• Molecules and Cells
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• 제26권5호
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• pp.427-435
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• 2008

In this review, we discuss the genes and the related signal pathways that regulate aging and longevity by reviewing recent findings of genetic longevity models in rodents in reference to findings with lower organisms. We also paid special attention to the genes and signals mediating the effects of calorie restriction (CR), a powerful intervention that slows the aging process and extends the lifespan in a range of organisms. An evolutionary view emphasizes the roles of nutrient-sensing and neuroendocrine adaptation to food shortage as the mechanisms underlying the effects of CR. Genetic and non-genetic interventions without CR suggest a role for single or combined hormonal signals that partly mediate the effect of CR. Longevity genes fall into two categories, genes relevant to nutrient-sensing systems and those associated with mitochondrial function or redox regulation. In mammals, disrupted or reduced growth hormone (GH)-insulin-like growth factor (IGF)-1 signaling robustly favors longevity. CR also suppresses the GH-IGF-1 axis, indicating the importance of this signal pathway. Surprisingly, there are very few longevity models to evaluate the enhanced anti-oxidative mechanism, while there is substantial evidence supporting the oxidative stress and damage theory of aging. Either increased or reduced mitochondrial function may extend the lifespan. The role of redox regulation and mitochondrial function in CR remains to be elucidated.

• Journal of Microbiology and Biotechnology
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• 제28권12호
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• pp.1999-2008
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• 2018

The compound 2,5-furandicarboxylic acid (FDCA), an important bio-based monomer for the production of various polymers, can be obtained from 5-hydroxymethylfurfural (HMF). However, efficient production of FDCA from HMF via biocatalysis has not been well studied. In this study, we report the identification of key genes that are involved in FDCA synthesis and then the engineering of Raoultella ornithinolytica BF60 for biocatalytic oxidation of HMF to FDCA using its resting cells. Specifically, previously unknown candidate genes, adhP3 and alkR, which were responsible for the reduction of HMF to the undesired product 2,5-bis(hydroxymethyl)furan (HMF alcohol), were identified by transcriptomic analysis. Combinatorial deletion of these two genes resulted in 85.7% reduction in HMF alcohol formation and 23.7% improvement in FDCA production (242.0 mM). Subsequently, an aldehyde dehydrogenase, AldH, which was responsible for the oxidation of the intermediate 5-formyl-2-furoic acid (FFA) to FDCA, was identified and characterized. Finally, FDCA production was further improved by overexpressing AldH, resulting in a 96.2% yield of 264.7 mM FDCA. Importantly, the identification of these key genes not only contributes to our understanding of the FDCA synthesis pathway in R. ornithinolytica BF60 but also allows for improved FDCA production efficiency. Moreover, this work is likely to provide a valuable reference for producing other furanic chemicals.

• Asian-Australasian Journal of Animal Sciences
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• 제32권7호
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• pp.1044-1051
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• 2019

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

• 한국환경독성학회:학술대회논문집
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• 한국환경독성학회 2003년도 춘계학술대회
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• pp.180-180
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• 2003

Transcript profiling is a particularly valuable tool in the field of steroid receptor biology, as these receptors are ligand-activated transcription factors and therefore exert their initial effects through altering gene expression in responsive cells. Also, an increased awareness of endocrine disrupting chemicals (EBCs) and their potential to affect wildlife and humans has produced a demand for practical screening methods to identify endocrine activity. Here we developed an in-house cDNA microarray, named KISTCHIP-400, with 401 clones, hormone related genes, factors, and ESTs, based on public database and research papers. Theses clones contained estrogen, androgen, thyroid hormone St receptors, sex hormone signal transduction ＆ regulation, c-fos, c-myc, ps2 gene, metabolism related genes etc. And to validate the KISTCHIP-400, we investigated gene expression profiles with reference hormones, 10$\^$-8/ M 17be1a-estradiol, 10$\^$-7/ M testosterone, 10$\^$-7/ M progesterone, and thyroxin in MCF-7 cell line. Although it is in first step of validation, low doses and combinations of EDCs need to be tested. Our preliminary results that indicate the developed microarray may be a useful laboratory tool for screening EDCs and elucidating endocrine disrupting mechanism.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.124-130
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• 2004

Microarray expression datasets are incessantly cumulated with the aid of recent technological advances. One of the first steps for analyzing these data under various experimental conditions is determining differentially expressed genes (DEGs) in each condition. Reasonable choices of thresholds for determining differentially expressed genes are used for the next -step-analysis with suitable statistical significances. We present a model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are tying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful network structure from microarray datasets.

• Genomics & Informatics
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• 제8권2호
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• pp.81-85
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• 2010

The aim of the study was to investigate pig reference families, generated from Korean native pigs (KNP) that were crossed with Yorkshire (YS) breeds, which were used to evaluate genetic markers to select breeding animals with superior pork quality. A set of five candidate genes (PRKAG3, MC4R, CAST, ESR, and PRLR ) was analyzed for association with pork quality traits. PRKAG3 (I199V) SNP genotypes were significantly associated with muscle moisture, protein, and fat contents. The MC4R D298N polymorphism was significantly associated with meat tenderness and color traits. The CAST polymorphism was significantly associated with muscle moisture and crude protein traits. These three genes have been associated with pork quality traits in other pig populations, and some of our results are consistent with earlier studies. In addition, two reproductive candidate genes (ESR and PRLR ) did not have significant associations. These results suggest that further study is warranted to investigate and develop more DNA markers associated with pork quality in our KNP-crossed pig families.

• 한국육종학회지
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• 제40권1호
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• pp.8-14
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• 2008

A complete diallel cross was performed to determine the inheritance of allelopathic potential and combining ability of six rice germplasm that showed different level of allelopathic potential against barnyardgrass. Parents and F1 of 30 crosses were assessed for allelophatic potential in field condition. Barnyardgrass (Echinochloa crus-galli (L.) Beauv. var. frumentaceae) was used for rice allelopathic potential indicator which was observed in height and shoot dry weight, then suppression percentage were calculated by comparing to barnyardgrass grown in control plot (no rice). It was found that general combining ability showed no significant effect, whereas specific combining ability and reciprocal effect were significant. Variance analysis confirmed that genetic control of allelopathic potential in rice against barnyardgrass was mostly directed by dominance gene effect. The dominant genes were associated with high allelopathic potential and recessive genes were associated with low allelopathic potential. Heritability in broad sense for barnyardgrass dry weight suppression was around 41%; whereas for barnyardgrass height suppression was 51%. However, heritability in narrow sense was very low. The finding suggests that accumulation of genes associated with allelopathic potential would be a strategy to develop promising varieties in reference with the specific combining ability of cross combinations.

• 한국발생생물학회지:발생과생식
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• 제27권1호
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• pp.47-56
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• 2023

Despite the commercialization of Next generation sequencing (NGS) gene testing, only a few studies have addressed the various ethical and legal problems associated with NGS testing in Korea Here, we reviewed the normative issues that emerged at each stage of the wet analysis and bioinformatics analysis of NGS gene testing. In particular, it was in mind to apply various international guidelines and the principles of bioethics to actual clinical practice. Considering the characteristics of NGS testing, wet analysis of additional testing can be justified if presumptive consent is recognized. Furthermore, the medical relationship between diseases needs to be established and it should be clear that the patient would have given consent if the patient had been aware of the correlation between genes. At the stage of bioinformatics analysis, the question of unsolicited findings arises. In case of unsolicited and relevant findings, according to American College of Medical Genetics and Genomics (ACMG), a recognized relationship between genes and diseases needs to be established. In case of unsolicited and not-relevant findings, it is almost impossible to determine whether knowing or not knowing the findings is more beneficial to the patient. However, it seems to be certain that the psychological harm an individual may suffer from such information is likely to be greater if the disease is severe and if there is no cure. The list of genes for which the ACMG guidelines impose reporting obligations is a good reference for judgment.

• Journal of Crop Science and Biotechnology
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• 제11권1호
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• pp.7-12
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• 2008

Quantitative trait loci, a genetic concept for explaining the inheritance of non-Mendelian traits in 1940s, have been realized as particular fragments of chromosome even unique genes in most crops in 21st century. However, only very a small portion of QTL has been screened out by geneticists comparing to a great number of genes underneath the quantitative traits. These identified QTL even have been seldom used into breeding program because crop breeders may not find the QTL in their breeding populations in their field station. Several key points will be proposed to meet the challenges of QTL analysis today: a fine mapping population and the related reference genetic map, QTL evaluation in multiple environments, recognizing real QTL with small genetic effect, map integration.

• 대한의생명과학회지
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• 제10권4호
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• pp.333-339
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• 2004

A multiplex PCR assay targeting the yst and 16S rRNA genes of Yersinia enterocolitica was developed to specifically identify pathogenic Y. enterocolitica from pure culture. Simultaneous amplification of 145 and 416 bp fragments of the yst and 16S rRNA genes of Y. enterocolitica was obtained using the primer pairs in a single reaction. Validation of the assay was performed with the reference Yersinia strains and other members of the family Enterobacteriaceae. The defined primer pairs amplified the targeted sequence from only pathogenic Y. enterocolitica strains, whereas none of the other bacterial species yielded any amplified fragments. Within an assay time of 4 h, this assay offers a very specific, reliable, and inexpensive alternative to the conventional phenotypic assays used in clinical laboratories to identify pathogenic Y. enterocolitica.