Botany - Research Publications

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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.
Monostroma: the Jeweled Seaweed for Future
(2011) Bast, Felix
Chromosomal location of non-hypersensitive leaf rust resistance genes in bread wheat cultivar PBW65 using microsatellite markers
(2012) Khan, M.A.; Kamaluddin, Saini, R.G.
Microsatellite or simple sequence repeat (SSRs) markers have been powerful tool for genetic mapping in wheat. Indian bread wheat (Triticum aestivum L.) cultivar PBW65 has shown significant level of resistance to most virulent race 77-5 of leaf rust (Puccinia triticina). It has been indicated that PBW65 expresses non-hypersensitive type of resistance against race 77-5. F2 and F3 crossing of PBW65 with WL711, a leaf rust susceptible wheat cultivar, and allelic tests with such already known genes (present in cultivars RL 6058 and HD 2009) revealed that cultivar PBW65 could be a potential source of novel nonhypersensitive leaf rust resistance genes. So far, only non-hypersensitive leaf rust resistance gene Lr34 was found to be effective under Indian conditions. Attempts to locate such durable leaf rust resistance genes in PBW65 through microsatellite markers showed 2B, 2D and 3D as critical chromosomes for PBW65. The primer Xgwm341 (3D) was found located 41.5 cM away from gene LrPBW1 in PBW65.
Temperature-stratified screening of chickpea (Cicer arietinum L.) genetic resource collections reveals very limited reproductive chilling tolerance compared to its annual wild relatives
(2012) Berger, J.D.; Kumar, Sanjeev; Nayyar, H.; Street, K. A.; Sandhu, J. S.; Henzell, J. M.; Kaur, J.; Clark, H.C.
Low reproductive chilling tolerance in chickpea impairs ovule fertilization, delaying pod set, exposing the crop to terminal drought throughout much of its distribution range. Despite this realization, little progress has been made because of the limited genetic variation available to breeders. To address this issue a wide range of domesticated (n= 1762) and wild Cicer (n= 200) germplasm collected from sites stratified by flowering phase temperature was extensively field evaluated, and compared with Lupinus angustifolius, a well-adapted Mediterranean winter annual. Chilling tolerance was estimated by regressing the time interval between pod set and first flower against mean post-anthesis temperature. Field screening was augmented by smaller scale experiments evaluating the effects of contrasting post-anthesis temperature regimes on plant growth and productivity, pollen function and subsequent pod set in temperature-controlled cabinets.Chickpea was less chilling tolerant than its wild relatives, the flower-pod interval increasing curvi-linearly as sites became cooler, with a strong effects between 11 and 16. ?C, tailing off after 17.5. ?C, but remaining statistically significant. There is little useful variation for chilling tolerance within domesticated chickpea. Small, albeit statistically significant differences in pod set delay in chickpea collected from contrasting flowering phase habitats, were marginal compared to more tolerant species such as Cicer bijugum, Cicer judaicum and L. angustifolius, and to a lesser extent Cicer reticulatum, Cicer pinnatifidum, and Cicer echinospermum. No differences were observed between desi and kabuli types. Field screening identified robust chilling tolerance in a C. echinospermum accession that commenced podding earlier, at lower temperatures (10.0. ?C), and yielded 5 times more than Rupali, the most productive chickpea. Controlled temperature experiments confirmed that in contrast to chickpea, pollen germination, viability, frequency on the stigma surface and subsequent pod set were unaffected by low post-anthesis temperatures (13/7. ?C) in C. echinospermum and L. angustifolius. Our results indicate that chickpea is even more chilling sensitive than previously thought. Because C. echinospermum is inter-fertile with chickpea, it has considerable potential both as a donor of robust chilling tolerance and as an agent for investigating resistance mechanisms. ? 2011.
Cancer phylogenetics: Computational modeling of tumor evolution
(Nova Science Publishers, Inc., 2012) Bast, Felix
The field of phylogenetics is one of the core areas of Bioinformatics which deals with computational methods to infer evolutionary heritage of organisms and genes. While phylogenetics has been extensively utilized in taxonomy and systematics of organisms, it is only very recently that the system started expanding to other fields- most importantly in cancer biology where it profoundly transformed our understanding of clonal evolution. Many of our findings in cancer phylogenetics credit to the fact that the tumor is not merely a collection of transformed cells with random mutation events; rather it is an evolving population. Many of the facets underpinning modern evolutionary synthesis can be applied to classify cancers and track its progression from initiating somatic mutation to symptomatic neoplasm. It is now widely accepted that all sub-clones within cancer are phylogenetically related and probability of a particular sub-clone progressing into neoplasm depending upon its time of initiation and evolutionary fitness. Computational models of tumor evolution have also contributed in identifying common clades- "cancer sub-types"- associated with particular cancers in different patients that in turn helped in translating our understanding of oncogeny to the development of "targeted therapeutics"- rationally designed drugs that are molecularly targeted to particular sub-types. Advent of next generation ultra-deep genome sequencing technologies has been rapidly trans-forming the very landscape of cancer phyogenetics. This chapter introduces the concept of cancer phylogenetics and reviews some of the recent advances in this field. This chapter also summarizes various phylogenetic approaches including distance matrix methods, parsimony, maximum likelihood, Bayesian methods and probabilistic inference that have potential applications in cancer research. ? 2012 Nova Science Publishers, Inc. All rights reserved.
Systematics and Taxonomic Keys for the Marine Green Algal Family Monostromataceae
(Nova Science Publishers, 2012) Bast, Felix
Marine green algal family Monostromataceae consists of single cell-layered green seaweeds distributed throughout the world, yet identification of it being one of the most challenging. Monostromatic green seaweeds are all edible and are commercially cultivated in Japan for centuries. A thorough understanding of its systematics is indeed a necessity for any empirical investigation. Working dichotomous taxonomic key for this family is presented for the first time for the ready benefit of field phycologists. Recent advances in the systematics of this family with a special emphasize on the Japanese varieties are also presented.
Synthesis of imine-pyrazolopyrimidinones and their mechanistic interventions on anticancer activity
(2013) Baviskar, Ashish T.; Banerjee, Uttam C.; Gupta, Mukesh; Singh, Rajveer; Kumar, Sunil; Gupta, Manish K.; Kumar, Sanjeev; Rout, Satish K.; Khullar, Madhu; Singh, Sandeep; Kumar, Raj
Design, synthesis and anticancer activity of a series of imine-pyrazolopyrimidinones is reported for the first time. Compounds 9d, 9n and 9o in the series show encouraging in vitro anticancer activity with low micromolar IC50 values against prostate (PC3) and breast (MCF7) cancer cell lines. Some notions about structure-activity relationships and plausible mechanism of biological activity are presented. ? 2013 Elsevier Ltd. All rights reserved.
Agronomy and cultivation methods for edible seaweeds
(Research India Publications, 2013) Bast, Felix
Seaweeds, by all means, are “future plants”; they have been projected as the future viand for ever-increasing human populations, viable and sustainable source for biofuel without disturbing global food scenario, as potential candidates for carbon capture and sequestration that is considered as a practical remedy for global warming, and they have a number of pharmaceutical, industrial and biotechnological applications. However, information on its cultivation methods or life history remain obscure to a majority of marine botanists, especially in India. While life histories of seaweeds have traditionally been an exotic topic for specialists- language of which is ciphered with scientific jargons incomprehensible to general scientific audience, its agronomy had been a trade secret for coastal communities in East Asian countries, especially Japan, the Philippines and Indonesia. In this mini-review, an overview of major coastal and offshore seaweed mariculture techniques are presented with the aid of clear-to-understand illustrations.
Sequence-based Phylogeography of Seaweeds: How Current Distribution is Shaped by Accumulation of Past?
(Graduate School of Kuroshio Science, Kochi University, 2013) Bast, Felix
State-of-the-art techniques of phylogeography are now routinely used to assess changes at DNA level accumulated over time, and thereby to study forces that might have influenced distribution patterns of organisms. Presented in this mini-review is the works on phylogeography of edible green seaweed Monostroma in Japan and how the current distribution pattern of this algae might have been influenced with the history of medieval Japan. Also presented herein is the striking revelations in ancient Japanese waka – a form of short poetry – that documents historical distribution patterns of this algae, and how these are congruent with findings in phylogeography reconstruction.
Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction
(Nature, 2013) Bast, Felix
This is a generic sequence analysis protocol suitable for plant and algal phylogeographic studies. Generated sequences from bidirectional Sanger sequencers are first assembled using Geneious. Sequence assembly is then trimmed and similarity search is conducted using BLASTn within Geneious. BLAST hits and other target taxa are selected and multiple sequence alignment is constructed. The alignment is then refined by checking using eye and exported as .fasta. Using MEGA, best-fitting nucleic acid substitution models will be calculated in MLModelTest. Model with lowest BIC score is selected and used for further phylogenetic analysis using MEGA or Geneious, which include distance matrix construction, phylogeny reconstruction using ML and BI.
Identification and characterization of novel UniGene-derived microsatellite markers in Podophyllum hexandrum (Berberidaceae).
(2013) Nag, Akshay; Bhardwaj, Pankaj; Ahuja, Paramvir Singh.; Sharma, Ram Kumar
Insulin receptor (IR) and insulin-like growth factor receptor 1 (IGF-1R) signaling systems: Novel treatment strategies for cancer
(Humana Press Inc., 2014) Singh, Pushpendra; Alex, Jimi Marin; Bast, Felix
Insulin and insulin-like growth factor (IGF) signaling system, commonly known for fine-tuning numerous biological processes, has lately made its mark as a much sought-after therapeutic targets for diabetes and cancer. These receptors make an attractive anticancer target owing to their overexpression in variety of cancer especially in prostate and breast cancer. Inhibitors of IGF signaling were subjected to clinical cancer trials with the main objective to confirm the effectiveness of these receptors as a therapeutic target. However, the results that these trials produced proved to be disappointing as the role played by the cross talk between IGF and insulin receptor (IR) signaling pathways at the receptor level or at downstream signaling level became more lucid. Therapeutic strategy for IGF-1R and IR inhibition mainly encompasses three main approaches namely receptor blockade with monoclonal antibodies, tyrosine kinase inhibition (ATP antagonist and non-ATP antagonist), and ligand neutralization via monoclonal antibodies targeted to ligand or recombinant IGF-binding proteins. Other drug-discovery approaches are employed to target IGF-1R, and IR includes antisense oligonucleotides and recombinant IGF-binding proteins. However, therapies with monoclonal antibodies and tyrosine kinase inhibition targeting the IGF-1R are not evidenced to be satisfactory as expected. Factors that are duly held responsible for the unsuccessfulness of these therapies include (a) the existence of the IR isoform A overexpressed on a variety of cancers, enhancing the mitogenic signals to the nucleus leading to the endorsement of cell growth, (b) IGF-1R and IR that form hybrid receptors sensitive to the stimulation of all three IGF axis ligands, and (c) IGF-1R and IR that also have the potential to form hybrid receptors with other tyrosine kinase to potentiate the cellular transformation, tumorigenesis, and tumor vascularization. This mini review is a concerted effort to explore and fathom the well-recognized roles of the IRA signaling system in human cancer phenotype and the main strategies that have been so far evaluated to target the IR and IGF-1R. ? 2013 Springer Science+Business Media New York.
Morphological and molecular assessment of native carrageenophyte Hypnea valentiae (Cystocloniaceae, Gigartinales) in Indian Subcontinent
(Phycological Society, 2014) Bast, Felix; Bhushan, Satej; John, Aijaz Ahmad
Hypnea valentiae is an important red alga commercially cultivated in various parts of the world for the production of carrageenan. Presented in this report is findings of morphological and molecular observations of naturally-occurring populations of this alga collected from west and east coasts of India. Both the isolates had similar external as well as microscopic morphology. Nuclear ribosomal DNA Internal Transcribed Spacer-1 (ITS1) sequences from these geographical isolates had 4.35 x 10 -1 Tamura-3-Parameter (T3P) pairwise distance between them, which indicate significant evolutionary differences accumulated over time. In comparison, T3P distance between related genera Kappaphycus and Eucheuma was 1.85 x 10 -1 . In our phylogeny reconstruction using Bayesian Inference, both the isolates formed a well- supported clade along with the only available accession of this genus at ITS1 locus, indicating affiliation of both the isolates in this genus. Interestingly, isolate from the west coast was more basal in the phylogram, which suggests phylogenetically primitive position of this population. Newly generated DNA barcodes of the geographic isolates of this native carragenophyte in this study is expected to be a key in tracing its further dispersal routes, either natural or deliberate. This is the first report on the comparative morphological and molecular assessment of Hypnea from India.
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.
Seaweeds in Japanese Culture: An analysis of medievalWakapoetry
(2014) Bast, Felix
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
Insilco Molecular Docking Study Of Natural Compounds On Wild and Mutated Epidermal Growth Factor Receptor.
(2014) Singh, Pushpendra; Bast, Felix.
Secret of waking-up fresh and having a great day!
(CSIR- NISCAIR, 2014) Bast, Felix
After a long night's sleep, now that you are sitting on a chair with morning cuppa and the Science Reporter-both indeed neuro-stimulants, and hoping to have a great day, no matter had you woke-up fresh or not. Believe it or not, seemingly perplexing conundrum the title of this write-up might have been, solutions have already been discovered by scientists (first part, almost four decades ago) albeit remained pretty much a coveted secret and mostly obscured from the public. So the purpose of this is straight forward; being a popular science enthusiast, let me divulge it, to make a bit of modern science-essence of three primary research papers that are filled with technical jargons and beyond the comprehension for most of us- improve our daily life.
An illustrated review on cultivation and life history of agronomically important seaplants
(Nova Science Publishers, Inc., 2014) Bast, Felix
Seaplants (a better alternative to the misnomer "Seaweeds"), by all means, are "future plants"; they have been projected as the future viand for ever-increasing human populations, viable and sustainable source for biofuel without disturbing global food scenario, as potential candidates for carbon capture and sequestration that is considered as a practical remedy for global warming, and they have a number of pharmaceutical, industrial and biotechnological applications. However, information on its cultivation methods or life history remains obscure to a majority of marine botanists. While life histories of seaweeds have traditionally been an exotic topic for specialists-language of which is ciphered with scientific jargons incomprehensible to general scientific audience, its agronomy had been a trade secret for coastal communities in East Asian countries, especially Japan, the Philippines and Indonesia. In this up-to-date illustrated review, current scientific understanding on the life-histories of agronomically pertinent seaweeds are presented in a fashion akin to popular science journalism with an overview of major coastal and offshore seaweed mariculture techniques, presented with the aid of clear-to-understand illustrations. Also discussed in this report are recent advances in the algal natural products; including uses in hydrocolloid and pharmaceutical industries, Integrated Multi Trophic Aquaculture, energy production, environmental impacts of the seafarming and its counter measures, before concluding with an overview of future research avenues. ? 2014 by Nova Science Publishers, Inc. All rights reserved.
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.