• Journal of KIISE:Computer Systems and Theory
• /
• v.29 no.7
• /
• pp.411-421
• /
• 2002

In this Paper we propose a new Image analysis algorithm for microarray processing and a method to locate the position of the grid cell using the topology of the grid spots. Microarray is a device which enables a parallel experiment of 10 to 100 thousands of test genes in order to measure the gene expression. Because of the huge data obtained by a experiment automated image analysis is needed. The final output of this microarray experiment is a set of 16-bit gray level image files which consist of grid-structured spots. In this paper we propose one algorithm which located the address of spots (spot indices) using graph structure from image data and a method which determines the precise location and shape of each spot by measuring the inclination of grid structure. Several experiments are given from real data sets.

• Journal of Pharmaceutical Investigation
• /
• v.34 no.4
• /
• pp.263-267
• /
• 2004

Branched and linear polyethylenimines (PEIs) have been studied as efficient and versatile agents for gene delivery in vitro and in vivo. PEIs exist in a linear or branched topology and are available in a wide range of molecular weight (Mw). Most studies have been done using PEIs with Mw higher than 10Kd. This study was aimed to test the transfection efficiency and the cell viability following gene delivery using PEI of Mw 2Kd, a relatively lower Mw cationic polymer. We used murine interleukin-2(mIL-2) plasmid DNA complexed with branched PEI 2Kd or 25Kd, and transfected them into a myoblast muscle cell line, C2C12. The cellular uptake of mIL-2 plasmid DNA was determined using quantitative polymerase chain reaction. RNA transcript levels were studied in the myoblast cells. Our results show that PEI 2Kd was as effective as PEI 25Kd in celluar gene delivery and transfection efficiency in C2C12 cells. Moreover, MTT assay indicated that PEI 2Kd/DNA complexes did not significantly reduce the cell viability regardless of N/P ratios. These results suggest that PEI of Mw 2Kd might play a role as effective and low toxic nonviral vector systems for muscular cell lines.

• Journal of Microbiology
• /
• v.33 no.2
• /
• pp.136-141
• /
• 1995

From a cluster of structural rRNA genes which has previsouly been cloned (Hwang and Kim, in submission; J. Microbiol. Biotechnol.), a 1.0-kb Eco RI fragment of DNA which shows significant homology to the 25S and rRNA s of Tricholoma matsutake was used for sequence analysis. Nucleotide sequence was bidirectionally determined using delection series of the DNA fragment. Comparing the resultant 1016-base sequence with sequences in the database, both the 3'end of 25S-rRNA gene and 5S rRNA gene were searched. The 5S rRNA gene is 118-bp in length and is located 158-bp downstream of 3'end of the 25S rRNA gene. IGSI and IGS2 (partial) sequences are also contained in the fragment. Multiple alignment of the 5S rRNA sequences was carried out with 5S rRNA sequences from some members of the subdivision Basidiomycotina obtained from the database. Polygenetic analysis with distance matrix established by Kimura's 2-parameter method and phylogenetic tree by UPGMA method proposed that T. matsutake is closely related to efibulobasidium allbescens. Secondary structure of 5S rRNA was also hypothesized to show similar topology with its generally accepted eukaryotic counterpart.

• Journal of the Korean Magnetic Resonance Society
• /
• v.17 no.1
• /
• pp.59-66
• /
• 2013

BldD, a developmental transcription factor from Streptomyces coelicolor, is a homodimeric, DNA-binding protein with 167 amino acids in each subunit. Each monomer consists of two structurally distinct domains, the N-terminal domain (BldD-NTD) responsible for DNA-binding and dimerization and the C-terminal domain (BldD-CTD). In contrast to the BldD-NTD, of which crystal structure has been solved, the BldD-CTD has been characterized neither in structure nor in function. Thus, in terms of structural genomics, structural study of the BldD-CTD has been conducted in solution, and in the present work, mainchain NMR assignments of the recombinant BldD-CTD (residues 80-167 of BldD) could be achieved by a series of heteronuclear multidimensional NMR experiments on a [$^{13}C/^{15}N$]-enriched protein sample. Finally, the secondary structure prediction by CSI and TALOS+ analysis using the assigned chemical shifts data identified a ${\beta}-{\alpha}-{\alpha}-{\beta}-{\alpha}-{\alpha}-{\alpha}$ topology of the domain. The results will provide the most fundamental data for more detailed approach to the atomic structure of the BldD-CTD, which would be essential for entire understanding of the molecular function of BldD.

• Fisheries and Aquatic Sciences
• /
• v.18 no.2
• /
• pp.173-181
• /
• 2015

We identified the $Na^+-K^+-2Cl^-$ cotransporter 2 (NKCC2) cDNA isoform from starry flounder, Platichthys stellate. The NKCC2 cDNA encoded a polypeptide of 1,043 amino acids representing 12 putative transmembrane domains based on the bioinformatic topology prediction. In addition, starry flounder NKCC2 possessed highly conserved residues within transmembrane domain 4, known as an essential site for its function. End-point reverse transcription-polymerase chain reaction analysis revealed that the NKCC2 transcript was moderately expressed only in the anterior and posterior intestines and the rectum. The NKCC2 mRNA level in the rectum, but not in other segments, was significantly induced 3 days post Streptococcus parauberis challenge, indicating that excess salt may be transported into the rectum. Taken together, our data indicate that an S. parauberis infection could tip the intestinal fluid balance in favor of fluid accumulation, indicating that bacterial pathogens can interfere with intestinal osmotic balance and normal mucosal immune homeostasis.

• Korean Journal of Plant Resources
• /
• v.24 no.4
• /
• pp.358-369
• /
• 2011

The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from genus Chrysosplenium were sequenced to address phylogenetic relationship. ITS including 5.8S sequence varied in length from 647 bp to 653 bp. Among them, 219 sites were variable sites with parsimony-informative. The aligned sequences were analyzed by maximum parsimony (MP) and neighbor-joining (NJ) methods. In the strict consensus trees of parsimony analysis, the monophyly of Chrysosplenium was supported by 100% bootstrap value. The first clade, C. pseudofauriei was at the basal position of the genus, and others formed two clades with high bootstrap support. The second clade included Ser. Pilosa and Ser. Oppositifolia and third clade included Ser. Alternifolia and Ser. Flagellifera. The NJ trees showed essentially the same topology. Finally, DNA sequences of ITS regions were useful phylogenetic marker in this genus. Based on the ITS and ridge seed morphological results, C. sphaerospermum Maxim. and C. valdepilosum (Ohwi) S.H. Kang & J.W. Han were discussed their scientific names and taxonomic positions.

• Proceedings of the Korean Biophysical Society Conference
• /
• 1996.07a
• /
• pp.11-11
• /
• 1996

The three-dimensional structure of the carboxyl-terminal domain of the E.coli RNA polymerase $\alpha$ subunit, which is regarded as the contact site for transcription activator proteins and the promoter UP element, was determined by NMR spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. (omitted)

• Asian-Australasian Journal of Animal Sciences
• /
• v.19 no.10
• /
• pp.1369-1378
• /
• 2006

This is the first study in which genetic variability and relationships of a large number of Japanese chicken breeds were revealed along with those of several foreign breeds by using microsatellite DNA polymorphisms. Twenty-eight breeds (34 populations) of native Japanese chickens and seven foreign breeds or varieties were analyzed. The mean number of alleles per locus, the proportion of the polymorphic loci, and the expected average heterozygosity ranged from 1.75 to 4.70, from 0.55 to 1.00, and from 0.21 to 0.67, respectively. Microsatellite alleles being unique to a particular population were detected in some populations. The $D_A$ genetic distance between populations was obtained from allele frequency for every pair of the populations to construct a neighbor-joining tree. According to the phylogenetic tree, excluding a few exceptions, native Japanese chicken breeds and foreign breeds were clearly separated from each other. Furthermore, the tree topology divided native Japanese chickens into four main classes, which was almost in accordance with the classification based on body morphology; that is, (1) Cochin type, (2) Malay type, (3) layer type, and (4) intermediate type between Malay and layer types. This is the first finding for native Japanese chickens.

• Korean Journal of Ichthyology
• /
• v.27 no.3
• /
• pp.165-182
• /
• 2015

The snailfishes (Scorpaenoidei: Liparidae) is a large group requiring taxonomic reviews because of a potential taxonomic confusion due to its great similarity in external morphology between species and a variation of its body color with size. Molecular phylogeny and taxonomic review were conducted for 10 species in 3 genera reported around the Korean waters, which facilitate understanding interrelationship within its family, and further management of fisheries resources. Molecular phylogeny using mitochondrial COI (mtCOI) and nuclear RAG2 (nRAG2) sequences indicates that the reciprocal monophyly of the three genera (Careproctus, Crystallichthys, and Liparis) were supported except Crystallichthys matsushimae, being closely related to Careproctus notosaikaiensis in only mtDNA COI topology. Liparis ingens Gilbert and Burke (1912) was reported as a distinct species differing from L. ochotensis. However, in the present study, comparing L. ingens from Korea with L. ochotensis from Japan and Russia, the two species were well corresponded in their morphology and molecule, therefore, we suggest L. ingens to be treated as a junior synonym of L. ochotensis.

• Journal of Life Science
• /
• v.23 no.7
• /
• pp.847-853
• /
• 2013

The genus Hemerocallis (family Xanthorthoeaceae) is a herbaceous species, some of which are very important in herbal medicines. We evaluated the rps16-trnK region of the chloroplast DNA of a representative sample of eight taxa in Korea to estimate phylogenetic relationships within the taxa of this genus. Due to differences in the number of inserted nucleotides, the aligned data for Hemerocallis ranged from 729 (H. aurantiaca) to 742 nucleotides (H. fulva var. kwanso), with a mean of 736. Although several small indels and 20 inserts were present, sequence variation within the Hemerocallis genus was mostly due to nucleotide substitutions. All rps16-trnK trees generated in Korea exhibited a well-solved topology, with high bootstrap support, irrespective of the methods (parsimony) and the setting used. The node of H. minor and H. littorea was strongly supported, with a high bootstrap value in three trees, and these two taxa were sistered with H. thunbergii. The number of chromosomes was not congruent with that found in a previous study with RAPD, but the number was in agreement with the results of this study.