• Genomics & Informatics
• /
• v.16 no.4
• /
• pp.30.1-30.6
• /
• 2018

There is urgent need for effective and cost-efficient data storage, as the worldwide requirement for data storage is rapidly growing. DNA has introduced a new tool for storing digital information. Recent studies have successfully stored digital information, such as text and gif animation. Previous studies tackled technical hurdles due to errors from DNA synthesis and sequencing. Studies also have focused on a strategy that makes use of 100-150-bp read sizes in both synthesis and sequencing. In this paper, we a suggest novel data encoding/decoding scheme that makes use of long-read DNA (~1,000 bp). This enables accurate recovery of stored digital information with a smaller number of reads than the previous approach. Also, this approach reduces sequencing time.

• Korean Journal of Microbiology
• /
• v.30 no.1
• /
• pp.8-14
• /
• 1992

Nucleotide Sequence of phnE Gene Encoding Extradiol Dioxygenase fromPseudomonas sp. Strain DJ77Kim, Young-Chang'.", Myeong-Su Shin1, Kil-Sang Younl, Young-Soon Park1, andUg-Hyeon Kim'.' (Department of Microbiology, C'hungbuk National University.Cheongju 360-763, KOREA. and 'Research Center for Molecular Microbiology,Seoul National University)nal University)

• Korean Journal of Microbiology
• /
• v.52 no.1
• /
• pp.110-115
• /
• 2016

A small plasmid (pDK4) from the Antarctic marine organism Pseudoalteromonas sp. PAMC 21150, was purified, sequenced and analyzed. pDK4 was determined to be 3,480 bp in length with a G+C content of 41.64% and contains three open reading frames encoding a replication initiation protein (RepA), a conjugative mobilization protein (Mob) and a hypothetical protein. PCR-amplified pDK4 was cloned in high-copy pUC19 to yield the fusion vector pDOC153. The chloramphenicol resistance gene was inserted into pDOC153 to give an ampicillin and chloramphenicol-resistant, Pseudoalteromonas - Escherichia coli shuttle vector (7,216 bp; pDOC155). The TonB-dependent receptor (chi22718_IV ) and exochitinase (chi22718_III ) genes from Arctic marine P. issachenkonii PAMC 22718 were cloned into pDOC155 to produce pDOC158 and pDOC165, respectively. Both vector derivatives were transferred into plasmid-free Pseudoalteromonas sp. PAMC 22137 by the triparental mating method. PCR experiments showed that the genes were stably maintained both in Pseudoalteromonas sp. PAMC 22137 and E. coli $DH5{\alpha}$ cells, indicating the potential use of pDOC155 as a new gene transfer system into marine Pseudoalteromonas spp.

• The Korean Journal of Pesticide Science
• /
• v.11 no.4
• /
• pp.320-330
• /
• 2007

Mitochondrial 16S DNA sequences of Bemisia tabaci which were collected on rose greenhouse of Iwol and Jinchen in Chungbuk and red pepper field of Miryang, Gyeongnam, were analyzed. The mtCOI PCR product of B. tabaci collected on red pepper field of Miryang were digested with EcoT14I (Sty I) into two fragments 555bp and 311bp, while the PCR product of B. tabaci collected on rose greenhouse of Iwol were digested with Sty I into two fragments of 560bp and 306bp. As a result, B. tabaci collected on red pepper reveal biotype Q and those on rose greenhouse was biotype B. These was difference between two biotypes in insecticide susceptibility, and the biotype B was more susceptible than biotype Q. As a result of foliar systemic test, root-uptake systemic test and residual effect, the biotype B was more susceptible. In case of inhibition effect on enzyme activities of fenitrothion (organophosphorous) and fenothiocarb (carbamate), those of biotype Q was higher than those of biotype B. These results indicate that biotype Q was more resistant than biotype B against 12 insecticides.

• Microbiology and Biotechnology Letters
• /
• v.26 no.1
• /
• pp.23-33
• /
• 1998

The entire sequence of a 4,214,810 bp genome of the Bacillus subtilis 168 has been determined by an international project, and the completion has been announced on July 19, 1997. For the sequencing project an international consortium was established and 25 European, 7 Japanese laboratories, 2 biotechnology companies, and our laboratory participated in the project. Within this framework we determined the complete nucleotide sequence of a 53,289 bp fragment upstream of the odhA gene (181 $^{\circ}$) of the B. subtilis 168 chromosome. On the basis of the published DNA sequences of the B. subtilis sspC and odhA genes, we obtained genomic fragments by plasmid rescue and long-range PCR. The sequenced fragment contains 56 putative open reading frames (designated yojA-yolI and 9 known genes (sspC, cge cluster, orfE5, orfRMl and odhA), in which we found many interesting features. In addition, the entire nucleotide sequence of a 53,289 bp region enabled us to revise the current genetic map of this region.

• Molecules and Cells
• /
• v.25 no.4
• /
• pp.467-478
• /
• 2008

Simple sequence repeats (SSRs) and interSSR (ISSR) marker systems were used in this study to reveal genetic changes induced by artificial selection for short/long larval duration in the tropical strain Nistari of the silkworm Bombyx mori. Artificial selection separated longer larval duration (LLD) ($29.428{\pm}0.723days$) and shorter larval duration (SLD) ($22.573{\pm}0.839days$) lines from a base, inbred population of Nistari (larval span of $23.143{\pm}0.35days$). SSR polymorphism was observed between the LLD and SLD lines at one microsatellite locus, Bmsat106 ($CA_7$) and at two loci of 1074 bp and 823 bp generated with the ISSR primer UBC873. Each of these loci was present only in the LLD line. The loci segregated in the third generation of selection and were fixed in opposite directions. In the $F_2$ generation of the $LLD{\times}SLD$ lines, the alleles of Bmsat106 and $UBC873_{1074bp}$ segregated in a 1:1 ratio and the loci were present only in the LLD individuals. $UBC873_{823bp}$ was homozygous. Single factor ANOVA showed a significant association between the segregating loci and longer larval duration. Together, the two alleles contributed to an 18% increase in larval duration. The nucleotide sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci had 67% A/T content and consisted of direct, reverse, complementary and palindromic repeats. The repeats appeared to be "nested" (59%) in larger repeats or as clustered elements adjacent to other repeats. Of 203 microsatellites identified, dinucleotides (67.8%) predominated and were rich in A/T and T/A motifs. The sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci showed similarity (E = 0.0) to contigs located in Scaffold 010774 and Scaffold 000139, respectively, of the B. mori genome. BLASTN analysis of the $UBC873_{1074bp}$ sequence showed significant homology of (nt.) 45-122 with upstream region of three exons from Bombyx. The complete sequence of this locus showed ~49% nucleotide conservation with transposon 412 of Drosophila melanogaster and the Ikirara insertions of Anopheles gambiae. The A + T richness and lack of coding potential of these small loci, and their absence in the SLD line, reflect the active process of genetic change associated with the switch to short larval duration as an adaptation to the tropics.

• Parasites, Hosts and Diseases
• /
• v.54 no.6
• /
• pp.751-758
• /
• 2016

This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out. Besides them, recently developed tools such as MAKER, PASA, Evidence Modeler, and Blast2GO were used. The scaffold DNA was obtained, the N50 was 108,950 bp, and the overall length was 341,776,187 bp. The N50 of the transcriptome was 940 bp, and its length was 53,046,952 bp. The GC content of the entire genome was 39.3%. The total number of genes was 20,178, and the total number of protein sequences was 22,358. Of the 22,358 protein sequences, 4,992 were newly observed in T. canis. Following proteins previously unknown were found: E3 ubiquitin-protein ligase cbl-b and antigen T-cell receptor, zeta chain for T-cell and B-cell regulation; endoprotease bli-4 for cuticle metabolism; mucin 12Ea and polymorphic mucin variant C6/1/40r2.1 for mucin production; tropomodulin-family protein and ryanodine receptor calcium release channels for muscle movement. We were able to find new hypothetical polypeptides sequences unique to T. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding of T. canis.

• Food Science of Animal Resources
• /
• v.41 no.2
• /
• pp.324-334
• /
• 2021

This study aimed at determining the genetic and virulence characteristics of the Listeria monocytogenes from smoked ducks. L. monocytogenes was isolated by plating, and the isolated colonies were identified by PCR. All the obtained seven L. monocytogenes isolates possessed the virulence genes (inlA, inlB, plcB, and hlyA) and a 385 bp actA amplicon. The L. monocytogenes isolates (SMFM2018 SD 1-1, SMFM 2018 SD 4-1, SMFM 2018 SD 4-2, SMFM 2018 SD 5-2, SMFM 2018 SD 5-3, SMFM 2018 SD 6-2, and SMFM 2018 SD 7-1) were inoculated in tryptic soy broth (TSB) containing 0.6% yeast extract at 60℃, followed by cell counting on tryptic soy agar (TSA) containing 0.6% yeast extract at 0, 2, 5, 8, and 10 min. We identified five heat resistant isolates compared to the standard strain (L. monocytogenes ATCC13932), among which three exhibited the serotype 1/2b and D-values of 5.41, 6.48, and 6.71, respectively at 60℃. The optical densities of the cultures were regulated to a 0.5 McFarland standard to assess resistance against nine antibiotics after an incubation at 30℃ for 24 h. All isolates were penicillin G resistant, possessing the virulence genes (inlA, inlB, plcB, and hlyA) and the 385-bp actA amplicon, moreover, three isolates showed clindamycin resistance. In conclusion, this study allowed us to characterize L. monocytogenes isolates from smoked ducks, exhibiting clindamycin and penicillin G resistance, along with the 385-bp actA amplicon, representing higher invasion efficiency than the 268-bp actA, and the higher heat resistance serotype 1/2b.

• Mycobiology
• /
• v.37 no.4
• /
• pp.251-257
• /
• 2009

We isolated and identified a strain of Eurotium rubrum from Meju that has not been reported in Korea. This fungus is yellowish brown; reverse dark brown on CYA and PDA while yellow on 2% MEA at $25{^{\circ}C}$. Cleistothecia are first bright yellow and gradually turned brown. Mycerial growth on CYA attained a diameter of 30 mm at $20{^{\circ}C}$, 37 mm at $25{^{\circ}C}$ and 32 mm at $30{^{\circ}C}$ after 15 days. The isolate grew slower on 2% MEA ($<$ 20 mm 15 days at $25{^{\circ}C}$) compared to CYA and PDA ($<$ 40 mm 15 days at $25{^{\circ}C}$). Cleistothecia are superficial, yellow to light brown, globose to subglobose, 40~75 ${\mu}m$ in diameter. Asci are 8-spored and globose to subglobose 8~11 ${\mu}m$. Ascospores are disciform, 4.0~5.0 ${\mu}m$ in length and 4.2~4.5 ${\mu}m$ in width. Conidia are ovate or bacillar, finely roughened to densely spinulose, 4.6~6.0 ${\mu}m$ in length and 3.0~4.3 ${\mu}m$ in width. Compared to known Eurotium rubrum, the Korean isolate showed 99% sequence similarity in ITS rDNA (554 bp) and calmodulin (750 bp) gene and 100% in $\beta$-tubulin (1016 bp) gene. The E. rubrum isolate also had weak $\beta$-glucosidase and protease activities.

• Analytical Science and Technology
• /
• v.33 no.6
• /
• pp.252-261
• /
• 2020

Currently, the potentiometric titration and the high pressure liquid chromatography (HPLC) method were utilized in Korean Pharmacopoeia XII (KP XII) as well as other pharmacopoeias (USP, EP, BP) for determination of loperamide hydrochloride in raw materials and capsules, respectively. The research objective is to overcome the remaining drawbacks from current methods such as solubility of mobile phase (KP XII), less scientific approach (USP 43) or using paired-ion chromatography reagent which shows some limitations (BP2017 and other formulation monographs). The proposed method was optimized by Design of Experiment (DoE) tool to obtain the satisfied method for determination of loperamide hydrochloride. The optimal condition was performed on the common C18 column (150 mm × 4.6 mm; 5 ㎛) using isocratic elution with the mobile phase containing 40 mM of potassium phosphate monobasic (pH 3.0) and acetonitrile (56:44), at a flow rate of 0.7 mL/min. The optimized method was validated and met the requirements of the International Conference on Harmonization. The developed method was applied to determine loperamide hydrochloride in capsules and can be used to update the current monograph in KP XII.