• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.11-11
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• 2014

Fungal pathogens have huge impact on health and economic wellbeing of human by causing life-threatening mycoses in immune-compromised patients or by destroying crop plants. A key determinant of fungal pathogenesis is their ability to undergo developmental change in response to host or environmental factors. Genetic pathways that regulate such morphological transitions and adaptation are therefore extensively studied during the last few decades. Given that epigenetic as well as genetic components play pivotal roles in development of plants and mammals, contribution of microbial epigenetic counterparts to this morphogenetic process is intriguing yet nearly unappreciated question to date. To bridge this gap in our knowledge, we set out to investigate histone modifications among epigenetic mechanisms that possibly regulate fungal adaptation and processes involved in pathogenesis of a model plant pathogenic fungus, Magnaporthe oryzae. M. oryzae is a causal agent of rice blast disease, which destroys 10 to 30% of the rice crop annually. Since the rice is the staple food for more than half of human population, the disease is a major threat to global food security. In addition to the socioeconomic impact of the disease it causes, the fungus is genetically tractable and can undergo well-defined morphological transitions including asexual spore production and appressorium (a specialized infection structure) formation in vitro, making it a model to study fungal development and pathogenicity. For functional and comparative analysis of histone modifications, a web-based database (dbHiMo) was constructed to archive and analyze histone modifying enzymes from eukaryotic species whose genome sequences are available. Histone modifying enzymes were identified applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 22,169 histone-modifying enzymes identified from 342 species including 214 fungal, 33 plants, and 77 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. Based on the database entries, functional analysis of genes encoding histone acetyltransferases and histone demethylases is under way. Here I provide examples of such analyses that show how histone acetylation and methylation is implicated in regulating important aspects of fungal pathogenesis. Current analysis of histone modifying enzymes will be followed by ChIP-Seq and RNA-seq experiments to pinpoint the genes that are controlled by particular histone modifications. We anticipate that our work will provide not only the significant advances in our understanding of epigenetic mechanisms operating in microbial eukaryotes but also basis to expand our perspective on regulation of development in fungal pathogens.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.261-271
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• 2016

Citrus is an economically important fruit crop widely growing worldwide. However, citrus production largely depends on natural hybrid selection and bud sport mutation. Unique botanical features including long juvenility, polyembryony, and QTL that controls major agronomic traits can hinder the development of superior variety by conventional breeding. Diverse factors including drastic changes of citrus production environment due to global warming and changes in market trends require systematic molecular breeding program for early selection of elite candidates with target traits, sustainable production of high quality fruits, cultivar diversification, and cost-effective breeding. Since the construction of the first genetic linkage map using isozymes, citrus scientists have constructed linkage maps using various DNA-based markers and developed molecular markers related to biotic and abiotic stresses, polyembryony, fruit coloration, seedlessness, male sterility, acidless, morphology, fruit quality, seed number, yield, early fruit setting traits, and QTL mapping on genetic maps. Genes closely related to CTV resistance and flesh color have been cloned. SSR markers for identifying zygotic and nucellar individuals will contribute to cost-effective breeding. The two high quality citrus reference genomes recently released are being efficiently used for genomics-based molecular breeding such as construction of reference linkage/physical maps and comparative genome mapping. In the near future, the development of DNA molecular markers tightly linked to various agronomic traits and the cloning of useful and/or variant genes will be accelerated through comparative genome analysis using citrus core collection and genome-wide approaches such as genotyping-by-sequencing and genome wide association study.

• Horticultural Science & Technology
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• v.33 no.1
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• pp.93-105
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• 2015

This study was performed to analyze genetic relationships of the four major cucurbitaceous crops including watermelon, melon, cucumber, and squash/pumpkin. Among 120 EST-SSR primer sets selected from the International Cucurbit Genomics Initiative (ICuGI) database, PCR was successful for 51 (49.17%) primer sets and 49 (40.8%) primer sets showed polymorphisms among eight Cucurbitaceae accessions. A total of 382 allele-specific PCR bands were produced by 49 EST-SSR primers from 24 Cucurbitaceae accessions and used for analysis of pairwise similarity and dendrogram construction. Assessment of the genetic relationships resulted in similarity indexes ranging from 0.01 to 0.85. In the dendrogram, 24 Cucurbitaceae accessions were classified into two major groups (Clade I and II) and 8 subgroups. Clade I comprised two subgroups, Clade I-1 for watermelon accessions [I-1a and I-1b-2: three wild-type watermelons (Citrullus lanatus var. citroides Mats. & Nakai), I-1b-1: six watermelon cultivars (Citrullus lanatus var. vulgaris S chrad.)] a nd C lade I -2 for melon and cucumber accessions [I-2a-1 : 4 melon cultivars(Cucumis melo var. cantalupensis Naudin.), I-2a-2: oriental melon cultivars (Cucumis melo var. conomon Makino.), and I-2b: five cucumber cultivars (Cucumis sativus L.)]. Squash and pumpkin accessions composed Clade II {II-1: two squash/ pumpkin cultivars [Cucurbita moschata (Duch. ex Lam.)/Duch. & Poir. and Cucurbita maxima Duch.] and II-2: two squash/pumpkin cultivars, Cucurbita pepo L./Cucurbita ficifolia Bouche.}. These results were in accordance with previously reported classification of Cucurbitaceae species, indicating that watermelon EST-SSRs show a high level of marker transferability and should be useful for genetic study in other cucurbit crops.

• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.844-854
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• 2005

We constructed a defined physical and genetic map of H. pylori strain 51, previously isolated from a Korean patient with a duodenal ulcer, by combining a restriction analysis by pulse-field gel electrophoresis with the construction of a BAC library. A Notl-digest of H. pylori strain 51 genome yielded seven fragments, from which the genomic size was estimated to be 1,698$\pm$24 kb. The BAC library was constructed from 50 to 200 kb fragments of HindIII-digested genomic DNA. From 700 BAC clones, an ordered overlapping maxi-set of 82 BAC clones was assembled that covered the entire genome. The positions of 15 genes were localized in the strain 51 genome with 4-22 kb of resolution and were compared with their orthologues in strain 26695 and strain J99. The arrangement of the 15 genes was identical in strain 51 and strain J99, except for flaA and hpaA. The plasticity zone of strain 51, like that of strain J99, was located in the single region, and was shorter than those of strain 26695 and strain J99. The strain 51 plasticity zone consisted of ORFs common only to strain 51 and J99 or to strain 51 and 26695, as well as strain 51-specific ORFs. Three genetic translocations and/or inversions were found between orthologue ORFs in strain 51 and strain J99. These results show that the chromosomal organization of strain 51 differs from Western strains such as strain 26695 and strain J99.

• Genomics & Informatics
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• v.6 no.1
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• pp.18-28
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• Journal of Microbiology
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• v.45 no.1
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• pp.21-28
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• 2007

In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China. The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on In(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori's growth and colonization in its host. In contrast, 522 (31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strain-specific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a vaccine for H. pylori.

• The Korea Journal of Herbology
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• v.31 no.5
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• pp.107-114
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• 2016

Objectives : Poria cocos Wolf has been widely used in Korean medicine as a medicinal fungus. In this study, we investigated that comparative anti-oxidant effects of ethanol extract from wild Poria cocos (WP) and plastic bag-cultivated Poria cocos (PBP).Methods : Total polyphenol and flavonoid contents in WP and PBP extract were monitored. And DPPH, ABTS, hydroxyl (·OH) free radical scavenging capacity, reducing power and xanthine oxidase inhibition activities of them were determined at 5, 1, 0.5 mg/ml concentrations.Results : Higher total polyphenol contents were found in the PBP extract (52.07±0.6 mg/TAEg) than in the WP extract (28.44±0.26 mg/TAEg). The flavonoid contents in WP and PBP extract were 17.29±0.30 mg/ RUEg, 21.36±0.40 mg/ RUEg, respectively. Also, DPPH, ABTS and ·OH free radical scavenging capacity of PBP extract in treated concentrations (5, 1, 0.5 mg/ml) significantly increased compared to those of WP-treated group. In particular, DPPH, ABTS free radical scavenging capacity and reducing power of PBP extract at 5 mg/ml concentration were similar to positive control (BHA or vit. C). Xanthine oxidase (XO) inhibition rate in both extract increased dose dependently. But it was significantly increased in PBP-treated group, only at 5 mg/ml, compared to those of WP-treated group. Then, their inhibition rate by PBP was similar to positive control (BHA).Conclusions : These results suggest that PBP extract is superior to WP extract in anti-oxidant capacity thus PBP can be applied in variable antioxidative products as a substitute for WP.

• Journal of Genetic Medicine
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• v.8 no.1
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• pp.28-34
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• 2011

Most clinicians understand clinical trials as the evaluation process for new medicine before their use. However, clinical trials can also be applied to laboratory diagnostic tests (LDTs) to verify diagnostic accuracy and efficacy before their clinical laboratory implementation for patients. The clinical trial of LDT has two distinctive characteristics that are different from the case of pharmaceuticals and thus worth special consideration. One of them is the level of evidence. The well-designed randomized controlled trials (RCTs) are known to provide the best evidence to prove the clinical efficacy of any pharmaceutical products. However, RCTs lose practicality when applied to LDTs due to various issues including ethical complications. For this reason, comparative study format is considered more feasible approach for LDTs. In addition pharmaceuticals and LDTs are different in that the user's intervention is not required for the former but critical to the latter. Moreover, in the case of pharmaceuticals, end-products are produced by manufacturers before being used by clinicians. However, in LDTs, once reagents and instruments are provided by manufacturers, they are first utilized by clinical laboratories to produce test results in order for clinicians to use them later. In other words, when it comes to LDTs, clinical laboratories play the role of manufacturers, providing reliable test results with improved quality assurance. Considering the distinctive characteristics of LDTs, we would like to offer detailed suggestions to successfully perform clinical trials in LDTs, which include analytical performance measures, clinical test performance measures, diagnostic test accuracy measures, clinical effectiveness measures, and post-implementation surveillance.

• Journal of Life Science
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• v.17 no.12
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• pp.1622-1626
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• 2007

This study was conducted to identify useful single nucleotide polymorphisms (SNPs) and determine their association with economically important traits in pig population. Four candidate gene analyses have identified important chromosomal regions and major genes associcated whit economic traits of the pig. For application of the chromosomal information to the pig industry using DNA technology, SNP markers were developed by comparative re-sequencing of polymerase chain reaction (PCR) products of 4 candidate genes (CSF2, IL4, MYOD, RIP140). PCR restriction fragment length polymorphism (PCR-RFLP) assays were developed for these 4 SNPs and used to genotype Berkshire pig populations in Korea.

• Animal Bioscience
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• v.37 no.6
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• pp.982-992
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• 2024

Objective: Jining Grey goat is a local Chinese goat breed that is well known for its high fertility and excellent meat quality but shows low meat production performance. Numerous studies have focused on revealing the genetic mechanism of its high fertility, but its highlighting meat quality and muscle growth mechanism still need to be studied. Methods: In this research, an integrative analysis of the genomics and transcriptomics of Jining Grey goats compared with Boer goats was performed to identify candidate genes and pathways related to the mechanisms of meat quality and muscle development. Results: Our results overlap among five genes (ABHD2, FN1, PGM2L1, PRKAG3, RAVER2) and detected a set of candidate genes associated with fatty acid metabolism (PRKAG3, HADHB, FASN, ACADM), amino acid metabolism (KMT2C, PLOD3, NSD2, SETDB1, STT3B, MAN1A2, BCKDHB, NAT8L, P4HA3) and muscle development (MSTN, PPARGC1A, ANKRD2). Several pathways have also been detected, such as the FoxO signaling pathway and Apelin signaling pathway that play roles in lipid metabolism, lysine degradation, N-glycan biosynthesis, valine, leucine and isoleucine degradation that involving with amino acid metabolism. Conclusion: The comparative genomic and transcriptomic analysis of Jining Grey goat and Boer goat revealed the mechanisms underlying the meat quality and meat productive performance of goats. These results provide valuable information for future breeding of goats.