised by the perfect blending of quinoline and a 2-benzothiazoleacetonitrile unit. The probe can selectively detects hydrazine and hypochlorite with two different outputs.
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- 2022
9. Genetic analysis of early seedling vigour in Oryza glaberrima accessions under laboratory and direct-seeded rice conditions
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Muralidhara Bharamappanavara, Anantha Siddaiah Madhyavenkatapura, Manoj Chikkahosahalli Appaiah, Basavaraj Siddanagouda Patil, Ajitha Vijjeswarapu, Ponnuvel Senguttuvel, Maganti Sheshu Madhav, Santosha Rathod, Tapan Kumar Mondal, Lokesha Ramappa, Umesh Rangappa Mathada, Raman Meenakshi Sundaram, Sreedevi Palakolanu, Brajendra Parmer, Mahender Kumar Rapolu, Lella Venkata Subba Rao, and Channappa Gireesh
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Physiology ,Genetics ,Agronomy and Crop Science - Published
- 2023
10. A novel carbazole-benzothiazole based chemodosimeter for chromogenic and fluorogenic recognition of CN
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Tapan Kumar Mondal, Atanu Maji, Amitav Biswas, Akash Das, Saswati Gharami, and Krishnendu Aich
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Materials Chemistry ,General Chemistry ,Catalysis - Abstract
A novel colorimetric and fluorescent sensing probe (E)-3-(4-(9H-carbazol-9-yl)phenyl)-2-(benzo[d]thiazol-2-yl)acrylonitrile (CBTA) was synthesized and characterized by spectroscopic techniques. CBTA displayed “turn off” fluorescence in the presence of cyanide with relatively high selectivity...
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- 2023
11. A biphenyl thiosemicarbazide based fluorogenic chemosensor for selective recognition of Cd2+: Application in cell bioimaging
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Tapan Kumar Mondal, Amitav Biswas, Debarpan Mitra, Rahul Naskar, Atanu Maji, Akash Das, and Nabendu Murmu
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General Chemical Engineering ,General Engineering ,Analytical Chemistry - Abstract
A diversified biphenyl thiosemicarbazide based chemosensor (HBMC) has been fabricated and reported towards specific detection of Cd2+ in MeOH:H2O (4:1) solution. Where we observed a chromogenic change from colorless to...
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- 2023
12. A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz)
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Tapan Kumar Mondal, Hukam C. Rawal, Nagandra Kumar Singh, Tilak Raj Sharma, Nisha Singh, and Ulavappa B. Angadi
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Statistics and Probability ,Germplasm ,Genetic diversity ,Genome evolution ,business.industry ,Haplotype ,food and beverages ,Biology ,Biochemistry ,Genome ,Computer Science Applications ,Biotechnology ,Computational Mathematics ,Computational Theory and Mathematics ,Camellia sinensis ,International HapMap Project ,Indel ,business ,Molecular Biology - Abstract
Motivation Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery. Results In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of ∼0.31× per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties. Supplementary information Supplementary data are available at Bioinformatics online.
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- 2021
13. Palladium(II) complex bearing benzothiazole based O,N,S donor pincer ligand: Study of in-vitro cytotoxicity, interaction with CT-DNA and BSA protein
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RAHUL NASKAR, PARAMITA GHOSH, SUBRATA MANDAL, SUBRATA JANA, NABENDU MURMU, and TAPAN KUMAR MONDAL
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General Chemistry - Published
- 2022
14. Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)
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Megha, Rohilla, Abhishek, Mazumder, Dipnarayan, Saha, Tarun, Pal, Shbana, Begam, and Tapan Kumar, Mondal
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Genetic Markers ,Plant Breeding ,Multidisciplinary ,Tea ,DNA Transposable Elements ,Humans ,Camellia sinensis ,Introns - Abstract
Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.
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- 2022
15. A new ratiometric switch 'two-way' detects hydrazine and hypochlorite
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Sangita, Das, Lakshman, Patra, Partha, Pratim Das, Kakali, Ghoshal, Saswati, Gharami, James W, Walton, Maitree, Bhattacharyya, and Tapan Kumar, Mondal
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Hydrazines ,Spectrometry, Fluorescence ,Leukocytes, Mononuclear ,Humans ,Fluorescent Dyes ,Hypochlorous Acid - Abstract
A new ratiometric fluorescent probe (
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- 2022
16. Manganese(II) complex with ONS donor redox non-innocent azo-thioether pincer ligand: synthesis, X-ray structure, electrochemistry and DFT computation
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Apurba Sau Mondal, Rahul Naskar, Chandan Kumar Manna, and Tapan Kumar Mondal
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General Chemistry - Published
- 2022
17. Identification and analysis of miRNAs‐lncRNAs‐mRNAs modules involved in stem‐elongation of deepwater rice ( Oryza sativa L.)
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Alok Kumar Panda, Hukam C. Rawal, Priyanka Jain, Vishnu Mishra, Jyoti Nishad, Soni Chowrasia, Ananda K. Sarkar, Priyabrata Sen, Soumendra Kumar Naik, and Tapan Kumar Mondal
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MicroRNAs ,Stress, Physiological ,Physiology ,Genetics ,Gene Regulatory Networks ,Oryza ,RNA, Long Noncoding ,RNA, Messenger ,Cell Biology ,Plant Science ,General Medicine - Abstract
Deepwater is an abiotic stress that limits rice cultivation worldwide due to recurrent floods. The miRNAs and lncRNAs are two non-coding RNAs emerging as major regulators of gene expressions under different abiotic stresses. However, the regulation of these two non-coding RNAs under deepwater stress in rice is still unexplored. In this study, small RNA-seq and RNA-seq from internode and node tissues were analyzed to predict deepwater stress responsive miRNAs and lncRNAs, respectively. Additionally, a competitive endogenous RNA (ceRNA) study revealed about 69 and 25 lncRNAs acting as endogenous target mimics (eTM) with the internode and node miRNAs, respectively. In ceRNA analyses, some of the key miRNAs such as miR1850.1, miR1848, and IN-nov-miR145 were upregulated while miR159e was downregulated, and their respective eTM lncRNAs and targets were found to have opposite expressions. Moreover, we have transiently expressed one module (IN-nov-miR145-Cc-TCONS_00011544-Os11g36430.3) in tobacco leaves. The integrated analysis has identified differentially expressed (DE) miRNAs, lncRNAs and their target genes, and the complex regulatory network, which might lead to stem elongation under deepwater stress. In this novel attempt to identify and characterize miRNAs and lncRNAs under deepwater stress in rice, we have provided, probably for the first time, a reference platform to study the interactions of these two non-coding RNAs with respective target genes through transient expression analyses.
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- 2022
18. Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea
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Tapan Kumar Mondal, Pooja Moni Baruah, Debasish B. Krishnatreya, Niraj Agarwala, Bhaskar Dowarah, and Soni Chowrasia
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0106 biological sciences ,0301 basic medicine ,Small RNA ,Science ,Arabidopsis ,RNA-dependent RNA polymerase ,Cell Cycle Proteins ,Biology ,Genes, Plant ,01 natural sciences ,Article ,Camellia sinensis ,Evolution, Molecular ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Gene expression ,Gene family ,Gene silencing ,Arabidopsis thaliana ,Gene ,Biotic ,Phylogeny ,Plant Proteins ,Genetics ,Multidisciplinary ,Abiotic ,Drought ,Arabidopsis Proteins ,food and beverages ,Argonaute ,biology.organism_classification ,RNA-Dependent RNA Polymerase ,Computational biology and bioinformatics ,030104 developmental biology ,Argonaute Proteins ,Medicine ,010606 plant biology & botany ,Genome-Wide Association Study - Abstract
Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.
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- 2021
19. Genome-wide identification and expression profiling of chitinase genes in tea (Camellia sinensis (L.) O. Kuntze) under biotic stress conditions
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Pooja Moni Baruah, Kuntala Sarma Bordoloi, Anuj Kumar Borah, Debasish B. Krishnatreya, Niraj Agarwala, and Tapan Kumar Mondal
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0106 biological sciences ,0301 basic medicine ,Physiology ,Plant Science ,Biology ,Polysaccharide ,01 natural sciences ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Exobasidium vexans ,Chitin ,Gene expression ,Camellia sinensis ,Molecular Biology ,Gene ,chemistry.chemical_classification ,fungi ,food and beverages ,Biotic stress ,biology.organism_classification ,030104 developmental biology ,chemistry ,Chitinase ,biology.protein ,010606 plant biology & botany - Abstract
Chitinases are a diverse group of enzymes having the ability to degrade chitin. Chitin is the second most abundant polysaccharide on earth, predominantly found in insect exoskeletons and fungal cell walls. In this study, we performed a genome-wide search for chitinase genes and identified a total of 49 chitinases in tea. These genes were categorized into 5 classes, where an expansion of class V chitinases has been observed in comparison to other plant species. Extensive loss of introns in 46% of the GH18 chitinases indicates that an evolutionary pressure is acting upon these genes to lose introns for rapid gene expression. The promoter upstream regions in 65% of the predicted chitinases contain methyl-jasmonate, salicylic acid and defense responsive cis-acting elements, which may further illustrate the possible role of chitinases in tea plant's defense against various pests and pathogens. Differential expression analysis revealed that transcripts of two GH19 chitinases TEA028279 and TEA019397 got upregulated during three different fungal infections in tea. While GH19 chitinase TEA031377 showed an increase in transcript abundance in the two insect infested tea tissues. Semi-quantitative RT-PCR analysis revealed that five GH19 chitinases viz. TEA018892, TEA031484, TEA28279, TEA033470 and TEA031277 showed significant increase in expression in the tea plants challenged with a biotrophic pathogen Exobasidium vexans. The study endeavours in highlighting biotic stress responsive defensive role of chitinase genes in tea.
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- 2021
20. Allantoin: Emerging Role in Plant Abiotic Stress Tolerance
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Soni Chowrasia, Tapan Kumar Mondal, Harmeet Kaur, and Vikram Singh Gaur
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0106 biological sciences ,0301 basic medicine ,Abiotic stress ,Catabolism ,Jasmonic acid ,fungi ,food and beverages ,Plant Science ,Biology ,01 natural sciences ,Superoxide dismutase ,03 medical and health sciences ,chemistry.chemical_compound ,Crosstalk (biology) ,030104 developmental biology ,Allantoin ,chemistry ,Biochemistry ,Biosynthesis ,biology.protein ,Molecular Biology ,Abscisic acid ,010606 plant biology & botany - Abstract
Allantoin is an intermediate product of purine catabolic pathway that helps in nitrogen mobilization in plants. It is ubiquitously present in the plant kingdom and serves as an important N form transported from source to sink. During the recent years, allantoin has emerged as a molecule involved in increasing stress tolerance in plants. Higher allantoin biosynthesis and accumulation in plants is correlated with an increase in different abiotic stress tolerance such as drought, salt, cold, heavy metals and irradiance. Increased allantoin accumulation subsequently activates ABA (abscisic acid) biosynthetic genes which in turn activate its hallmark downstream stress-related genes such as RD26 and 29 (response to desiccation), CAT2 (catalase2), Mn/Fe/Cu/Zn superoxide dismutases and SOS1 (salt overly sensitive 1). External application of allantoin on plants acts as signalling molecule that induces a complex crosstalk between ABA and JA (Jasmonic acid) pathway resulting in increased stress tolerance in plants. Recently, allantoin has been attributed to the role of kin recognition in plants, which highlights its role as a signal molecule that facilitates inter-plant interactions. In this review, we present the up to date understanding of this Nitrogen carrying compound, which has recently emerged as a molecule that plays important roles in abiotic stress tolerance in plants.
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- 2021
21. Nested Association Mapping (NAM) Populations: Present Status and Future Prospects in the Genomics Era
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Manish K. Pandey, Sujay Rakshit, Siddaiah M. Anantha, Barbadikar M. Kalyani, Tapan Kumar Mondal, Kondajji R. Yathish, Mallikarjuna Swamy, Raman Meenakshi Sundaram, Santosha Rathod, Ellur Ranjith, Maganti Sheshu Madhav, L. V. Subbarao, Channappa Gireesh, and P. Senguttuvel
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0106 biological sciences ,0301 basic medicine ,Genetic dissection ,education.field_of_study ,Population ,Genomics ,Genome-wide association study ,Plant Science ,Quantitative trait locus ,Biology ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Nested association mapping ,education ,010606 plant biology & botany - Abstract
Development of mapping population is a prerequisite for genetic dissection of genomic regions underlying complex traits. Nested Association Mapping (NAM) is an integrated multi-parent population ap...
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- 2021
22. IN-VITRO STUDY OF MORINGA OLEIFERA AND CASIA FISTULA ON MULTI DRUG RESISTANT BACTERIA, ISOLATED FROM BOVINE MASTITIS MILK
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Shatabdi Das, Tapan Kumar Mondal, Sayani Marick, Sandhimita Mondal, Jayanta Chowdhury, Nilanjana Dey, and Arnab Ganguli
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Moringa ,Traditional medicine ,Multi drug resistant bacteria ,Fistula ,General Engineering ,medicine ,In vitro study ,Biology ,medicine.disease ,Mastitis - Published
- 2020
23. Integrated computational approach toward discovery of multi-targeted natural products from Thumbai (Leucas aspera) for attuning NKT cells
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Aparoopa Das, Vishwa Jyoti Baruah, Bhaswati Sarmah, Rasana Paul, Tapan Kumar Mondal, Dhrubajyoti Gogoi, Nirmal Mazumder, and Subrata Chakraborty
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0303 health sciences ,biology ,Molecular model ,030303 biophysics ,Leucas aspera ,General Medicine ,Computational biology ,biology.organism_classification ,Natural killer T cell ,Thymidylate kinase ,03 medical and health sciences ,Structural Biology ,Potential source ,Pharmacophore ,Molecular Biology ,Biological network ,Function (biology) - Abstract
A multi-omics-based approach targeting the plant-based natural products from Thumbai (Leucas aspera), an important yet untapped potential source of many therapeutic agents for myriads of immunological conditions and genetic disorders, was conceptualized to reconnoiter its potential biomedical application. A library of 79 compounds from this plant was created, out of which 9 compounds qualified the pharmacokinetics parameters. Reverse pharmacophore technique for target fishing of the screened compounds was executed through which renin receptor (ATP6AP2) and thymidylate kinase (DTYMK) were identified as potential targets. Network biology approaches were used to comprehend and validate the functional, biochemical and clinical relevance of the targets. The target-ligand interaction and subsequent stability parameters at molecular scale were investigated using multiple strategies including molecular modeling, pharmacophore approaches and molecular dynamics simulation. Herein, isololiolide and 4-hydroxy-2-methoxycinnamaldehyde were substantiated as the lead molecules exhibiting comparatively the best binding affinity against the two putative protein targets. These natural lead products from L. aspera and the combinatorial effects may have plausible medical applications in a wide variety of neurodegenerative, genetic and developmental disorders. The lead molecules also exhibit promising alternative in diagnostics and therapeutics through immuno-modulation targeting natural killer T-cell function in transplantation-related pathogenesis, autoimmune and other immunological disorders.Communicated by Ramaswamy H. Sarma.
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- 2020
24. Pan-genomic, transcriptomic, and miRNA analyses to decipher genetic diversity and anthocyanin pathway genes among the traditional rice landraces
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Pankaj Kumar Singh, Hukam C. Rawal, Alok Kumar Panda, Joy Roy, Tapan Kumar Mondal, and Tilak Raj Sharma
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Anthocyanins ,MicroRNAs ,Gene Expression Regulation, Plant ,Genetics ,Genetic Variation ,India ,Oryza ,Genomics ,Transcriptome - Abstract
Black rice is famous for containing high anthocyanin while Joha rice is aromatic with low anthocyanin containing rice from the North-Eastern Region (NER) of India. However, there are limited reports on the anthocyanin biosynthesis in Manipur Black rice. Therefore, the present study was aimed to understand the origin, domestication and anthocyanin biosynthesis pathways in Black rice using the next generation sequencing approaches. With the sequencing data, various analyses were carried out for differential expression and construction of a pan-genome. Protein coding RNA and small RNA sequencing analysis aided in determining 7415 and 131 differentially expressed transcripts and miRNAs, respectively in NER rice. This is the first extensive study on identification and expression analysis of miRNAs and their target genes in regulating anthocyanin biosynthesis in NER rice. This study will aid in better understanding for decoding the theory of high or low anthocyanin content in different rice genotypes.
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- 2022
25. Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by
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Jayanth, Kallugudi, Vikram Jeet, Singh, Kunnumal Kurungara, Vinod, Subbaiyan Gopala, Krishnan, Shekharappa, Nandakumar, Brijesh Kumar, Dixit, Ranjith Kumar, Ellur, Haritha, Bollinedi, Mariappan, Nagarajan, Amit, Kumar, Mridul, Chakraborti, Rakesh Kumar, Seth, Tapan Kumar, Mondal, Prolay Kumar, Bhowmick, and Ashok Kumar, Singh
- Abstract
The exploitation of heterosis through intersubspecific hybridisation between
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- 2022
26. Human peripheral blood mononuclear cells targeted multidimensional switch for selective detection of HSO3− anion
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Sabu Thomas, James W. Walton, Sangita Das, Partha Pratim Das, Tapan Kumar Mondal, Lakshman Patra, Kakali Ghoshal, and Maitree Bhattacharyya
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Solvent ,chemistry.chemical_compound ,Aqueous solution ,chemistry ,Carbazole ,Chromogenic ,Process Chemistry and Technology ,General Chemical Engineering ,Luminophore ,Conjugated system ,Photochemistry ,Fluorescence ,Malononitrile - Abstract
A new ratiometric π-conjugated luminophore with donor-acceptor (D- π- A) network CM {(E)-2-(4-(2-(9-butyl-9H-carbazol-3-yl)vinyl)benzylidine)malononitrile} has been synthesized by malononitrile conjugated carbazole dye with an intervening p-styryl spacer. Here, p-styryl conjugated malononitrile is used as a recognition site for the detection of HSO3− with a fast response time (within 50 s). In a mixed aqueous solution, CM reacts with HSO3− to give a new product 1-(9-butyl-9H-carbazol-3-yl)-2-(4-(2, 2-dicyanovinyl)phenyl)ethane-1-sulfonic acid. The probe exhibits positive solvatofluorochromism with solid state red fluorescence. The restriction of intermolecular rotation of p-styryl conjugated malononitrile unit enhances the typical solid state fluorescence properties. The probe (CM and its corresponding aldehyde CA) also demonstrates a strong solvent dependence yielding blue to green to pink and even red fluorescence in commonly used organic solvents like n-hexane, toluene, diethyl ether (DEE), THF, DCM, Dioxane, CH3CN and MeOH. The chemodosimetric approach of HSO3− selectively takes place at the olefinic carbon exhibiting a prominent chromogenic as well as ratiometric fluorescence change with a 147 nm blue-shift in the fluorescence spectrum. CM can detect HSO3− as low as 1.21 × 10−8 M. Moreover, the CM can be successfully applied to detect intrinsically generated intracellular HSO3− in human peripheral blood mononuclear cells (PBMCs). CM has shown sharp intensities (2628 ± 511.8) when the cells are HSO3− untreated. At green channel (at 486 nm) almost negligible fluorescence intensities are found (423 ± 127.5) for HSO3− untreated samples. However, the green fluorescence (2863 ± 427.5) increases significantly (p < 0.05), and simultaneously the red fluorescence gets significantly (p < 0.05) diminished (515 ± 113.2) after addition of HSO3−. The CM has been effectively utilized for evaluating the bisulfite ions in food samples as well. The concentrations of HSO3− in diluted sugar samples have been determined with the recovery of 97.6–9.12%.
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- 2022
27. Low expression of carotenoids cleavage dioxygenase 1 (ccd1) gene improves the retention of provitamin-A in maize grains during storage
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Aanchal Baveja, Devendra K. Yadava, Tapan Kumar Mondal, Rajkumar U. Zunjare, Rashmi Chhabra, Firoz Hossain, Suman Dutta, and Vignesh Muthusamy
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0106 biological sciences ,0301 basic medicine ,Beta-Cryptoxanthin ,Gene Dosage ,Gene Expression ,Cleavage (embryo) ,Zea mays ,01 natural sciences ,Dioxygenases ,03 medical and health sciences ,Dioxygenase ,Genotype ,Genetics ,Inbreeding ,Food science ,Allele ,Vitamin A ,Molecular Biology ,Gene ,Carotenoid ,Alleles ,Proa ,Plant Proteins ,chemistry.chemical_classification ,biology ,Hydrolysis ,Provitamins ,General Medicine ,beta Carotene ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,Provitamin a ,chemistry ,Genome, Plant ,010606 plant biology & botany - Abstract
Provitamin-A (proA) is essentially required for vision in humans but its deficiency affects children and pregnant women especially in the developing world. Biofortified maize rich in proA provides new opportunity for sustainable and cost-effective solution to alleviate malnutrition, however, significant loss of carotenoids during storage reduces its efficacy. Here, we studied the role of carotenoid cleavage dioxygenase 1 (ccd1) gene on degradation of carotenoids in maize. A set of 24 maize inbreds was analyzed for retention of proA during storage. At harvest, crtRB1-based maize inbreds possessed significantly high proA (β-carotene: 12.30 µg/g, β-cryptoxanthin: 4.36 µg/g) than the traditional inbreds (β-carotene: 1.74 µg/g, β-cryptoxanthin: 1.28 µg/g). However, crtRB1-based inbreds experienced significant degradation of proA carotenoids (β-carotene: 20%, β-cryptoxanthin: 32% retention) following 5 months. Among the crtRB1-based genotypes, V335PV had the lowest retention of proA (β-carotene: 1.63 µg/g, β-cryptoxanthin: 0.82 µg/g), while HKI161PV had the highest retention of proA (β-carotene: 4.17 µg/g, β-cryptoxanthin: 2.32 µg/g). Periodical analysis revealed that ~ 60-70% of proA degraded during the first three months. Expression analysis revealed that high expression of ccd1 led to low retention of proA carotenoids in V335PV, whereas proA retention in HKI161PV was higher due to lower expression. Highest expression of ccd1 was observed during first 3 months of storage. Copy number of ccd1 gene varied among yellow maize (1-6 copies) and white maize (7-35 copies) while wild relatives contained 1-4 copies of ccd1 gene per genome. However, copy number of ccd1 gene did not exhibit any correlation with proA carotenoids. We concluded that lower expression of ccd1 gene increased the retention of proA during storage in maize. Favourable allele of ccd1 can be introgressed into elite maize inbreds for higher retention of proA during storage.
- Published
- 2020
28. ‘Green revolution’ dwarf genesd1of rice has gigantic impact
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Tilak Raj Sharma, Tapan Kumar Mondal, Giresh Channappa, Vikram Singh Gaur, and Mridul Chakraborti
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0106 biological sciences ,0301 basic medicine ,General Medicine ,Biology ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,030104 developmental biology ,Botany ,Genetics ,Molecular Biology ,Gene ,Green Revolution ,010606 plant biology & botany - Abstract
Rice (Oryza sativa L.) is one of the most important cereal that has fed the world over a longer period. Before green revolution, cultivated rice is believed to have consisted of thousands of landraces each adapted to its specific climatic conditions by surviving against different abiotic and biotic selection pressure. However, owing to the low yield, photo-period sensitivity, late maturity and sensitivity to lodging of these landraces grown world-wide, serious concerns of impending global food crisis was felt during the 1960s because of (i) unprecedented increase of the population and (ii) concomitant decline in the cultivable land. Fortunately, high-yielding varieties developed through the introgression of the semi-dwarf1 gene (popularly known as sd1) during the 1960s led to significant increments in the food grain production that averted the apprehensions of nearing famine. This historical achievement having deep impact in the global agriculture is popularly referred as ‘Green Revolution.’ In this paper, we reviewed, its genetics as well as molecular regulations, evolutionary relationship with orthologous genes from other cereals as well as pseudo-cereals and attempted to provide an up-to-date information about its introgression to different rice cultivars of the world.
- Published
- 2020
29. Current status of genomic resources on wild relatives of rice
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Richa Kamboj, Tapan Kumar Mondal, Balwant Singh, and Deepak Singh Bisht
- Subjects
0106 biological sciences ,0301 basic medicine ,Resource (biology) ,media_common.quotation_subject ,Introgression ,Genomics ,Plant Science ,Review ,Biology ,Oryza ,01 natural sciences ,Adaptability ,03 medical and health sciences ,Genetics ,genomics ,wild rice ,Domestication ,database ,media_common ,rice ,food and beverages ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Identification (biology) ,Gene pool ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.
- Published
- 2020
30. A fluorescent 'ON–OFF–ON' switch for the selective and sequential detection of Hg2+and I−with applications in imaging using human AGS gastric cancer cells
- Author
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Krishnendu Aich, Tapan Kumar Mondal, Paramita M. Ghosh, Saswati Gharami, Lakshman Patra, and Nabendu Murmu
- Subjects
Inorganic Chemistry ,Detection limit ,Chemistry ,Live cell imaging ,Microscopy ,Cancer cell ,Biophysics ,X-ray ,Time-dependent density functional theory ,Fluorescence ,Gastric cancer cell - Abstract
A new fluorescent "on-off-on" probe (BIPQ) is designed and developed which selectively binds with Hg2+; its emission intensity is quenched almost 40-fold at 455 nm without interference from other metal cations. On gradual addition of I- to the solution of BIPQ-Hg2+, the emission reverts to its original intensity. The limits of detection of BIPQ for Hg2+ and I- are found to be on the order of 3.12 × 10-9 and 5.48 × 10-8 M, respectively, which shows clearly that BIPQ can sense Hg2+ at a very minute level. DFT and TDDFT studies are conducted with the probe to establish similarity between theoretical and experimental outcomes. Finally, to demonstrate its practical benefit in biological fields, live cell imaging experiments with BIPQ are carried out to detect Hg2+ in human AGS gastric cancer cell lines.
- Published
- 2020
31. Dhani (Oryza coarctata): A Wild Relative of Rice is a Potential Source of Coastal Salinity Tolerance Genes Suitable for Rice Breeding
- Author
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Swati Mishra, Soni Chowrasia, and Tapan Kumar Mondal
- Published
- 2022
32. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms
- Author
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Shakir Ali, Hukam C. Rawal, and Tapan Kumar Mondal
- Subjects
Small RNA ,ved/biology ,ved/biology.organism_classification_rank.species ,RNA ,Computational biology ,Plants ,Biology ,Genome ,MicroRNAs ,RNA, Transfer ,Transfer RNA ,Identification (biology) ,Model organism ,Molecular Biology ,Organism ,Information Systems ,Reference genome - Abstract
In recent years, microRNAs (miRNAs) and tRNA-derived RNA fragments (tRFs) have been reported extensively following different approaches of identification and analysis. Comprehensively analyzing the present approaches to overcome the existing variations, we developed a benchmarking methodology each for the identification of miRNAs and tRFs, termed as miRNA Prediction Methodology (miRPreM) and tRNA-induced small non-coding RNA Prediction Methodology (tiRPreM), respectively. We emphasized the use of respective genome of organism under study for mapping reads, sample data with at least two biological replicates, normalized read count support and novel miRNA prediction by two standard tools with multiple runs. The performance of these methodologies was evaluated by using Oryza coarctata, a wild rice species as a case study for model and non-model organisms. With organism-specific reference genome approach, 98 miRNAs and 60 tRFs were exclusively found. We observed high accuracy (13 out of 15) when tested these genome-specific miRNAs in support of analyzing the data with respective organism. Such a strong impact of miRPreM, we have predicted more than double number of miRNAs (186) as compared with the traditional approaches (79) and with tiRPreM, we have predicted all known classes of tRFs within the same small RNA data. Moreover, the methodologies presented here are in standard form in order to extend its applicability to different organisms rather than restricting to plants. Hence, miRPreM and tiRPreM can fulfill the need of a comprehensive methodology for miRNA prediction and tRF identification, respectively, for model and non-model organisms.
- Published
- 2021
33. Facile Aerial Oxidation of Redox Non-innocent Organic Molecules on Silica Surface
- Author
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Poulami Sengupta, Tapan Kumar Mondal, and Samaresh Bhattacharya
- Abstract
Redox non-innocent organic substrates, viz. 3,5-di-tert-butylcatechol (3,5-DBC) and 2-aminophenol (2-AP), undergo facile aerial oxidation on silica surface to exclusively afford 3,5-di-tert-butyl-1,2-benzoquinone (3,5-DBQ) and 2-amino-3H-phenoxazin-3-one (APX) respectively.
- Published
- 2021
34. Two New Quinoline‐Benzothiazole Blended ‘Off‐On’ Type Fluorescent Probes Exclusively Detect Cd 2+
- Author
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Krishnendu Aich, Saswati Gharami, Lakshman Patra, Sangita Das, and Tapan Kumar Mondal
- Subjects
chemistry.chemical_compound ,Benzothiazole ,Chemistry ,Quinoline ,General Chemistry ,Fluorescence ,Combinatorial chemistry - Published
- 2019
35. Tissue specific long non-coding RNAs are involved in aroma formation of black tea
- Author
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Deepti Varshney, Tapan Kumar Mondal, Hukam C. Rawal, Biswajit Bera, P. Mohan Kumar, Himanshu Dubey, Nagendra K. Singh, and Tanoy Bandyopadhyay
- Subjects
0106 biological sciences ,010405 organic chemistry ,In silico ,Apical dominance ,food and beverages ,RNA ,Computational biology ,Biology ,01 natural sciences ,Genome ,0104 chemical sciences ,Biological pathway ,Axillary bud ,microRNA ,KEGG ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
With the progress of sequencing technology coupled with in silico approaches, disclosure of long non-coding RNA (lncRNAs) from RNAseq data has become easy and reliable. Till today, no methodical investigation of lncRNAs and their regulatory roles in tea have been studied. In this study, using 170 RNAseq data (˜7157 million reads) of 11 harvestable tissues, 33,400 putative high certainty lncRNAs were discovered, among which 99.76% were found to be putative novel lncRNAs. The expression analysis of lncRNAs from 53 RNAseq data of 7 tissues (axillary bud, a bud and a leaf, a bud and 2 leaves, apical bud and 2 leaves, 2nd leaf, 4th leaf, and 6th leaf) demonstrated their tissue-specific expression. Further, around 1,654 lncRNAs were found to be endogenous target mimics of miRNAs that interacted with 698 mRNAs of tea genome. Based on their target i.e. coding-gene partners by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway showed that 378 lncRNAs are involved in major aroma formation pathway of tea. Present study also provides valuable information to uncover the various molecular functions of lncRNAs that regulate aroma formation of tea.
- Published
- 2019
36. Advances in understanding salt tolerance in rice
- Author
-
Showkat Ahmad Ganie, Kutubuddin A. Molla, Tapan Kumar Mondal, Robert J Henry, and Kangila Venkataraman Bhat
- Subjects
0106 biological sciences ,Genomics ,Oryza ,01 natural sciences ,Genome ,Epigenesis, Genetic ,Metabolomics ,Genetics ,Plant breeding ,Codon ,biology ,business.industry ,food and beverages ,Salt Tolerance ,General Medicine ,biology.organism_classification ,Biotechnology ,Salinity ,Plant Breeding ,Phenotype ,business ,Literature survey ,Agronomy and Crop Science ,Functional genomics ,010606 plant biology & botany - Abstract
This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1–6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.
- Published
- 2019
37. Synthesis of a rhodium(III) triphenylphosphine complex via C S bond cleavage of an azo-thioether ligand: X-ray structure, electrochemistry and catalysis towards transfer hydrogenation of ketones
- Author
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Chandan Kumar Manna, Puspendu Roy, Tapan Kumar Mondal, and Rahul Naskar
- Subjects
010405 organic chemistry ,Ligand ,chemistry.chemical_element ,010402 general chemistry ,Transfer hydrogenation ,01 natural sciences ,0104 chemical sciences ,Rhodium ,Catalysis ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Thioether ,chemistry ,Octahedral molecular geometry ,Materials Chemistry ,Physical and Theoretical Chemistry ,Triphenylphosphine ,Bond cleavage - Abstract
A new rhodium(III) triphenylphosphine complex having the general formula [Rh(PPh3)2(L)Cl] (1) was synthesized by C S bond cleavage of an ONS donor azo-thioether ligand (L-CH2Ph). The complex was thoroughly characterized by various spectroscopic techniques. Its single crystal X-ray structure exhibits an octahedral geometry around the rhodium(III) center. A cyclic voltammogram of the complex exhibits ligand based quasi-irreversible oxidative and reductive responses. The electronic structure, redox properties and electronic excitations in the complex were interpreted by DFT and TDDFT calculations. The complex effectively catalyzed the transfer hydrogenation reaction of ketones with high yields in i-PrOH in the presence of a base.
- Published
- 2019
38. An ESIPT based chromogenic and fluorescent ratiometric probe for Zn2+ with imaging in live cells and tissues
- Author
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Saswati Gharami, Krishnendu Aich, Paramita M. Ghosh, Tapan Kumar Mondal, Nabendu Murmu, and Deblina Sarkar
- Subjects
inorganic chemicals ,Absorption (pharmacology) ,Detection limit ,Chemistry ,Chromogenic ,02 engineering and technology ,General Chemistry ,Time-dependent density functional theory ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Fluorescence ,Catalysis ,0104 chemical sciences ,Blueshift ,Live cell imaging ,Materials Chemistry ,Biophysics ,Density functional theory ,skin and connective tissue diseases ,0210 nano-technology - Abstract
A new ESIPT based fluorescent probe has been introduced for selective detection of Zn2+ in human breast cancer cells. The designed probe exhibits a prominent ratiometric fluorescence change along with a sharp blue shift of ∼71 nm which can be attributed to the hampering of the ESIPT process. The probe is efficient enough to detect Zn2+ solely in the presence of other biologically relevant cations with a limit of detection value of 1.6 × 10−7 M. The experimentally observed changes in the structure and absorption properties of the probe after complete addition of Zn2+ were further studied by density functional theory (DFT) and time dependent density functional theory (TDDFT) calculations. Moreover, the dip-stick experiment with this probe displays both absorption and fluorescence color changes after exposure to Zn2+ which also turns out to be a potential application for the probe. Live cell imaging studies have been carried out using human breast cancer cells (MCF-7) and tissues.
- Published
- 2019
39. Facile detection of organophosphorus nerve agent mimic (DCP) through a new quinoline-based ratiometric switch
- Author
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Krishnendu Aich, Saswati Gharami, Lakshman Patra, Tapan Kumar Mondal, and Sangita Das
- Subjects
Detection limit ,Analyte ,Cyan ,Quinoline ,02 engineering and technology ,General Chemistry ,Time-dependent density functional theory ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Combinatorial chemistry ,Catalysis ,0104 chemical sciences ,Diethyl chlorophosphate ,chemistry.chemical_compound ,chemistry ,Yield (chemistry) ,Materials Chemistry ,Nucleophilic substitution ,0210 nano-technology - Abstract
In this paper, a quinoline-based (BIMQ) probe was developed, and it displayed ratiometric detection of organophosphorus (OP) chemical vapor threat DCP. Upon addition of the nerve agent mimic diethyl chlorophosphate (DCP), a fluoroscence color change from blue to cyan was observed. The chemodosimeter BIMQ underwent nucleophilic substitution with DCP, followed by a ring closure to yield the final product and showed an explicit fluorescence response towards DCP. The probe BIMQ selectively detected DCP in the presence of other toxic analytes. The detection limit of BIMQ for DCP was established to be in the order of 10−8 M in the solution phase, which suggests that BIMQ can efficiently detect DCP at a very low level. This ratiometric switch has a potential application as a portable kit for detecting DCP vapour with high sensitivity. TDDFT calculations were carried out in order to unveil the electronic properties theoretically.
- Published
- 2019
40. Simple fabrication of a carbaldehyde based fluorescent 'turn-on' probe for the selective and sole detection of Pd2+: application as test strips
- Author
-
Saswati Gharami, Tapan Kumar Mondal, Krishnendu Aich, Chandan Kumar Manna, and Lakshman Patra
- Subjects
Detection limit ,Fabrication ,Chemistry ,Analytical chemistry ,02 engineering and technology ,General Chemistry ,Time-dependent density functional theory ,Electronic structure ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Binding constant ,Fluorescence ,Catalysis ,0104 chemical sciences ,Test strips ,Turn (geometry) ,Materials Chemistry ,0210 nano-technology - Abstract
A new fluorescent “turn-on” probe (DHMC) has been designed and synthesized to selectively detect Pd2+ among other cations at physiological pH. Upon incremental addition of Pd2+ into the probe solution, a “turn-on” emission enhancement was noticed with a ∼69 nm red shift at 562 nm in CH3CN/H2O (4/1, v/v) solution. The limit of detection and binding constant values have been determined and found to be on the order of 7.4 × 10−8 M and 1.7 × 105 M−1 respectively, which clearly suggests that the probe is very efficient in detecting Pd2+ at very minute levels and also the DHMC–Pd2+ complexation is stable enough too. A brilliant application of the probe has been explored which indicates that DHMC can detect Pd2+ in the solid state too. DFT and TDDFT calculations are carried out to interpret the electronic structure and sensing mechanism.
- Published
- 2019
41. Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica-japonica Hybridization in Rice
- Author
-
Jayanth Kallugudi, Vikram Jeet Singh, Kunnumal Kurungara Vinod, Subbaiyan Gopala Krishnan, Shekharappa Nandakumar, Brijesh Kumar Dixit, Ranjith Kumar Ellur, Haritha Bollinedi, Mariappan Nagarajan, Amit Kumar, Mridul Chakraborti, Rakesh Kumar Seth, Tapan Kumar Mondal, Prolay Kumar Bhowmick, and Ashok Kumar Singh
- Subjects
indica-japonica ,wide compatible varieties ,S5n ,inter sub-species hybridization ,Ecology ,Plant Science ,Ecology, Evolution, Behavior and Systematics - Abstract
The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding.
- Published
- 2022
42. Palladium(II) complexes with thioether based ONS donor ligand: Synthesis, characterization, X-ray structure, DFT study and anti-cancer activity
- Author
-
Rahul Naskar, Paramita Ghosh, Chandan Kumar Manna, Nabendu Murmu, and Tapan Kumar Mondal
- Subjects
Inorganic Chemistry ,Materials Chemistry ,Physical and Theoretical Chemistry - Published
- 2022
43. The core set of sequence-tagged microsatellite sites markers between halophytic wild rice Oryza coarctata and Oryza sativa complex
- Author
-
LK Bose, BC Marndi, Sutapa Sarkar, M. K. Kar, Krishnendu Chattopadhyay, BC Patra, Soham Ray, Motilal Behera, SK Dash, Dipti Ranjan Pani, Koushik Chakraborty, Chinmay Pradhan, Mridul Chakraborti, Joshitha Vijayan, Deepa, Tapan Kumar Mondal, and Debashree Dalai
- Subjects
0106 biological sciences ,0301 basic medicine ,Oryza sativa ,biology ,food and beverages ,Plant Science ,Horticulture ,Oryza ,biology.organism_classification ,01 natural sciences ,Genome ,Intraspecific competition ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Genetics ,Microsatellite ,Identification (biology) ,Gene pool ,Agronomy and Crop Science ,Gene ,010606 plant biology & botany - Abstract
For breeding of salinity tolerant rice, halophytic species Oryza coarctata is considered as a valuable resource. Non-availability of molecular markers in the species is a major limitation and identification of markers applicable with wider gene pool will be resource-saving. Even after the recent advancement in high throughput genotyping techniques, sequence-tagged microsatellite sites (STMS) markers are considered as valuable resource for pre-breeding, especially when usable for a large number of species. Using a novel bioinformatics pipeline for cross transferable marker identification, whole genome sequences of nine Oryza species were surveyed with 23,499 STMS markers of rice. With this highly reproducible strategy, band sizes or polymorphism prediction among different species is possible before in-vitro validation. Only 359 STMS markers were cross-transferable to O. coarctata and 77 of those were common with O. sativa complex. These core markers were distributed over 11 chromosomes and nearly 76% were located within various genes of Oryza. The markers also showed unique genome specific polymorphism pattern with high levels of inter- and intraspecific variations in “AA” genome and complete absence of intra- or inter-population variations in O. coarctata (KKLL). The numbers of microsatellite motifs and the repeat numbers in different motifs were much lesser in O. coarctata leading to the exceptionally high level of polymorphism with all “AA” genome species. Two markers are also useful for species identification. The hyper-variable markers are effective resource for pre-breeding of O. sativa, O. glaberrima and new rice for Africa involving O. coarctata or any other species of O. sativa complex.
- Published
- 2021
44. Oryza coarctata is a triploid plant with initial events of C4 photosynthesis evolution
- Author
-
Tapan Kumar Mondal, Jyoti Nishad, Rakesh Pandey, and Soni Chowrasia
- Subjects
0106 biological sciences ,0301 basic medicine ,Plant Science ,Biology ,Photosynthesis ,01 natural sciences ,Carbon Cycle ,03 medical and health sciences ,Halophyte ,Botany ,Genetics ,Mitosis ,C4 photosynthesis ,Obligate ,food and beverages ,Oryza ,General Medicine ,Vascular bundle ,Biological Evolution ,Triploidy ,Chloroplast ,Plant Leaves ,030104 developmental biology ,Ploidy ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Oryza coarctata is an obligate halophyte of wild species of rice which thrives well under high saline as well as submerged conditions. We report here for the first time that O. coarctata is triploid (2n = 3x = 36), though it was previously known as tetraploid (2n = 4x = 48). The chromosome number of O. coarctata was determined from mitotic plates of root tips and ploidy level was determined by flow cytometer, where it was found to be triploid (2n = 3x = 36). In addition, this species was found to possess several unique anatomical features in leaves such as presence of Kranz-anatomy, increased vein density and higher ratio of bundle sheath to mesophyll cell area as compared to rice variety (IR-29). Ultra-structure of leaf showed the presence of bundle sheath cells with significant number of chloroplasts and mitochondria which were arranged centrifugally. Chloroplasts lack grana in bundle sheath cell whereas, mesophyll cell contain well-developed grana. These anatomical and ultra structural characteristics indicate that this plant is in initial stage of evolving towards C4 photosynthesis due to high selection pressure which might help it to survive in wide range of ecological conditions i.e. from submerged saline to non-saline terrestrial condition.
- Published
- 2021
45. RNA Interference (RNAi) in Functional Genomics of Wheat
- Author
-
Tapan Kumar Mondal, Priyabrata Sen, Kanti Kiran, and Charu Lata
- Subjects
RNA interference ,Mechanism (biology) ,Gene silencing ,Context (language use) ,Computational biology ,Biology ,biology.organism_classification ,Functional genomics ,Gene ,Function (biology) ,Caenorhabditis elegans - Abstract
Post-genomic era of biology is faced with a major challenge in deciphering the gene function out of enormous amount of data generated by NGS technology, in addition to large number of EST sequences, available in the public domain. Among many approaches, one important approach is to knock out the gene and analysis of the visible effect of loss of gene function. RNA interference (RNAi), as a reverse genetic approach currently in use for studies of gene function, holds a great promise in this context. The efficacy of RNAi as tool for functional genomics study has already been successfully demonstrated in Caenorhabditis elegans. With the availability of comprehensive resources of genomic sequence data and knowledge of the biological mechanism of RNAi, use of RNAi in functional genomics is quickly gaining space and popularity. Results from the study of transgene-induced RNAi suggests many variables that should be considered while designing experiment to decipher gene function.
- Published
- 2021
46. Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea
- Author
-
Hukam C. Rawal, Biswajit Bera, Tilak Raj Sharma, R. Victor J. Ilango, Sangeeta Borchetia, S Soundararajan, Nagendra K. Singh, Anoop Kumar Barooah, and Tapan Kumar Mondal
- Subjects
0106 biological sciences ,0301 basic medicine ,China ,Science ,India ,Biology ,01 natural sciences ,Genome ,Article ,Camellia sinensis ,Evolution, Molecular ,03 medical and health sciences ,Plant evolution ,Genus ,Genome, Chloroplast ,Chinese tea ,Phylogeny ,Multidisciplinary ,Phylogenetic tree ,food and beverages ,Camellia ,Chloroplast ,030104 developmental biology ,Evolutionary biology ,Codon usage bias ,Medicine ,Microsatellite ,Plant sciences ,Genome, Plant ,010606 plant biology & botany ,Microsatellite Repeats - Abstract
Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.
- Published
- 2021
47. Integrated computational approach toward discovery of multi-targeted natural products from Thumbai (
- Author
-
Vishwa Jyoti, Baruah, Rasana, Paul, Dhrubajyoti, Gogoi, Nirmal, Mazumder, Subrata, Chakraborty, Aparoopa, Das, Tapan Kumar, Mondal, and Bhaswati, Sarmah
- Subjects
Molecular Docking Simulation ,Biological Products ,Lamiaceae ,Natural Killer T-Cells ,Molecular Dynamics Simulation - Abstract
A multi-omics-based approach targeting the plant-based natural products from Thumbai (
- Published
- 2020
48. Genome-wide identification and expression profiling of chitinase genes in tea (
- Author
-
Kuntala Sarma, Bordoloi, Debasish B, Krishnatreya, Pooja Moni, Baruah, Anuj Kumar, Borah, Tapan Kumar, Mondal, and Niraj, Agarwala
- Subjects
fungi ,food and beverages ,Research Article - Abstract
Chitinases are a diverse group of enzymes having the ability to degrade chitin. Chitin is the second most abundant polysaccharide on earth, predominantly found in insect exoskeletons and fungal cell walls. In this study, we performed a genome-wide search for chitinase genes and identified a total of 49 chitinases in tea. These genes were categorized into 5 classes, where an expansion of class V chitinases has been observed in comparison to other plant species. Extensive loss of introns in 46% of the GH18 chitinases indicates that an evolutionary pressure is acting upon these genes to lose introns for rapid gene expression. The promoter upstream regions in 65% of the predicted chitinases contain methyl-jasmonate, salicylic acid and defense responsive cis-acting elements, which may further illustrate the possible role of chitinases in tea plant’s defense against various pests and pathogens. Differential expression analysis revealed that transcripts of two GH19 chitinases TEA028279 and TEA019397 got upregulated during three different fungal infections in tea. While GH19 chitinase TEA031377 showed an increase in transcript abundance in the two insect infested tea tissues. Semi-quantitative RT-PCR analysis revealed that five GH19 chitinases viz. TEA018892, TEA031484, TEA28279, TEA033470 and TEA031277 showed significant increase in expression in the tea plants challenged with a biotrophic pathogen Exobasidium vexans. The study endeavours in highlighting biotic stress responsive defensive role of chitinase genes in tea.
- Published
- 2020
49. Identification and functional prediction of long non-coding RNAs of rice (Oryza sativa L.) at reproductive stage under salinity stress
- Author
-
Tapan Kumar Mondal, Jyoti Nishad, Himanshu Dubey, Deepak Singh Bisht, Tilak Raj Sharma, Priyanka Jain, and Samreen Hussian
- Subjects
0301 basic medicine ,Propanols ,Biology ,Plant Roots ,Salt Stress ,03 medical and health sciences ,0302 clinical medicine ,Gene Expression Regulation, Plant ,Genotype ,microRNA ,Gene expression ,Genetics ,RNA, Messenger ,RNA, Small Interfering ,Molecular Biology ,Oryza sativa ,Gene Expression Profiling ,Reproduction ,food and beverages ,Oryza ,General Medicine ,Exons ,Long non-coding RNA ,Salinity ,Plant Leaves ,Metabolic pathway ,MicroRNAs ,030104 developmental biology ,030220 oncology & carcinogenesis ,RNA, Long Noncoding ,Adaptation ,Genome, Plant - Abstract
Salinity adversely affects the yield and growth of rice (Oryza sativa L.) plants severely, particularly at reproductive stage. Long non-coding RNAs (lncRNAs) are key regulators of diverse molecular and cellular processes in plants. Till now, no systematic study has been reported for regulatory roles of lncRNAs in rice under salinity at reproductive stage. In this study, total 80 RNA-seq data of Horkuch (salt-tolerant) and IR-29 (salt-sensitive) genotypes of rice were used and found 1626 and 2208 transcripts as putative high confidence lncRNAs, among which 1529 and 2103 were found to be novel putative lncRNAs in root and leaf tissue respectively. In Horkuch and IR-29, 14 and 16 lncRNAs were differentially expressed in root tissue while 18 and 63 lncRNAs were differentially expressed in leaf tissue. Interaction analysis among the lncRNAs, miRNAs and corresponding mRNAs indicated that these modules are involved in different biochemical pathways e.g. phenyl propanoid pathway during salinity stress in rice. Interestingly, two differentially expressed lncRNAs such as TCONS_00008914 and TCONS_00008749 were found as putative target mimics of known rice miRNAs. This study indicates that lncRNAs are involved in salinity adaptation of rice at reproductive stage through certain biochemical pathways.
- Published
- 2020
50. Mapping QTL hotspots associated with weed competitive traits in backcross population derived from Oryza sativa L. and O. glaberrima Steud
- Author
-
Brajendra Parmar, M. D. Tuti, Basavaraj Patil, Senguttuvel Ponnuvel, Suneetha Kota, Sreedevi Banugu, Tapan Kumar Mondal, Manoj Appaiah, Muralidhara Bharamappanavara, Santosha Rathod, L. V. Subbarao, Raman Meenakshi Sundaram, Sheshu Madhav Maganti, Gireesh Channappa, Anantha M. Siddaiah, Shashidhar Kadadanamari Shankarappa, Kalyani M. Barbadikar, and Lokesha Ramappa
- Subjects
0106 biological sciences ,0301 basic medicine ,Molecular biology ,Science ,Weed Control ,Population ,Quantitative Trait Loci ,Plant Weeds ,Biology ,Quantitative trait locus ,01 natural sciences ,Genetic analysis ,Article ,03 medical and health sciences ,parasitic diseases ,Genetics ,Cultivar ,Allele ,education ,Alleles ,education.field_of_study ,Multidisciplinary ,Oryza sativa ,fungi ,food and beverages ,Chromosome Mapping ,Oryza ,respiratory system ,030104 developmental biology ,Phenotype ,Agronomy ,Seeds ,Trait ,Medicine ,Weed ,Plant sciences ,Edible Grain ,010606 plant biology & botany ,Microsatellite Repeats - Abstract
To improve grain yield under direct seeded and aerobic conditions, weed competitive ability of a rice genotype is a key desirable trait. Hence, understanding and dissecting weed competitive associated traits at both morphological and molecular level is important in developing weed competitive varieties. In the present investigation, the QTLs associated with weed competitive traits were identified in BC1F2:3 population derived from weed competitive accession of O. glaberrima (IRGC105187) and O. sativa cultivar IR64. The mapping population consisting of 144 segregating lines were phenotyped for 33 weed competitive associated traits under direct seeded condition. Genetic analysis of weed competitive traits carried out in BC1F2:3 population showed significant variation for the weed competitive traits and predominance of additive gene action. The population was genotyped with 81 genome wide SSR markers and a linkage map covering 1423 cM was constructed. Composite interval mapping analysis identified 72 QTLs linked to 33 weed competitive traits which were spread on the 11 chromosomes. Among 72 QTLs, 59 were found to be major QTLs (> 10% PVE). Of the 59 major QTLs, 38 had favourable allele contributed from the O. glaberrima parent. We also observed nine QTL hotspots for weed competitive traits (qWCA2a, qWCA2b, qWCA2c, qWCA3, qWCA5, qWCA7, qWCA8, qWCA9, and qWCA10) wherein several QTLs co-localised. Our study demonstrates O. glaberrima species as potential source for improvement for weed competitive traits in rice and identified QTLs hotspots associated with weed competitive traits.
- Published
- 2020
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