• Journal of Mycology and Infection
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• 제24권2호
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• pp.37-44
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• 2019

To date, hundreds of fungal genomes have been sequenced, and many more are underway. Recently developed cutting-edge techniques generate very large amounts of data, and the field of fungal genomics in dermatology has consequently evolved substantially. Methodological improvements have broadened the scope of large-scale ecological studies in dermatology, including biodiversity assessments and genomic identification of fungi. Here, we aimed to provide a brief introduction to bioinformatic approaches to fungal genomics in the field of dermatology. We described the history and basic concepts of fungal genomics and presented sequencing-based techniques for fungal identification, including a list of the revised taxa of dermatophytes, as determined by current phylogenetic analysis. Finally, we discussed the emerging trends in fungal genomics in dermatology, such as next-generation sequencing.

• Genomics & Informatics
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• 제20권4호
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• pp.49.1-49.7
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• 2022

Many packages for a meta-analysis of genome-wide association studies (GWAS) have been developed to discover genetic variants. Although variations across studies must be considered, there are not many currently-accessible packages that estimate between-study heterogeneity. Thus, we propose a python based application called Beta-Meta which can easily process a meta-analysis by automatically selecting between a fixed effects and a random effects model based on heterogeneity. Beta-Meta implements flexible input data manipulation to allow multiple meta-analyses of different genotype-phenotype associations in a single process. It provides a step-by-step meta-analysis of GWAS for each association in the following order: heterogeneity test, two different calculations of an effect size and a p-value based on heterogeneity, and the Benjamini-Hochberg p-value adjustment. These methods enable users to validate the results of individual studies with greater statistical power and better estimation precision. We elaborate on these and illustrate them with examples from several studies of infertility-related disorders.

• 한국식물학회:학술대회논문집
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• 한국식물학회 2001년도 춘계학술발표대회:발표눈문요지록
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• pp.7-7
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• 2001

• Asian-Australasian Journal of Animal Sciences
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• 제24권1호
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• pp.110-124
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• 2011

Anatomically separate fat depots differ in size, function, and contribution to pathological states such as the metabolic syndrome. We isolated pre-adipocytes from different adipose depots, omental, subcutaneous and intramuscular, of beef cattle, and cultured in vitro to determine the basis for the variations and attribute these variations to the inherent properties of adipocyte progenitors. The proliferating cells from all depots before the confluence were harvested and the proteome was analyzed by a functional proteomic approach, involving 2-DE and MALDI-TOF/TOF. More than 252 protein spots were identified, selected and analyzed by Image Master (ver 7.0) and MALDI-TOF/TOF. Further, our analysis showed that there were specific differences in proteome expression patterns among proliferating precursor cells from the three depots. Sixteen proteins were found to be differentially expressed and these were identified as proteins involved in cellular processes, heat shock/chaperones, redox proteins, cytoskeletal proteins and metabolic enzymes. The results also enabled us to understand the basic roles of these proteins in different inherent properties exhibited by adipose tissue depots.

• Journal of Plant Biotechnology
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• 제35권4호
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• pp.265-274
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• 2008

Glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family divided into Phi, Tau, Theta, Zeta, Lambda and DHAR classes on the basis of sequence identity. The Phi(F) and Tau(U) classes are plant-specific and ubiquitous. Their roles have been defined as herbicide detoxification and responses to biotic and abiotic stresses. Fifty-two members of the GST super-family were identified in the Arabidopsis thaliana genome, 13 members of which belong to the Phi class of GSTs (AtGSTFs). Based on the sequence similarities of AtGSTFs, 11 BAC clones were identified from Brassica rapa. Seven unique sequences of ORFs designated the Phi class candidates of GST derived from B. rapa (BrGSTFs) were detected from these 11 BAC clones by blast search and sequence alignment. Some of BrGSTFs were present in the same BAC clones indicating that BrGSTFs could also be clustered as usual in plant. They were mapped on B. rapa linkage group 2, 3, 9 and 10 and their nucleotide and amino acid sequences were highly similar to those of AtGSTFs. In addition, in silico analysis of BrGSTFs using Korea Brassica Genome Project 24K oligochip and microarray database for cold, salt and drought stresses revealed 15 unigenes to be highly similar to AtGSTFs and six of these were identical to one of BrGSTFs identified in the BAC clones indicating their expression. The sequences of BrGSTFs and unigenes identified in this study will facilitate further studies to apply GST genes to medical and agriculture purposes.

• BMB Reports
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• 제43권5호
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• pp.349-354
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• 2010

Previously, we reported that overexpression of Opa (Neisseria gonorrhoeae opacity-associated)-interacting protein 5 (OIP5) caused multi-septa formation and growth defects, both of which are considered cancer-related phenotypes. To evaluate OIP5 as a possible cancer therapeutic target, we examined its expression level in 66 colorectal cancer patients. OIP5 was upregulated about 3.7-fold in tumors and over 2-fold in 58 out of 66 colorectal cancer patients. Knockdown of OIP5 expression by small interfering RNA specific to OIP5 (siOIP5) resulted in growth inhibition of colorectal and gastric cancer cell lines. Growth inhibition of SNU638 by siOIP5 caused an increase in sub-G1 DNA content, as measured by flow cytometry, as well as an apoptotic gene expression profile. These results indicate that knockdown of OIP5 may induce apoptosis in cancer cells. Therefore, we suggest that OIP5 might be a potential cancer therapeutic target, although the mechanisms of OIP5-induced carcinogenesis should be elucidated.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.79.2-80
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• 2003

To better understand plant defense responses against pathogen attack, we identified the transcription factor-encoding genes in the hot pepper Capsicum annuum that show altered expression patterns during the hypersensitive response raised by challenge with bacterial pathogens. One of these genes, Ca1244, was characterized further. This gene encodes a plant-specific Type IIIA - zinc finger protein that contains two Cys$_2$His$_2$zinc fingers. Ca1244 expression is rapidly and specifically induced when pepper plants are challenged with bacterial pathogens to which they are resistant. In contrast, challenge with a pathogen to which the plants are susceptible only generates weak Ca1244 expression. Ca1244 expression is also strongly induced in pepper leaves by the exogenous application of ethephon, an ethylene releasing compound. Whereas, salicylic acid and methyl jasmonate had moderate effects. Pepper protoplasts expressing a Ca1244-smGFP fusion protein showed Ca1244 localizes in the nucleus. Transgenic tobacco plants overexpressing Ca1244 driven by the CaMV 355 promoter show increased resistance to challenge with a tobacco-specific bacterial pathogen. These plants also showed constitutive upregulation of the expression of multiple defense-related genes. These observations provide the first evidence that an Type IIIA - zinc finger protein, Ca1244, plays a crucial role in the activation of the pathogen defense response in plants.

• BMB Reports
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• 제41권4호
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• pp.300-304
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• 2008

The Dazl gene encodes a germ-cell-specific RNA-binding protein which is essential for spermatogenesis. It has been proposed that this protein (DAZL) binds to RNA in the cytoplasm of germ cells and controls spermatogenesis. Using the specific nucleic acids associated with proteins (SNAAP) technique, we identified 17 target mRNAs bound by mDAZL. Among these transcripts, we focused on TSSK2, which encodes a testis-specific serine/threonine kinase. To date, five TSSK family members have been cloned, and all are exclusively expressed in the testis. We demonstrated that in addition to the TSSK1 3'UTR, the 3'UTRs of TSSKs 2 and 4 were bound by human and mouse DAZL, and that human DAZL (hDAZL) bound to the 3'UTR of human TSSK5 (hTSSK5). Our results suggest that the Dazl gene may play different roles in human and mouse spermatogenesis by regulating different members of the downstream gene family.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.210-210
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• 2022

Silybum marianum is an annual or biennial plant from the Asteraceae family. It can grow in low-nutrient soil and drought conditions, making it easy to cultivate. From the seed, a specialized plant metabolite called silymarin (flavonolignan complex) is produced and is known to alleviate the liver from hepatitis and toxins damages. To infer the phylogenetic placement of a Korean milk thistle, we conducted a chloroplast assembly and annotation following by a comparison with existing Chinese reference genome (NC_028027). The chloroplast genome structure was highly similar with an assembly size of 152,642 bp, an 153,202 bp for Korean and Chinese milk thistle respectively. Moreover, there were similarities at the gene level, coding sequence (n = 82), transfer RNA (n = 31) and ribosomal RNA (n = 4). From all coding sequences gene set, the phylogenetic tree inference placed the Korean cultivar into the milk thistle clade; corroborating the expected tree. Moreover, an investigation the tree based only on the ycf1 gene confirmed the same tree; suggesting that ycf1 gene is a potential marker for DNA barcoding and population diversity study in milk thistle genus. Overall, the provided data represents a valuable resource for population genomics and species-centered determination since several species have been reported in the Silybum genus.

• 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.