• Journal of the Korea Society of Computer and Information
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• v.25 no.10
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• pp.1-14
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• 2020

In this paper, we propose to solve the problem of increasing system memory usage due to an increase in the number of mapping information management when using a NAND flash memory-based storage device in an existing sector-based file system. The proposed technique is to store only mapping information in page units based on index blocks and manage them in block units. To this end, the proposed technique uses a sequential offset for storing and managing a plurality of mapping information in one page in a small block, and a reverse offset for a spare page corresponding to a change in mapping information in the block. Through this, the proposed technique has the advantage that the number of block-unit deletions is less than that of the existing technique, and the system memory usage required for mapping information management is low. Reduced by about 32%.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7343-7350
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• 2015

Genetic changes associated with acute lymphoblastic leukemia (ALL) provide very important diagnostic and prognostic information with a direct impact on patient management. Detection of chromosome abnormalities by conventional cytogenetics combined with fluorescence in situ hybridization (FISH) play a very significant role in assessing risk stratification. Identification of specific chromosome abnormalities has led to the recognition of genetic subgroups based on reciprocal translocations, deletions and modal number in B or T-cell ALL. In the last twelve years 102 newly diagnosed childhood/adult ALL bone marrow samples were analysed for chromosomal abnormalities with conventional G-banding, and FISH (selected cases) using specific probes in our hospital. G-banded karyotype analysis found clonal numerical and/or structural chromosomal aberrations in 74.2% of cases. Patients with pseudodiploidy represented the most frequent group (38.7%) followed by high hyperdiploidy group (12.9%), low hyperdiploidy group (9.7%), hypodiploidy (<46) group (9.7%) and high hypertriploidy group (3.2%). The highest observed numerical chromosomal alteration was high hyperdiploidy (12.9%) with abnormal karyotypes while abnormal 12p (7.5%) was the highest observed structural abnormality followed by t(12;21)(p13.3;q22) resulting in ETV6/RUNX1 fusion (5.4%) and t(9;22)(q34.1;q11.2) resulting in BCR/ABL1 fusion (4.3%). Interestingly, we identified 16 cases with rare and complex structural aberrations. Application of the FISH technique produced major improvements in the sensitivity and accuracy of cytogenetic analysis with ALL patients. In conclusion it confirmed heterogeneity of ALL by identifying various recurrent chromosomal aberrations along with non-specific rearrangements and their association with specific immunophenotypes. This study pool is representative of paediatric/adult ALL patients in Oman.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.5
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• pp.1977-1980
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• 2015

Objective: The Von Hippel-Lindau syndrome (VHLD), an inherited neoplastic syndrome predisposing to central nervous system hemangioblastoma (CNS), pheochromocytoma (PCC), renal cell carcinoma(RCC), retinal hemangioma (RA) and renal cysts, is caused by mutations or deletions of the VHL tumor-suppressor gene. To assess VHL genotype-phenotype correlations with function of pVHL a gene mutation analysis of members in a Chinese family with non-syndromic PCCs and individuals with apparently sporadic pheochromocytoma (ASP) was performed. Materials and Methods: DNA samples of 20 members from the Chinese family with non-syndromic PCCs and 41 patients with ASP were analyzed by polymerase chain reaction and direct sequencing, confirmed by Taqman probe. Results: Three novel mutations (H125P, 623(^TTTGTtG) and R120T) were identified in the Chinese family and in 3 among 41 ASP patients. The mutations were all located in exon 2 of VHL gene encoding ${\beta}$-domain of pVHL. The tumor type in H125P carriers and R120T carriers was VHL type 2C. And 623(^TTTGTtG) carriers presented VHL type 2B or type 2C. Conclusions: VHL gene abnormalities were identified in the Chinese family with non-syndromic PCCs and patients with APS, resulting in dysfunction of pVHL. H125P and R120T could be associated with VHL type 2C, while 623(^TTTGTtG) might be linked with VHL type 2B or type 2C. Not only is the genetic analysis helpful for early diagnosis and treatment of patients with VHLD, it is also benefitial for research intoVHLD pathogenesis.

• KSBB Journal
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• v.10 no.1
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• pp.89-96
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• 1995

An Avabidofsis thaliana gene encoding phosphoribosyl anthranilate transferase is shown to be the gene that is defective in blue fluorescent trp 1 mutant plants. This gene, named PAT1, coding region is homologous to those for the phosphoribosyl anthranilate transferase from many microorganisms. This is due to a defect in tryptophan biosynthesis that leads to an accumulation of anthranilate, a fluorescent intermediate in the tryptophan pathway. PAT1 is a single-copy gene that complements all of the visible phenotypes of the different trp1 mutants. Experiments to determine the regulation of the PAT1 gene are in progress. The wild-type PAT1 promoter and several promoter deletions of PAT1 gene have been transformed into Arabidopsis tryptophan mutants. These constructs might identify promoter elements that control this patterns. We have isolated the homozygous lines in T3 seeds and analysed the protein levels using PAT antibody and PAT protein level increased two fold in pHSl07. Finally, the potential of using PAT1 as a selectable marker or visible reporter of gene expression is being explored.

• Molecules and Cells
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• v.23 no.1
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• pp.39-48
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• 2007

Charcot-Marie-Tooth (CMT) disease and hereditary neuropathy with liability to pressure palsies (HNPP) are frequent forms of genetically heterogeneous peripheral neuropathies. Reciprocal unequal crossover between flanking CMT1A-REPs on chromosome 17p11.2-p12 is a major cause of CMT type 1A (CMT1A) and HNPP. The importance of a sensitive and rapid method for identifying the CMT1A duplication and HNPP deletion is being emphasized. In the present study, we established a molecular diagnostic method for the CMT1A duplication and HNPP deletion based on hexaplex PCR of 6 microsatellite markers (D17S921, D17S9B, D17S9A, D17S918, D17S4A and D17S2230). The method is highly time-, cost- and sample-saving because the six markers are amplified by a single PCR reaction and resolved with a single capillary in 3 h. Several statistical and forensic estimates indicated that most of these markers are likely to be useful for diagnosing the peripheral neuropathies. Reproducibility, as determined by concordance between independent tests, was estimated to be 100%. The likelihood that genotypes of all six markers are homozygous in randomly selected individuals was calculated to be $1.6{\times}10^{-4}$, which indicates that the statistical error rate for this diagnosis of HNPP deletion is only 0.016%.

• The Plant Pathology Journal
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• v.18 no.2
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• pp.98-101
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• 2002

Using phytoplasma universal primer pair Pl and P7, a fragment of about 1.8 kb nucleotide sequences of 16S rRNA gene and 16S-23S rRNA intergenic spacer region, and a portion of 23S rRNA gene of jujube witches'broom (JWB) and mulberry dwarf(MD) phytoplasmas were determined. The nucleotide sequences of JWB and MD were 1,850 bp and 1,831 bp long, respectively. The JWB phytoplasma sequence was aligned with the homologous sequence of MD phytoplasma. Twenty-eight base insertions and nine base deletions were found in the JWB phytoplasma sequence compared with that of MD phytoplasma. The similarity of the aligned sequences of JWB and MD was 84.8%. The near-complete 16S rRNA gene DNA sequences of JWB and MD were 1,529 bp and 1,530 bp in length, respectively, and revealed 89.0% homology. The 16S-23S rRNA intergenic spacer region DNA sequences were 263 bp and 243 bp in lengths respectively, while homology was only 70% and the conserved tRNA-lle gene of JWB and MD was located into the intergenic space region between 16S-23S rRNA gene. The nucleotide sequences were 77 bp long in both JWB and MD, and showed 97.4% sequence homology. Based on the phylogenetic analysis of the two phytoplasmas, the JWB phytoplasma belongs to the Elm yellow phytoplasma group (16S rV), whereas, the MD phytoplasma belongs to the Aster yellow group (16S rI).

• Journal of Korean Neurosurgical Society
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• v.29 no.2
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• pp.188-195
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• 2000

Objective : Essential tremor(ET) is the most common movement disorder, however, there has been little agreement in the neurologic literature regarding diagnostic criteria for ET. Familial ET is an autosomal dominant disorder presenting as an isolated postural tremor. The main feature of ET is postural tremor of the arms with later involvement of the head, voice, or legs. In previous studies, it was reported that ET susceptibility was inherited in an autosomal dominant inheritance. As previous results, it would suggest that ET might be associated with defect of mitochondrial or nuclear DNA. Recent studies are focusing on molecular genetic detection of movement disorders, such as essential tremor and restless legs syndrome. Moreover, authors have analysed mitochondrial DNA(mtDNA) from the blood cell of positive control(PC) and ET patients via long and accurate polymerase chain reaction(LA PCR). Materials & Methods : Blood samples were collected from PC and 9 ET patients. Total DNA was extracted twice with phenol followed by chloroform : isoamylalcohol. For the analysis of mtDNA, LA PCR was performed by mitochondrial specific primers. Results : With this technique, deletions of large quantities were detected within several regions of mtDNA in ET patients except for D-loop and CO I regions. Conclusion : The authors believe that ET is a genentic disorder with deficiency of mitochondrial DNA multicomplexes and mitochondiral dysfunction could be one of major causative factors of ET. Mitochondrial dysfunction may play an important role in the pathogenesis and possibility of disease progression among familial group with ET patients.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.183-192
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• 2003

With the availability of complete whole-genomes such as the human, mouse, fugu and chimpanzee chromosome 22, comparative analysis of large genomes from cross-species at varying evolutionary distances is considered one of a powerful approach for identifying coding and functional non-coding sequences. Here we describe a fast and efficient global alignment method especially for large genomic regions over mega bases pair. We used an approach for identifying all similarity regions by HSP (Highest Segment Pair) regions using local alignments and then large syntenic genome based on the both extension of anchors at HSP regions in two species and global conservation map. Using this alignment approach, we examined rearrangement loci in human chromosome 21 and chimpanzee chromosome 22. Finally, we extracted syntenic genome 30 Mb of human chromosome 21 with chimpanzee chromosome 22, and then identified genomic rearrangements (deletions and insertions ranging h size from 0.3 to 200 kb). Our experiment shows that all jnsertion/deletion (indel) events in excess of 300 bp within chimpanzee chromosome 22 and human chromosome 21 alignments in order to identify new insertions that had occurred over the last 7 million years of evolution. Finally we also discussed evolutionary features throughout comparative analyses of Ka/ks (non-synonymous / synonymous substitutions) rate in orthologous 119 genes of chromosome 21 and 53 genes of MHC-I class in human and chimpanzee genome.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.118-125
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• 2006

The region responsible for replication of the megaplasmid pAtC58 in the nopaline-type Agrobacterium tumefaciens strain C58 was determined. A derivative ofa Co1E1 vector, pBluscript SK-, incapable of autonomous replication in Agrobacterium spp, was cloned with a 7.6-kb Bg1II-HindIII fragment from a cosmid clone of pAtC58, which contains a region adjacent to the operon for the utilization of deoxyfructosyl glutamine (DFG). The resulting plasmid conferred resistance to carbenicillin on the A. tumefaciens strain UIA5 that is a plasmidfree derivative of C58. The plasmid was stably maintained in the strain even after consecutive cultures for generations. Analysis of nested deletions of the 7.6-kb fragment showed that a 4.3-kb BglII-XhoI region sufficiently confers replication of the derivative of the ColE1 vector on UIA5. The region comprises three ORFs, which have high homologies with repA, repB, and repC of plasm ids in virulent Agrobacterium spp. including pTiC58, pTiB6S3, pTi-SAKURA, and pRiA4b as well as those of symbiotic plasmids from Rhizobium spp. Phylogenie analysis showed that rep genes in pAtC58 are more closely related to those in pRiA4 than to pTi plasmids including pTiC58, suggesting that the two inborn plasmids, pTiC58 and pAtC58, harbored in C58 evolved from distinct origins.

• Journal of Microbiology and Biotechnology
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• v.8 no.2
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• pp.152-157
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• 1998

To analyze the role of the C and D domains in the cyclization activity of cyclodextrin glucanotransferase (CGTase), two plasmids, pKB1ΔC300 and pKB1ΔD96, were constructed in which DNA regions encoding 100 and 32 amino acids, respectively, from the C and D domains of B. stearothermophilus NO2 CGTase were deleted. The mutated CGTase from the pKBlΔC300 produced much lower amounts of ${\alpha}$-, ${\beta}$-, and $\gamma$-cyclodextrin (CD) than the parental CGTase. However, the mutated CGTase from the pKBlΔD96 showed a similar production pattern of CDs to wild-type CGTase. The production ratios of the ${\alpha}$-, ${\beta}$- and $\gamma$-CDs were not affected by the deletions, when compared to those of parental CGTase. The optimum temperature of the mutated CGTase from the pKBlΔC300 was decreased from $60^{\circ}C$ to $55^{\circ}C$. The optimum pH of the mutated CGTase from the pKB1D96 was shifted from 6.0 to 7.0. The thermostability of the two mutant CGTases were not changed. From these results, it is suggested that the C and D domains are not related to cyclization activity directly because mutant-enzymes deleted C or D domains still possessed their activity. However, they are important for other enzymatic properties such as productivity and pH optimum as a partition of CGTase tertiary structure.