• Genomics & Informatics
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• v.21 no.3
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• pp.37.1-37.11
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• 2023

Systemic lupus erythematosus (SLE) is an inflammatory-autoimmune disease with a complex multi-organ pathogenesis, and it is known to be associated with significant morbidity and mortality. Various genetic, immunological, endocrine, and environmental factors contribute to SLE. Genomic variants have been identified as potential contributors to SLE susceptibility across multiple continents. However, the specific pathogenic variants that drive SLE remain largely undefined. In this study, we sought to identify these pathogenic variants across various continents using genomic and bioinformatic-based methodologies. We found that the variants rs35677470, rs34536443, rs17849502, and rs13306575 are likely damaging in SLE. Furthermore, these four variants appear to affect the gene expression of NCF2, TYK2, and DNASE1L3 in whole blood tissue. Our findings suggest that these genomic variants warrant further research for validation in functional studies and clinical trials involving SLE patients. We conclude that the integration of genomic and bioinformatic-based databases could enhance our understanding of disease susceptibility, including that of SLE.

• Animal Bioscience
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• v.37 no.4
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• pp.591-599
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• 2024

Objective: Sumba Ongole (SO) cattle are valuable breed due to their important role in the development of Indonesian cattle. Despite rapid advances in molecular technology, no genomic studies on SO cattle have been conducted to date. The aim of this study is to provide genomic profile related to the population diversity, admixture, and demographic trends of SO cattle. Methods: Genomic information was gathered from 79 SO cattle using the Illumina Bovine SNP50 v3 Beadchip, and for comparative purposes, additional genotypes from 209 cattle populations worldwide were included. The expected and observed heterozygosity, inbreeding coefficient, pairwise fixation indices between-population, and Nei's genetic distance were examined. Multidimensional scaling, admixture, and treemix analyses were used to investigate the population structure. Based on linkage disequilibrium and effective population size calculations, the demographic trend was observed. Results: The findings indicated that the genetic diversity of SO cattle was similar to that of other indicine breeds. SO cattle were genetically related to indicines but not to taurines or Bali cattle. The study further confirmed the close relationship between SO, Ongole, and Nellore cattle. Additionally, a small portion of the Ongole mixture were identified dominant in the SO population at the moment. The study also discovered that SO and Bali cattle (Bos javanicus) could have been ancestors in the development of Ongole Grade cattle, which corresponds to the documented history of Ongolization. Our finding indicate that SO cattle have maintained stability and possess unique traits separate from their ancestors. Conclusion: In conclusion, the genetic diversity of the SO cattle has been conserved as a result of the growing significance of the present demographic trend. Consistent endeavors are necessary to uphold the fitness of the breed.

• KOGO NEWS
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• v.5 no.4
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• pp.9-16
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• 2005

Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic expression data transforms the challenges m biomedical research into ones in bioinformatics. Clinical informatics has long developed technologies to imp개ve biomedical research by integrating experimental and clinical information systems. Biomedical informatics, powered by high throughput techniques, genomic-scale databases and advanced clinical information system, is likely to transform our biomedical understanding forever much the same way that biochemistry did to biology a generation ago. The emergence of healthcare and biomedical informatics revolutionizing both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics and prognostics.

• Genomics & Informatics
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• v.11 no.2
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• pp.68-75
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• 2013

Anaplastic thyroid cancer (ATC) belongs to the most malignant and rapidly progressive human thyroid cancers and its prognosis is very poor. Also, it shows high resistance to cancer treatments, so that effective treatment for ATC has not been found to date, and virtually all patients terminate their life rapidly after diagnosis. Although targeted treatment of genetic alterations has emerged as an extremely promising approach to human cancers, such as BRAF in metastatic melanoma, it remains unclear that how commonly genomic alterations are influenced in ATC tumorigenesis. In recent years, genome wide approaches have been exploited to find genetic alterations associated with complex diseases, including cancer. Here, we reviewed the comprehensive genetic alterations in ATC and recent approaches in the context of identifying genomic alterations associated with ATC. Since surprisingly few reports have been published on the genome wide study of ATC, this review puts emphasis on the urgent needs of genomic research for the prevention and treatment of ATC.

• Genomics & Informatics
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• v.21 no.1
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• pp.11.1-11.5
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• 2023

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis.

• Genomics & Informatics
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• v.1 no.1
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• pp.50-54
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• 2003

Genome of an extreme thermophile, Thermus caldophilus GK24 has been analyzed to construct the genomic map. The genomic DNAs encapsulated in agarose gel were digested with SspI, EcoRI, SpeI, and HpaI restriction endonucleases, and then the resulting genomic DNA fragments were analyzed by pulsed-field gel electrophoresis. Its restriction map has been constructed by analyzing sizes of the restriction fragments obtained from both complete and partial digestions. The circular form of its genome was composed of about 1.98 Mbp and a megaplasmid. The genomic loci for the genes of xylose isomerase, thioredoxin, tRNA-16S rRNA, 23S rRNA, L5 ribosomal protein, ADP-glucose pyrophosphorylase, DNA-ligase, and Tca DNA polymerase were determined by both Southern hybridization and PCR.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.187-192
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• 2010

In order to monitor the possibility of horizontal gene transfer between transgenic rice and microorganisms in a paddy rice field, the gene flow from a bifunctional fusion (TPSP) rice containing trehalose-6-phosphate synthase and phosphatase to microorganisms in soils was investigated. The soil samples collected from the paddy rice field during June 2004 to March 2006 were investigated by multiplex PCR, Southern hybridization, and amplified fragment length polymorphism (AFLP). The TPSP gene from soil genomic DNAs was not detected by PCR. Soil genomic DNAs did not show homologies on the Southern blotting data, indicating that gene transfer did not occur during the last two years in the paddy rice field. In addition, the AFLP band patterns produced by soil genomic DNAs from both transgenic and non-transgenic rice fields appeared similar to each other when analyzed by the NTSYSpc program. Thus, these data suggest that transgenic rice does not give a significant impact on the communities of soil microorganisms, although long-term observation may be needed.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1065-1070
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• 2006

The avian uncoupling protein (avUCP) is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. The sequencing analysis method was used to identify nucleotide polymorphisms within the avUCP gene in Korean native chicken (KNC). This study identified ten single nucleotide polymorphisms (SNPs) in the avUCP gene. We analyzed the SNPs of the avUCP gene to investigate whether polymorphism in the gene might be responsible for quantitative variations in economic traits in KNC. Three significant polymorphic sites for economic traits were avUCP C+282T (mean body weight, p<0.05), avUCP C+433T (daily percent lay, p<0.05), and avUCP T+1316C (daily percent lay, p<0.05). The frequency of each SNP was 0.125 (C+282T in avUCP gene exon 1 region), 0.150 (C+433T in avUCP gene intron 1 region), and 0.15 (T+1316C in avUCP gene exon 3 region), respectively. Among the identified SNPs, one pair of SNPs (genotype CC, C+282T and TT, avUCP C+433T) showed the highest daily percent lay (p<0.05) and mean body weight (p<0.05) and the frequency was 0.067. This study of the avUCP gene could be useful for genetic studies of this gene and selection on economic traits for KNC.

• The Korean Journal of Mycology
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• v.28 no.1
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• pp.26-31
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• 2000

We isolated genomic clone of FVFD16 and FVFD30 gene specifically expressed during fruit body formation of Flammulina velutipes [(Curt: Fr.) Sing] and determinated the sequences. The FVFD16 gene is including two introns in open reading frame, and FVFD30 gene is including four introns. The introns were matched GT/AG rule. The FVFD16 and FVFD30 genes contained CAAT box with similarity arrange and TATA box. CT-rich region was presented before the transcription start point. FVFD30 gene is investigated that expected the most activity of CCACC arrange. The result of FVFD16 gene analysis showed 80% homology by cDNA clone that is gene family. From the results of genomic southern blot analysis, we presumed more than two copy number gene family of FVFD16 and FVFD30 gene.

• BMB Reports
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• v.37 no.1
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• pp.107-113
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• 2004

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.