• Proceedings of the Korean Society of Sericultural Science Conference
• /
• 2003.04a
• /
• pp.47-48
• /
• 2003

The development of cDNA microarray has permitted the analysis of thousands of genes simultaneously. cDNA microarray has been used to analyze gene expression profiles during developmental stage in both single and multicellular organisms. Two significant factors contributing to the limitation of the development of cDNA microarray in the Bombyx mori are the shortage of accessible repositories of cDNA clones and ESTs and the relative scarcity of facilities to produce microarrays and analyze the data generated. (omitted)

• KSBB Journal
• /
• v.26 no.2
• /
• pp.131-138
• /
• 2011

Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.

• Molecular & Cellular Toxicology
• /
• v.2 no.1
• /
• pp.60-66
• /
• 2006

Methylmercury (MeHg), one of the heavy metal compounds, can cause severe damage to the central nervous system in humans. Many reports have shown that MeHg is poisonous to human body through contaminated foods and has released into the environment. Despite many studies on the pathogenesis of MeHg-induced central neuropathy, no useful mechanism of toxicity has been established so far. This study, using of suppression subtractive hybridization (SSH) method, was peformed to identify differentially expressed genes by MeHg in SH-SY5Y human neuroblastoma cell line. We prepared to total RNA from SH-SY5Y cells treated with solvent (DMSO) and $6.25\;{\mu}M\;(IC_{50})$ MeHg and performed forward and reverse SSH. Differentially expressed cDNA clones were screened by dot blot, sequenced and confirmed that individual clones indeed represent differentially expressed genes with real time RT-PCR. These sequences were identified by BLAST homology search to known genes or expressed sequence tags (ESTs). Analysis of these sequences may provide an insight into the biological effects of MeHg in the pathogenesis of neurodegenerative disease and a possibility to develop more efficient and exact monitoring system of heavy metals as ubiquitous environmental pollutants.

• Journal of the Architectural Institute of Korea Structure & Construction
• /
• v.34 no.2
• /
• pp.67-74
• /
• 2018

Resource leveling minimizes resource fluctuations by deferring the earliest start times (ESTs) of non-critical activities within their corresponding total float. The intentional float-consumption for resource leveling purpose reduces the schedule delay contingency. This paper presents a method called Genetic Algorithm based Resource Leveling (GARL) that minimizes resource fluctuations and float-consumption impact over project duration. It identifies activities that are less sensitive to float-consumption and performs resource leveling using those activities. The study is of value to project scheduler because GARL identifies the set of activities to be deferred and the number of shift day(s) of each and every activities in the set within its total float expeditiously. It contributes to establish a baseline schedule which implements an optimal resource leveling plan. A case study is presented to verify the validity and usability of the method. It was confirmed that GARL satisfies the project duration constraint by considering resource fluctuations and float-consumption over project duration.

• Proceedings of the Korean Aquaculture Society Conference
• /
• 2003.10a
• /
• pp.44-44
• /
• 2003

Gene expression in five tissues of the abalone (Haliotis discus hannai) was investigated using an expressed sequence tag (EST) analysis. Randomly selected clones were obtained from cDNA libraries constructed with gill (GI), digestive diverticula(DD), hepatopancreas (HP), foot/mucus (FM) and rectangular muscle (RM). Of 1,235 clonesanalyzed (288 clones for GI, DD, HP each,166 for FM, and 205 for RM), 741 (60.0%) clones in total turned out to share significant similarity with the sequences from NCBI GenBank (less than 10/sup -3/ of e-values), 423 sequences showed poor similarity (> 10/sup -3/), and 71 sequences didn't match with any sequences in GenBank. The percent unique sequence (singleton) was ranged from 56.1% (RM) to 74.7% (FM) among libraries. On the other hand, overall percent singleton was 55.3% when all the ESTs from five libraries were assembled into contigs. Analysis of the organisms represented by the best hit for each EST (e-values < 10/sup -3/) showed that 23.8% matched with mammalian entries, 24.0% with mollusks, 14.4% with insects, 11.6% with fish and 26.2% with others. The expressed patterns differed among the tissues when judged by the categorization of the sequences from each library into 10 broad functional classes. In all the libraries, the class I (no hit o. poor similarity) was the largest category with an average of 40.1%. This largest class was followed by class V (general metabolisms) in DD (21.9%), GI (14.6%) and HP (16.7%), while the 'cell structure and motility'(class VI) was the second largest class in remaining two libraries (31.2% for RM and 9.6% for FM). The class IX (cell division and proliferation) was the smallest class in all the libraries (less than 3%). This report provides the first tissue-specific lists of expressed abalone genes, which could be a fundamental basis for genomics program of abalone species.

• Journal of Life Science
• /
• v.19 no.5
• /
• pp.587-592
• /
• 2009

A dramatic morphological change of embryos occurs at peri-implantation. Maternal and embryonic cross-talk during this period, initiated by signals from embryo(s), provides signals for maternal recognition of pregnancy and establishing and maintaining the pregnancy. However, the cellular, biochemical and genetic processes that direct embryo remodeling in mammalian species are not well studied or understood. In order to identify potential genes responsible for morphological change and cross-talk between embryo and uterus, an initial EST analysis was performed. A catalog of expressed genes (Transcriptome) from the d12 peri-implanting porcine embryos was constructed. Six clones were chosen from the initial ESTs for elucidation of their expression patterns during embryogenesis in early pregnancy. A number of these genes demonstrated unique expression profiles in a tissue, cell-type, and temporal fashion, indicating dynamic regulation of embryonic and endometrial gene expressions at different stages of pregnancy. Cross-talk between the embryo and endometrium of the pregnant uterus has provided a suitable micro-environment for the embryo's rapid and dramatic morphological changing process at the peri-implantation stage.

• Asian-Australasian Journal of Animal Sciences
• /
• v.23 no.1
• /
• pp.17-24
• /
• 2010

In the antral follicle phase, several layers of cumulus cells surround the oocyte and play an important support and regulation role in oocyte development and maturation via intercellular communications and interactions between oocytes and cumulus cells. However, information on stage specific gene expression in swine during the phase is not well understood. To investigate the function of cumulus cells during in vitro maturation of porcine oocytes and gene expression, suppression subtractive hybridization (SSH) was performed to screen genes that were differentially expressed between cumulus-oocyte complexes (COCs) and naked oocytes (NOs). Utilizing mRNAs from in vitro maturation oocytes, a SSH cDNA library from COCs as the tester and NOs as the driver was constructed. The SSH cDNA library was then screened using dot blot analysis. Results showed that a total of 70 clones randomly selected from the library were differentially expressed. Among these, 41 exhibited high homology to known genes and 11 were novel expressed sequences tags (ESTs). Four differentially expressed genes, including bfgf, sprouty 2, egr and btc, were further studied by real time quantitative PCR; results confirmed an increased expression of respective mRNA in COCs compared with NOs, which suggests that these factors may play an important role in oocyte development and maturation.

• BMB Reports
• /
• v.40 no.4
• /
• pp.501-510
• /
• 2007

Sex-related genes expressed in vitellogenic ovaries of the giant tiger shrimp, Penaeus monodon, were identified by an EST approach. A total of 1051 clones were unidirectionally sequenced from the 5 terminus. Nucleotide sequences of 743 EST (70.7%) significantly matched known genes previously deposited in the GenBank (E-value <$10^{-4}$) whereas 308 ESTs (29.3%) were regarded as newly unidentified transcripts (E-value >$10^{-4}$). A total of 559 transcripts (87 contigs and 472 singletons) were obtained. Thrombospondin (TSP) and peritrophin (79 and 87 clones accounting for 7.5 and 8.3% of clones sequenced, respectively) predominated among characterized transcripts. everal full length transcripts (e.g. cyclophilin, profillin and thioredoxin peroxidase) were also isolated. A gene homologue encoding chromobox protein (PMCBX, ORF of 567 nucleotides encoding a protein of 188 amino acids) which is recognized as a new member of the HP1 family was identified. Expression patterns of 14 of 25 sex-related gene homologues in ovaries and testes of P. monodon broodstock were examined by RT-PCR. Female sterile and ovarian lipoprotein receptor homologues were only expressed in ovaries whereas the remaining transcripts except disulfide isomerase related P5 precursor and adenine nucleotide translocator 2 were higher expressed in ovaries than testes of P. monodon broodstock. A homologue of ubiquitin specific proteinase 9, X chromosome (Usp9X) revealed a preferential expression level in ovaries than testes of broodstock-sized P. monodon (N = 13 and 11, P<0.05) but was only expressed in ovaries of 4-month-old shrimp (N = 5 for each sex).

• BMB Reports
• /
• v.43 no.2
• /
• pp.115-121
• /
• 2010

A large data set of Hanwoo (Korean cattle) ESTs was analyzed to obtain differential gene expression results for the following three libraries: intramuscular fat, longissimus dorsi muscle and liver. To better understand the gene expression profiles, we identified differentially expressed genes (DEGs) via digital gene expression analysis. Hierarchical clustering of genes was performed according to their relative abundance within the six separate groups (Hanwoo fat versus non-Hanwoo fat, Hanwoo muscle versus non-Hanwoo muscle and Hanwoo liver versus non-Hanwoo liver), producing detailed patterns of gene expression. We determined the quantitative traits associated with the highly expressed genes. We also provide the first list of putative regulatory elements associated with differential tissue expression in Hanwoo cattle. In addition, we conducted evolutionary analysis that suggests a subset of genes accelerated in the bovine lineage are strongly correlated with their expression in Hanwoo muscle.

• Development and Reproduction
• /
• v.17 no.3
• /
• pp.231-240
• /
• 2013

Olive flounder (Paralichthys olivaceus) is one of the commercial important flatfish species in Korea. The ocular signal transduction pathway is important in newly hatched flounders because it is closely involved in the initial feeding phase thus essential for survival during the juvenile period. However, the study of gene expression during ocular development is incomplete in olive flounder. Therefore we examined the expression analysis of specifically induced genes during the development of the visual system in newly hatched flounders. We searched ocular development-involved gene in the database of expressed sequence tags (ESTs) from olive flounder eye and this gene similar to arrestin with a partial sequence homology. Microscopic observation of retinal formation corresponded with the time of expression of the arrestin gene in the developmental stage. These results suggest that arrestin plays a vital role in the visual signal transduction pathway of the retina during ocular development. The expression of arrestin was strong in the ocular system during the entirety of the development stages. Our findings regarding arrestin have important implications with respect to its biological role and evolution of G-protein coupled receptor (GPCR) signaling in olive flounder. Further studies are required on the GPCR-mediated signaling pathway and to decipher the functional role of arrestin.