• Journal of Microbiology
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• v.37 no.4
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• pp.224-228
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• 1999

Benzaldehyde dehydrogenase (BZDH), an enzyme involved in the degradation of toluene and xylenes, is encoded by the phnN gene of Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1,803 base pairs which included the phnN gene. The fragment contained an open reading frame of 1,506 base pairs to accommodate th 55 kDa sized enzyme encoding BZDH. The enzyme efficiently oxidized benzaldehyde, salicylaldehyde, m-tolualdehyde and ps-tolualdehyde.

• Journal of Korean Academy of Oral and Maxillofacial Radiology
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• v.29 no.1
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• pp.299-308
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• 1999

Purpose: The purpose of this study was to compare the qualities of the four different processing chemicals (solutions). Materials and Methods: With EP 21 films(Ektaspeed plus film, Kodak Co., USA), nine unexposed and nine exposed films of a step wedge were processed utilizing automatic film processor(XR 24, Durr Co., Germany) for 5 days. During 5 days, the total number of processed films including out-patient' s intraoral films were about 400-500 for each brand. Base plus fog density, film density, contrast of processed films were measured with densitometer(model 07-443 digital densitometer, Victoreen Co., USA). These measurements were analyzed for comparison. Results: The results were as follows, 1. For the base plus fog density. there was significant difference among the four chemicals (p<0.05). The sequence of the base plus fog densities was in ascending order by Kodak, X-dol 90. Agfa and Konica. 2. For the film density. all chemicals showed useful range of photographic densities(0.25-2.5). The sequence of the film densities was in ascending order by Kodak, X-dol 90, Konica and Agfa. But there was no statistically significant difference of film density between X-dol and Kodak (p<0.05). 3. The sequence of the contrasts was in ascending order by Konica, X-dol 90, Kodak and Agfa. But there was no statistically significant difference of contrast between X-dol and Konica (p<0.05). Conclusion: These results indicated that the four processing chemicals had clinically useful film density and contrast. but only Kodak processing chemical had useful base plus fog density.

• Journal of the Korean Mathematical Society
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• v.47 no.4
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• pp.861-877
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• 2010

The works of Erd$\ddot{o}$s et al. about expansions of 1 with respect to a non-integer base q, referred to as q-expansions, are investigated to determine how far they continue to hold when the number 1 is replaced by a positive number x. It is found that most results about q-expansions for real numbers greater than or equal to 1 are in somewhat opposite direction to those for real numbers less than or equal to 1. The situation when a real number has a unique q-expansion, and when it has exactly two q-expansions are studied. The smallest base number q yielding a unique q-expansion is determined and a particular sequence is shown, in certain sense, to be the smallest sequence whose corresponding base number q yields exactly two q-expansions.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.22 no.7
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• pp.1505-1514
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• 1997

In this paper, a temporally adaptive layered image sequence coding technique employing H.261 is proposed. In the proposed technique, the frame rate of the base layer is adjusted according to the temporal activity measure based on the rate-distortion function. The base layer is encoded using the H.261. Then, the full frame-rate error image is formed by comparing the original image and the interpolated version of the reconstructed base layer image. The enhancement layer is algo encoded using H.261 but with leaky prdiction to provide robust error resilience. The simulation results show that the proposed technique provides better performance than the twin-H.261 with leaky prediction in both the fixed-rate and variable-rate systems.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.2
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• pp.76-80
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• 2013

The TCP domain is a DNA-binding domain present in plant transcription factors and has a similar structural feature to the bHTH motif of eukaryotic transcription factors. The imino proton exchange study has been performed for the DNA duplex containing the consensus DNA-binding site for the AtTCP11 transcription factor. The first two base pairs in the consensus 5'-GTGGG-3' sequence are relatively very unstable but lead to greater stabilization of the neighboring two G C base pairs. These unique dynamic features of the five base pairs in the consensus DNA sequence might play crucial roles in the effective DNA binding of the AtTCP11 protein.

• Journal of Microbiology and Biotechnology
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• v.30 no.10
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• pp.1583-1591
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• 2020

CRISPR/Cpf1 has emerged as a new CRISPR-based genome editing tool because, in comparison with CRIPSR/Cas9, it has a different T-rich PAM sequence to expand the target DNA sequence. Single-base editing in the microbial genome can be facilitated by oligonucleotide-directed mutagenesis (ODM) followed by negative selection with the CRISPR/Cpf1 system. However, single point mutations aided by Cpf1 negative selection have been rarely reported in Corynebacterium glutamicum. This study aimed to introduce an amber stop codon in crtEb encoding lycopene hydratase, through ODM and Cpf1-mediated negative selection; deficiency of this enzyme causes pink coloration due to lycopene accumulation in C. glutamicum. Consequently, on using double-, triple-, and quadruple-base-mutagenic oligonucleotides, 91.5-95.3% pink cells were obtained among the total live C. glutamicum cells. However, among the negatively selected live cells, 0.6% pink cells were obtained using single-base-mutagenic oligonucleotides, indicating that very few single-base mutations were introduced, possibly owing to mismatch tolerance. This led to the consideration of various target-mismatched crRNAs to prevent the death of single-base-edited cells. Consequently, we obtained 99.7% pink colonies after CRISPR/Cpf1-mediated negative selection using an appropriate single-mismatched crRNA. Furthermore, Sanger sequencing revealed that single-base mutations were successfully edited in the 99.7% of pink cells, while only two of nine among 0.6% of pink cells were correctly edited. The results indicate that the target-mismatched Cpf1 negative selection can assist in efficient and accurate single-base genome editing methods in C. glutamicum.

• The KIPS Transactions:PartA
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• v.9A no.3
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• pp.387-398
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• 2002

As whole genome sequences of many organisms have been revealed by small-scale genome projects, the intensive research on individual genes and their functions has been performed. However on-memory algorithms are inefficient to analysis of whole genome sequences, since the size of individual whole genome is from several million base pairs to hundreds billion base pairs. In order to effectively manipulate the huge sequence data, it is necessary to use the indexed data structure for external memory. In this paper, we introduce a workbench system for analysis and visualization of whole genome sequence using string B-tree that is suitable for analysis of huge data. This system consists of two parts : analysis query part and visualization part. Query system supports various transactions such as sequence search, k-occurrence, and k-mer analysis. Visualization system helps biological scientist to easily understand whole structure and specificity by many kinds of visualization such as whole genome sequence, annotation, CGR (Chaos Game Representation), k-mer, and RWP (Random Walk Plot). One can find the relations among organisms, predict the genes in a genome, and research on the function of junk DNA using our workbench.

• Journal of Microbiology and Biotechnology
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• v.3 no.3
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• pp.139-145
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• 1993

The nucleotide sequence of the xylanase gene (xynS) from alkali-tolerant Bacillus sp. YA.14 was determined and analyzed. A 639 base pairs open reading frame for xynS gene was observed and encoded for a protein of 213 amino acids with a molecular weight of 23, 339. S1 nuclease mapping showed that the transcription initiation site of the xynS gene did not exist in the cloned DNA. Ribosome binding site sequence with the free energy of -18.8 Kcal/mol was observed 8 base pairs upstream from the initiation codon, ATG. The proposed signal sequence consisted of 28 amino acids, of which 3 were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YA-14 xylanase showed 48% homology with Bacillus sp. YC-335 xylanase and 96% homology with xylanases from B. subtilis and B. circulans.

• Journal of Microbiology and Biotechnology
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• v.3 no.4
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• pp.224-231
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• 1993

The nucleotide sequence of the xylanase gene (xynY) from alkalophilic Bacillus sp. YC-335 was determined and analyzed. An open reading frame of 1, 062 base pairs for xynY gene was observed and encoded for a protein of 354 amino acids with a molecular weight of 38, 915. S1 nuclease mapping showed that the transcription initiation sites of the xynY gene were different in Bacillus sp. YC-335 and Escherichia coli HB101 (pYS55). S1 mapping also showed that -10 region of the xynY gene recognized by RNA polymerases of E. coli and Bacillus sp. YC-335 were TACAGT and TATGAT , respectively. A ribosome binding site sequence with the free energy of -17.0 Kcal/mol was observed 9 base pairs upstream from the unusual initiation codon, TTG. The proposed signal sequence consisted of 27 amino acids, 2 of which were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YC-335 xylanase showed more than 50% homology with xylanases from B. pumilus, B. subtilis, and B. circulans.

• Korean Journal of Microbiology
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• v.36 no.3
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• pp.192-195
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• 2000

Degenerate primevs corresponding to the consensus sequences of the copper-binding regions in the N- and Cterminal domains of fungal laccases were used to isolate laccase gene-specific sequences froin a white rot rungus Ganodern~a lucidrm w-hich has been known to strengthen the imnnne system. A 1.6 Kbp fragment was amplified by PCR and its base sequence was detenuiued. Locating seven iutrous within the base sequence, we could deduce its amino acid sequence. The nucleotide sequence witl~out introlls was 47Y0 identical to that of lee1 gene of Pametes wllosa; lhe identity in amino acid sequences of the two was 7994 The deduced amino acid seqoence was also sunilar to those of Coriolus versicolo~ kc3 (79%); Co~,iolz~s hirsutus phenolouiduse (78%), Trainetes vel.srcoloi. lccl (77%), Trametes ~!i/Iosa Ice2 (77%) and Trametes vemicolor kc4 (66%).