• Plant Biotechnology Reports
• /
• v.5 no.1
• /
• pp.9-17
• /
• 2011

With the development of next-generation sequencing technology, ever-expanding databases of genetic information from various organisms are available to researchers. However, our ability to study the biological meaning of genetic information and to apply our genetic knowledge to produce genetically modified crops and animals is limited, largely due to the lack of molecular tools to manipulate genomes. Recently, targeted cleavage of the genome using engineered DNA scissors called zinc finger nucleases (ZFNs) has successfully supported the precise manipulation of genetic information in various cells, animals, and plants. In this review, we will discuss the development and applications of ZFN technology for genome engineering and highlight recent reports on its use in plants.

• Journal of Microbiology
• /
• v.38 no.1
• /
• pp.44-47
• /
• 2000

The cDNA of VP2/NS junction region on segment A of the marine birnavirus (MBV) isolated from flounder (DS strain) was amplified using the reverse transcription (RT)-polymerase chain reaction (PCR). Its cDNA nucleotide and deduced amino acid sequences were analyzed, and compared with the reference strains of MBV and infectious pancreatic necrosis virus (IPNV). Analyses of the nucleotide and deduced amino acid sequences revealed that the DS strain is very similar to the reference strains of MBV, distant from the IPNV.

• Parasites, Hosts and Diseases
• /
• v.53 no.3
• /
• pp.329-333
• /
• 2015

The emergence of dirofilarial infections in Asia including Vietnam is a clinically significant threat to the community. We here report a rare case of subcutaneous Dirofilaria repens infection on the posterior thoracic wall in a young woman presenting a painful, itchy, and palpable nodule. The adult worm was identified by mitochondrial cox1 and nuclear ITS-2 sequence determination. The diagnosis was additionally confirmed by 16S rRNA sequencing of the endosymbiont Wolbachia pipientis commonly co-existing with D. repens. This is a rare case of subcutaneous human infection on the posterior thoracic region caused by D. repens.

• Journal of Korean Institute of Industrial Engineers
• /
• v.17 no.2
• /
• pp.1-16
• /
• 1991

This paper deals with some critical activities of CAPP system such as generation of part description database, part feature recognition, process and operation selection, and sequencing method for turning operation of symmetric rotational parts. The part description database is generated by data conversion module from CAD data, and the part feature is recognized by using both pattern primitives and feature recognition rules. Machining processes and operations are selected based on machining surface features and its sequence is determined by rules acquired from process planning expert. AutoCAD is employed as CAD system and computer program is developed by using Turbo-C on IBM PC/AT compatible system.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.11
• /
• pp.5535-5538
• /
• 2012

Background: There have been case reports of oral squamous cell carcinoma arising from gingival overgrowth induced by phenytoin - an antiepileptic drug. However, a detailed analysis for the presence of mutations in p53 and ras genes, which are the two most frequently mutated genes in cancers, in phenytoin induced gingival overgrowth tissues has hitherto not been performed. Methods: Cellular DNA isolated from twenty gingival overgrowth tissues collected from patients undergoing phenytoin therapy were amplified using primers for p53 (exons 5-8) and H-ras (exons 1-2) genes. The PCR amplicons were then gel purified and subjected to direct sequencing analysis to screen for mutations. Results: Direct sequencing of twenty samples of phenytoin induced gingival growth did not identify mutations in any of the exons of p53 and H-ras genes that were analyzed. Conclusion: Our result indicates that mutational alteration of p53 and H-ras genes is infrequent in phenytoin induced gingival growth, which thus suggests a non malignant nature of this pathology. The findings in the present study are clinically significant as a large number of epileptic patients are treated with phenytoin.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.1
• /
• pp.78-84
• /
• 2017

Objective: The aim of this study was to examine shifts in the composition of the bacterial population in the intestinal tracts (ITs) of weaning piglets by antibiotic treatment using high-throughput sequencing. Methods: Sixty 28-d-old weaning piglets were randomly divided into two treatment groups. The Control group was treated with a basal diet without antibiotics. The Antibiotic group's basal diet contained colistin sulfate at a concentration of 20 g per ton and bacitracin zinc at a concentration of 40 g per ton. All of the pigs were fed for 28 days. Then, three pigs were killed, and the luminal contents of the jejunum, ileum, cecum, and colon were collected for DNA extraction and high-throughput sequencing. Results: The results showed that the average daily weight gain of the antibiotic group was significantly greater (p<0.05), and the incidence of diarrhea lower (p>0.05), than the control group. A total of 812,607 valid reads were generated. Thirty-eight operational taxonomic units (OTUs) that were found in all of the samples were defined as core OTUs. Twenty-one phyla were identified, and approximately 90% of the classifiable sequences belonged to the phylum Firmicutes. Forty-two classes were identified. Of the 232 genera identified, nine genera were identified as the core gut microbiome because they existed in all of the tracts. The proportion of the nine core bacteria varied at the different tract sites. A heat map was used to understand how the numbers of the abundant genera shifted between the two treatment groups. Conclusion: At different tract sites the relative abundance of gut microbiota was different. Antibiotics could cause shifts in the microorganism composition and affect the composition of gut microbiota in the different tracts of weaning piglets.

• Asian-Australasian Journal of Animal Sciences
• /
• v.22 no.8
• /
• pp.1091-1101
• /
• 2009

In an attempt to understand the biochemical mechanism for the synthesis of the anabolic steroid, 19-nortestosterone, produced by prepubertal boar testes and its physiological role, normalized complementary DNA (cDNA) from boar testes was generated. DNA sequencing of 2,016 randomly selected clones yielded 794,116 base pairs of high quality nucleotide sequence. Computer-assisted assembly of the nucleotide sequence of each clone resulted in 423 contigs and 403 singletons including several genes for steroidogenic enzymes and molecules related to steroid metabolism. Analysis of gene expression pattern by use of the presently-fabricated cDNA microarray identified a number of genes that were differentially expressed during the postnatal development period in boar testes. Two genes of unknown function were identified to be highly expressed in the testis of 2-weeks-old neonatal boar. In addition, the sequencing of open reading frames of these genes revealed their homology with human alpha hemoglobin and Homo sapiens hypothetical LOC643669, transcript variant 1. Moreover, the transcripts of these genes were also detected in porcine muscle and adipocytes, in addition to Leydig cells of pigs.

• BMB Reports
• /
• v.51 no.10
• /
• pp.481-483
• /
• 2018

Glioblastoma (GBM) is the most common and aggressive form of human adult brain malignancy. The identification of the cell of origin harboring cancer-driver mutations is the fundamental issue for understanding the nature of GBM and developing the effective therapeutic target. It has been a long-term hypothesis that neural stem cells in the subventricular zone (SVZ) might be the origin-of-cells in human glioblastoma since they are known to have life-long proliferative activity and acquire somatic mutations. However, the cell of origin for GBM remains controversial due to lack of direct evidence thereof in human GBM. Our recent study using various sequencing techniques in triple matched samples such as tumor-free SVZ, tumor, and normal tissues from human patients identified the clonal relationship of driver mutations between GBM and tumor-free SVZ harboring neural stem cells (NSCs). Tumor-free SVZ tissue away from the tumor contained low-level GBM driver mutations (as low as 1% allelic frequency) that were found in the dominant clones in its matching tumors. Moreover, via single-cell sequencing and microdissection, it was discovered that astrocyte-like NSCs accumulating driver mutations evolved into GBM with clonal expansion. Furthermore, mutagenesis of cancer-driving genes of NSCs in mice leads to migration of mutant cells from SVZ to distant brain and development of high-grade glioma through the aberrant growth of oligodendrocyte precursor lineage. Altogether, the present study provides the first direct evidence that NSCs in human SVZ is the cell of origin that develops the driver mutations of GBM.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.20
• /
• pp.8883-8886
• /
• 2014

Background: Tetracycline is an antibiotic widely used for the treatment of Helicobacter pylori infection, but its effectiveness is decreasing due to increasing bacterial resistance. The aim of this study was to investigate the occurrence of 16S rRNA mutations associated with resistance or reduced susceptibility to tetracycline ofHelicobacter pylori by real-time PCR (RT-PCR) assays from culture. Materials and Methods: Tetracycline susceptibility and minimal inhibition concentration (MIC) was determined by the Epsilometer test (Etest) method. A LightCycler assay developed to detect these mutations was applied to DNA extracted from culture. The 16S rRNA of these isolates was sequenced and resistance-associated mutations were identified. From 104 isolates of H. pylori examined, 11 showed resistance to tetracycline. Results: LightCycler assay was applied to DNA extracted from 11 tetracycline-susceptible and 11 tetracycline resistance H. pylori isolates. In our study the sequencing of the H. pylori wild types in 16 s rRNA gene were AGA 926-928 with MIC (0.016 to $0.5{\mu}g/ml$), while the sequencing and MIC for resistant were GGA and AGC, (0.75 to $1.5{\mu}g/ml$), respectively. Also we found a novel mutation in 2 strains with $84^{\circ}C$ as their melting temperatures and exhibition of an A939C mutation. Conclusions: We conclude that real-time PCR is an excellent method for determination of H. pylori tetracycline resistance related mutations that could be used directly on biopsy specimens.

• Animal Bioscience
• /
• v.34 no.12
• /
• pp.1921-1929
• /
• 2021

Objective: The intestinal microbiota enhances nutrient absorption in the host and thus promotes heath. Qinghai semi-fine wool sheep is an important livestock raised in the Qinghai-Tibetan Plateau; however, little is known about the bacterial microbiota of its intestinal tract. The aim of this study was to detect the microbial characterization in the intestinal tract of the Qinghai semi-fine wool sheep. Methods: The bacterial profiles of the six different intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of Qinghai semi-fine wool sheep were studied using 16S rRNA V3-V4 hypervariable amplicon sequencing. Results: A total of 2,623,323 effective sequences were obtained, and 441 OTUs shared all six intestinal segments. The bacterial diversity was significantly different among the different intestinal segments, and the large intestine exhibited higher bacterial diversity than the small intestine. Firmicutes, Bacteroidetes, and Patescibacteria were the dominant phyla in these bacterial communities. Additionally, at the genus level, Prevotella_1, Candidatus_Saccharimonas, and Ruminococcaceae_UCG-005 were the most predominant genus in duodenal segment, jejunal and ileal segments, and cecal, colonic, and rectal segments, respectively. We predicted that the microbial functions and the relative abundance of the genes involved in carbohydrate metabolism were overrepresented in the intestinal segments of Qinghai semi-fine wool sheep. Conclusion: The bacterial communities and functions differed among different intestinal segments. Our study is the first to provide insights into the composition and biological functions of the intestinal microbiota of Qinghai semi-fine wool sheep. Our results also provide useful information for the nutritional regulation and production development in Qinghai semi-fine wool sheep.