• Molecules and Cells
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• v.26 no.3
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• pp.278-284
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• 2008

An open reading frame, designated GerGTII and located downstream of the polyketide synthase genes, has been identified as a chalcosyltransferase by sequence analysis in the dihydrochalcomycin biosynthetic gene cluster of Streptomyces sp. KCTC 0041BP. The deduced product of gerGTII is similar to several glycosyltransferases, authentic and putative, and it displays a consensus sequence motif that appears to be characteristic of a sub-group of these enzymes. Specific disruption of gerGTII within the S. sp. KCTC 0041BP genome by insertional in-frame deletion method, resulted complete abolishment of dihydrochalcomycin and got the 20-O-mycinosyl-dihydrochalconolide as intermediate product in dihydrochalcomycin biosynthesis which was confirmed by electron spray ionization-mass spectrometry and liquid chromatography-mass spectrometry. Dihydrochalcomycin also was recovered after complementation of gerGTII.

• Parasites, Hosts and Diseases
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• v.42 no.3
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• pp.145-148
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• 2004

We compared the DNA sequence difference of isolates of Clonorchis sinensis from one Korean (Kimhae) and two Chinese areas (Guangxi and Shenyang), The sequences of nuclear rDNA (18S, internal transcribed spacer 1 and 2: ITS1 and ITS2) and mitochondrial DNA (cytochrome c oxidase subunit 1: cox1) were compared. A very few intraspecific nucleotide substitution of the 18S, ITS1, ITS2 and cox1 was found among three isolates of C. sinensis and a few nucleotide insertion and deletion of ITS1 were detected. The 18S, ITS1, ITS2 and cox1 sequences were highly conserved among three isolates. These findings indicated that the Korean and two Chinese isolates are similar at the DNA sequence level.

• Korean Journal of Plant Taxonomy
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• v.52 no.3
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• pp.156-172
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• 2022

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• Korean Journal of Veterinary Research
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• v.32 no.4
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• pp.555-567
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• 1992

In this study gene encoding structural proteins of a CPV isolate was cloned and sequenced to elucidate the molecular genetical properties of the canine parvoviruses isolated from the field. Six recombinant plasmids of pEP3, p1471, p2070, pEP069, pEP338 and p14711p were constructed from the map positions 22 to 98 of RF DNA to clone the VP1 and VP2 genes of CPV-V20. Sequentialy the gene comprising 3780 nucleotides were sequenced by dideoxy chain termination method. When nucleotide sequence of gene encoding the structural proteins of CPV-V20 was compared with those of other strains, CPV-N, CPV-d and CPV-780929 published previously, DNA, homologies to CPV-V20 were 99.87% with CPV-N, 99.73% with CPV-d, 96.85% with CPV-780929 and 98.4% with FPLV-Carl, respectively. The DNA sequence data of CPV-V20 showed seven point mutations and also deletion of 135 nucleotides from the nucleotide position 4745 to 4879 located in the 3'-noncoding region of CPV-N.

• Korean Journal of Veterinary Research
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• v.60 no.3
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• pp.109-116
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• 2020

This study aimed to develop a semi-nested polymerase chain reaction assay for the direct detection of Mycoplasma synoviae (M. synoviae) from clinical samples using three newly designed oligonucleotide primers specific to the variable lipoprotein haemagglutinin (vlhA) gene and differentiate M. synoviae field strains based on a nucleotide deletion or the insertion of the proline-rich repeat (PRR) region of the vlhA gene. The developed semi-nested polymerase chain reaction (PCR) assay revealed positive results in 12 out of 100 clinical samples collected from chickens showing lameness and joint swelling. Six positive samples were selected randomly for sequencing, and sequence analysis revealed 96.3-100% nucleotide identities compared to the reference sequences. Phylogenetic analysis showed that sequences of the strains in this study were closely related to WVU1853 (Spain), CK.MS.UDL.PK.2014.2 (Pakistan), and F10-2AS (USA) strains, but they were distinct from the M. synoviae-H vaccine strain sequence. M. synoviae obtained from these samples were identified as types A and C with a length of 38 and 32 amino acids, respectively. These results indicated that the specific and sensitive semi-nested PCR could be a useful diagnostic tool for the direct identification of clinical samples, and the sequence analysis of the partial vlhA gene can be useful for typing M. Synoviae.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.237-242
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• 2007

Genome duplication(i.e. polyploidy) is a common phenomenon in the evolution of plants. The objective of this study was to achieve a comprehensive understanding of genome duplication for SNP discovery by Thymine/Adenine(TA) cloning for confirmation. Primer pairs were designed from 793 EST contigs expressed in the roots of a supernodulating soybean mutant and screened between 'Pureunkong' and 'Jinpumkong 2' by direct sequencing. Almost 27% of the primer sets were failed to obtain sequence data due to multiple bands on agarose gel or poor quality sequence data from a single band. TA cloning was able to identify duplicate genes and the paralogous sequences were coincident with the nonspecific peaks in direct sequencing. Our study confirmed that heterogeneous products by the co-amplification of a gene family member were the main cause of obtaining multiple bands or poor quality sequence data in direct sequencing. Counts of amplified bands on agarose gel and peaks of sequencing trace suggested that almost 27% of nonrepetitive soybean sequences were present in as many as four copies with an average of 2.33 duplications per segment. Copy numbers would be underestimated because of the presence of long intron between primer binding sites or mutation on priming site. Also, the copy numbers were not accurately estimated due to deletion or tandem duplication in the entire soybean genome.

• Korean Journal of Microbiology
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• v.32 no.2
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• pp.115-119
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• 1994

Replication control region of pSBK203, a chloramphenicol acetyltransferase conferring plasmid from Staphylococus aureus was cloned and its nucleotide sequence has been determined. Base sequence homology of this copy control region with those of plasmids belonging to pT181 family was obtained and analyzed. Copy number of four copy mutants derived by addtion or deletion of nucleotides in unique XbaI recognition site in copy control region of pSBK203 was also determined.

• Speech Sciences
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• v.9 no.1
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• pp.193-206
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• 2002

The aim of this study is to find out how the labiovelar onglide /w/ in English kwV sequences that have minimal pairs with kV sequences is pronounced differently among Korean EFL learners based on acoustic evidence. This study tries to identify /w/ sound in English kwV sequences through spectrograms and to examine the duration ratios of each segment in kwV words to compare the patterns of an English native speaker with those of Korean speakers of English. In spectrographic analyses, the complete deletion of /w/ and partial pronunciation of /w/ dubbed [$k^{w}$] were identified as well as the targetappropriate production of /w/. The general production patterns with respect to the duration ratios in English [kw] sequence words showed that the subjects who produced /w/ had similar ratio patterns that the native speaker had in that the vowel duration ratio in kwV sequences was shorter than that in kV sequences. By contrast, the subjects who deleted [w] had a long ratio of the onset [$k^{h}$] while the speaker with a partial pronunciation of /w/ had a long ratio of the following vowel.

• Clinical and Experimental Pediatrics
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• v.56 no.6
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• pp.265-268
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• 2013

Wiskott-Aldrich syndrome (WAS) is an inherited X-linked disorder. The WAS gene is located on the X chromosome and undergoes mutations, which affect various domains of the WAS protein, resulting in recurrent infection, eczema, and thrombocytopenia. However, the clinical features and severity of the disease vary according to the type of mutations in the WAS gene. Here, we describe the case of a 4-year-old boy with a history of marked thrombocytopenia since birth, who presented with recurrent herpes simplex infection and late onset of eczema. Examination of his family history revealed that older brother, who died from intracranial hemorrhage, had chronic idiopathic thrombocytopenia. Therefore, we proceeded with genetic analysis and found a new deletion mutation in the WAS gene: c.858delC (p.ser287Leufs$^*21$) as a hemizygous form.