• BMB Reports
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• v.37 no.1
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• pp.75-82
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• 2004

Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.282-285
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• 2004

The polyene antibiotics including nystatin, pimaricin, amphotericin and candicidin are a family of most promising antifungal polyketide compounds, typically produced by rare actinomycetes species. The biosynthetic gene clusters for these polyenes have been previously investigated, revealing the presence of highly homologous biosynthetic genes among polyene-producers such as polyketide synthase (PKS) and cytochrome P450 hydroxylase (CYP) genes. Based on amino acid sequence alignment among actinomycetes CYP genes, the highly-conserved regions specific for only polyene CYP genes were identified and chosen for degenerate PCR primers, followed by the PCR-screening with various actinomycetes genomic DNAs. Among tested several polyene non-producing actinomycetes strains, Pseudonorcardia autotrophica strain was selected based on the presence of PCR product with polyene-specific CYP gene primers, and then confirmed to contain a cryptic novel polyene hydroxylase gene in the chromosome. These results suggest that the polyene-specific hydroxylase gene PCR should be an efficient way of screening and isolating potentially-valuable cryptic polyene antibiotic biosynthetic genes from various microorganisms including rare actinomycetes.

• Korean Journal of Veterinary Service
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• v.39 no.1
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• pp.59-63
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• 2016

Duck circovirus (DuCV) has been recognized as a contagious immunosuppressive virus affecting many duck species worldwide. To determine the prevalence of DuCV infection in ducks, we investigated 104 samples collected from 50 duck farms in Jeonbuk province with the polymerase chain reaction (PCR). Among collected samples, 40 (38.5%) were positive for DuCV. The prevalence of DuCV PCR-positive samples increased with age. Genomic sequences of 15 DuCV strains were determined and compared with previously available DuCV sequences in public databases. Phylogenetic analysis revealed that all strains were clustered into DuCV-1 group.

• Environmental Mutagens and Carcinogens
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• v.19 no.1
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• pp.28-33
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• 1999

The SNF2 family includes proteins from a variety of species with roles I cellular processes such as transcriptional regulation, recombination and various types of DNA repair. Several proteins with unknown function are also included in this family. Here, we report the cloning and characterization of hrp 2+ gene (helicase related gene from S. pombe) which was isolated by PCR amplication using the conserved domain of SNF2 motifs within the ERCC6 gene which encodes a protein involved in DNA excision repair. The hrp2+ gene was isolated by screening with yeast S. pombe genomic library. The isolated cloned contained 6.5 kb insert DNA. Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as hrp2+ gene and this gene exists as a single copy in S. pombe genome. The 4.7 kb transcript of mRNA was identified by Northern blot. To examined the transcriptional regulation of hrp2+ gene, DNA damaging agents were treated. These results indicated that the hrp2+ gene may not be directly involved in DNA replication, but may be involved in damage response pathway.

• Proceedings of the Korean Aquaculture Society Conference
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• 2002.08a
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• pp.171-172
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• 2002

Genomic DNA from the muscle of marsh clam (Corbicula leana)from Gochang was extrected in order to identify genetic differences and similarity by randomly amplified polymorphic DNAs-polymerase chain reaction. 3.28 of the 23.0 polymorphic bands per lane were found to be polymorphic in marsh clam. Also, about 4.34% of total polymorphic bands were either specific to marsh clam. The major common bands of 0.28 kb generated by primer OPB-15 (GGAGGGTGTT) were present in every individuals, respectively, which were polymorphic. This common bands which present in every individuals should be diagnostic of specific strains, species and-or their relatedness. Primer OPB-19 (ACCCCCGAAG) produced the highest number of specific bands, which was 12. The specific minor band of 0.07 kb was present in lane 22, which were polymorphic. Especially, only a specific band (1.35kg) identifying individuals was observed in lane 22.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.4
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• pp.587-596
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• 2001

In the last decade, rapid developments in molecular biotechnology and of genomic tools have enabled the creation of dense linkage maps across whole genomes of human, plant and animals. Successful development and implementation of interval mapping methodologies have allowed detection of the quantitative trait loci (QTL) responsible for economically important traits in experimental and commercial livestock populations. The candidate gene approach can be used in any general population with the availability of a large resource of candidate genes from the human or rodent genomes using comparative maps, and the validated candidate genes can be directly applied to commercial breeds. For the QTL detected from primary genome scans, two incipient fine mapping approaches are applied by generating new recombinants over several generations or utilizing historical recombinants with identity-by-descent (IBD) and linkage disequilibrium (LD) mapping. The high resolution definition of QTL position from fine mapping will allow the more efficient implementation of breeding programs such as marker-assisted selection (MAS) or marker-assisted introgression (MAI), and will provide a route toward cloning the QTL.

• BMB Reports
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• v.44 no.5
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• pp.291-297
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• 2011

Aging is one of the most complicated biological processes in all species. A number of different model organisms from yeast to monkeys have been studied to understand the aging process. Until recently, many different age-related genes and age-regulating cellular pathways, such as insulin/IGF-1-like signal, mitochondrial dysfunction, Sir2 pathway, have been identified through classical genetic studies. Parallel to genetic approaches, genome-wide approaches have provided valuable insights for the understanding of molecular mechanisms occurring during aging. Gene expression profiling analysis can measure the transcriptional alteration of multiple genes in a genome simultaneously and is widely used to elucidate the mechanisms of complex biological pathways. Here, current global gene expression profiling studies on normal aging and age-related genetic/environmental interventions in widely-used model organisms are briefly reviewed.

• Journal of Microbiology and Biotechnology
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• v.24 no.4
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• pp.563-567
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• 2014

Pseudomonas syringae pv. syringae (Psy) is a major bacterial pathogen of many economically important plant species. Despite the severity of its impact, the genome sequence of the type strain has not been reported. Here, we present the draft genome sequence of Psy ATCC 19310. Comparative genomic analysis revealed that Psy ATCC 19310 is closely related to Psy B728a. However, only a few type III effectors, which are key virulence factors, are shared by the two strains, indicating the possibility of host-pathogen specificity and genome dynamics, even under the pathovar level.

• Genomics & Informatics
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• v.7 no.1
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• pp.26-31
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• 2009

Heat shock proteins are a class of molecular chaperones that can be found in nearly all organisms from Bacteria, Archaea and Eukarya domains. Heat shock proteins experience increased transcription during periods of heat induced osmotic stress and are involved in protein disaggregation and refolding as part of a cell's danger signaling cascade. Heat shock protein, Hsp20 is a small molecular chaperone that is approximately 20kDa in weight and is hypothesized to prevent aggregation and denaturation. Hsp20 can be found in several strains of Proteobacteria, which comprises the largest phyla of the Bacteria domain and also contains several medically significant bacterial strains. Genomic analyses were performed to determine a common evolutionary pattern among Hsp20 sequences in Proteobacteria. It was found that Hsp20 shared a common ancestor within and among the five subclasses of Proteobacteria. This is readily apparent from the amount of sequence similarities within and between Hsp20 protein sequences as well as phylogenetic analysis of sequences from proteobacterial and non-proteobacterial species.

• BMB Reports
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• v.41 no.11
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• pp.757-764
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• 2008

The genomic sequences of a huge number of species have been determined. Typically, these genome sequences and the associated annotation data are accessed through Internet-based genome browsers that offer a user-friendly interface. Intelligent use of the data should expedite biological knowledge discovery. Such activity is collectively called data mining and involves queries that can be simple, complex, and even combinational. Various tools have been developed to make genome data mining available to computational and experimental biologists alike. In this mini-review, some tools that have proven successful will be introduced along with examples taken from published reports.