• The Plant Pathology Journal
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• v.17 no.2
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• pp.67-70
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• 2001

Medicago truncatula is a diploid legume plant related to the forage crop alfalfa. Recently, it has been chosen as a model species for genomic studies due to its small genome, self-fertility, short generation time, and high transformation efficiency. M. truncatula engages in symbiosis with nitrogen-fixing soil bacterium Rhizobium meliloti. M. truncatula mutants that are defective in nodulation and developmental processes have been generated. Some of these mutants exhibited altered phenotypes in symbiotic responses such as root hair deformation, expression of nodulin genes, and calcium spiking. Thus, the genes controlling these traits are likely to encode functions that are required for Nod-factor signal transduction pathways. To facilitate genome analysis and map-based cloning of symbiotic genes, a bacterial artificial chromosome library was constructed. An efficient polymerase chain reaction-based screening of the library was devised to fasten physical mapping of specific genomic regions. As a genomics approach, comparative mapping revealed high levels of macro- and microsynteny between M. truncatula and other legume genomes. Expressed sequence tags and microarray profiles reflecting the genetic and biochemical events associated with the development and environmental interactions of M. truncatula are assembled in the databases. Together, these genomics programs will help enrich our understanding of the legume biology.

• Korean Journal of Environmental Biology
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• v.39 no.3
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• pp.383-389
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• 2021

The Erythropeltidales are a common group of small, mostly epiphytic, marine red algae. However, they are little known in Korea. Many of the described species of Erythropeltidales differ subtly in morphology, and often the morphological differences are due to the substrate or environmental changes. Integration of molecular data with standardized culture conditions has been recommended to account for these algae. A Madagascaria species was first collected from the western coast of Korea and was identified as Madagascaria erythrocladioides based on the morphological and molecular characteristics. Morphological characteristics conformed well with its original description, and the phylogenetic analysis based on rbcL sequence showed Korean M. erythrocladioides nests in the same clade with the original species described in Japan with a genetic distance of 0.0-0.1%. This species was isolated from a red alga, Pterocladiella capillacea, in laboratory culture. The thallus ontogeny and host preference were examined by a co-culture with 13 different species of algae. Results showed a relatively broad host preference in mono-spore attachment and epiphyte development of Madagascaria erythrocladioides. Mono-spores of M. erythrocladioides attached to most of the red algal hosts' surfaces but no crustose thalli developed on some of the algal hosts even after one month of co-culture.

• 한국균학회소식:학술대회논문집
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• 2006.10a
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• pp.32-44
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• 2006

To investigate non-aflatoxin-production of A. oryzae at the molecular level, an aflatoxin biosynthesis gene homolog cluster of RIB 40 was analyzed. Although most genes in the corresponding cluster exhibited from 97 to 99 % similarity to those of Aspergillus flavus, three genes shared 93 % similarity or less. In addition, although slight expression of aflR, positive transcriptional regulator gene, was detected in some A. oryzae strains having seven aflatoxin biosynthesis homologous genes, other genes related to aflatoxin production were not detected. RIB strains were mainly divided into group 1, having seven aflatoxin biosynthesis homologous genes (aflT, nor-i, aflR, norA, avnA, verB, and vbs), and group 2, having three homologous (avnA, verB, and vbs). Partial aflatoxin homologous gene cluster of RIB62 from group 2 was sequenced and compared with that of RIB40 from group 1. RIB62 showed a large deletion upstream of ver-1 with more than half of the aflatoxin homologous gene cluster missing including aflR, a positive transcriptional regulatory gene. Adjacent to the deletion of the aflatoxin homologous gene cluster, RIB62 has a unique sequence of about 8kb and a telomere. Southern analysis of A. oryzae RIB strains with four kinds of probe derived from the unique sequence of RIB62 showed that all group 2 strains have identical hybridizing signals. Polymerase chain reaction with specific primer set designed to amplify the junction between ver-1 and the unique sequence of RIB62 resulted in the same size of DNA fragment only from group 2 strains. Based on these results, we developed a useful genetic tool that distinguishes A. oryzae group 2 strains from the other groups' strains and propose that it might have differentiated from the ancestral strains due to chromosomal breakage.

• The Plant Pathology Journal
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• v.34 no.2
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• pp.139-142
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• 2018

Pyrenophoratritici-repentis is the causal agent of tan spot. According to their ability to produce necrosis and/or chlorosis on a set of four differential bread wheats, the isolates of this fungus are currently grouped into eight races. When durum wheat genotypes were added to the differential set, a new virulence type was identified in Algeria. The isolates showing this virulence pattern are unable to attack bread wheat while they cause necrosis in durum genotypes. In this work, characterization of those isolates was based on pathological and molecular aspects. This included inoculation of bread and durum wheat, and virulence gene analysis using PCR and sequencing. The results showed that all isolates caused a resistance on all bread wheats of the differential set, while they produced necrosis in durum. ToxA and ToxB genes were amplified in all isolates, whereas toxb was absent. Sequence analysis for both genes showed no differences with those found in the two functional genes. The presence of two genes, ToxA and ToxB, despite the absence of symptoms usually caused by their products, suggests the existence of a new homologous for these two genes yet unknown. The presence of ToxA in the isolate unable to produce necrosis in Glenlea is reported for the first time.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.381-388
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• 2008

An X-linked skeletal disorder, SEDT (spondyloepiphyseal dysplasia tarda) is a genetic disease characterized by a disproportionately short trunk and short stature caused by mutations in the SEDL gene. This gene is evolutionarily conserved from yeast to human. The yeast SEDL protein ortholog, Trs20p, has been isolated as a member of a large multi-protein complex called the transport protein particle (TRAPP), which is involved in endoplasmic reticulum (ER)-to-Golgi transport. The interaction between SEDL and partner proteins is important in order to understand the molecular mechanism of SEDL functions. We isolated several SEDL-binding proteins derived from rat cells by an immobilized GST-fusion method. Furthermore, the SEDL-homologue proteins were identified using motif based methods. Common motifs between SEDL-binding proteins and SEDL-homologue proteins were classified into seven types and 78 common motifs were revealed. Sequence similarities were contracted to seven types using phylogenetic trees. In general, types I-III and VI were classified as having the function of acetyl-CoA carboxylase, glycogen phosphorylase, isocitrate dehydrogenase, and enolase, respectively, and type IV was found to be functionally related to the GST protein. Types V and VII were found to contribute to TRAPP vesicle trafficking.

• The Plant Pathology Journal
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• v.18 no.5
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• pp.251-258
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• 2002

A potyvirus was isolated from cultivated Iris plants showing leaf streak mosaic symptom. Reverse transcription and polymerase chain reaction (RT-PCR) product of 1 kb long which encoded partial nuclear inclusion B and N-terminal region of viral coat protein (CP) genes for potyviruses was successfully amplified with a set of potyvirus-specific degenerate primers with viral RNA samples from the infected leaves: The RT-PCR product was cloned into the plasmid vector and its nucleotide sequences were determined. The nucleotide sequence of a CDNA clone revealed that the virus was an isolate of Ornithogalum moseic virus (OrMV) based on BLAST search analysis and was denoted as OrMV Korean isolate (OrMV-Ky). To further characterize the CP gene of the virus, a pair of OrMV-specific primers was designed and used for amplification of the entire CP gene of OrMV-Kr, The virus was easily and reliably detected from virus-infected Iris leaves by using the RT-PCR with the set of virus-specific primers. The RT-PCR product of the CP gene of the virus was cloned and its sequences were determined from selected recombinant CDNA clones. Sequence analysis revealed that the CP of OrMV-Kr consisted of 762 nucleotides, which encoded 253 amino acid residues. The CP of OrMV-Ky has 94.1-98.0% amino acid sequence identities (20 amino acid alterations) with that of other three isolates of OrMV, Two NT rich potential N-glycosylation motif sequences, NCTS and NWTM, and a DAC triple box responsible for aphid transmission were conserved in CPs of all the strains of OrMV. The virus has 58.5-86.2% amino acid sequence identities with that of other 16 potyviruses, indicating OrMV to be a distinct species of the genus. OrMV-Ky was the most related with Pterostylia virus Yin the phylogenetic tree analysis of CP at the amino acid level. This is the first report on the occurrence of OrMV in Iris plants in Korea. Data in this study indicate that OrMV is found in cultivated Iris plants, and may have mixed infection of OrMV and Iris severe mosaic virus in Korea.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2010.10a
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• pp.18-18
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• 2010

Molecular insights on the role of plant growth promoting rhizobacteria (PGPR) in potato tuberization are reported in the present study. The PGPRwere isolated from the soil collected from potato fields of Highland Agricultural Research Centre, Pyeongchang, Korea and they were identified to the genus level based on the 16S rRNA sequence analysis. These PGPR were heat-killed, filtered and the filtrates were addedindividually at a concentration of $10^7\;cfu\;mL^{-1}$ in MS (Murashige and Skoog's) medium supplemented with 7% (w/v) sucrose to study their influence on in vitro potato tuberization. Tuber initiation occurred early in untreated control, while tuber growth was pronounced in case of PGPR treatments. The control explants showed tuber formation as a result of sub-apical swelling of stolons while several sessile tubers formed directly in the axils of nodal cuttings in case of PGPR treatments, which is an indication of strong induction for tuberization. Theexplants cultured on MS medium supplemented with bacterial isolate 6 (Bacillus firmus strain 40) showed highest average tuber yield (Ca. 12.56 g per treatment) after 30 days of culture, which was 3 folds increase over the untreated control. A significant increase in lipoxygenase (LOX1) mRNA expression and activity of LOX enzyme were also detected in the tubers induced on PGPR treatments as compared to untreated control. This LOX expression level correlated with increased tuber growth and tuber yield. Further studies focused on the role of bacteria cell wall components, growth regulators and signal molecules released by PGPR are under investigation to elicit clues for PGPR-mediated signal pathway controlling potato tuberization.

• Journal of Mushroom
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• v.20 no.2
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• pp.43-49
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• 2022

Pleurotus ostreatus is a globally cultivated mushroom crop. Cap color is a quality factor in P. ostreatus. However, cap color can spontaneously mutate, degrading the quality of the mushroom on the market. Early detection and removal of mutant strains is the best way to maintain the commercial value of the crop. To detect the cap color mutant Gonji7ho, molecular markers were developed based on insertion/deletions (InDels) derived from the comparison of mitogenomes of Gonji7ho and Gonji7hoM mushrooms. Sequencing, assembly, and comparative analysis of the two mitogenomes revealed genome sizes of 73,212 bp and 72,576 bp with 61 and 57 genes or open reading frames (ORFs) in P. ostreatus Gonji7ho and Gonji7hoM, respectively. Fourteen core protein-encoding genes, two rRNA, and 24 tRNA with some OFRs were predicted. Of the 61 genes or OFRs in the wild type, dpo, rpo, and two orf139 were missing (or remnant) in the mutant strain. Molecular markers were developed based on the sequence variations (InDels) between the two mitogenomes. Six polymorphic molecular markers could detect the mutated mitochondria by PCR. These results provide basic knowledge of the mitogenomes of wild-type and mutant P. ostreatus, and can be applied to discriminate mutated mitochondria.

• Journal of Microbiology and Biotechnology
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• v.26 no.8
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• pp.1375-1382
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• 2016

The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.

• International Journal of Industrial Entomology and Biomaterials
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• v.39 no.1
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• pp.14-21
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• 2019

Genome editing by CRISPR/Cas9, a third-generation gene scissor in molecular breeding at the genome level, is attracting much attention as one of the breeding techniques of the future. In this study, genetic and phenotypic analysis was used to examine the responsiveness of the Bakokjam variety of the silkworm Bombyx mori to molecular breeding using CRISPR/Cas9 in editing the white egg 2 (w-2) gene. The nucleotide sequence of the w-2 gene was analyzed and three different guide RNAs (gRNA) were prepared. The synthesized gRNA was combined with Cas9 protein and then analyzed by T7 endonuclease I after introduction into the Bm-N silkworm cell line. To edit the silkworm gene, W1N and W2P gRNA and Cas9 complexes were microinjected into silkworm embryos. Based on the results of microinjection, the hatching rate was 16-24% and the incidence of mutation was 33-37%. The gene mutation was verified in the heterozygous F1 generation, but no phenotypic change was observed. In F2 homozygotes generated by F1 self-crosses, a mutant phenotype was observed. These results suggest that silkworm molecular breeding using the CRISPR/Cas9 system is possible and will be a very effective way to shorten the time required than the traditional breeding process.