• Asian-Australasian Journal of Animal Sciences
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• 제23권7호
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• pp.833-847
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• 2010

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.

• Investigative Magnetic Resonance Imaging
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• 제12권2호
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• pp.131-141
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• 2008

목적: 물체 내부의 온도를 비침습적으로 측정할 수 있는 양성자 공명 주파수 이동에 의한 MR 온도영상의 재구성에 center array-sequencing 위상펼침(PU) 기법을 적용시켜 그 성능 및 유용성을 평가하고자 하였다. 대상 및 방법: MR 온도 영상에 앞서 잡음 수준이 다른 타원형 팬텀들을 컴퓨터 모의 실험으로 제작하고 제안된 PU방 법을 적용시켜 잡음에 대한 성능을 평가하였다. MR 실험은 PU 실험과 이를 이용한 온도분포영상획득 실험으로 구분하여 수행되었다. 1.5T MR 영상장치에서 무릎코일과 $T2^*$ 경사자장에코 펄스열을 이용하여 MR 영상을 얻었다. 물통, 오렌지, 아가젤 등의 팬텀을 실험 대상으로 하였고 자체 제작된 온수펌프 장치로 팬텀의 온도를 조절하였다. T 형 열전쌍 온도측정장치로 팬텀 온도를 측정하고 MR 온도영상 결과와 비교하였다. 획득된 MR영상의 위상분포는 제안된 PU방법으로 위상을 편 후 온도분포 영상을 재구성하였다. 가열 전 후의 온도변화와 MR 영상의 위상변화 관계를 이용하여 아가젤 팬텀 내의 MR온도분포 영상을 구하였다. 결과: 제안된 center array-sequencing PU 알고리즘을 이용하여 여러 팬텀에 대한 MR 위상영상의 접힘 현상을 기존 방법보다 간편하고 빠르게 제거할 수 있었고 이를 이용하여 MR 온도영상을 획득할 수 있었다. 결론: 본 연구는 제안된 center array-sequencing 위상펼침 방법이 잡음에 강하고 처리 속도가 빠를 뿐만 아니라 양성자 공명 주파수 이동의 성질을 이용한 MR 온도 영상 획득에 성공적으로 적용될 수 있음을 보였다.

• 한국방사선학회논문지
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• 제3권2호
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• pp.23-26
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• 2009

본 연구는 향상된 중심배열 정렬 위상 펼침 방법(ICASPL)을 제안하고 자기공명 위상 영상을 재구성하여 성능을 평가하였다. 제안된 방법을 수행하기 위해 2% 한천젤에 0.6mM/l를 첨가한 팬텀을 제작하여 임상용젠작하5T 자기공명영상와젠상용화된 무릎코일을 이용하여 MR위상영상을 얻었다. 획득된 k 공간 자료는 PC로 옮긴 뒤 매트랩 프로그램을 이용하여 영상을 재구성하였다. 제안된 ICASPU의 오차를 2차 회귀분석읕 이용하여 기존의 중심배열 정렬 위상 펼침과 비교 평가하였다. 그 결과 기존의 ICASPU방법에 비해 제안된 ICASPU방법이 5배 정도 오차가 향상된 것을 확인할 수 있었다. 본 연구는 향상된 중심배열 정렬 위상 펼침 방법을 이용한 위상영상 펼침의 유용성을 확인하였으며, 향후 위상 정보를 포함한 영상 적용에 매우 유용할 것이라 기대된다.

• Genomics & Informatics
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• 제11권2호
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• pp.76-82
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• 2013

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

• BMB Reports
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• 제31권5호
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• pp.475-483
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• 1998

Many antibiotics contain partially deoxygenated sugar components that are usually essential for biological activity, affinity, structural stability, and solubility of antibiotics. Gene probes of the biosynthetic genes related with the deoxysugar were obtained from PCR. Primers were designed from the conserved peptide sequences of the known dTDP-D-glucose 4,6-dehydratases, which are the key step enzymes in the biosynthesis of deoxysugar. The primers were applied to amplify parts of dehydratase genes to 27 actinomycetes that produce the metabolites containing deoxysugar as structural constituents. About 180 and 340 bp DNA fragments from all of the actinomycetes were produced by PCR and analyzed by Southern blot and DNA sequencing. The PCR products were used as gene probes to clone the biosynthetic gene clusters for the antibiotic mithramycin, rubradirin, spectinomycin, and elaiophyrin. This method should allow for detecting of the biosynthetic gene clusters of a vast array of secondary metabolites isolated from actinomycetes because of the widespread existence of deoxysugar constituents in secondary metabolites.

• Journal of Korean Neurosurgical Society
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• 제67권4호
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• pp.418-430
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• 2024

Objective : Isoflurane, a widely used common inhalational anesthetic agent, can induce brain toxicity. The challenge lies in protecting neurologically compromised patients from neurotoxic anesthetics. Choline alfoscerate (L-α-Glycerophosphorylcholine, α-GPC) is recognized for its neuroprotective properties against oxidative stress and inflammation, but its optimal therapeutic window and indications are still under investigation. This study explores the impact of α-GPC on human astrocytes, the most abundant cells in the brain that protect against oxidative stress, under isoflurane exposure. Methods : This study was designed to examine changes in factors related to isoflurane-induced toxicity following α-GPC administration. Primary human astrocytes were pretreated with varying doses of α-GPC (ranging from 0.1 to 10.0 µM) for 24 hours prior to 2.5% isoflurane exposure. In vitro analysis of cell morphology, water-soluble tetrazolium salt-1 assay, quantitative real-time polymerase chain reaction, proteome profiler array, and transcriptome sequencing were conducted. Results : A significant morphological damage to human astrocytes was observed in the group that had been pretreated with 10.0 mM of α-GPC and exposed to 2.5% isoflurane. A decrease in cell viability was identified in the group pretreated with 10.0 µM of α-GPC and exposed to 2.5% isoflurane compared to the group exposed only to 2.5% isoflurane. Quantitative real-time polymerase chain reaction revealed that mRNA expression of heme-oxygenase 1 and hypoxia-inducible factor-1α, which were reduced by isoflurane, was further suppressed by 10.0 µM α-GPC pretreatment. The proteome profiler array demonstrated that α-GPC pretreatment influenced a variety of factors associated with apoptosis induced by oxidative stress. Additionally, transcriptome sequencing identified pathways significantly related to changes in isoflurane-induced toxicity caused by α-GPC pretreatment. Conclusion : The findings suggest that α-GPC pretreatment could potentially enhance the vulnerability of primary human astrocytes to isoflurane-induced toxicity by diminishing the expression of antioxidant factors, potentially leading to amplified cell damage.

• Genomics & Informatics
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• 제8권3호
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• pp.131-137
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• 2010

Genome-wide association studies (GWASs) have greatly contributed to the identification of common variants responsible for numerous complex traits. There are, however, unavoidable limitations in detecting causal and/or rare variants for traits in this approach, which depends on an LD-based tagging SNP microarray chip. In an effort to detect potential casual and/or rare variants for complex traits, such as type 2 diabetes (T2D) and triglycerides (TGs), we conducted a targeted resequencing of loci identified by the Korea Association REsource (KARE) GWAS. The target regions for resequencing comprised whole exons, exon-intron boundaries, and regulatory regions of genes that appeared within 1 Mb of the GWA signal boundary. From 124 individuals selected in population-based cohorts, a total of 0.7 Mb target regions were captured by the NimbleGen sequence capture 385K array. Subsequent sequencing, carried out by the Roche 454 Genome Sequencer FLX, generated about 110,000 sequence reads per individual. Mapping of sequence reads to the human reference genome was performed using the SSAHA2 program. An average of 62.2% of total reads was mapped to targets with an average 22X-fold coverage. A total of 5,983 SNPs (average 846 SNPs per individual) were called and annotated by GATK software, with 96.5% accuracy that was estimated by comparison with Affymetrix 5.0 genotyped data in identical individuals. About 51% of total SNPs were singletons that can be considered possible rare variants in the population. Among SNPs that appeared in exons, which occupies about 20% of total SNPs, 304 nonsynonymous singletons were tested with Polyphen to predict the protein damage caused by mutation. In total, we were able to detect 9 and 6 potentially functional rare SNPs for T2D and triglycerides, respectively, evoking a further step of replication genotyping in independent populations to prove their bona fide relevance to traits.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.1-1
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• 2003

It is clear that computers will play a key role in the biology of the future. Even now, it is virtually impossible to keep track of the key proteins, their names and associated gene names, physical constants(e.g. binding constants, reaction constants, etc.), and hewn physical and genetic interactions without computational assistance. In this sense, computers act as an auxiliary brain, allowing one to keep track of thousands of complex molecules and their interactions. With the advent of gene expression array technology, many experiments are simply impossible without this computer assistance. In the future, as we seek to integrate the reductionist description of life provided by genomic sequencing into complex and sophisticated models of living systems, computers will play an increasingly important role in both analyzing data and generating experimentally testable hypotheses. The future of bioinformatics is thus being driven by potent technological and scientific forces. On the technological side, new experimental technologies such as microarrays, protein arrays, high-throughput expression and three-dimensional structure determination prove rapidly increasing amounts of detailed experimental information on a genomic scale. On the computational side, faster computers, ubiquitous computing systems, high-speed networks provide a powerful but rapidly changing environment of potentially immense power. The challenges we face are enormous: How do we create stable data resources when both the science and computational technology change rapidly? How do integrate and synthesize information from many disparate subdisciplines, each with their own vocabulary and viewpoint? How do we 'liberate' the scientific literature so that it can be incorporated into electronic resources? How do we take advantage of advances in computing and networking to build the international infrastructure needed to support a complete understanding of biological systems. The seeds to the solutions of these problems exist, at least partially, today. These solutions emphasize ubiquitous high-speed computation, database interoperation, federation, and integration, and the development of research networks that capture scientific knowledge rather than just the ABCs of genomic sequence. 1 will discuss a number of these solutions, with examples from existing resources, as well as area where solutions do not currently exist with a view to defining what bioinformatics and biology will look like in the future.

• Asian Pacific Journal of Cancer Prevention
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• 제17권7호
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• pp.3309-3315
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• 2016

Helicobacter pylori as the second most common cause of gastric cancer in the world infects approximately half of the developed countries population and 80% of the population living in developing countries. Integrons as genetic reservoirs play major roles in dissemination of antimicrobial resistance genes. To the best of our knowledge, this is the first study to report carriage of class 1 and 2 integrons and associated gene cassettes in H. pylori isolates from Iran. This cross-sectional study was conducted in Tehran among 110 patients with H. pylori infection. Antimicrobial susceptibility testing (AST) for H. pylori strains were assessed by the micro broth dilution method. Class 1 and 2 integrons were detected using PCR. In order to determine gene cassettes, amplified fragments were subjected to DNA sequencing of both amplicon strands. The prevalence of resistance to clarithromycin, metronidazole, clarithromycin, tetracycline, amoxicillin, rifampin, and levofloxacin were 68.2% (n=75), 25.5% (n=28), 24.5% (n=27), 19.1% (n=21), 18.2% (n=20) and 16.4% (n=18), respectively. Frequency of multidrug resistance among H. pylori isolates was 12.7%. Class 2 integron was detected in 50 (45.5%) and class 1 integron in 10 (9.1%) H. pylori isolates. The most predominant gene cassette arrays in class 2 integron-bearing H. pylori were included sat-era-aadA1, dfrA1-sat2-aadA1, blaoxa2 and, aadB whereas common gene cassette arrays in class 1 integron were aadB-aadA1-cmlA6, aacA4, blaoxa2, and catB3. The high frequency of class 2 integron and multidrug resistance in the present study should be considered as a warning for clinicians that continuous surveillance is necessary to prevent the further spread of resistant isolates.

• Journal of Animal Science and Technology
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• 제52권5호
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• pp.357-366
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• 2010

한우의 유전체 전장의 정보를 Illumina BeadArray$^{TM}$ Bovine SNP50 assay를 이용하여 단일염기다형 현상을 조사한 결과, 유전적 다양성을 보이는 좌위가 약 32,567 좌위 이상에서 다양성을 보이고 있었으며 약 5,554 좌위에서 다양성이 조사되지 않았다. 이는 조사된 자료의 가계집단의 수가 크게 제한되었기 때문에 기인될 수 있으며 또 다른 원인으로는 한우 종축집단의 크기가 작을 수 있다는 현상을 반증한다고 사료된다. 유전분석의 기초가 되는 혈통기록에 의한 개체간 혈연관계를 유전체 정보에 의한 혈연관계와 비교하여 본 결과, 유전체 정보에 의한 혈연관계의 크기가 혈통기록에 의한 혈연관계보다 좀 더 정확하게 추정될 수 있다는 장점이 있으며 혈통기록상의 오류로 그릇된 혈연관계의 크기를 유전체 정보를 통하여 보완할 수 있다는 장점이 있다. 이러한 장점을 활용하면 유전체정보를 이용한 유전능력 평가의 정확성을 크게 향상시킬 수 있을 것으로 사료되었다.