BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.

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Somaclonal variations and their applications in horticultural crops improvement

Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

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Advances in plant gene-targeted and functional markers: a review

Members of the genus Curcuma L. have been used in traditional medicine for centuries for treating gastrointestinal disorders, pain, inflammatory conditions, wounds, and for cancer prevention and antiaging, among others. Many of the biological activities of Curcuma species can be attributed to nonvolatile curcuminoids, but these plants also produce volatile chemicals. Essential oils, in general, have shown numerous beneficial effects for health maintenance and treatment of diseases. Essential oils from Curcuma spp., particularly C. longa, have demonstrated various health-related biological activities and several essential oil companies have recently marketed Curcuma oils. This review summarizes the volatile components of various Curcuma species, the biological activities of Curcuma essential oils, and potential safety concerns of Curcuma essential oils and their components.

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Chemical Composition and Biological Activities of Essential Oils of Curcuma Species.

Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.

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Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies.

Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10). Resequencing of Suvarna variety has generated 5 Gbases raw data with 75 bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with accession number SRR4042181. Reads were assembled using Cufflinks-2.2.1 tool which ended up with 42994 numbers of transcripts. The length of transcripts ranged from 83 to15565, with a N50 value 1216 and median transcript length 773. The transcripts were annotated through number of databases. For the first time transcriptome profiling of cultivar Suvarna has been done, which could help towards identification of single nucleotide polymorphisms (SNPs) between Suvarna and other turmeric cultivars for its authentic identification.

Transcriptome profiling of Curcuma longa L. cv. Suvarna

Eclipta prostrata (Linn.) (Family: Asteraceae) is an important Indian medicinal herb having myriad therapeutic potential. In the present study, the essential oil was extracted from the aerial parts...

Electron Ionization Based Detection of Volatile Constituents of Aerial Parts of Eclipta prostrata (Linn.) by One Dimensional Gas Chromatography and Mass Spectrometry

Objective: The aim of this investigation was to carry out the qualitative evaluation of selected high drug yielding elite genotypes of turmeric to add to their eliteness. Methods: 131 turmeric genotypes collected from 10 different agroclimatic zones were analysed for curcumin content. Leaves and rhizomes of these plants were collected for extraction of essential oil. Curcumin percentage of the sample was estimated according to the ASTA method. Essential oil was extracted by hydro-distillation of fresh leaves and rhizomes following the method of Guenther (1972). Initial screening of elite genotypes was done on the basis of curcumin content (≥5%), rhizome oil content (≥1.5%) and leaf oil content (≥0.5%). Selected elite genotypes were subjected to qualitative evaluation of essential oil through GC-MS analysis. Results: The five high rhizome oil yielding genotypes, TR1, TR2, TR3 and TR5 containing high rhizome oil yield of 2.1%, 1.7%, 1.6% and 1.5% respectively were considered to be elite clones containing tumerone as the major constituent of rhizome essential oil along with all desirable constituents. On the basis of leaf oil yield, genotypes TL1 and TL2 with 1.9% and 1.1% leaf oil were proved as elite clones with α–phellandrene as the major constituent along with other desirable constituents. GC-MS analysis of 3 selected high curcumin yielding genotypes TC1, TC2 and TC3 with curcumin content 7.3, 7.2 and 7.0% respectively revealed TC1 and TC2 as elite genotypes containing high quality rhizome and leaf oil. Conclusion: The present investigation reveals that eight genotypes of turmeric selected with high drug yield and high quality essential oil would have enough significance for boosting the production and export of value added products in the national and international market.

Gc-ms analysis of essential oil of some high drug yielding genotypes of turmeric (curcuma longa l.)

The antioxidant and antimicrobial activities of the essential oil and extract of Alpinia nigra (Gaertn.) Burtt (Zingiberaceae) were assessed in vitro. Besides total phenolic and flavonoid content o...

Phytoconstituents Analysis and Bioactivity Study of Alpinia nigra (Gaertn.) Burtt

Plant NBS-LRR R-genes recognizes several pathogen associated molecular patterns (PAMPs) and limit pathogen infection through a multifaceted defense response. CzR1, a coiled-coil-nucleotide-binding-site-leucine-rich repeat R-gene isolated from Curcuma zedoaria L exhibit constitutive resistance to different strains of P. aphanidermatum. Majority of the necrotrophic oomycetes are characterized by the presence of carbohydrate PAMPs β-glucans in their cell walls which intercat with R-genes. In the present study, we predicted the 3D (three dimensional) structure of CzR1 based on homology modeling using the homology module of Prime through the Maestro interface of Schrodinger package ver 2.5. The docking investigation of CzR1 with β-glucan using the Glide software suggests that six amino acid residues, Ser186, Glu187, Ser263, Asp264, Asp355 and Tyr425 act as catalytic residues and are involved in hydrogen bonding with ligand β-(1,3)-D-Glucan. The calculated distance between the carboxylic oxygen atoms of Glu187–Asp355 pair is well within the distance of 5A suggesting a positive glucanase activity of CzR1. Elucidation of these molecular characteristics will help in in silico screening and understanding the structural basis of ligand binding to CzR1 protein and pave new ways towards a broad spectrum rhizome rot resistance development in the cultivated turmeric.

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Molecular modeling and docking characterization of CzR1, a CC-NBS-LRR R-gene from Curcuma zedoaria Loeb. that confers resistance to Pythium aphanidermatum.

Basudeba Kar

Papers

Transcriptome profiling of Curcuma longa L. cv. Suvarna

Electron Ionization Based Detection of Volatile Constituents of Aerial Parts of Eclipta prostrata (Linn.) by One Dimensional Gas Chromatography and Mass Spectrometry

Gc-ms analysis of essential oil of some high drug yielding genotypes of turmeric (curcuma longa l.)

Phytoconstituents Analysis and Bioactivity Study of Alpinia nigra (Gaertn.) Burtt

Molecular modeling and docking characterization of CzR1, a CC-NBS-LRR R-gene from Curcuma zedoaria Loeb. that confers resistance to Pythium aphanidermatum.