• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.60-60
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• 2015

Hybrid histidine kinase is a part of two-component system that is required for various stress responses and pathogenesis of pathogenic fungi. In the present study, Tco1, a homologue of human pathogen Cryptococcus neoformans Tco1 encoding a hybrid histidine kinase, was identified in corn smut pathogen Ustilago maydis by bioinformatic analysis. To explore the role of Tco1 in the virulence of U. maydis, mutants in which the tco1 gene was partially deleted were constructed by allelic exchange. The U. maydis tco1 mutants did show unaltered growth rate on axenic medium but were unable to produce conjugation tubes and develop fuzzy filaments, resulting in impaired mating of compatible strains. The expression levels of prf1, pra1, and mfa1 which are involved in the pheromone pathway significantly decreased in the tco1 mutants. In inoculation tests to host, the tco1 mutants showed significantly reduced ability in the production of anthocyanin pigments and tumor development on maize leaves. Overall, the combined results indicated that Tco1 plays important roles in sexual development and virulence of U. maydis by regulating the expression of the genes involved in the pheromone pathway.

• Molecules and Cells
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• v.27 no.1
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• pp.119-123
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• 2009

Porcine endogenous retroviruses (PERVs) gamma1 in the pig genome have the potential to act as harmful factors in xenotransplantation (pig-to-human). Long terminal repeats (LTRs) are known to be strong promoter elements that could control the transcription activity of PERV elements and the adjacent functional genes. To investigate the transcribed PERV gamma1 LTR elements in pig tissues, bioinformatic and experimental approaches were conducted. Using RT-PCR amplification and sequencing approaches, 69 different transcribed LTR elements were identified. And 69 LTR elements could be divided into six groups (15 subgroups) by internal variation including tandem repeated sequences, insertion and deletion (INDEL). Remarkably, all internal variations were indentified in U3 region of LTR elements. Taken together, the identification and characterization of various PERV LTR transcripts allow us to extend our knowledge of PERV and its transcriptional study.

• Journal of fish pathology
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• v.24 no.3
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• pp.297-305
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• 2011

A trap identification system for isolating functional sequences to allow the constitutive expression of foreign protein from Edwardsiella tarda was developed. Using the green fluorescent protein (GFP) reporter-based trap system, various functional sequences to drive heterologous expression of the GFP were selectable in Escherichia coli host. However from the bioinformatic sequence analysis, all the segments predicted as regulatory regions were not native promoters actually existing upstream of endogenous E. tarda genes. Instead, a number of non-authentic sequences, possibly resulted from the random shuffling and/or intermolecular ligation were also proven to be able to display a potent GFP expression in the recombinant E. coli. Further analysis with selected clones showed that both authentic and non-authentic sequences could function in as a constitutive promoter, leading quite a consistent and stable GFP expression after repetitive subcultures. Microscopic examination also confirmed the uniform pattern of GFP expression in every host bacterium. Semi-quantitative assay of GFP showed that there was no clear relationship between expression levels and organizational features of the promoters trapped. Functional promoter-like elements achieved in the present study could be a good starting material for multivalent genetic engineering of E. tarda in order to produce recombinant vaccines in a cost-effective fashion.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.41-44
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• 2005

Cytokines play a crucial role in the immune and inflammatory responses. But because of the high evolutionary rate of these proteins, the similarity between different members of their family is very low, which makes the identification of novel members of cytokines very difficult. According to this point, a new bioinformatic strategy to identify novel cytokine of the short-chain and long-chain 4${\alpha}$ helix cytokine using hidden markov model (HMM) is proposed in the paper. As a result, two motifs were created on the two train data sets, which were used to search three different databases. In order to improve the result, a strict criterion is established to filter the novel cytokines in the subject proteins. Finally, according to their E-value, scores and the criterion, four subject proteins are predicted to be possible novel cytokines for each family respectively.

• Mycobiology
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• v.42 no.3
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• pp.241-248
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• 2014

NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferric-chelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bioinformatic approaches used to identify Nox-encoding genes. Further, most studies on fungal Nox genes have focused mainly on functionality, rather than sequence properties, and consequently clear differentiation among the various Nox isoforms has not been achieved. We conducted an extensive sequence analysis to identify putative Nox genes among 34 eukaryotes, including 28 fungal genomes and one Oomycota genome. Analyses were performed with respect to phylogeny, transmembrane helices, di-histidine distance and glycosylation. Our analyses indicate that the sequence properties of fungal Nox genes are different from those of human and plant Nox genes, thus providing novel insight that will enable more accurate identification and characterization of fungal Nox genes.

• BMB Reports
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• v.37 no.1
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• pp.93-106
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• 2004

The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, 'systems biology' studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).

• Fisheries and Aquatic Sciences
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• v.20 no.12
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• pp.31.1-31.11
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• 2017

Background: Liver-expressed antimicrobial peptide-2 (LEAP-2) is an important component of innate immune system in teleosts. In order to understand isoform-specific involvement and regulation of LEAP-2 genes in mud loach (Misgurnus mizolepis, Cypriniformes), a commercially important food fish, this study was aimed to characterize gene structure and expression characteristics of two paralog LEAP-2 isoforms. Results: Mud loach LEAP-2 isoforms (LEAP-2A and LEAP-2B) showed conserved features in the core structure of mature peptides characterized by four Cys residues to form two disulfide bonds. The two paralog isoforms represented a tripartite genomic organization, known as a common structure of vertebrate LEAP-2 genes. Bioinformatic analysis predicted various transcription factor binding motifs in the 5'-flanking regions of mud loach LEAP-2 genes with regard to development and immune response. Mud loach LEAP-2A and LEAP-2B isoforms exhibited different tissue expression patterns and were developmentally regulated. Both isoforms are rapidly modulated toward upregulation during bacterial challenge in an isoform and/or tissue-dependent fashion. Conclusion: Both LEAP-2 isoforms play protective roles not only in embryonic and larval development but also in early immune response to bacterial invasion in mud loach. The regulation pattern of the two isoform genes under basal and stimulated conditions would be isoform-specific, suggestive of a certain degree of functional divergence between isoforms in innate immune system in this species.

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.130-136
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• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• Genomics & Informatics
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• v.11 no.3
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• pp.102-113
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• 2013

Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.29-44
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• 2001

DNA damage by physical insult including UV and g-radiation might provoke genetic alterations in cells, which is followed by either acute cell death or tumorigenesis. The responsiveness to g-radiation depends on cellular context of target cells. To understand the mechanisms of checkpoint control, repair and cell death following genotoxic stimu]i, cDNA microarray can provide the gene expression profile. To make a profile of gene expression in irradiated Jurkat T cells, we hybridized the cDNA microarray using cDNA from g-irradiated Jurkat T cells. Jurkat T cells were exposed to 4Gy to 16Gy, and total RNA were extracted at 4 to 24 hrs after irradiation. The hybridization of the microarray to fluorescence-labeled cDNA from treated and untreated cells was analyzed by bioinformatic analysis to address relative changes in expression levels of the genes present in the array. Responses varied widely in different time points, suggesting acute stress response and chronic restoration or cell death. From these results we could select 384 genes related to radiation response in Tcells, and radiation response might be different in various types of cells. Using Radchip, we could separate "the exposed" from control PBMCs. We propose that Radchip might be useful to check the radiation research as well as radiation carcinogenesis.