• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2000.11a
• /
• pp.21-22
• /
• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.

• International Journal of Concrete Structures and Materials
• /
• v.18 no.3E
• /
• pp.173-181
• /
• 2006

The objectives of this study are to evaluate the reliability of an existing nonlinear analysis program for predicting the inelastic behavior of reinforced concrete frame with seismic details and to observe the redistribution of the internal forces, which can not be easily measured by an experiment. In order to carry out this task, the nonlinear analysis program of IDARC 2D(3) was run on a 2-bay, 2-story moment-resisting reinforced concrete plane frame with seismic details. (1) The effort to obtain the results of the analysis similar to those of experiment was made by determining the appropriate values of model parameters. The comparison of the analysis results with those of experiment and the observation of the distribution of internal forces obtained through nonlinear analysis points to the following conclusions. (1) The overall relationship between lateral load and lateral displacement given by the analysis is similar to that of experiment. However, the values of initial stiffness and the amount of energy dissipation in the initial displacement steps given by the analysis show larger values than those of experiment. (2) The analysis provided detailed information on the distribution and redistribution of internal forces and proved useful in elucidating the crack pattern, the sequence of the occurrence of plastic hinges, and the failure or yielding mechanism for the whole structure. (3) In spite of the similarity in overall behavior of analysis and experiment, there exists a significant discrepancy in some local behaviors. Furthermore, the hysteresis in the relationship between moment and curvature in some column ends have shown sudden deteriorations in strength, which can not be interpreted satisfactorily at the present time. Therefore, it is necessary to develop a better analytical model to fill this knowledge gap.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.55 no.2
• /
• pp.151-158
• /
• 2010

Camelina sativa L., known as popular names "gold-of-pleasure" or "false flax" is an alternative oilseed crop that can be grown under different climatic and soil conditions. Up to date, however, the genomic information of Camelina has not been studied in detail. Therefore, a cDNA library was constructed and characterized from young leaves. The constructed cDNA library incorporated of 1334 cDNA clones and the size of the insertion fragments average was 736 base pair. We generated a total of 1269 high-quality expressed sequence tags (ESTs) sequences. The result of cluster analysis of EST sequences showed that the number of unigene was 851. According to subsequent analysis, the 476 (55.9%) unigenes were highly homologous to known function genes and the other 375 (44.1%) unigenes were unknown. Remaining 63 (7.4%) unigenes had no homology with any other peptide in NCBI database, indicating that these seemed to be novel genes expressed in leaves of Camelina. The database-matched ESTs were further classified into 17 categories according to their functional annotation. The most abundant of categories were "protein with binding function or cofactor requirement (27%)", "metabolism (11%)", "subcellular localization (11%)", "cellular transport, transport facilities and transport routes (7%)", "energy (6%)", "regulation of metabolism and protein function (6%)". Our result in this study provides an overview of mRNA expression profile and a basal genetic information of Camelina as an oilseed crop.

• BMB Reports
• /
• v.31 no.4
• /
• pp.364-369
• /
• 1998

Insect plasma protein is abundant in the hemolymph of holometabolous insect larvae and is used as a source of amino acids and energy for construction of adult structures during metamorphosis. In order to understand the mechanism of decomposition of larval plasma proteins by hemocyte protease, we tried to purify a cysteine protease from the hemocyte lysate by using Carbobenzoxy-L-Phenylalanyl-L-Arginine-4-Methyl-Coumaryl-7-Amide (Z-Phe-Arg-MCA) as substrate and to identify plasma proteins that are selectively susceptible to the purified protease. Here, we describe the purification and characterization of a cysteine protease that specifically hydrolyzes the plasma protein of the coleopteran insect, Tenebrio molitor, larvae. The molecular mass of this enzyme was 25 kDa, as determined by SDS-PAGE under reducing conditions. The amino acids sequence of its $NH_{2}-terminus$ was determined to be Leu-Pro-Gly-Gln-Ile-Asp-Trp-Arg-Asp-Lys-Gly. This sequence contained Pro, Asp, and Arg residues, conserved in many papain superfamily enzymes. The specific cysteine protease inhibitors, such as E-64 and leupetin, inhibited its hydrolytic activity. One plasma protein with a molecular mass of 48 kDa was selectively hydrolyzed within 3 h when the purified enzyme and plasma proteins were incubated in vitro. However, the 48 kDa protein was not hydrolyzed by the purified 25 kDa protease in the presence of E-64. Western blotting analysis at various developmental stages showed that the purified enzyme was detected at larvae, pupae, and adult stages, but not the embryo stage.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.6
• /
• pp.771-780
• /
• 2014

A putative lipolytic enzyme gene, named as est9x, was obtained from a marine microbial metagenome of the South China Sea. Sequence analysis showed that Est9X shares lower than 27% sequence identities with the characterized lipolytic enzymes, but possesses a catalytic triad highly conserved in lipolytic enzymes of the ${\alpha}/{\beta}$ hydrolase superfamily. By phylogenetic tree construction, Est9X was grouped into a new lipase/esterase family. To understand Est9X protein in depth, it was recombinantly expressed, purified, and biochemically characterized. Within potential hydrolytic activities, only lipase/esterase activity was detected for Est9X, confirming its identity as a lipolytic enzyme. When using p-nitrophenol esters with varying lengths of fatty acid as substrates, Est9X exhibited the highest activity to the C2 substrate, indicating it is an esterase. The optimal activity of Est9X occurred at a temperature of $65^{\cric}C$, and Est9X was pretty stable below the optimum temperature. Distinguished from other salt-tolerant esterases, Est9X's activity was tolerant to and even promoted by as high as 4 M NaCl. Our results imply that Est9X is a unique esterase and could be a potential candidate for industrial application under extreme conditions.

• Journal of Sericultural and Entomological Science
• /
• v.38 no.1
• /
• pp.13-18
• /
• 1996

To secure the genetic resources of silkworm, Bomyx mori, the cDNA library was constructed with mRNA isolated from fifth instar larvae. Titer of the cDNA library was about 1.3 X 106 plaques in total. We presumed that the titer covered all transcripts existed in Bombyx mori. Meanwhile, it is knowen that partial cDNA sequences, Expressed Sequence Tags(ESTs), have a good value for the discovery of novel genes and the elucidation of their structures. For this purpose, partial cDNA sequencing was carried out from randomly selected cDNA clones in the library. Partial cDNA sequences of 37 clones were determined and an average of 212 nucleotides of sequence can be read from the clone. The ESTs were searched in GenBAnk database and fifteen ESTs showed significant similarities to enlisted sequences. They included the genes of storage protein, heat shock protein, actin, catalase and so forth. We presumed that the 22 unmatched ESTs were novel genes.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.2
• /
• pp.256-263
• /
• 2006

In the model legume Medicago truncatula, two mutants, sickle and sunn, exhibit morphologically and genetically distinct hypernodulation phenotypes. However, efforts to isolate the single recessive and single semidominant genes for sickle and sunn, respectively, by map-based cloning have so far been unsuccessful, partly due to the absence of clones that enable walks from linked marker positions. To help resolve these difficulties, a new bacterial artificial chromosome (BAC) library was constructed using BamHI-digested genomic fragments. A total of 23,808 clones were collected from ligation mixtures prepared with double-size-selected high-molecular-weight DNA. The average insert size was 116 kb based on an analysis of 88 randomly selected clones using NotI digestion and pulsed-field gel electrophoresis. About 18.5% of the library clones lacked inserts. The frequency of the BAC clones carrying chloroplast or mitochondrial DNA was 0.98% and 0.03%, respectively. The library represented approximately 4.9 haploid M. truncatula genomes. Hybridization of the BAC clone filters with a $C_{0}t-l$ DNA probe revealed that approximately 37% of the clones likely carried repetitive sequence-enriched DNA. An ordered array of pooled BAC DNA was screened by polymerase chain reactions using 13 sequence-characterized molecular markers that belonged to the eight linkage groups. Except for two markers, one to five positive BAC clones were obtained per marker. Accordingly, the sickle- and sunn-linked BAC clones identified herein will be useful for the isolation of these biotechnologically important genes. The new library will also provide clones that fill the gaps between preexisting BAC contigs, facilitating the physical mapping and genome sequencing of M. truncatula.

• Journal of the Korea institute for structural maintenance and inspection
• /
• v.21 no.1
• /
• pp.40-48
• /
• 2017

RC flat plates may be governed by a serviceability as well as a strength condition, and a construction sequence and its impact on the distributions of gravity loads among slabs tied by shores are decisive factors influencing short and long term behaviors of flat plate. Over-loading and tensile cracking in early-aged slabs significantly increase the deflection of a flat plate system under construction, and a reshoring work may be helpful in reducing slab deflections by controlling the vertical distributions of loads in a multi-shored flat plate system. In this study, a effect of reshoring works on short and long term deflections of flat plate systems are analyzed. The slab construction loads with various reshoring schemes and slab design and construction conditions are defined by a simplified method, and the practical calculation of slab deflections with considering construction sequences and concrete cracking and long term effects is applied. From parametric studies, the reshoring works are verified to reduce slab deflections, and the optimized conditions for the reshoring works and slab design and constructions are discussed.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.17 no.3
• /
• pp.677-683
• /
• 2016

In urban areas, underground tunnel construction sites have spread widely to accommodate rapidly increasing traffic volume along with a high-degree economic growth. Earth tunneling might be adapted frequently for the underground space securing, and various tunneling methods have been developed to stabilize the tunnel face and crown. Among them, the DSM (divided shield method) is gaining popularity for its enhanced stability and construction efficiency. This method has its foundation from the Messer Shield method, which is one of the trenchless special tunneling methods. This study examined the effects of face reinforcement on construction the sequence through a large scale soil chamber test and numerical analyses. The chamber has a size of a 1/2 scale of the real tunnel. Surface settlements were measured according the tunneling process. Commercially available software, MIDAS GTS, was used for numerical analysis and its result was compared with the values obtained from the chamber test. The results of the study show that both settlements of the embanked soils and the stress of the tunnel girder are located within the safe criteria. Overall, this study provides basic data and the potential of using a reinforced tunnel face to enhance DSM applications.

• Journal of Korean Society of Steel Construction
• /
• v.29 no.1
• /
• pp.49-60
• /
• 2017

As well as the strength check, fatigue life check is also mainly required for designing mooring lines of the floating structures. In general, forces which induce dynamic structural response significantly affect to fatigue design of the mooring lines. So, waves are mainly considered as the governing loading for fatigue design of the mooring lines. In this study, characteristics of the fatigue damage of the mooring lines for submerged floating tunnels (SFT) under irregular waves are investigated. For this study time domain hydrodynamic analysis is used to obtain motion of the tunnel and tension and stresses of the mooring lines under the specific environmental conditions. Also, the Rainflow-counting method, the Palmgren-Miner's rule, and S-N curves for floating offshore structures presented by DNV recommendation is applied to calculate the fatigue damage due to the fluctuating stresses. Referring to the design plactice of the tendon pipes for TLP (tension-leg platform), which is very similar structural system to SFT, it is assumed that a 100 year return period wave attacks the SFT systems during 48 hours and the fatigue damages due to the environmental loading are calculated. Following the analysis sequence, the effects of the tunnel draft, spacing and initial inclination angle of the mooring lines on the fatigue damage under the specific environmental loadings are investigated.