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Research Interests

  Classification of fungi

  Interaction between organisms

  Molecular mechanism of evolution

  Artificial gene evolution

  Metabolic engineering

  Evolution in silico

Research Experience 

  Phylogenetic analysis

  Molecular biology

  Directed evolution

  Evolutionary Biology

Publication

Patents

Presentation

Research Interests

 

Classification of fungi

I want to construct polyphasic fungal classification system based on morphological, physiological, biochemical, and molecular characteristics. I expect that stable and natural classification system that reflects evolutionary relationships among organisms can be achieved from these studies. I am also interested in establishment of rapid and reliable identification systems of fungi including human or crop pathogens using molecular systematics and various fingerprinting methods such as AFLP, ARDRA and Ribotyping. Molecular ecological studies and population studies of fungi can be achieved from these studies.

 

Searching for interaction between organisms

I think that the most important driving force of evolution is the interaction between organisms including competition and cooperation. There are numerous patterns of interaction between organisms. Among them, the most interesting one to me is the interaction between plant and fungi. I am interested in studying patterns and distribution, physiological phenomenon, genomic evolution, and driving forces of plant-fungi interactions

 

Molecular mechanism of evolution

I want to study molecular mechanisms of evolution. In particular, I am interested in mechanisms of rapid evolutionary changes such as acquisition of antibiotic or chemical resistance and horizontal transfer of genes between organisms.

 

Application of evolutionary mechanisms to evolve genes or organisms artificially

Directed evolution using DNA shuffling method revolutionized the field of protein engineering. The method is based on the principles of natural evolution. I am interested in applying various principles of natural evolution including recombination, DNA mobility, horizontal gene transfer and selection of fittest to evolve genes and organisms in artificial environments.

 

Metabolic engineering

I am now constructing metagenomic libraries from natural environments using BAC or plasmid vector. Cloning of genes using metagenome enable me to study population structure, functional diversity of un-culturable microorganisms that represent 99% of natural population. It is also possible to clone industrially useful genes from metagenomic libraries. I am planning to develop useful enzymes through metagenome screening and directed evolution methods. Using the products of metagenome and directed evolution research, I want to develop industrially useful organisms, especially bio-energy producing organisms.

 

Evolution in silico

Evolution is a very long-term process and it is not easy to study mechanisms of evolution in vivo or in vitro. I think that simulation of evolution using computer is one possible solution to study mechanisms of evolution. I also pay attention to the application of evolutionary algorithms in other fields.

 

 

Research Experience 

 

Phylogenetic analysis of fungi and bacteria

I have extensive experiences in classification of fungi, including mushrooms, brackets, moulds, and yeasts. I have been doing field survey and identification works based on host relationships, macro- and micro-morphological, cultural, physiological, biochemical, and molecular characteristics for brackets, mushrooms, moulds and yeasts since 1991. I am now participating in the project for searching biodiversity of yeasts in various natural resources. In the course of biodiversity survey, I have found several new species of yeasts and written manuscripts describing them.

Related papers: Lim, Hong, and Jung (1999), Hong, Chun, Oh, and Bae (2001), Hong, Lee, and Bae (2002), Hong, Bae, Hetzberg, Titze, and Lachance (in press), some unpublished results

 

I have also experience in bacterial systematics and molecular ecological analysis through cooperation with bacterial taxonomists and ecologists.

Related papers: Lee, Hong, Lee, Kim, and Bae (2001), Lee, Chang, Hong, Oh, Pyun, and Bae (in press), Sohn, Hong, Bae, and Chun (submitted)

 

I have extensive experiences in phylogenetic analysis. I have used various experimental techniques including mitochondrial DNA RFLP, AFLP, and sequencing. I have also used various analytical methods including distance analysis, parsimony, and maximum likelihood using computer programs such as PAUP, PHYLIP, MacClade, GelCompar, and Phydit. I have deep understanding for theoretical background of phylogenetic analyses including distance analysis, parsimony, and maximum likelihood. Using various experimental and analytical methods, I have analyzed phylogenetic relationships of polypore fungi, the genus Ganoderma, the family Sporobolomycetaceae, and the genus Penicillium. During the phylogenetic analysis of Ganoderma spp., I have found that some species of Ganoderma have group II introns in the conserved loop position. From the parsimony rule and comparison of gene phylogeny and intron phylogeny, the intron mobility was deduced

Related papers: Hong and Jung (1994), Ko, Hong and Jung (1997), Ko, Hong and Jung (1997), Hong, Chun, Nam, Park and Bae (2000), Hong, Park, Jeong and Bae (2000), Hong and Jung (in revision), some unpublished results.

 

I am now conducting a project for phylogenic analysis and identification of Pleurotus spp. and moulds contaminating mushroom cultivation bed such as Trichoderma and Hypocrea. This project include sequence analyses of mitochondrial SSU rDNA and ITS rDNA, AFLP fingerprint analysis, analyses of morphological and cultural characteristics, and developing species- and strain-specific probes and detection methods for Pleurotus spp., Trichoderma spp., and Hypocrea spp.

 

Molecular biology

I have conducted a project analyzing mitochondrial genome of Trimorphomyces papilionaceus, the basidiomycetous yeast. This work included cloning of restriction fragments, restriction mapping, transcript mapping, and sequencing. It also included gene finding using computer programs, secondary structure analyses of rRNAs, tRNAs and introns, analysis of codon usage, and comparison of sequences and gene structure with other mitochondrial genomes including those of Saccharomyces cerevisiae, Posospora anserina, Emericella nidulans, and Homo sapiens.

Related papers: Hong, Kang and Jung (1993), Jeoung, Hong, Kang, and Jung (1995), some unpublished results

 

In order to design universal primers for mitochondrial small subunit rDNA of fungi belonging to Hymenomycetes, I have cloned, sequenced, and analyzed mitochondrial small subunit rRNA gene from four representative fungal species, Ganoderma lucidum, Bjerkandera adusta, Phlebiopsis gigantean, and Phellinus laevigatus. Primers designed based on the conserved sequences worked well for various hymenomycetous fungi. I have analyzed phylogenetic informativeness of mtSSU rDNA sequences based on the number of informative sites, skewness, and CI index.

Related papers: Hong, Jeong and Jung (in press)

 

Through these works, I have plentiful experiences in nearly all kinds of general molecular biological techniques including library construction, Southern and Northern analysis, PCR, sequencing, restriction mapping, sequence analysis using computer program etc. I am now involved in the project for construction of BAC and plasmid library of uncultured bacterial DNA from various natural sources and expression in E. coli. Through these works, I expect to have experiences in BAC vector, PFGE, and expression of genes in E. coli.

 

Directed evolution

I have developed two new techniques based on PCR method to evolve proteins, promoters, or viruses in vitro. These techniques were submitted for patents. I am trying to evolve some protein genes through these methods and a new screening method I have developed.

Related patents: Korea Patent, 2001-28442, Korea Patent, 2002-889 and PCT patent, KR02/01011

 

Evolutionary Biology

I have deep and sound conceptual foundation of evolutionary theory through extensive paper and book reading for behavioral, physiological, and molecular evolution. I started my first step as an evolutionist with the book entitled "Toward a new philosophy of Biology" written by Ernst Mayr. I have translated the book into Korean language with my colleges, although it was not pressed. Since then, I have read many literatures about organismal and molecular evolution.

 

Mathematics and Computer

I have learned several mathematical subjects including linear algebra, statistics, and differential equation in undergraduate and have solid mathematical concepts. Recently, I have learned ?Visual Basic? program language. Although I have no experience of program coding, I have plentiful knowledge for the structure of computer program and can communicate with programmers well

 

 

Publication

  1. Sohn, K., Hong, S. G., Bae, K. S., and Chun, J. (2002) Transfer of Hongia koreensis Lee et al. 2000 to the genus Kriebbella Park et al. 1999 as Kribbella koreensis comb. nov. Int. J. Syst. Evol. Microbiol. In press  pdf
  2. Hong, S. G., Bae, K. S., Hetzberg, M., Titze, A., and Lachance, M.-A. (2002) Candida kunwiensis sp. nov. a yeast associated with flowers and bumblebees. Int. J. Syst. Evol. Microbiol 53: 367-372. pdf
  3. Lee, J. S., Chang, Y. H., Hong, S. G., Oh, H. W., Pyun, Y. R. and Bae, K. S. (2002) Paenibacillus daejeonensis sp. nov., a new alkali-tolerant bacteria from soil. Int. J. Syst. Evol. Microbiol 52: 2107-2111. pdf
  4. Hong, S.G., Jeong, W., and Jung, H.S. (2002) Amplification of mitochondrial small subunit ribosomal DNA of polypores and its potential for phylogenetic analysis. Mycologia. 94(5): 823-833 pdf
  5. Hong, S. G., Lee, K. H. and Bae, K. S. (2002) Diversity of yeasts associated with natural environments in Korea. J. Microbiol. 40 (1): 55-62. pdf
  6. Rho, M. C., Lee, H. S., Chang, K. T., Song, H. Y., Kwon, O. E., Lee, S. W., Ko, J. S., Hong, S. G., and Kim, Y. K. (2002) Phenylpyropene C, a new inhibitor of acyl-CoA: Cholesterol acyltransferase produced by Penicillium griseofulvum F1959. J. Antiobiot. 55(2): 211-214. pdf
  7. Song, K. H., Lee, J. K., Song, J. Y., Hong, S. G., Baek, H., Kim, S.Y. and Hyun, H. H.. (2002) Production of mannitol by a novel strain of Candida magnoliae. Biotech. Letter 24(1): 9-12. pdf
  8. Hong, S. G., Chun, J., Oh, H. W. and Bae, K. S. (2001) Metschnikowia koreensis sp. nov., a new yeast species isolated from flowers in Korea. Int. J. Syst. Evol. Microbiol. 51(5): 1927-1931. pdf
  9. Lee, M. S., Hong, S. G., Lee, D. H., Kim, C. K., and Bae, K. S. (2001) Microbial diversity in the mud flat of Suncheon Bay, Chunnam province, by 16S rRNA gene analysis. Kor. J. Microbiol. 37(2): 137-144. pdf
  10. Hong, S. G., Park, Y.-D., Jeong, W. and Bae, K. S. (2000) Sequence comparison of mitochondrial small subunit ribosomal DNA in Penicillium. J. Microbiol. 38(2): 62-65. pdf
  11. Hong, S.G., Chun, J., Nam, J.S., Park, Y.-D., and Bae, K.S. (2000) Phylogenetic analysis of the genus Sporobolomyces based on partial sequences of 26S rDNA. J. Microbiol. Biotechnol. 10(3): 363-366 pdf
  12. Lim, Y.W., Hong, S.G. and Jung, H.S. (1999) Taxonomic study on Korean Aphyllophorales (IV) - on some unrecorded wood-rotting fungi. Kor. J. Mycol. 27(1): 68-72. pdf
  13. Ko, K.S., Hong, S.G. and Jung, H.S. (1997) Phylogenetic analysis of Trichaptum based on nuclear 18S, 5.8S and ITS ribosomal DNA sequences. Mycologia 89(5): 727-734. pdf
  14. Ko, K.S., Hong, S.G., and Jung, H.S. (1997) Phylogenetic study of Trichaptum inferred from nuclear ribosomal DNA sequences. J. Microbiol. 35(2): 79-86. pdf
  15. Jeoung, W., Hong, S.G., Kang, Y.-W. and Jung, H.S. (1995) Restriction and transcription maps of mitochondrial DNA of Trimorphomyces papilionaceus. J. Microbiol. 33(2): 149-153. pdf
  16. Hong, S.G. and Jung, H.S. (1994) Phylogeny of Ganoderma based on the restriction enzyme analysis of mitochondrial DNA. Kor. J. Microbiol. 32(4): 245-251. pdf
  17. Hong, S.G., Kang, Y.-W. and Jung, H.S. (1993) Sequence analysis of the small subunit ribosomal RNA gene of Trimorphomyces papilionaceus mitochondria. Kor. J. Microbiol. 31(6): 471-477. pdf

 

 

Patents

  1. PCT patent, KR02/01011 (Appl. No.), Method for constructing a chimeric library using a single strand specific DNase.
  2. Korea Patent, 10-2002-0000889 (Appl. No.), Method for constructing chimeric DNA library using Exonuclease VII.
  3. Korea Patent, 10-2001-0028442 (Appl. No.), Method for constructing a chimeric DNA library using a single strand specific DNase

 

 

Presentation

  1. Hong, S. G. Bae, K. S. (2002) Development of a new method for constructing a chimeric DNA library. Poster presentation. 9th International Symposium on the Genetics of Industrial Microorganisms. Gyeongju, Korea.
  2. Hong, S. G., Min, J.-Y. and Bae, K. S. (2002) Phylogenetic analysis of the genus Pleurotus and related species based on mitochondrial small subunit rDNA sequences. Poster presentation. Mycological Society of America 2002 Annual Meeting, Corvallis, Oregon.
  3. Hong, S. G., Lee, K. H. and Bae, K. S. (2002) Diversity of yeasts associated with natural environments in Korea. Oral presentation. Spring meeting of the Korean Society of Mycology, Kwangju, Korea.
  4. Hong, S. G., Lee, K. H. and Bae, K. S. (2002) Diversity of yeasts associated with natural environments in Korea. Poster presentation. The 5th filamentous fungi conference, Choong Ju, Korea.
  5. Hong, S. G., Jung, H. S., and Bae, K. S. (2001) Evolution of group II introns in the mitochondrial small subunit ribosomal RNA gene of Ganoderma. Poster presentation. Spring meeting of the Korean Society of Microbiology. Seoul Korea.
  6. Min, J. Y., Hong, S. G., Lee, K. H., Ryu, S. H., and Bae, K. S. (2001) Phylogenetic analysis of the genus Pleurotus based on sequences of mitochondrial small subunit ribosomal DNA. Poster presentation. Spring meeting of the Korean Society of Mycology, Seoul, Korea.
  7. Min, J. Y., Hong, S. G., and Bae, K. S. (2001) Phylogenetic analysis of Pleurotus based on sequences of mitochondrial small subunit ribosomal DNA. Poster presentation, The 4th filamentous fungi conference, Choong Ju, Korea.
  8. Hong, S. G., Chun, J. and Bae, K. S. (2000) Sporobolomyces koreensis sp. nov., a novel yeast species isolated from Lilium sp. in Korea. Poster presentation, Taejon, Korea
  9. Hong, S. G., Chun, J. and Bae, K. S. (2000) Metschnikowia koreensis sp. nov., a new yeast species isolated from sweet potato flower in Korea. Poster presentation, Tenth International Symposyum on Yeast, Arnhem, The Netherlands.
  10. Hong, S. G., Jeong, W., Park, Y.-D., Chun, J., and Bae, K. S. (2000) Candida kunwiensis a new yeast isolated from sweet potato flower in Kunwi. Poster presentation, Spring meeting of the Korean Society of Mycology, Kyungju, Korea.
  11. Hong, S. G., Jeong, W., Chun, J., and Bae, K. S. (2000) A new osmotolerant yeast isolated from sweet potato flower in Kunwi. Poster presentation, Spring meeting of the Korean Society of Microbiology, Seoul, Korea.
  12. Hong, S. G., Jeong, W. and Bae, K. S. (2000) Phylogenetic analysis of the genus Sporobolomyces based on partial sequences of 26S rDNA. Oral presentation, The 3rd filamentous fungi conference, Choong Ju, Korea.
  13. Hong, S. G. and Jung, H. S. (1999) Phylogenetic analysis of Ganoderma based on mitochondrial ribosomal DNA sequences. Oral presentation, Spring meeting of the Korean Society of Mycology, Suwon, Korea.
  14. Lim, Y. W., Hong, S. G., and Jung, H. S. (1999) Taxonomic study for several unrecorded species of Aphyllophorales of Korea (VI) Poster presentation, Spring meeting of the Korean Society of Mycology, Suwon, Korea.
  15. Hong, S. G. and Jung, H. S. (1998) Cloning and Sequence Analysis of Mitochondrial Small Subunit rRNA Genes from Bjerkandera adusta, Ganoderma lucidum, Peniophora gigantea and Stereum gausapatum. Poster presentation, Spring meeting of the Microbiology Society of Korea. Seoul, Korea.
  16. Hong, S. G. and Jung, H. S. (1998) Phylogeny of the Genus Ganoderma. Poster presentation, Autumn meeting of the Microbiology Society of Korea. Seoul, Korea.
  17. Lim, Y. W., Hong, S. G., and Jung, H. S. (1998) Taxonomic study for several unrecorded species of Aphyllophorales of Korea (IV) Oral presentation, Spring meeting of the Korean Society of Mycology, Cheonju, Korea.
  18. Ko, K. S., Hong, S. G., and Jung, H. S. (1996) Phylogenetic analysis of Trichaptum based on nuclear small subunit ribosomal RNA gene and ITS1-5.8S-ITS2 region sequences. Poster presentation, APS/MSA Joint Annual Meeting, Indianapolis, Indiana, USA
  19. Hong, S. G. and Jung, H. S. (1995) Phylogenetic analysis of the genus Ganoderma based on the 18S rDNA sequences. Poster presentation, Spring meeting of the Microbiology Society of Korea. Seoul, Korea.
  20. Ko, K. S., Hong, S. G., and Jung, H. S. (1995) Phylogenetic analysis of Trichaptum based on 18S and ITS1-5.8S-ITS2 ribosomal DNA sequences. Poster presentation, Seoul, Korea
  21. Hong, S. G. and Jung, H. S. (1994) Phylogenetic analysis of the genus Ganoderma based on RFLP pattern of mitochondrial DNA. Poster presentation, Spring meeting of the Microbiology Society of Korea. Seoul, Korea.
  22. Hong, S. G., Kang, Y. W., and Jung, H. S. (1993) Sequence and secondary analysis of mitochondrial small subunit ribosomal RNA of Trimorphomyces papilionaceus. Poster presentation, Autumn Meeting of the Microbiology Society of Korea. Korea
  23. Hong, S. G., Kang, Y. W., and Jung, H. S. (1993) Systematics of a basidiomycetous yeast, Trimorphomyces papilionaceus, based on the small subunit rRNA gene sequence of mitochondria. Poster presentation, MSA Annual Meeting
  24. Hong, S. G., Kang, Y. W., and Jung, H. S. (1993) Structure of mitochondrial large subunit ribosomal RNA gene of Trimorphomyces papilionaceus. Poster presentation, Spring meeting of Microbiology Society of Korea, Korea
  25. Hong, S. G., Kang, Y. W., and Jung, H. S. (1992) Sequence analysis of mitochondrial small subunit ribosomal RNA of Trimorphomyces papilionaceus. Poster presentation, Autumn Meeting of the Microbiology Society of Korea. Korea.
  26. Hong, S. G., Jeong, W., Kang, Y. W., and Jung, H. S. (1992) Transcript mapping of mtDNA from a dikaryotic strain of Trimorphomyces papilionaceus. Poster presentation, Spring Meeting of the Microbiology Society of Korea. Korea.
  27. Jeong, W., Hong, S. G., Kim, Y. H., Kang, Y. W., and Jung, H. S. (1992) Restriction mapping and cloning of mtDNA from a dikaryotic strain of Trimorphomyces papilionaceus. Poster presentation, Spring Meeting of the Microbiology Society of Korea. Korea.

 

 

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