Institutional Publications

Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11

Browse

Author: search.filters.author.Sharma, VishakhaHas files: Yes

Search Results

Now showing 1 - 10 of 28
  • Thumbnail Image
    Item
    Ebola virus disease: Biology, diagnosis, treatment and prevention of epidemics
    (Indian National Science Academy, 2017) Kumar, Sushil; Kumari, Renu; Pandey, Richa; Sharma, Vishakha
    Ebola virus disease (EVD) is a highly lethal contagious disease caused by the negative RNA strand Ebola virus. Reservoired in wild forest animals of Africa, Ebola virus infects humans that come in direct contact of diseased animals and outbreaks of EVD result from person to person spread of infection. A recent EVD outbreak in West Africa has killed several thousand persons. Since Ebola infection will persist in animals, EVD epidemics are expected to continue to occur in future. Infected travellers from Africa can initiate/import outbreaks in countries of other continents. This review describes the properties of the Ebola virus and EVD, the ongoing attempts to develop diagnostics, vaccines and medicines for prevention and cure of EVD and the supportive care that saves some EVD patients. Also discussed are measures that can stop and prevent EVD outbreaks. Need for inclusion of EVD in the education, research, drug and medical equipment manufacturing programmes, of the densly populated countries such as India, is emphasised.
  • Thumbnail Image
    Item
    Coevolution mechanisms that adapt viruses to genetic code variations implemented in their hosts
    (Indian Academy of Sciences, 2016) Kumar, Sushil; Kumari, Renu; Sharma, Vishakha
    Viruses, the preponderant species, are the agents of horizontal gene transfer between cellular organisms, a major means for generation of genetic variability that drives evolution in varying environments. Recent work on virus × host interaction has led to revision of the conventional idea that the genetic code of the virus and host must be same so that the host translational system facilitates efficient, accurate and complete expression of the infecting viral genome. There is evidence now that differences between the genetic codes of viruses and their hosts are not an absolute barrier to virus multiplication. The recent work on mechanisms by which viruses overcome the mismatch in codon usage of host versus theirs is discussed here contextually. Examples of coevolution of viruses and their hosts, in terms of genetic code usage, discussed here agree with the concept that their evolution is reciprocally driven and therefore suggestive of a kind of long-term interdependent symbiotic relationship between them.
  • Thumbnail Image
    Item
    An analysis of vascular system in the compound tendrilled afila leaf in Pisum sativum
    (National Institute of Science Communication and Information Resources-NISCAIR, 2014) Sharma, Vishakha; Kumar, Arvind; Kumar, Sushil
    Recent work on the venation patterning and morphogenesis of leaf/leaflet has posed the question how different are these in tendrils, which are another type of vegetative lateral organ. Here, the venation patterns of leaflets, stipules and tendrils were compared in the model species, P. sativum. Unlike reticulated venation in leaflets and stipules, venation in tendrils comprised of one or more primary veins. A few secondaries were attached to a primary vein, mostly distally. Bilaterally symmetrical secondary veins were rare. The primary veins in tendrils were daughter strands from dichotomously divided mother veins in rachis, connected finally to vascular strands in stem. A tendril received primary vein from one or more mother strands. Some mother strands contributed primary veins to proximal, distal and terminal domain tendrils of af leaf. The tendrils shared the multi-primary vein character with stipules. Vein redundancy provided a mechanism for survival of tendril/leaf against injury to some of the veins/mother veins. The presence of aborted primary veins that did not reach apex, rows of cambium cells attached to primary vein(s) at apex, the pattern of attachment of primary veins to mother veins and cessation of vein growth in apical direction in aborted tendrils of af lld genotype indicated that the growth of primary veins and tendril was acropetal. Loss-of-function of AF extended the repression of TL and MFP genes on leaflet development from distal and apical domains to proximal domain of leaves in af mutants.
  • Thumbnail Image
    Item
    Genetics of dioecy and causal sex chromosomes in plants
    (Indian Academy of Sciences, 2014) Kumar, Sushil; Kumari, Renu; Sharma, Vishakha
    Dioecy (separate male and female individuals) ensures outcrossing and is more prevalent in animals than in plants. Although it is common in bryophytes and gymnosperms, only 5% of angiosperms are dioecious. In dioecious higher plants, flowers borne on male and female individuals are, respectively deficient in functional gynoecium and androecium. Dioecy is inherited via three sex chromosome systems: XX/XY, XX/X0 and WZ/ZZ, such that XX or WZ is female and XY, X0 or ZZ are males. The XX/XY system generates the rarer XX/X0 and WZ/ZZ systems. An autosome pair begets XY chromosomes. A recessive loss-of-androecium mutation (ana) creates X chromosome and a dominant gynoecium-suppressing (GYS) mutation creates Y chromosome. The ana/ANA and gys/GYS loci are in the sex-determining region (SDR) of the XY pair. Accumulation of inversions, deleterious mutations and repeat elements, especially transposons, in the SDR of Y suppresses recombination between X and Y in SDR, making Y labile and increasingly degenerate and heteromorphic from X. Continued recombination between X and Y in their pseudoautosomal region located at the ends of chromosomal arms allows survival of the degenerated Y and of the species. Dioecy is presumably a component of the evolutionary cycle for the origin of new species. Inbred hermaphrodite species assume dioecy. Later they suffer degenerate-Y-led population regression. Cross-hybridization between such extinguishing species and heterologous species, followed by genome duplication of segregants from hybrids, give rise to new species.
  • Thumbnail Image
    Item
    The lld mutation in Pisum sativum used as a genetic tool to discern the plant leaflet/leaf developmental process
    (NISCAIR-CSIR, India, 2013) Sharma, Vishakha; Tripathi, Bhumi Nath; Kumar, Sushil
    Leaves of P. sativum the double mutant genotype tendril-less (tl) leaflet-development (lld), due to the action of lld mutation, produce many leaflets that are aborted at different stages of development. Morphological, vein pattern and histological observations showed that aborted leaflets became cup/bell/trumpet (cup) shaped because of segmental differentiation in the leaflet primordium. Cup's inside lamina surface was adaxial and outer surfaces of cup and its stem were abaxial. The lld cups were phenotypically homologous to aborted leaves described in Arabidopsis thaliana mutants, angustifolia and those which underexpressed the HD-ZIP III proteins. Leaflet primordium was found to grow and establish three dimensional polarities apex-downwards. Primordium produced lateral outgrowth on one side of midvein. Differentiation, in the outgrowth of secondary veins, whose xylem tissues faced each other, established the adaxial-abaxial polarity. Lateral outgrowth then developed a cavity which got bounded by future adaxial epidermis. Further growth, veinlet formation, differentiation of palisade parenchyma and spongy parenchyma followed. Opening of lateral outgrowth at its outer midline produced a flat leaflet with lateral lamina spans. The structural and functional correspondence between leaflet and simple leaves suggested commonality between leaf and leaflet development mechanisms. A molecular model for the lld led leaflet abortion was also provided.
  • Thumbnail Image
    Item
    Parallelismic homoplasy of leaf and stipule phenotypes among genetic variants of Pisum sativum and Medicago truncatula and some taxa of papilionoideae, caesalpinioideae and mimosoideae subfamilies of the leguminosae flora of Delhi
    (Springer, 2013) Sharma, Vishakha; Kumar, Sushil
    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.
  • Thumbnail Image
    Item
    Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus
    (Indian Academy of Sciences, 2013) Kumari, Renu; Yadav, Gitanjali; Sharma, Vishakha; Sharma, Vinay; Kumar, Sushil
    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 ethylation 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.
  • Thumbnail Image
    Item
    Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance
    (Indian Academy of Sciences, 2013) Kumari, Renu; Sharma, Vishakha; Sharma, Vinay; Kumar, Sushil
    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.
  • Thumbnail Image
    Item
    Common and distinguishing characteristics of genes and genomes and their evolution in the genome sequenced legumes
    (Indian National Science Academy, 2013) Kumar, Sushil; Kumari, Renu; Sharma, Vishakha; Yadav, Gitanjali
    By March 2013, genome sequences have been published for five legume species- Cicer arietinum (pulse crop chickpea), Cajanus cajan (pulse crop pigeonpea), Glycine max (pulse-cum-oil seed crop soybean), Lotus japonicus and Medicago truncatula (both model plants). The genome sequenced legumes belong to the subfamily papilionoideae of the angiosperm family leguminoseae, C. arietinum, L. japonicus and M. truncatula to the galegoid clade and C. cajan and G. max to millettioid clade. These diploid species have 2n number varying from 12 in L. japonicus, 16 in M. truncatula and C. arietinum, 22 in C. cajan and 40 in G. max. Comparisons among their genome sequences have revealed several important properties about structure and evolution of their genomes. Thirty five to 60% of genome is in the form of repititive elements, mainly transposons. Genome carries less than 50,000 protein-coding genes, 56 to 87% in two or more copies. All the five species arose from a common pre-papilionoid parent produced by inter-species hybridization accompanied by whole genome duplication (WGD or allotetraploidy) about 58 million years ago (Mya). Separation of clades and speciation occurred via sequence changes, over a period of > 40 million years. Individual genes underwent substitution and frameshift mutations. Chromosomal level rearrangements involved deletions, inversions, translocations, fission and fusions. There was spread of individual genes or blocks of genes followed by their tandem duplication. Deletion of orthologues was also involved in lineage specific changes. Ancestors of Glycine underwent an allotetraploid event after separation of C. cajan in the millettioid clade about 13 Mya. Developments relating to the applications of legume genome sequence knowledge are also discussed.
  • Thumbnail Image
    Item
    Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants
    (Indian Academy of Sciences, 2013) Kumar, Sushil; Kumari, Renu; Sharma, Vishakha; Sharma, Vinay
    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 orC) 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.