Hyoungseok Lee

Genetic association study of adiponectin polymorphisms with risk of Type 2 diabetes mellitus in Korean population

Aims  To investigate any association between Type 2 diabetes mellitus and two single nucleotide polymorphisms (SNPs) in the adiponectin gene, T45G and G276T, in the Korean population.

Transcriptomics and comparative analysis of three antarctic notothenioid fishes.

For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.

Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes

Next-generation sequencing has become the most widely used sequencing technology in genomics research, but it has inherent drawbacks when dealing with high-GC content genomes. Recently, single-molecule real-time sequencing technology (SMRT) was introduced as a third-generation sequencing strategy to compensate for this drawback. Here, we report that the unbiased and longer read length of SMRT sequencing markedly improved genome assembly with high GC content via gap filling and repeat resolution.

Characterization of four isolates of Bombyx mori nucleopolyhedrovirus.

Summary. Bombyx mori nucleopolyhedroviruses (BmNPVs), isolated from a sericultural Korean farm, were purified and characterized by their DNA restriction pattern, virus replication, polyhedra production and gene structures. The EcoR I and Sal I fragments showed similar overall patterns with minor difference but distinguishable patterns in each isolate. There was no significant difference in the virus replication pattern, yield of total polyhedra production and polyhedra morphology, but the yield of released polyhedra by BmNPV-K1 in Bm5 cells was 2 to 5 times higher than that of other isolates. In comparative studies of p10 gene, BmNPV-K1 and K3 had same structure and they encoded a protein consisting of 94 amino acids. Although BmNPV-K2 encoded the same length of amino acids with BmNPV-K1 and K3, it had different structure, and BmNPV-K4 had the p10 gene encoding 70 amino acids.

Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia antarctica Desv.

Background Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been researched as an important ecological marker and as an extremophile plant for studies on stress tolerance. Despite its importance, little genomic information is available for D. antarctica. Here, we report the complete chloroplast genome, transcriptome profiles of the coding/noncoding genes, and the posttranscriptional processing by RNA editing in the chloroplast system. Results The complete chloroplast genome of D. antarctica is 135,362 bp in length with a typical quadripartite structure, including the large (LSC: 79,881 bp) and small (SSC: 12,519 bp) single-copy regions, separated by a pair of identical inverted repeats (IR: 21,481 bp). It contains 114 unique genes, including 81 unique protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Sequence divergence analysis with other plastomes from the BEP clade of the grass family suggests a sister relationship between D. antarctica, Festuca arundinacea and Lolium perenne of the Poeae tribe, based on the whole plastome. In addition, we conducted high-resolution mapping of the chloroplast-derived transcripts. Thus, we created an expression profile for 81 protein-coding genes and identified ndhC, psbJ, rps19, psaJ, and psbA as the most highly expressed chloroplast genes. Small RNA-seq analysis identified 27 small noncoding RNAs of chloroplast origin that were preferentially located near the 5′- or 3′-ends of genes. We also found >30 RNA-editing sites in the D. antarctica chloroplast genome, with a dominance of C-to-U conversions. Conclusions We assembled and characterized the complete chloroplast genome sequence of D. antarctica and investigated the features of the plastid transcriptome. These data may contribute to a better understanding of the evolution of D. antarctica within the Poaceae family for use in molecular phylogenetic studies and may also help researchers understand the characteristics of the chloroplast transcriptome.

Cloning and Expression Analysis of 2-on-2 Hemoglobin from Soybean

Hemoglobins (Hbs) are heme proteins found in all five kingdoms of living organisms. In plants, three different classes of Hbs have been identified-nonsymbiotic Hbs from diverse species, symbiotic Hbs from nitrogen-fixing plants, and so-called 2-on-2 Hbs. Here, we report the cloning and expression analysis of the 2-on-2 Hb gene,GmGLB3, from soybean. TheGmGLB3 cDNA clone encodes a protein for 172 amino acid residues. Its deduced amino acid sequence shows the highest identity (74%) with 2-on-2 Hb fromMedicago truncatula. Multiple sequence alignment confirms the conserved and signature amino acid residues previously reported with plant 2-on-2 Hbs. Genomic Southern hybridization demonstrates thatGmGLB3 has two copies in the soybean genome. Based on our northern hybridization, theGmGLB3 gene is specifically expressed in root nodules, with levels increasing in the late stage during nodule development. Its transcript level is also increased under flooding and kinetin treatments in the roots, or under flooding and 2-iP treatments in the stems. However, no transcript is detected in the leaves regardless of treatment. Therefore, we propose that theGmGLB3 gene is specifically expressed in root nodules and that its expression in other plant organs is regulated by cytokinin and/or flooding.

Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been studied as an extremophile that has successfully adapted to marginal land with the harshest environment for terrestrial plants. However, limited genetic research has focused on this species due to the lack of genomic resources. Here, we present the first de novo assembly of its transcriptome by massive parallel sequencing and its expression profile using D. antarctica grown under various stress conditions. Total sequence reads generated by pyrosequencing were assembled into 60,765 unigenes (28,177 contigs and 32,588 singletons). A total of 29,173 unique protein-coding genes were identified based on sequence similarities to known proteins. The combined results from all three stress conditions indicated differential expression of 3,110 genes. Quantitative reverse transcription polymerase chain reaction showed that several well-known stress-responsive genes encoding late embryogenesis abundant protein, dehydrin 1, and ice recrystallization inhibition protein were induced dramatically and that genes encoding U-box-domain-containing protein, electron transfer flavoprotein-ubiquinone, and F-box-containing protein were induced by abiotic stressors in a manner conserved with other plant species. We identified more than 2,000 simple sequence repeats that can be developed as functional molecular markers. This dataset is the most comprehensive transcriptome resource currently available for D. antarctica and is therefore expected to be an important foundation for future genetic studies of grasses and extremophiles.

Isolation and Characterization of a Root Nodule-Specific Cysteine Proteinase cDNA from Soybean

We have determined that a nodule-specific cDNA clone (GmCysP1), obtained from a soybean root nodule-specific EST pool, encodes cysteine proteinase. Its amino acid sequence homology, as well as the conservation of typical motifs and amino acid residues involved in active site formation, shows that GmCysP1 can be classified as a legumain (C13) family cysteine proteinase, belonging to clan CD. Moreover, based on its expression patterns,GmCysP1 is a nodule-specific cysteine proteinase gene that is possibly associated with nodule development or senescence. Our genomic Southern analysis also suggests thatGmCysP1 is a member of a multigene family. Therefore, we propose that GmCysP1 is the first to be identified as a nodule-specific and senescence-related cysteine proteinase that belongs to the legumain family from soybean.

Estimation of antioxidant, antimicrobial activity and brine shrimp toxicity of plants collected from Oymyakon region of the Republic of Sakha (Yakutia), Russia

BackgroundSeveral plants are reported to be produced various biological active compounds. Lichens from the extreme environments such as high altitude, high UV, drought and cold are believed to be synthesized unique types of secondary metabolites than the other one. Several human pathogenic bacteria and fungi have been muted into drug resistant strains. Various synthetic antioxidant compounds have posed carcinogenic effects. This phenomenon needs further research for new effective drugs of natural origin. This manuscript aimed to screen new source of biological active compounds from plants of subarctic origin.ResultsA total of 114 plant species, including 80 species of higher plants, 19 species of lichens and 15 species of mosses, were collected from Oymyakon region of the Republic of Sakha (Yakutia), Russia (63˚20′N, 141˚42′E–63˚15′N, 142˚27′E). Antimicrobial, DPPH free radical scavenging and brine shrimp (Artemia salina) toxicity of all crude extract were evaluated. The obtained result was analyzed and compared with commercial standards. A total of 28 species of higher plants showed very strong antioxidant activity (DPPH IC50, 0.45-5.0 μg/mL), 13 species showed strong activity (DPPH IC50, 5-10 μg/mL), 22 species showed moderate antioxidant activity (DPPH IC50,10-20 μg/mL) and 17 species showed weak antioxidant activity (DPPH IC50 more than 20 μg/mL). Similarly, 3 species of lichen showed strong antioxidant activity, one species showed moderate and 15 species showed weak DPPH reducing activity. In addition, 4 species of mosses showed moderate antioxidant activity and 11 species showed weak antioxidant activity. Similarly, extracts of 51 species of higher plants showed antimicrobial (AM) activity against Staphylococcus aureus and 2 species showed AM activity against Candida albicans. Similarly, 11 species of lichen showed AM activity against S. aureus and 3 species showed AM activity against Escherichia coli. One species of moss showed AM activity against S. aureus. And finally, one species of higher plant Rheum compactum and one species of lichen Flavocetraria cucullata showed the toxicity against Brine shrimp larvae in 100 μg/mL of concentration.ConclusionThe experimental results showed that subarctic plant species could be potential sources of various biologically active natural compounds.

Reference genes validation for qPCR normalization in Deschampsia antarctica during abiotic stresses.

Abstract Quantitative real time PCR is the most sensitive and widely used method for the analysis of gene expression. The choice of one or several reference genes is very important for a normalization process, which should not fluctuate under stress conditions, to reduce error rate and bias during experimental procedure. In the present study, the expression stability of nine reference genes (two actins, two tubulins, two elongation factor 1α, two ubiquitins, and cyclophilin) during abiotic stresses such as cold, salt, and PEG treatments, was evaluated on Deschampsia antarctica plants using geNorm software. Results from various experimental conditions indicated that cyclophilin and elongation factor 1α were the most stable genes in the leaf and the root, respectively. The expression of the other reference genes varied under stress. The relative quantification of the TACR7 gene varied according to the kind and the number of reference genes used, suggesting the importance of considering the implications of a combination of reference genes under different stress conditions and in different tissues.