• BMB Reports
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• v.37 no.4
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• pp.460-465
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• 2004

A 16-residue polypeptide model with the sequence acetyl-YALSLAATLLKEAASL-OH was derived by rational de novo peptide design. The designed sequence consists of amino acid residues with high propensity to adopt an alpha helical conformation, and sequential order was arranged to produce an amphipathic surface. The designed sequence was chemically synthesized using a solid-phase method and the polypeptide was purified by reverse-phase liquid chromatography. Molecular mass analysis by electro-spray ionization mass spectroscopy confirmed the correct designed sequence. Structural characterization by circular dichroism spectroscopy demonstrated that the peptide adopts the expected alpha helical conformation in 50% acetonitrile solution. Liposome binding assay using Small Unilamellar Vesicle (SUV) showed a marked release of entrapped glucose by interaction between the lipid membrane and the tested peptide. The channel-forming activity of the peptide was revealed by a planar lipid bilayer experiment. An analysis of the conducting current at various applied potentials suggested that the peptide forms a cationic ion channel with an intrinsic conductance of 188 pS. These results demonstrate that a simple rational de novo design can be successfully employed to create short peptides with desired structures and functions.

• Genomics & Informatics
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• v.10 no.1
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• pp.1-8
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• 2012

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/ Solexa systems, along with bioinformation analysis technologies of whole-genome $de$ $novo$ assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing $de$ $novo$ assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least $2{\times}$ and $30{\times}$ depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through $de$ $novo$ assembly in any whole-genome sequenced species. The $20{\times}$ and $50{\times}$ coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average $30{\times}$ coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

• Journal of Genetic Medicine
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• v.8 no.2
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• pp.135-138
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• 2011

The authors of the present study report the prenatal detection of a chromosomal abnormality with additional satellites on the distal short arm of chromosome 8. A 35-year-old woman was referred for amniocentesis because of her advanced maternal age and positive result for maternal serum screening test. Cytogenetic analysis of cultured amniocytes showed a satellite 8p chromosome. The satellite 8p chromosome was positive for nucleolus organizer region (NOR) staining. The parents' karyotypes were normal. Fluorescence in situ hybridization (FISH) study for metaphases of fetal amniocytes revealed a cryptic translocation of chromosomes 8p and 22p. The fetal karyotype was described as 46,XY,8ps.ish t(8;22)(p23.3;p11.2) (D8S504-;D8S504+)dn. The parents decided to continue the pregnancy and a phenotypically normal boy was born at 38 weeks of gestation. In case of de novo terminal NORs detected prenatally, more accurate cytogenetic and molecular analysis should be performed in order to rule out cryptic chromosomal rearrangement among other chromosomes.

• The Korean Journal of Food And Nutrition
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• v.9 no.4
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• pp.430-433
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• 1996

The activity of PAL, an initial and key regulatory enzyme in biosynthesis of phenolics, peaked during ripening stage. The enzyme activities were 5.60 and 4.25 units/100g fr. wt. in ripening and overripening stages. The increase in PAL activity in ripening strawberry fruits is due to de novo synthesis of the enzyme. PAL extracts from ripe strawberry fruits have a native molecular weight of about 260, 000 Da.

• Journal of Microbiology and Biotechnology
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• v.7 no.2
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• pp.138-143
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• 1997

We have designed and constructed a gene encoding novel high essential amino acid encoding protein(HEAAE). The resultant DNA fragment was tested for in vitro and in vivo expression and then cloned into plant expression vector pBI121, under the control of the cauliflower mosaic virus 35S promoter. Agrobacterium tumefaciens, strain LBA4404, was subsequently transformed with this new construct and Nicotiana tabacum var. Xanthi transgenic plants were obtained. DNA analysis by Southern procedure confirmed the presence of the multi-copy number of genes in the transformed plants. Analysis of RNA and protein synthesized in these transgenic plants demonstrated the stable expression of this gene.

• Clinical and Experimental Pediatrics
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• v.50 no.3
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• pp.311-315
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• 2007

This is the first case of a de novo balanced translocation 46, XY, t(3;17)(p12.2;q25) associated with multiple musculoskeletal abnormalities, including Sprengel's deformity (congenital undescended scapula to be reported). This translocation has not been described previously with this congenital anomaly in Korea.

• YAKHAK HOEJI
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• v.43 no.1
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• pp.61-67
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• 1999

Geranyllinalool, a polyisoprenoid compound, was found to block the early biosynthetic pathway of sphingolipids in LLC-PKl cells. Sphinganine, an intermediate in sphingolipid biosynthetic pathway, was abruptly accumulated in LLC-PKl cells at $2{\;}{\mu}M$ of fumonisin B1(FB1), a specific inhibitor of sphinganine N-acyltransferase, for 24 hr. Geranyllinalool lowered the $B_1(FB_1)$, a specific inhibitor of sphinganine N-acyltransferase, for 24 hr. Geranyllinalool lowered th FB1 and $50{\;}\mu$M geranyllinalool. l-Cy-closerine, an inhibitor of serine-palmitoyl transferase, was used as a positive control to evaluate the inhibitory effect of geranyllinalool. These results suggest that geranyllinalool may inhibit the serine-palmitoyl transferase, the first enzyme in de novo sphingolipid biosynthesis, resulting in the altered regulation of sphingolipid metabolism.

• Molecules and Cells
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• v.27 no.2
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• pp.135-142
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• 2009

The centrosome, an organelle comprising centrioles and associated pericentriolar material, is the major microtubule organizing center in animal cells. For the cell to form a bipolar mitotic spindle and ensure proper chromosome segregation at the end of each cell cycle, it is paramount that the cell contains two and only two centrosomes. Because the number of centrosomes in the cell is determined by the number of centrioles, cells have evolved elaborate mechanisms to control centriole biogenesis and to tightly coordinate this process with DNA replication. Here we review key proteins involved in centriole assembly, compare two major modes of centriole biogenesis, and discuss the mechanisms that ensure stringency of centriole number.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.105.2-105.2
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• 2003

Recently, several reports suggest that ceramide formation has been implicated in the apoptosis signaling in response to chemotherapeutic agents. In this study, to enhance paclitaxel-mediated cytotoxicity and endogenous ceramide levels, we blocked ceramide metabolism using an inhibitor of glucosylceramide synthase, l-phenyl-2- dacanoylamino-3-morpholino-l-propanol(PDMP) and SM synthase, D609. Exposure of human breast cancer cells to paclitaxel accumulated de novo ceramide synthesis by enhancement of SPT activity 1.2-fold, whereas ceramide synthase activity was not altered. (omitted)

• Genomics & Informatics
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• v.19 no.3
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• pp.32.1-32.10
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• 2021

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.