Botany - Research Publications

Permanent URI for this collectionhttps://kr.cup.edu.in/handle/32116/32

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End date: 2017

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Now showing 1 - 10 of 95
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    Insilco Molecular Docking Study of Natural Compounds On Wild and Mutated Epidermal Growth Factor Receptor
    (Springer, 2014) Singh, Pushpendra; Bast, Felix
    The role played by overexpression of tyrosine kinase epidermal growth factor receptor (EGFR), the transmembrane receptor central to numerous cellular processes comprising cell migration, adhesion, apoptosis, and cell proliferation, has been highlighted in various cancers such as prostate, breast, lung, and ovarian cancers as well as in mutations in the EGFR kinase domain. Although many therapeutic approaches have targetted EGFR, the mutations occurring in the EGFR kinase domain including L858 EGFR and T790/L858R had led to the amplification of EGFR signals, consequently leading to increased cell proliferation and cell growth. The strategies involving the inhibition of EGFR L858 and T790M have been accredited with limited achievement in addition to being associated with unwanted adverse effects as a result of crosstalk of wild-type EGFR. All current EGFR tyrosine kinase inhibitors have been identified as ATP competitive inhibitors of wild-type EGFR possessing aniline and quinazoline moiety on the ligands skeleton. Our results obtained by performing molecular docking study on Maestro 9.3 molecular docking suite indicated that CID5280343 possesses better energy conformation against wild-type EGFR as well as two mutated EGFR. Moreover, it was discovered in this study that the natural compounds CID72276, CID5280445, CID441794, and CID72277 and InterBioScreen's library STOCK1N-78657, STOCK1N-78976, and STOCK1N-78847 have better binding conformation against gatekeeper T790M mutated EGFR concluded to be brought about by means of flexible ligands/receptor-based molecular docking protocol. Miraculous features of these compounds are their various pharmacokinetic and pharmacodynamic parameters which were found to be satisfactory as drug-like molecules. This molecular docking study also summarizes docking free energy, protein-ligands interaction profile, and pharmacokinetic and pharmacodynamic parameter of lead molecules which were tremendously helpful in enhancing the activity of these natural compounds against EGFR.
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    Strong endemism of bloom-forming tubular Ulva in Indian west coast, with description of Ulva paschima Sp Nov (Ulvales, Chlorophyta)
    (PLOS One, 2014) Bast, Felix; John, Aijaz Ahmad; Bhushan, Satej
    Ulva intestinalis and Ulva compressa are two bloom-forming morphologically-cryptic species of green seaweeds widely accepted as cosmopolitan in distribution. Previous studies have shown that these are two distinct species that exhibit great morphological plasticity with changing seawater salinity. Here we present a phylogeographic assessment of tubular Ulva that we considered belonging to this complex collected from various marine and estuarine green-tide occurrences in a ca. 600 km stretch of the Indian west coast. Maximum Likelihood and Bayesian Inference phylogenetic reconstructions using ITS nrDNA revealed strong endemism of Indian tubular Ulva, with none of the Indian isolates forming part of the already described phylogenetic clades of either U. compressa or U. intestinalis. Due to the straightforward conclusion that Indian isolates form a robust and distinct phylogenetic clade, a description of a new bloom-forming species, Ulva paschima Bast, is formally proposed. Our phylogenetic reconstructions using Neighbor-Joining method revealed evolutionary affinity of this new species with Ulva flexuosa. This is the first molecular assessment of Ulva from the Indian Subcontinent.
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    DNA Barcoding of a new record of epi-endophytic green algaeUlvellaleptochaete(Ulvellaceae, Chlorophyta) in India
    (Indian Academy of Science, 2014) Bast, Felix; Bhushan, Satej; John, Aijaz Ahmad
    Epi-endophytic green algae comprise one of the most diverse and phylogenetically primitive groups of green algae and are considered to be ubiquitous in the world's oceans; however, no reports of these algae exist from India. Here we report the serendipitous discovery of Ulvella growing on intertidal green algae Cladophora glomerata and benthic red algae Laurencia obtusa collected from India. DNA barcodes at nuclear ribosomal DNA Internal Transcriber Spacer (nrDNA ITS) 1 and 2 regions for Indian isolates from the west and east coasts have been generated for the first time. Based on morphology and DNA barcoding, isolates were identified as Ulvella leptochaete. Phylogenetic reconstruction of concatenated dataset using Maximum Likelihood method differentiated Indian isolates from other accessions of this alga available in Genbank, albeit with low bootstrap support. Monophyly of Ulvella leptochaete was obvious in both of our phylogenetic analyses. With this first report of epi-endophytic algae from Indian territorial waters, the dire need to catalogue its cryptic diversity is highlighted and avenues of future research are discussed.
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    SSR marker based DNA fingerprinting and diversity assessment in superior tea germplasm cultivated in western Himalaya
    (Indian National Academic Science, 2014) Bhardwaj, Pankaj; Sharma, Rajesh Kumar; Kumar, Rajendra; Sharma, Hemlata; Ahuja, Paramvir Singh
    Twenty one microsatellites (genomic & genic) markers were used to evaluate genetic diversity and DNA fingerprinting of 15 popular tea accessions. Each accession had a unique marker profile, indicating that microsatellite markers were useful in differentiation studies among the tea collections. A total of 127 polymorphic alleles were scored with an allele frequency of 6.05 per primer. The polymorphism information content (PIC) ranged from 0.2 (CamsinM1) to 0.60 (TUGMS12), with an average of 0.359. SSR markers analysis detected a high level of heterozygosity (av Ho 0.775; He 0.847) in tea. The Jaccard's similarity coefficients ranged from 0.15 to 0.56 with an average similarity index (ASI) of 0.234. The first two coordinate explained 54.33% of the total variance. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram and the PCoA (Principle coordinate analysis) indicated that the populations formed two major groups with exclusive China and China hybrids (I) and Assam types (II). The collections from western Himalayan possessed a moderate to high level of genetic diversity which could provide valid guidelines for genetic improvement of tea
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    Creatures of India: Guide to Animals in India with up-to-date systematics
    (New Delhi Publishers, 2014) Bast, Felix
    Indian Biodiversity, albeit being one of the richest in the world with three of the 32 �Biodiversity Hotspots�, is unfortunately in a serious sate of neglect from the administration and the general public alike. Four big-sized animals, Pink-headed Duck, Himalayan Mountain Quail, Lesser Indian Rhinoceros and Indian Cheetah, have gone extinct in the last century alone. IUCN enlist India at 7th rank of shame-list, countries struggling to protect its biodiversity. With almost 18% of world population cramming into less than 2% of area, sub-continental forest cover has been steadily shrinking, so as its biodiversity. This report is first of its kind in India, a comprehensive assessment of status and trends of commonly found animals in the subcontinent with its up-to-date taxonomic positions, overview on the systematics, bio-prospecting and conservation. This work also serves as a �binomen dictionary�-for looking up binomial names of virtually every animal species that you might encounter in daily life in India. The idea to write this book sprang from one of the class assignments as part of BSS.506: Biosystematics and Biodiversity course here at the Central University of Punjab, Bathinda. The assignment was to make a database of Indian Biodiversity. While I appreciate the passion that my students put in the creation of database, most of their entries were well-described taxa from North America and Europe-presumably obtained through online resources, highlighting the dire need to categorize Indian Biodiversity. Zoological Survey of India (ZSI) has published few checklists of animal taxa in India but those did not include several of the important animal phyla. Checklists merely enlist scientific names without common name or any other information and therefore their utility in practical identification is extremely limited. This inspired me to write a book with following focuses: 1. Limit to the macroscopic extant species that are commonly found in nature throughout the subcontinent. 2. Species of human importance; a note on bio-prospecting that highlights commercially cultivated/medicinally important/culturally significant taxa discussed in each chapter introduction. 3. Species of conservation importance; a note on conservation discussed in each chapter introduction and common names are appropriately superscribed throughout (CR: Critically Endangered, EN: Endangered, VU: Vulnerable and NT: Near Threatened.) 4. Example families and genera covering all iconic metazoan phyla and phylogenetic trees to illustrate evolutionary relationships between them; to aid in understanding and appreciation of animal systematics. 5. Designated animals representing national and state level administration. This book is still incomplete; as a privileged reader who appreciates the biodiversity, a column in all the tables are waiting for you to complete; �Name in Regional Language�. With seventeen official languages, India is so linguistically diverse that if I sought out to include a multilingual list of taxa covered in this book, it would have doubled the weight of this book and wasted a number of pages! Instead I made this book like a class-activity notebook; it is for you to find, identify and complete the name in local dialect/regional language in the space provided (Activity: 1), a simple, yet pedagogically-sound method.
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    Monostroma: the Jeweled Seaweed for Future Cultivation methods, Ecophysiology, Phylogeography and Molecular Systematics
    (Lambert Academic Publishing, 2011) Bast, Felix
    This thesis aims at providing a comprehensive picture of the reproductive physiology, growth, phylogeography, and phylogenetics of M. latissimum-nitidum complex in Southern Japan. A review on agronomy and utilization of seaweeds is provided as Chapter 2 to present a comprehensive overview of the seaweed biology and applications. Seasonality in the growth and occurrence of Monostroma sp. at three environmentally distinct habitats along Tosa Bay, Kochi Prefecture, Japan is explored and results of correlation analyses between environmental conditions and thallus size are presented in Chapter 3. Also investigated in the same chapter is the homology of nuclear encoded rDNA Internal Transcribed Spacer (ITS) sequences between naturally occurring and commercially cultivated populations. Findings of the culture studies sought to identify the species naturally occurring at the study sites are also summarized in Chapter 2. In the course of research, I observed that thalli of the naturally occurring populations of M. latissimum, changes its color during maturation, as reported elsewhere in the literature. Further to that observation, a thorough cytological investigation on the gametangial ontogeny of naturally occurring M. latissimum is presented in Chapter 4 and possible taxonomic implications of this finding are discussed. Once the thalli of M. latissimum release gametes, which mode of syngamy do they have? Is sex of the progenies environmentally determined? These are some of the questions being investigated in Chapter 5. Reported in the Chapter 6 is a serendipitous discovery of an asexually reproducing ecotype of M. latissimum in the marginal populations at low-saline habitat. Findings of the culture studies to complete its life cycle are presented. Molecular studies to investigate homogeneity of nrDNA ITS sequences between the two ecot ypes (i.e., sexual vs asexual) are also investigated in the same chapter. Results of phylogenetic analyses of the newly generated ITS sequence of M. latissimum with that of the related monostromatic green algal taxa retrieved from GenBank are also presented in Chapter 6 to understand relative taxonomical position of this species in the class Ulvophyceae. Chapter 7 is an investigation on the morphologic and genetic homogeneity of natural and cultivated populations of the two closely related species M. latissimum and M. nitidum along the Southern Japanese coast where the warm-water Kuroshio Current influences throughout the year. Combined phylogeographical analysis of nuclear encoded first internal transcribed spacer (ITS1) sequences and rDNA 18s gene are presented in addition to the comparison of morphological traits, to understand if they belong to the same taxa. In the final experimental chapter, Chapter 8, taxonomic hypothesis for Monostromataceae were tested and the systematic position of this family is explored using multi-local phylogeny. Relationships of this family with over 40 Ulvophycean genera were investigated and phylogeny reconstruction was conducted using five independent genetic markers; viz., nrDNA ITS1, nrDNA ITS2, nrDNA 5.8S, nrDNA 18S and cpDNA rbcL. Chapter 9 summarizes and discusses the results of this thesis, places them in a regional context and discusses avenues of future work.
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    Alternate mild drought stress (−0.1 MPa PEG) immunizes sensitive chickpea cultivar against lethal chilling by accentuating the defense mechanisms
    (Polish Academy of Sciences, 2016) Kaur S.; Jairath A.; Singh I.; Nayyar H.; Kumar S.
    The changes in climate particularly, the rise in temperature and humidity affect the physiological functions of plants subsequently affecting crop productivity adversely. A strategy is required which can be directly implemented in fields to induce the tolerance in crop plants. In present study, two chickpea varieties with contrasting sensitivity PDG3 (Tolerant) and GPF2 (Sensitive) were raised hydroponically, preconditioned with mild drought stress (0.1 MPa PEG-6000) for 3 days (above 0.1 MPa is lethal) and subsequently recovered for double time (6 days) and finally exposed to lethal cold stress (4 °C) for 3 days. We hypothesize that preconditioning with non-lethal drought stress may immunize the plants to combat lethal cold stress. Membrane integrity improved in root and shoot, lipid peroxidation decreased to control level in preconditioned seedlings. Cellular respiration ability (% TTC reduction) increased in the preconditioned seedlings to almost 90 % in the shoot and 60 % in the root, concurrently it was 45 % in non-preconditioned seedlings. Proline content also increased in preconditioned seedlings, especially roots. Carbohydrate had a shift in terms of a high amount of total, reducing sugars and starch in non-preconditioned seedlings compared to preconditioned. Both PDG3 and GPF2 showed enhanced SOD, CAT and GPOX activity indicating tolerance against cold-induced oxidative stress and preconditioning induced improvement against lethal cold stress.
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    Starch: A precise account covering its multidimensional aspects
    (Nova Science Publishers, Inc., 2017) Majeed, A.; Ul Rehman, W.; Najar, R.A.; Choudhary, S.; Thakur, S.; Singh, A.; Sharma, G.; Bhardwaj, P.
    Starch is the main storage carbohydrate of plants and is composed of glucose residues linked together by ? 1-4 glycosidic bonds. The starch molecule consists of a linear amylose and highly branched amylopectin. Starch forms the main energy source in human diets and is present in large quantities in our common foods like rice, wheat, maize, etc. Granule-bound starch synthase is responsible for amylose synthesis while amylopectin requires the action of starch synthases plus branching enzymes. The degradation of starch requires another set of enzymes including ?-amylase and debranching enzyme. Microorganisms can be employed to produce the starch degrading enzymes thereby yielding the high glucose and fructose syrups. Starch is a good candidate for generating electricity in microbial fuel cells. Besides, ethanol production is yet another application for energy production that can lessen the pressure on conventional petroleum-based fuels. The hydrogels and composites of starch are widely used in pharmaceutical and cosmetic industries, agriculture and medicine especially tissue engineering. Besides the starch itself, its derivatives have a wide range of industrial applications. This chapter focuses on starch structure, synthesis, derivatives, composites, hydrogels, energy production, cosmetic and other industrial applications. ? 2017 Nova Science Publishers, Inc.