• Journal of Dairy Science and Biotechnology
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• v.40 no.2
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• pp.86-91
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• 2022

Chryseobacterium mulctrae KACC 21234^T is a novel species isolated from raw bovine milk. Psychrotrophic bacteria are considered contaminants and are hypothesized to originate from the environment. In this investigation, the C. mulctrae KACC 21234^T genome was determined to be 4,868,651 bp long and assembled into four contigs with a G+C ratio of 33.8%. In silico genomic analyses revealed the presence of genes encoding proteases (endopeptidase Clp, oligopeptidase b, carboxypeptidase) and lipases (phospholipase A(2), phospholipase C, acylglycerol lipase) that can catalyze the degradation of the proteins and lipids in milk, causing its quality to deteriorate. Additionally, antimicrobial resistance and putative bacteriocin genes were detected, potentially intensifying the pathogenicity of the strain. The genomic evidence presented highlights the need for improved screening protocols to minimize the potential contamination of milk by proteolytic and lipolytic psychrotrophic bacteria.

• The Korean Journal of Pharmacology
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• v.24 no.1
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• pp.1-10
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• 1988

To obtain information about the structure of the human phenylethanolamin N-methyltransferase (PNMT) and to further define the extent of the evolutionary relationships among PNMT molecules of several spesies, a full length cDNA clone for bovine adrenal PNMT was used to screen a charon 4A genomic library. One phage was isolated and identified, which included the entire PNMT gene. The length of inserted genomic DNA was 13.1-Kilobase (Kb) containing two internal EcoRI sites. Construction of a restriction map and subsequent Southern and dot blot analysis with 5'-and3'-specific cDNA probes allowed the identification of exon-containing fragments. This is the first report of the cloning of gene for human epinephrine synthesizing enzyme.

• Korean Journal Plant Pathology
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• v.11 no.3
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• pp.271-277
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• 1995

The RNA nucleotide sequences of the 3/-noncoding regions (3'-NCRs) of two Korean strains of turnip mosaic virus (TuMV), Ca and cqs, have been determined from their cDNA clones that encompassed the 3'-terminal regions of the viral genomic RNAs. The 3'-NCRs of both strains were 209 nucleotides long, terminated with GAC residues and poly (A) tails. The potential polyadenylational signal motif, UAUGU, was located 140 nucleotides upstream from the poly (A) tail in each of the virus. A highly conserved hexanucleotide sequence [A G U G A/U G/C], which was common in the 3'-NCRs of the potyvirus RNAs, was also found at the regions of 119 bases upstream from the 3'-end. Comparison of the 3'-NCRs of the two Korean isolates with those of four strains from Canada, China and Japan showed significantly identical genotypes (94.3∼99.5%). The secondary structure of three loops with long stems was found within the 3'-NCRs by sequence analysis. The substituted bases in the region among the six TuMV strains did not alter their secondary structures. Length of the 3'-NCRs of the know 11 potyviral RNAs and TuMV RNAs was different from one another and their nucleotide sequences showed 55.7% to 24.0% of homology. The 3'-NCR, therefore, is considered to be useful for phylogenetic studies in potyviruses.

• Korean journal of applied entomology
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• v.46 no.1 s.145
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• pp.169-173
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• 2007

Root-knot nematode damage was found on yam, Dioscorea bulbifera in Andong Korea. From the root-knots, female nematodes were isolated and subjected to DNA sequence analysis. Sequence of cytochrome oxidase subunit II (COII) was analyzed from the genomic DNA of the isolate. COII locus size and sequence of the nematode isolate were similar to those of Meloidogyne javanica or M. incognita. However, an analysis of HinfI restriction site, a species-specific character between these two species, showed that the isolate did not match to either M. javanica or M. incognita.

• Korean Journal of Medicinal Crop Science
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• v.12 no.2
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• pp.154-162
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• 2004

Hairy roots were induced from Korean ginseng (Panax ginseng C. A. Meyer) root explants and studied for their gene expression. A total of 3,000 ESTs (expressed sequence tags) from ginseng hairy root were determined and about 2,700 ESTs have a length of readable sequence, which result in 1,352 unique ESTs sequences. The 879 ESTs showed significant similarities to known nucleotide or amino acid sequences in other plant species, which were divided into eleven categories depending upon gene function. The remaining 473 sequences showed no significant matches, which are likely to be transcripts or to be matched to other organisms. The results indicated that the analysis of the ginseng hairy root ESTs by partial sequencing of random cDNA clones may be an efficient approach to isolate genes that are functional in ginseng root in a large scale. Our extensive EST analysis of genes expressed in ginseng hairy root not only contributes to the understanding of the dynamics of genome expression patterns in root organ but also adds data to the repertoire of all genomic genes.

• Journal of Photoscience
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• v.7 no.2
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• pp.73-78
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• 2000

To analyze molecular traits determining pigmentation between Pharbitis nill violet and white, Amplified Fragment Length Polymorphism(AFLP) and Differential Display Reverse Transcription(DDRT) experiments were carried out with either genomic DNAs or total RNAs isolated from both plants. Results of AFLP experiment in combination of 8 EcoRⅠ primers with 6 MseⅠ primers showed 41 violet-and 60 white-specific DNA bands. In the subsequent experiment, 22 violet-and 22 white-specific DNA fragments were amplified by PCR with DNAs eluted. The sizes of the fragments range from 200 to 600bp. DDRT using total RNA produced 19 violet-and 17 white-specific cDNA fragments, ranging from 200 to 600bp. The fragments obtained by both AFLP and DDRT had been cloned into pGEM T-easy vector, amplified and subjected to the nucleotide sequence analyses. As a result of Blast sequence analysis, most of them sequenced up to date showed no similarity to any Known gene, while few has similarity to known animal or plant genes. An AFLP clone V6, for example, has a strong sequence similarity to the human transcription factor LZIP-alpha mRNA and a DDRT clone W19 to Solanum tuberosum 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA.

• Journal of fish pathology
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• v.19 no.3
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• pp.227-233
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• 2006

Olive flounder immunoreceptor DAP10 homologue cDNA was cloned from a peripheral blood lymphocytes (PBLs) cDNA library. The length of the olive flounder DAP10 cDNA is 473bp and it contains an open reading frame of 234bp. The predicted polypeptide sequence is 78 amino acids, consisting of a 22-amino acid leader, an 11-amino acid extracellular domain, a 21-amino acid transmembrane segment, and a 24-amino acid cytoplasmic domain. The amino acid sequence of olive flounder DAP10 has 56%, 50%, 32%, 31%, and 31% sequence identity with zebrafish DAP10, catfish DAP10, cattle DAP10, rat DAP10 and Monkey DAP10, respectively. Olive flounder DAP10 has a conserved aspartic acid in the transmembrane domain and a phophatidylinositol-3 kinase-binding site (YxxM/V) in the cytoplasmic region. Genomic organization reveals that olive flounder DAP10 comprises five exons and four introns. A phylogenetic analysis based on the deduced amino acid sequence grouped the olive flounder DAP10 with other species DAP10. In RT-PCR analysis, DAP10 transcripts were detected predominantly in PBLs, kidney, spleen and intestine.

• Journal of Marine Life Science
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• v.6 no.1
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• pp.38-46
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• 2021

The blood clam, Tegillarca granosa, is economically important in marine bivalve and is used in fisheries industry among western Pacific Ocean Coasts especially in Korea, China, and Japan. The number of chromosomes in the blood clam is known as 2n=38, but the genome size and genetic information of the genome are not still clear. In order to predict the genomic size of the T. granosa, the in-silico analysis analysed the genomic size using short DNA sequence information obtained using the NGS Illumina HiSeq platform. As a result, the genomic size of T. granosa was estimated to be 770.61 Mb. Subsequently, a draft genome assembly was performed through the MaSuRCA assembler, and a simple sequence repeat (SSR) analysis was done by using the QDD pipeline. 43,944 SSRs were detected from the genome of T. granosa and 69.51% di-nucleotide, 16.68% trinucleotide, 12.96% tetra-nucleotide, 0.82% penta-nucleotide, and 0.03% hexa-nucleotide were consisted. 100 primer sets that could be used for genetic diversity studies were selected. In the future, this study will help identify the genetic diversity of T. granosa and population genetic studies, and further identify the classification of origin between homogenous groups.

• Journal of Internet Computing and Services
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• v.5 no.5
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• pp.1-15
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• 2004

In this paper, we explain the design and implementation of GWB(Gene WorkBench), which is a web-based, integrated system for efficiently managing and analyzing genomic sequences, Most existing software systems handling genomic sequences rarely provide both managing facilities and analyzing facilities. The analysis programs also tend to be unit programs that include just single or some part of the required functions. Moreover, these programs are widely distributed over Internet and require different execution environments. As lots of manual and conversion works are required for using these programs together, many life science researchers suffer great inconveniences. in order to overcome the problems of existing systems and provide a more convenient one for helping genomic researches in effective ways, this paper integrates both managing facilities and analyzing facilities into a single system called GWB. Most important issues regarding the design of GWB are how to integrate many different analysis programs into a single software system, and how to provide data or databases of different formats required to run these programs. In order to address these issues, GWB integrates different analysis programs byusing common input/output interfaces called wrappers, suggests a common format of genomic sequence data, organizes local databases consisting of a relational database and an indexed sequential file, and provides facilities for converting data among several well-known different formats and exporting local databases into XML files.

• Bulletin of the Korean Chemical Society
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• v.27 no.5
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• pp.699-704
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• 2006

Escherichia coli RNase P is a ribonucleoprotein composed of M1 RNA and C5 protein. Previously, analysis of RNA aptamers selected for C5 protein from a synthetic RNA library showed that C5 protein could bind various RNA molecules as an RNA binding protein. In this study, we searched cellular RNA motifs that could be recognized by C5 protein by a genomic SELEX approach. We found various C5 protein-binding RNA motifs derived from E. coli genomic sequences. Our results suggest that C5 protein interacts with various cellular RNA species in addition to M1 RNA.