• Animal cells and systems
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• v.15 no.3
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• pp.251-258
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• 2011

Ciliates are considered one of the most diverse protozoa and play significant roles in ecology. For successful taxonomic study of these microscopic eukaryotes, a staining procedure is necessary, due mainly to intrinsic difficulties in recognizing characteristics from living cells. Although molecular taxonomy has been used to resolve the ambiguities associated with traditional morphology-based taxonomy, extraction of genomic DNA from stained ciliate cells is not available yet. In the present study, we describe a method to extract genomic DNA from a single protargol-impregnated euplotid cell. By using $HgCl_2$ as a fixative and modulating the exposure time of bleach solution in the protargol impregnation, high-quality genomic DNA can successfully be extracted from a stained single cell with minimal loss of morphological integrity. This technique will contribute to the effectiveness of combined approaches of molecular and morphological taxonomy from single ciliate cells.

• Animal Bioscience
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• v.37 no.3
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• pp.451-460
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• 2024

Objective: The objective is to identify genomic regions and candidate genes associated with age to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) in Yorkshire pig. Methods: This study used a total of 104,380 records and 11,854 single nucleotide polymorphism (SNP) data obtained from Illumina porcine 60K chip. The estimated genomic breeding values (GEBVs) and SNP effects were estimated by single-step genomic best linear unbiased prediction (ssGBLUP). Results: The heritabilities of AGE, ADG, BF, and EMA were 0.50, 0.49, 0.49, and 0.23, respectively. We identified significant SNP markers surpassing the Bonferroni correction threshold (1.68×10^-6), with a total of 9 markers associated with both AGE and ADG, and 4 markers associated with BF and EMA. Genome-wide association study (GWAS) analyses revealed notable chromosomal regions linked to AGE and ADG on Sus scrofa chromosome (SSC) 1, 6, 8, and 16; BF on SSC 2, 5, and 8; and EMA on SSC 1. Additionally, we observed strong linkage disequilibrium on SSC 1. Finally, we performed enrichment analyses using gene ontology and Kyoto encyclopedia of genes and genomes (KEGG), which revealed significant enrichments in eight biological processes, one cellular component, one molecular function, and one KEGG pathway. Conclusion: The identified SNP markers for productive traits are expected to provide valuable information for genetic improvement as an understanding of their expression.

• BMB Reports
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• v.49 no.11
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• pp.607-611
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• 2016

The Cancer Genome Atlas (TCGA) has compiled genomic, epigenomic, and proteomic data from more than 10,000 samples derived from 33 types of cancer, aiming to improve our understanding of the molecular basis of cancer development. Availability of these genome-wide information provides an unprecedented opportunity for uncovering new key regulators of signaling pathways or new roles of pre-existing members in pathways. To take advantage of the advancement, it will be necessary to learn systematic approaches that can help to uncover novel genes reflecting genetic alterations, prognosis, or response to treatments. This minireview describes the updated status of TCGA project and explains how to use TCGA data.

• Genomics & Informatics
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• v.1 no.1
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• pp.1-6
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• 2003

In conclusion, the seemingly fuzzy and disorganized data of biology with thousands of different layers ranging from molecule to the Internet have refused so far to be mapped precisely and predicted successfully by mathematicians, physicists or computer scientists. Genomics and bioinformatics are the fields that process such complex data. The insights on the nature of biological entities as complex interaction networks are opening a door toward a generalization of the representation of biological entities. The main challenge of genomics and bioinformatics now lies in 1) how to data mine the networks of the domains of bioinformatics, namely, the literature, metabolic pathways, and proteome and structures, in terms of interaction; and 2) how to generalize the networks in order to integrate the information into computable genomic data for computers regardless of the levels of layer. Once bioinformatists succeed to find a general principle on the way components interact each other to form any organic interaction network at genomic scale, true simulation and prediction of life in silico will be possible.

• Biomedical Science Letters
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• v.20 no.4
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• pp.185-193
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• 2014

Cancers are based upon an array of orchestrated genetic changes and the identification of changes causally related to the carcinogenic process. To elucidate the mechanism of cancer carcinogenesis, it is necessary to reconstruct these molecular events at each level. Microarray technologies have been extensively used to evaluate genetic alterations associated with cancer onset and progression in clinical oncology. The clinical impact of the genomic alterations identified by microarray technologies are growing rapidly and array analysis has been evolving into a diagnostic tool to better identify high-risk patients and predict patient outcomes from their genomic profiles. Here, we discuss the state-of-the-art microarray technologies and their applications in clinical oncology, and describe the potential benefits of these analysis in the clinical implications and biological insights of cancer biology.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.58-58
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• 2017

The advent of next generation sequencing technology has elicited plenty of sequencing data available in agriculturally relevant plant species. For most crop species, it is too expensive to obtain the whole genome sequence data with sufficient coverage. Thus, many approaches have been developed to bring down the cost of NGS. Genotyping-by-sequencing (GBS) is a cost-effective genotyping method for complex genetic populations. GBS can be used for the analysis of genomic selection (GS), genome-wide association study (GWAS) and constructing haplotype and genetic linkage maps in a variety of plant species. For efficiently dealing with plant GBS data, the TASSEL-GBS pipeline is one of the most popular choices for many researchers. TASSEL-GBS is JAVA based a software package to obtain genotyping data from raw GBS sequences. Here, we describe application of GBS and bioinformatics pipeline of TASSEL-GBS for analyzing plant genetics data.

• Archives of Plastic Surgery
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• v.47 no.3
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• pp.203-208
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• 2020

Vascular anomalies are congenital localized abnormalities that result from improper development and maintenance of the vasculature. The lesions of vascular anomalies vary in location, type, and clinical severity of the phenotype, and the current treatment options are often unsatisfactory. Most vascular anomalies are sporadic, but patterns of inheritance have been noted in some cases, making genetic analysis relevant. Developments in the field of genomics, including next-generation sequencing, have provided novel insights into the genetic and molecular pathophysiological mechanisms underlying vascular anomalies. These insights may pave the way for new approaches to molecular diagnosis and potential disease-specific therapies. This article provides an introduction to genetic testing for vascular anomalies and presents a brief summary of the etiology and genetics of vascular anomalies.

• Journal of Genetic Medicine
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• v.12 no.1
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• pp.6-11
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• 2015

Intellectual disability (ID) is the most common disability among people under the age of 20 years. In the absence of obvious non-genetic causes of ID, the majority of cases of severe ID are thought to have a genetic cause. The advent of technologies such as array comparative genomic hybridization, single nucleotide polymorphism genotyping arrays, and massively parallel sequencing has shown that de novo copy number variations and single nucleotide variations affecting coding regions are major causes of severe ID. This article reviews the genetic causes of ID along with diagnostic approaches for this disability.

• Journal of Plant Biotechnology
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• v.7 no.1
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• pp.1-15
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• 2005

Salinity is one of the major limiting factors for agricultural productivity. In plants, accumulation of osmolytes plays a pivotal role in abiotic stress tolerance. Likewise, exclusion or compartmentation of $Na^+$ ions into vacuoles provides an efficient mechanism to avert deleterious effects of $Na^+$ in the cytosol. Both vacuolar and plasma membrane sodium transporters and $H^+-ATPases$ can provide the necessary ion homeostasis. A variety of crop plants were engineered with respect to the synthesis of osmoprotectants and ion-compartmentation, but there are other cellular pathways involved in the salinity responses that are still not completely explored. Genomics approaches are increasingly used to identify genes and pathway changes involved in salt-tolerance. The new knowledge may be used via guided genetic engineering of multiple genes to create crop plants with significantly increased productivity in saline soils. This review surveys how plants deal with high salt conditions and how salt tolerance can be improved by transgenic approaches.

• Korean Journal of Agricultural Science
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• v.43 no.1
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• pp.1-13
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• 2016

Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.