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

http://www.bio-nica.info/Biblioteca/Meudt2007AFLPApplicationAnalysis.pdf

Almost forgotten or latest practice? AFLP applications, analyses and advances.

MicroRNAs (miRNA) are approximately 21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.

/pdf/pmrd-plant-microrna-database-4lwfqwbvgf.pdf

PMRD: plant microRNA database

Natural protective glue protein, sericin bioengineered by silkworms: Potential for biomedical and biotechnological applications ☆

To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from mature leaves and developing roots, shoots, and inflorescences. Using a spatial clustering algorithm, we identified 36,780 genomic groups of small RNAs. Most consisted of 24-nt RNAs that are expressed in all four tissues and enriched in repeat regions of the genome; 1029 clusters were composed primarily of 21-nt small RNAs and, strikingly, 831 of these contained phased RNAs and were preferentially expressed in developing inflorescences. Thirty-eight of the 24-mer clusters were also phased and preferentially expressed in inflorescences. The phased 21-mer clusters derive from nonprotein coding, nonrepeat regions of the genome and are grouped together into superclusters containing 10-46 clusters. The majority of these 21-mer clusters (705/831) are flanked by a degenerate 22-nt motif that is offset by 12 nt from the main phase of the cluster. Small RNAs complementary to these flanking 22-nt motifs define a new miRNA family, which is conserved in maize and expressed in developing reproductive tissues in both plants. These results suggest that the biogenesis of phased inflorescence RNAs resembles that of tasiRNAs and raise the possibility that these novel small RNAs function in early reproductive development in rice and other monocots.

/pdf/clusters-and-superclusters-of-phased-small-rnas-in-the-ag9aiw40kl.pdf

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice.

Nineteen cashew accessions were analysed with 50 random primers, 12 ISSR primers and 6 AFLP primer pairs to compare the efficiency and utility of these techniques for detecting variation in cashew ...

Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India.

SummaryRandom amplified polymorphic DNA analysis was carried out in 29 Indian mango cultivars comprising popular landraces and some advanced cultivars. PCR amplification with 24 primers generated 314 bands, 91.4% of which were polymorphic. Jaccard’s similarity between pairs of cultivars ranged between 0.318 and 0.75 with a mean of 0.565. A UPGMA dendrogram showed the majority of the cultivars from northern and eastern regions of India clustering together and separate from southern and western cultivars. Analysis of molecular variance revealed that 94.7% of the genetic diversity in mango existed within regions. However, differences among regions were significant; northern and eastern regions formed one zone and western and southern regions formed another zone of mango diversity in India.

Analysis of genetic diversity of Indian mango cultivars using RAPD markers

We studied microsatellite frequency and distribution in 21.76-Mb random genomic sequences, 0.67-Mb BAC sequences from the Z chromosome, and 6.3-Mb EST sequences of Bombyx mori. We mined microsatellites of ≥15 bases of mononucleotide repeats and ≥5 repeat units of other classes of repeats. We estimated that microsatellites account for 0.31% of the genome of B. mori. Microsatellite tracts of A, AT, and ATT were the most abundant whereas their number drastically decreased as the length of the repeat motif increased. In general, tri- and hexanucleotide repeats were overrepresented in the transcribed sequences except TAA, GTA, and TGA, which were in excess in genomic sequences. The Z chromosome sequences contained shorter repeat types than the rest of the chromosomes in addition to a higher abundance of AT-rich repeats. Our results showed that base composition of the flanking sequence has an influence on the origin and evolution of microsatellites. Transitions/transversions were high in microsatellites of ESTs, whereas the genomic sequence had an equal number of substitutions and indels. The average heterozygosity value for 23 polymorphic microsatellite loci surveyed in 13 diverse silkmoth strains having 2–14 alleles was 0.54. Only 36 (18.2%) of 198 microsatellite loci were polymorphic between the two divergent silkworm populations and 10 (5%) loci revealed null alleles. The microsatellite map generated using these polymorphic markers resulted in 8 linkage groups. B. mori microsatellite loci were the most conserved in its immediate ancestor, B. mandarina, followed by the wild saturniid silkmoth, Antheraea assama.

/pdf/survey-and-analysis-of-microsatellites-in-the-silkworm-4ey9p6god1.pdf

Survey and analysis of microsatellites in the silkworm, Bombyx mori: frequency, distribution, mutations, marker potential and their conservation in heterologous species.

Microsatellite markers are employed for genotyping of Basmati varieties and assaying purity of market samples. However, employment of diverse electrophoresis techniques across laboratories has resulted in inconsistent allele sizes, creating doubts about the suitability of the assay. This study evaluated agarose gel electrophoresis, slab gel electrophoresis, and capillary electrophoresis techniques for their efficiency in the detection and quantification of adulteration in Basmati samples. Comparative analysis across 8 microsatellite loci in 12 rice varieties demonstrated that the capillary electrophoresis method showed less error (±0.73 bp) in the estimation of allele sizes compared to slab gel (±1.59 bp) and agarose gel (±8.03 bp) electrophoretic methods. Capillary electrophoresis showed greater reproducibility ( 3 bp) based methods. Capillary electrophoresis was significantly superior in quantification of the adulterant, with a mean error of ±3....

Capillary electrophoresis is essential for microsatellite marker based detection and quantification of adulteration of Basmati rice (Oryza sativa).

Indian cashew breeding programme has produced 24 selections and 11 hybrids with increased yield and excellent nut characters. Molecular profiles of these varieties were developed using a combination of five RAPD and four ISSR primers pre-selected for maximum discrimination and repeatability. A total of 94 markers were generated which discriminated all the varieties with a probability of identical match by chance of2.8 × 10-11. There was no correlation between the relationships based on molecular data and the pedigree of the varieties. Narrow range of average similarity values among major cashew breeding centres with only 3.6% of molecular variance partitioned between them was attributed to the exchange of genetic material in developing varieties. Difference in the average similarity coefficients between selections and hybrids was low indicating the need and scope for identification of more parental lines in enhancing the effectiveness of hybridisation programme.

Sunil Archak

Papers

Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India.

Analysis of genetic diversity of Indian mango cultivars using RAPD markers

Survey and analysis of microsatellites in the silkworm, Bombyx mori: frequency, distribution, mutations, marker potential and their conservation in heterologous species.

Capillary electrophoresis is essential for microsatellite marker based detection and quantification of adulteration of Basmati rice (Oryza sativa).

DNA fingerprinting of Indian cashew (Anacardium occidentale L.) varieties using RAPD and ISSR techniques