SKA Institution for Research

Delhi, India

SKA Institution for Research

Delhi, India
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Kumari R.,National Institute of Plant Genome Research NIPGR | Kumari R.,Banasthali University | Sharma V.,National Institute of Plant Genome Research NIPGR | Sharma V.,SKA Institution for Research | And 3 more authors.
Journal of Genetics | Year: 2013

In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants of Mendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein-coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed. © 2013 Indian Academy of Sciences.


Kumar S.,National Institute of Plant Genome Research NIPGR | Kumar S.,SKA Institution for Research | Kumari R.,National Institute of Plant Genome Research NIPGR | Kumari R.,Banasthali University | And 3 more authors.
Journal of Genetics | Year: 2013

Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants. © 2013 Indian Academy of Sciences.


Kumari R.,National Institute of Plant Genome Research NIPGR | Kumari R.,Banasthali University | Yadav G.,National Institute of Plant Genome Research NIPGR | Sharma V.,National Institute of Plant Genome Research NIPGR | And 4 more authors.
Journal of Genetics | Year: 2013

The 5S and 18S rDNA sequences of Catharanthus roseus cv 'Nirmal' (wild type) and its leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill) single mutants and lli egd, lli ill and egd ill double mutants were characterized. The lli, egd and ill mutants of Mendelian inheritance bore the names after their most conspicuous morphological feature(s). They had been chemically induced and isolated for their salt tolerance. The double mutants were isolated as morphological segregants from crosses between single mutants. The morphological features of the two parents accompanied salt tolerance in the double mutants. All the six mutants were hypomethylated at repeat sequences, upregulated and downregulated for many genes and carried pleiotropic alterations for several traits. Here the 5S and 18S rDNAs of C. roseus were found to be relatively low in cytosine content. Cytosines were preponderantly in CG context (53%) and almost all of them were methylated (97%). The cytosines in CHH and CHG (where H = A, T or C) contexts were largely demethylated (92%) in mutants. The demethylation was attributable to reduced expression of RDR2 and DRM2 led RNA dependant DNA methylation and CMT3 led maintenance methylation pathways. Mutants had gained some cytosines by substitution of C at T sites. These perhaps arose on account of errors in DNA replication, mediated by widespread cytosine demethylation at CHG and CHH sites. It was concluded that the regulation of cytosine methylation mechanisms was disturbed in the mutants. ILL, EGD and LLI genes were identified as the positive regulators of other genes mediating the RdDM and CMT3 pathways, for establishment and maintenance of cytosine methylation in C. roseus. © 2013 Indian Academy of Sciences.


Sharma V.,National Institute of Plant Genome Research NIPGR | Kumar S.,SKA Institution for Research
Indian Journal of Experimental Biology | Year: 2013

In the wild type P. sativum, each of the adult plant stem nodes, bears a pair of sessile foliaceous stipules and a petiolated unipinnately compound leaf of 4 to 6 leaflets and 7-9 tendrils. The stipule-reduced (st) and cochleata (coch) single null mutants and coch st double null mutant differ fom the wild type in respectively having sessile stipules of much reduced size, petiolated simple and/or compound leaf-like stipules and no stipules. It is also known that coch leaves are somewhat bigger than st and wild type leaves. Here, pleiotropic phenotype of coch st double mutant was investigated. The morphologies of stipules and leaf were quantified in the field grown plants and microcultured shoots, latter in the presence and absence of gibberellic acid and N-1-naphthylphthalamic acid. The observations showed that as compared to the corresponding plants or shoots of COCH ST (WT) genotype, (a) coch st plants bore leaves in which all the organs were hypertrophied; (b) full complement of leaflets and 3-5 tendrils were formed on leaf; (c) the microcultured coch st shoots were taller despite lower number of nodes, and (d) they also produced leaves in which all the organs were bigger and the ratio of leaflets/tendrils was higher. It was concluded that in coch st double mutant (a) ST function is essential for stipule primordium differentiation, in the absence of COCH function and (b) absence of negative feedback loops between simple stipules and compound leaf for metabolite utilization allows hypertrophied growth in leaves.


Kumar S.,National Institute of Plant Genome Research NIPGR | Kumar S.,SKA Institution for Research | Mishra R.K.,National Institute of Plant Genome Research NIPGR | Kumar A.,National Institute of Plant Genome Research NIPGR | And 7 more authors.
Journal of Genetics | Year: 2012

In Pisum sativum, the completely penetrant leaflet development (lld) mutation is known to sporadically abort pinnae suborgans in the unipinnate compound leaf. Here, the frequency and morphology of abortion was studied in each of the leaf suborgans in 36 genotypes and in presence of auxin and gibberellin, and their antagonists. Various lld genotypes were constructed by multifariously recombining lld with a coch homeotic stipule mutation and with af, ins, mare, mfp, tl and uni-tac leaf morphology mutations. It was observed that the suborgans at all levels of pinna subdivisions underwent lld-led abortion events at different stages of development. As in leafblades, lld aborted the pinnae in leaf-like compound coch stipules. The lld mutation interacted with mfp synergistically and with other leaf mutations additively. The rod-shaped and trumpet-shaped aborted pea leaf suborgans mimicked the phenotype of aborted leaves in HD-ZIP-III-deficient Arabidopsis thaliana mutants. Suborganwise aborted morphologies in lld gnotypes were in agreement with basipetal differentiation of leaflets and acropetal differentiation in tendrils. Altogether, the observations suggested that LLD was the master regulator of pinna development. On the basis of molecular markers found linked to lld, its locus was positioned on the linkage group III of the P. sativum genetic map. © 2012 Indian Academy of Sciences.


Kumar S.,SKA Institution for Research | Kumar S.,National Institute of Plant Genome Research NIPGR | Kumari R.,SKA Institution for Research | Kumari R.,National Institute of Plant Genome Research NIPGR | Pandey R.,Indian Institute of Chemical Technology
Protoplasma | Year: 2015

New challenges posed by the development of resistance against artemisinin-based combination therapies (ACTs) as well as previous first-line therapies, and the continuing absence of vaccine, have given impetus to research in all areas of malaria control. This review portrays the ongoing progress in several directions of malaria research. The variants of RTS,S and apical membrane antigen 1 (AMA1) are being developed and test adapted as multicomponent and multistage malaria control vaccines, while many other vaccine candidates and methodologies to produce antigens are under experimentation. To track and prevent the spread of artemisinin resistance from Southeast Asia to other parts of the world, rolling circle-enhanced enzyme activity detection (REEAD), a time- and cost-effective malaria diagnosis in field conditions, and a DNA marker associated with artemisinin resistance have become available. Novel mosquito repellents and mosquito trapping and killing techniques much more effective than the prevalent ones are undergoing field testing. Mosquito lines stably infected with their symbiotic wild-type or genetically engineered bacteria that kill sympatric malaria parasites are being constructed and field tested for stopping malaria transmission. A complementary approach being pursued is the addition of ivermectin-like drug molecules to ACTs to cure malaria and kill mosquitoes. Experiments are in progress to eradicate malaria mosquito by making it genetically male sterile. High-throughput screening procedures are being developed and used to discover molecules that possess long in vivo half life and are active against liver and blood stages for the fast cure of malaria symptoms caused by simple or relapsing and drug-sensitive and drug-resistant types of varied malaria parasites, can stop gametocytogenesis and sporogony and could be given in one dose. Target-based antimalarial drug designing has begun. Some of the putative next-generation antimalarials that possess in their scaffold structure several of the desired properties of malaria cure and control are exemplified by OZ439, NITD609, ELQ300 and tafenoquine that are already undergoing clinical trials, and decoquinate, usnic acid, torin-2, ferroquine, WEHI-916, MMV396749 and benzothiophene-type N-myristoyltransferase (NMT) inhibitors, which are candidates for future clinical usage. Among these, NITD609, ELQ300, decoquinate, usnic acid, torin-2 and NMT inhibitors not only cure simple malaria and are prophylactic against simple malaria, but they also cure relapsing malaria. © 2014, Springer-Verlag Wien.


Kumar S.,National Institute of Plant Genome Research NIPGR | Kumar S.,SKA Institution for Research | Sharma V.,National Institute of Plant Genome Research NIPGR | Sharma V.,SKA Institution for Research
Proceedings of the National Academy of Sciences India Section B - Biological Sciences | Year: 2013

Simple petiolated leaves are formed on the wild type plants of apocynaceous medicinal-cum-floricultural species Catharanthus roseus. A C. roseus variant line homozygous for two loss-of-function mutations, an induced leafless inflorescence (lli) mutations and a natural bisected leaf (bil) mutation, was isolated on account of its unique leaf bisection phenotype which was characterized. The lli bil phenotype was highly penetrant but poorly expressed. Only about one-fourth of leaves of lli bil plants were bisected. Leaf bisection was correlated with premature termination of midvein. Degree of bisection varied from a nick at the apex of lamina to formation of two complete leaflets. The notch in 43 % of the bisected leaves bore a pin-like apical adventitious growth. The features of bisected leaves showed that midvein was essential for symmetrical development of smooth lamina spans on its either side; although the development of spans was independent. Several lateral veins emerged from proximal midvein and grew acropetally. Lamina development in the proximal region failed in the absence of local lateral veins. Bisected leaves were also formed as bi-lobed simple leaves, each lobe having its own primary (mid) vein arising from proximally bifurcated midvein. Also formed were completely bisected leaves. In these binately compound leaves, each leaflet had its own petiolule attached to the leaf petiole. The lli bil genotype of C. roseus perhaps provides the only example of a compound leaved variant evolving from a simple leaved species. This phenotype of lli bil leaves supports the suggestion that simple leaf form was ancestral in angiosperms. © 2012 The National Academy of Sciences, India.


Sharma V.,National Institute of Plant Genome Research NIPGR | Sharma V.,SKA Institution for Research | Kumar S.,National Institute of Plant Genome Research NIPGR | Kumar S.,SKA Institution for Research
Plant Systematics and Evolution | Year: 2013

The leguminous flora of Delhi comprises 78 Papilionoideae, 24 Caesalpinioideae and 24 Mimosoideae species; 80 of them are perennials. Five types of imparipinnate and two types of paripinnate compound leaves were observed in the species. The paripinnate leaves are bipinnate in 25 species (mostly mimosoid) and bifoliate in two species. The imparipinnate leaves were trifoliate or multifoliate in 59 papilionoid species and multifoliate in 16 caesalpinioid species; four of the papilionoid species produced leafletted and tendrilled unipinnate leaves. Leaves were bifacially simple in 22 species, simple with ectopic terminal growth in one species and simple tendril in one species. Twenty-one species (mostly mimosoid) were devoid of stipules. In 82 species stipules were small and free. Stipules were large and lobed in 17 species and large and adnate in four species. Two species of Caesalpinioideae produce compound leaf-like stipules. All four stipule phenotypes of 126 species corresponded with stipular phenotypes observed in wild type, coch, st and coch st genotypes of the model legume P. sativum. The seven leaf phenotypes observed in 126 species corresponded with phenotypes expected among combinations of uni (uni-tac), af, ins, mfp and tl mutants of P. sativum and sgl1, cfl1, slm1 and palm1 mutants of M. truncatula, also an IRL model legume. All the variation in leaf and stipule morphologies observed in the leguminous flora of Delhi could be explained in terms of the gene regulatory networks already revealed in P. sativum and M. truncatula. It is hypothesized that the ancestral gene regulatory networks for leaves and stipules produced in Leguminosae were like that prevalent in P. sativum. © 2013 Springer-Verlag Wien.


Bahl J.R.,Central Institute of Medicinal and Aromatic Plants | Bansal R.P.,Central Institute of Medicinal and Aromatic Plants | Goel R.,Krishna Institute of Engineering and Technology | Kumar S.,National Institute of Plant Genome Research | Kumar S.,SKA Institution for Research
Indian Journal of Natural Products and Resources | Year: 2015

Seeds of Silybum marianum cv SMB-5, an Indian cultivar of dwarf habit and high seed yield, were characterized for their oil content and was examined for its physico-biochemical properties. The seed oil content was low at 20±2%. The oil had acid value of 1.5, specific gravity at 27 0C was 0.885, saponification value as 199 and iodine value equal to 97. The main fatty acid composition was: palmitic acid, 9.6%; stearic acid, 4.7%; oleic acid, 3.9%; linoleic acid, 45.8% and linolenic acid, 5.3%. The properties of the oil of Indian genotype largely correspond with those of S. marianum oil of Canadian, Greek, Egytian, Iraqi, Iranian and Pakistani genotypes. In comparison to the commercial oils of soybean, Indian mustard, canola, groundnut, sunflower, safflower and flex, the fatty acid compositional properties of S. marianum oil were found to be unique being rich in linoleic acid. © 2015, Indian Journal of Natural Products and Resources. All right reserved.


PubMed | SKA Institution for Research
Type: Journal Article | Journal: Protoplasma | Year: 2015

New challenges posed by the development of resistance against artemisinin-based combination therapies (ACTs) as well as previous first-line therapies, and the continuing absence of vaccine, have given impetus to research in all areas of malaria control. This review portrays the ongoing progress in several directions of malaria research. The variants of RTS,S and apical membrane antigen 1 (AMA1) are being developed and test adapted as multicomponent and multistage malaria control vaccines, while many other vaccine candidates and methodologies to produce antigens are under experimentation. To track and prevent the spread of artemisinin resistance from Southeast Asia to other parts of the world, rolling circle-enhanced enzyme activity detection (REEAD), a time- and cost-effective malaria diagnosis in field conditions, and a DNA marker associated with artemisinin resistance have become available. Novel mosquito repellents and mosquito trapping and killing techniques much more effective than the prevalent ones are undergoing field testing. Mosquito lines stably infected with their symbiotic wild-type or genetically engineered bacteria that kill sympatric malaria parasites are being constructed and field tested for stopping malaria transmission. A complementary approach being pursued is the addition of ivermectin-like drug molecules to ACTs to cure malaria and kill mosquitoes. Experiments are in progress to eradicate malaria mosquito by making it genetically male sterile. High-throughput screening procedures are being developed and used to discover molecules that possess long in vivo half life and are active against liver and blood stages for the fast cure of malaria symptoms caused by simple or relapsing and drug-sensitive and drug-resistant types of varied malaria parasites, can stop gametocytogenesis and sporogony and could be given in one dose. Target-based antimalarial drug designing has begun. Some of the putative next-generation antimalarials that possess in their scaffold structure several of the desired properties of malaria cure and control are exemplified by OZ439, NITD609, ELQ300 and tafenoquine that are already undergoing clinical trials, and decoquinate, usnic acid, torin-2, ferroquine, WEHI-916, MMV396749 and benzothiophene-type N-myristoyltransferase (NMT) inhibitors, which are candidates for future clinical usage. Among these, NITD609, ELQ300, decoquinate, usnic acid, torin-2 and NMT inhibitors not only cure simple malaria and are prophylactic against simple malaria, but they also cure relapsing malaria.

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