• Korean journal of food and cookery science
• /
• v.23 no.4 s.100
• /
• pp.530-536
• /
• 2007

In this study, rice flour sponge cakes were prepared by replacing 50% of the sucrose with oligosaccharides. Isomaltooligosaccharide and fructooligosaccharide were used as the oligosaccharides. The effects of oligosaccharides on the physical, textural and sensory properties of the cakes were then examined. The oligosaccharides increased batter viscosity and decreased batter specific gravity and baking loss. The moisture content, specific loaf volume and loaf volume index of the cake increased by replacing 50% of the sucrose with oligosaccharides. Internal and exterior color determinations showed that the 'L' value of the sponge cake with oligosaccharides was lower than that of the control, indicating a darker crust and crumb with the oligosaccharide substitution. Decreases in textual hardness, chewiness, and brittleness occurred with the oligosaccharides. Sensory panels perceived that the oilgosaccharide darkened the crust of the rice flour sponge cake and the panelists rated the cakes with the oilgosaccharide substitutions as sweeter, softer and more moist. The rice flour sponge cakes with isomaltooligosaccharides had a significantly higher acceptability then the others.

• BMB Reports
• /
• v.37 no.3
• /
• pp.292-297
• /
• 2004

The current model for the mechanism of action of the Bacillus thuringiensis Cry $\delta$-endotoxins involves the penetration of the ${\alpha}4-{\alpha}5$ hairpin into the target midgut epithelial cell membranes, followed by pore formation. In this study, PCR-based mutagenesis was employed to identify a critical residue within the ${\alpha}4-{\alpha}5$ loop of the 130-kDa Cry4A mosquito-larvicidal protein. Alanine-substitutions of two charged (Asp-198 and Asp-200) and four polar (Asn-190, Asn-195, Tyr-201 and Tyr-202) residues in the ${\alpha}4-{\alpha}5$ loop were performed. Like the wild-type, all of the mutant toxins were over-expressed as inclusion bodies in Escherichia coli. When E. coli cells expressing each mutant toxin were bioassayed against Aedes aegypti larvae, larvicidal activity was completely abolished for the substitution of only Tyr-202, while replacements at the other positions still retained a high level of toxicity. Further replacement of Tyr-202 with an aromatic side chain, phenylalanine, did not affect the toxicity. These results revealed a crucial role in toxin activity for the conserved aromatic residue at the 202 position within the ${\alpha}4-{\alpha}5$ loop of the Cry4A toxin.

• Radiation Oncology Journal
• /
• v.33 no.2
• /
• pp.149-154
• /
• 2015

Purpose: We performed exome sequencing in a breast cancer family without BRCA mutations. Materials and Methods: A family that three sisters have a history of breast cancer was selected for analysis. There were no family members with breast cancer in the previous generation. Genetic testing for BRCA mutation was negative, even by the multiplex ligation-dependent probe amplification method. Two sisters with breast cancer were selected as affected members, while the mother of the sisters was a non-affected member. Whole exome sequencing was performed on the HiSeq 2000 platform with paired-end reads of 101 bp in the three members. Results: We identified 19,436, 19,468, and 19,345 single-nucleotide polymorphisms (SNPs) in the coding regions. Among them, 8,759, 8,789, and 8,772 were non-synonymous SNPs, respectively. After filtering out 12,843 synonymous variations and 12,105 known variations with indels found in the dbSNP135 or 1000 Genomes Project database, we selected 73 variations in the samples from the affected sisters that did not occur in the sample from the unaffected mother. Using the Sorting Intolerant From Tolerant (SIFT), PolyPhen-2, and MutationTaster algorithms to predict amino acid substitutions, the XCR1, DLL1, TH, ACCS, SPPL3, CCNF, and SRL genes were risky among all three algorithms, while definite candidate genes could not be conclusively determined. Conclusion: Using exome sequencing, we found 7 variants for a breast cancer family without BRCA mutations. Genetic evidence of disease association should be confirmed by future studies.

• Korean Journal of Materials Research
• /
• v.23 no.9
• /
• pp.537-542
• /
• 2013

Two types of Tb- and Na-substituted green phosphors $Ca_{(1-1.5x)}WO_4:Tb_x^{3+}$: and $Ca_{(1-2x)}WO_4:Tb_x^{3+},Na_x^+$ were synthesized with various x values, using a solid-state reaction. The former phosphors contained both substitutional and vacancy point defects, while the later had only substitutional defects. X-ray diffraction results showed that the main diffraction peak, (112), was centered at $2{\theta}=28.72^{\circ}$ and indicated that there was no basic structural deformation caused by substitutions or vacancies. The photoluminescence emission and photoluminescence excitation spectra revealed the optical properties of trivalent terbium ions, $Tb^{3+}$. Typical transitions, $^5D_3{\rightarrow}^7F_6,\;^7F_5,\;^7F_4$ and $^5D_4{\rightarrow}^7F_6,\;^7F_5,\;^7F_4,\;^7F_3$, and cross relaxations were observed. Subtle differences in the photoluminescence of green phosphors were observed as a result of the point defects. The FT-IR spectra indicated that some of the ungerade vibrational modes had shifted positions and changed shapes, spreading out over a wide range of frequencies. This change can be attributed to the different masses of $Tb^{3+}$ and $Na^+$ ions and $V_{Ca}$" vacancies compared to $Ca^{2+}$ ions. The gerade normal modes of the Raman spectra exhibited subtle differences resulting from point defects in $Ca_{(1-1.5x)}Tb_xWO_4$ and $Ca_{(1-2x)}Tb_xNa_xWO_4$.

• The Korean Journal of Zoology
• /
• v.39 no.3
• /
• pp.231-238
• /
• 1996

Several types of human lung and pancreatic carcinoma cell lines were cultured and their chromosomal DNAs were extracted. These DNAs were then partially amplified by PCR (Polymerase Chain Reaction) and sequenced to analyze the types and frequency of mutations, and their possible relation in the oncogene, K-ras and suppressor gene, p53. Regardless of the cell line origin, 81% were found to possess at least one mutation. Among the cell lines analyzed, 54.5% of the mutations were found in either K-ras or p53. Except for one nonsense mutation, all mutations were missense with either base insertions or substitutions. Furthermore, besides the p53 codons Known to be mutated simultaneously with' ras to enhance tumor growth, p53 164-165 and 248 were found to be mutated simultaneously with K-ms. Regardless of the site of p53 mutation, all K-ras mutations found in these cases occurred at exon 1, codon 12.

• BMB Reports
• /
• v.44 no.4
• /
• pp.238-243
• /
• 2011

We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean Jindo dog. An additional 365,909 ESTs from other dog breeds were identified from the NCBI dbEST database, and all ESTs were clustered into 28,514 consensus sequences using StackPack. We selected the 7,305 consensus sequences that could be assembled from at least five ESTs and estimated that 12,533 high-quality single nucleotide polymorphisms (SNPs) were present in 97,835 putative SNPs from the 7,305 consensus sequences. We identified 58 Jindo dog-specific SNPs in comparison to other breeds and predicted seven synonymous SNPs and ten non-synonymous SNPs. Using PolyPhen, a program that predicts changes in protein structure and potential effects on protein function caused by amino acid substitutions, three of the non-synonymous SNPs were predicted to result in changes in protein function for proteins expressed by three different genes (TUSC3, ITIH2, and NAT2).

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.37 no.5
• /
• pp.414-422
• /
• 2004

To infer phylogenetic relationships among Epinephelus species inhabiting coastal regions of Korean peninsula, mitochondrial cytochrome b genes from 9 species belonging to the subfamily Epinephelinae were PCR-amplified, cloned and sequenced. Aligned cytochrome b sequences of 10 species containing one additional sequence from GenBank were 1,140 base pairs in length, including 439 variable and 330 parsimony informative sites. The cytochrome b genes of 10 species, as other vertebrates studied to date, exhibit unequal base compositions: an entirely low G content ($15.2{\pm}0.3{\%}$on average) and almost equal T, C and A contents ($29.3{\pm}0.8{\%},\;30.7{\pm}1.0{\%},\;and\;24.8{\pm}0.5{\%}$ on average, respectively).In third codon positions, transitional substitutions especially between Epinephelus species and outgroup species are almost certainly saturated or near saturation. Phylogenetic analyses were performed with sequence data from 8 Epinephelus species and 2 outgroup species (Cephalopholis urodela and Vaviola louti) by using distance-based (neighbor-joining and minimum evolution) and parsimony-based (maximum parsimony) methods. The results showed that the monophyly of the genus Epinephelus was supported by relatively high bootstrap values. However, phylogenetic relationships among E. areolatus, E. moara, E. septemfasciatus, and Epinephelus sp were poorly resolved. Within the genus Epinephelus, three resolved monophyletic groups were found: clade 1 included E. akaara and E. awoara;, clade 2 included E. fasciatus and E. merra; and clade 3 included E. akaara, E. awoara, E. fasciatus, E. merra, E. areolatus, E. moara, E. septemfasciatus and Epinephelus Sp.

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

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.23
• /
• pp.10433-10438
• /
• 2015

Background: Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children and represents approximately 25% of cancer diagnoses among those younger than 15 years of age. Aim and Objectives: This study investigated substitutions in the ATP synthase subunit 6 gene of mitochondrial DNA (mtDNA) as a potential diagnostic biomarker for early detection and diagnosis of acute lymphoblastic leukemia. Based on mtDNA from 23 subjects diagnosed with acute lymphoblastic leukemia, approximately 465 bp of the ATP synthase subunit 6 gene were amplified and sequenced. Results: The sequencing revealed thirty-one mutations at 14 locations in ATP synthase subunit 6 of mtDNA in the ALL subjects. All were identified as single nucleotide polymorphisms (SNPs) with a homoplasmic pattern. The mutations were distributed between males and females. Novel haplotypes were identified in this investigation: haplotype (G) was recorded in 34% in diagnosed subjects; the second haplotype was (C) with frequency of 13% in ALL subjects. Neither of these were observed in control samples. Conclusions: These haplotypes were identified for the first time in acute lymphoblastic leukemia patients. Five mutations able to change amino acid synthesis for the ATP synthase subunit 6 were associated with acute lymphoblastic leukemia. This investigation could be used to provide an overview of incidence frequency of acute lyphoblastic leukemia (ALL) in Saudi patients based on molecular events.

• Korean Journal of Plant Taxonomy
• /
• v.42 no.1
• /
• pp.13-23
• /
• 2012

The trnL-F region islocated in the large single-copy region of the chloroplast genome. It consists of the trnL gene, the trnL intron, and the trnL-F IGS. Molecular evolution and phylogenetic relationships in Korean Thalictrum L. were investigated using data from the cpDNA trnL-F region. Bayesian and parsimony analyses of the data set with the gap characteristics recovered well-resolved trees that are topologically similar, with clades supported by some indels evolution. Indel events of cpDNA trnL-F in Korean Thalictrum were interpreted as phylogenetically informative characteristics. Sect. Physocarpum (excluding T. osmorhizoides) was an early-diverging group with in the genus and the remaining section formed strongly supported clades. Korean Thalictrum has various evolutionary patterns, such as the spatial distribution of the nucleotide diversity and transversion-type base substitutions in the trnL-F region.