• Research in Plant Disease
• /
• v.21 no.4
• /
• pp.337-340
• /
• 2015

During July to November 2014, severe rust infection was consistently found on Peucedanum japonicum growing farm in Yeosu, Korea. The rust was observed mainly on lower leaf surfaces. Symptoms of typical plants included yellow-orange rust pustules were observed on the petiole and leaf surface with small yellowish to chlorotic lesions on the upper surface. No symptom was observed on flowers. Uredinia were occurred amphigenous on leaf surface, and occasionally caulicolous, scattered or loosely aggregate, rounded to oblong, 0.4 to 4 mm in diameter, covered by epidermis, then naked, surrounded by ruptured epidermis, pulverulent, and brown. Urediniospores were ovate-ellipsoid, ellipsoid or subglobose, light brown, 20 to $45{\times}15$ to $35{\mu}m$, walls 2 to $4{\mu}m$ thick. The resulting sequences were deposited in GenBank with accession No. KT778808, KT778809, and KT778810, respectively. Since this was the first accession of 28S sequence Puccinia jogashimensis, there was no exact match in GenBank nucleotide database. On the basis of the morphological characteristics and phylogenetic analyses of 28S rDNA, the fungus was identified as P. jogashimensis. To our knowledge, this is the first confirmed report on the occurrence of P. jogashimensis on P. japonicum in Korea.

• Research in Plant Disease
• /
• v.19 no.4
• /
• pp.326-330
• /
• 2013

During the 2012 growing season, 154 leaf samples were collected from sweet cherry trees in Hwaseong, Pyeongtaek, Gyeongju, Kimcheon, Daegu, Yeongju and Eumseong and tested for the presence of Cherry green ring mottle virus (CGRMV). PCR products of the expected size (807 bp) were obtained from 6 samples. The PCR products were cloned and sequenced. The nucleotide sequences of the clones showed over 88% identities to published coat protein sequences of CGRMV isolates in the GenBank database. The sequences of CGRMV isolates, CGR-KO 1-6 shared 98.8 to 99.8% nucleotide and 99.6 to 100% amino acid similarities. Phylogenetic analysis indicated that the Korean CGRMV isolates belong to the group II of CGRMV coat protein genes. The CGRMV infected sweet cherry trees were also tested for Apple chlorotic leaf spot virus (ACLSV), Apple mosaic virus (ApMV), Cherry necrotic rusty mottle virus (CNRMV), Cherry mottle leaf virus (CMLV), Cherry rasp leaf virus (CRLV), Cherry leafroll virus (CLRV), Cherry virus A (CVA), Little cherry virus 1 (LChV1), Prune dwarf virus (PDV) and Prunus necrotic ringspot virus (PNRSV) by RT-PCR. All of the tested trees were also infected with ACLSV.

• Journal of Conservation Science
• /
• v.23
• /
• pp.81-93
• /
• 2008

The analysis of ancient DNA (aDNA) in paleogenetics has become an increasingly important subject of archaeological, anthropological, biological as well as public interest. In this study, paleogenetic analyses were carried out on the human skeletal remains from a historical cemetery site in Myeongam-ri, Asan, Korea. Archaeological records show that this particular location had been used as a habitation or mortuary site as early as the Bronze Age and up until the Joseon Dynasty. Human remains of twenty individuals out of forty-nine tombs from the Goryeo to Joseon Dynasty were selected for the analysis of this study. In order to identify the genealogy of the population and traditional burial pattern of the cemetery, we conducted comparative analyses of the hyper variable regions (HVRs) in mitochondrial DNA (mtDNA) of each sample. A number of cautious steps were taken at all experimental stages in order to avoid erroneous recombination by the segmental and modern contaminations derived from the researchers. We sequenced segmental amplicons of HVRs andassigned relevant haplogroups according to the sequence polymorphism on the basis of the known mtDNA database. The result shows that diverse haplogroups were unexpectedly present in the small population group of the Myeongam-ri site. This diversity appears to be related to the geographical conditions and archaeological properties of the Myeongam-ri site.

• Microbiology and Biotechnology Letters
• /
• v.39 no.2
• /
• pp.133-139
• /
• 2011

In this study, we determined the changes in microbial numbers in solar salts according to the manufacturing process and storage duration. The salt samples were harvested from salt farms in Shinan (area 2) and Yeonggwang (area 1). They were serially diluted ten-fold and then placed on 4 kinds of cultivable media (mannitol salt agar, eosin methylene blue, plate count agar, and trypticase soy agar). After incubation, we obtained 62 halophilic isolates from the salt samples. Coliform and general bacteria were not detected in all salt samples. By 16S rRNA sequencing analysis, we found 12 kinds of halophilic bacteria belonging to the genera Halobacillus, Halomonas, Bacillus, Idiomarina, Marinobacter, Pseudoalteromonas, Vibrio, Salinivibrio, Virgibacillus, Alteromonas, Staphylococcus and some un-known stains. In our study, we discovered two novel species that have a 16S rDNA sequence similarity below 97%.

• Weed & Turfgrass Science
• /
• v.7 no.1
• /
• pp.15-21
• /
• 2018

Since sulfonylurea (SU) herbicide-resistant Monochoria korsakowii in Seosan reclaimed land in 1998 was reported first, herbicide-resistant weed species and their area of occurrence have been steadily increasing. In recent years, Sagittaria trifolia resistant to SU herbicides has been reported in Gimhae, Gyeongnam province. While collecting S. trifolia for constructing barcode database of major weeds we were suspicious by the continuous variation in the leave morphology of the species. In order to identify the S. trifolia from S. aginash we barcoded the species collected from domestic using ITS and compared the sequence variation with the ITS sequences of S. aginash downloaded from NCBI. As a result, it was found that the plants collected from the domestic did not have any variation among individuals although they showed wide morphological variation. On the other hand, interspecific variation between S. trifolia and S. aginash was 4.6%. Plants that are difficult to identify using morphological characters can be identified quickly and accurately using the barcode technique. Herbicide-resistant weeds may require different management practices depending on the species even in the same genus. Domestic herbicide-resistant weeds are steadily increasing. Therefore, accurate identification of these species must be preceded for effective weed control.

• Molecules and Cells
• /
• v.28 no.6
• /
• pp.529-536
• /
• 2009

Genome sequencing of the pig is being accelerated because of its importance as an evolutionary and biomedical model animal as well as a major livestock animal. However, information on expressed porcine genes is insufficient to allow annotation and use of the genomic information. A series of expressed sequence tags of 5' ends of five full-length enriched cDNA libraries (SUSFLECKs) were functionally characterized. SUSFLECKs were constructed from porcine abdominal fat, induced fat cells, loin muscle, liver, and pituitary gland, and were composed of non-normalized and normalized libraries. A total of 55,658 ESTs that were sequenced once from the 5′ ends of clones were produced and assembled into 17,684 unique sequences with 7,736 contigs and 9,948 singletons. In Gene Ontology analysis, two significant biological process leaf nodes were found: gluconeogenesis and translation elongation. In functional domain analysis based on the Pfam database, the beta transducin repeat domain of WD40 protein was the most frequently occurring domain. Twelve genes, including SLC25A6, EEF1G, EEF1A1, COX1, ACTA1, SLA, and ANXA2, were significantly more abundant in fat tissues than in loin muscle, liver, and pituitary gland in the SUSFLECKs. These characteristics of SUSFLECKs determined by EST analysis can provide important insight to discover the functional pathways in gene networks and to expand our understanding of energy metabolism in the pig.

• Development and Reproduction
• /
• v.7 no.2
• /
• pp.127-136
• /
• 2003

The present study was conducted to investigate gene expression profile of mouse ovaries during the primordial-primary follicle transition. We isolated total RNA from mouse ovaries at day1(contains only primordial follicles) and day5(contains both primordial and primary follicles) and synthesized cDNA using annealing control primers(ACP, Seegene, Inc., Seoul, Korea). Using 80 different ACPs for PCR, we cloned, sequenced, and analyzed identities of 41 differentially expressed genes(DEGs). According to BLAST analysis, sequences of 33 clones significantly matched database entries, 4 clones were novel, and 4 clones were ESTs. We selected 8 DEGs with interesting functions, Anx11 and Pepp2-Pending highly expressed in day1 ovary, while Apg3/Autlp-like, BPOZ, Ches1, Kcmf1, NHE3, Nid2, Ninj1, SENP3, Suil-rsl, and TIAP/m-survivin highly expressed in days ovary, and confirmed their different expression between day1 ovaries and days ovaries using semi-quantitative RT-PCR. There was no false positive result. Using in situ hybridization, we found that almost all of genes studied were expressed in the oocyte from primordial follicle stage but expression decreased from primary follicle stage. Meanwhile their expression was increased in cuboidal granulosa cells. Different expression of BPOZ and TIAP/m-survivin between primordial and primary follicles was confirmed by using laser capture microdissection followed by real-time PCR BPOZ and TIAP/m-survivin expressed 4.5 and 3.4 fold higher in primary than primordial follicles, respectively. List of genes obtained from the present study will provide insights for the study of mechanism regulating primordial-primary follicle transition.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.140-140
• /
• 2017

Nutritious and functional foods from crop have received great attention in recent years. Colored-grain wheat contains high phenolic compound and a large number of flavonoid. The anthocyanin and polyphenolic synthesis and accumulation is generally stimulated in response to biotic or abiotic stresses. Here, we analyzed genome wide transcripts in seedling of colored-grain wheat response to ABA and PEG treatment. About 900 and 1500 transcripts (p-value < 0.05) from ABA and PEG treatment were aligned to IWGSC1+popseq DB which is composed of over 110,000 transcripts including 100,934 coding genes. NR protein sequences of Poaceae from NCBI and protein sequence of transcription factors originated from 83 species in plant transcription factor database v3.0 were used for annotation of putative transcripts. Gene ontology analysis were conducted and KEGG mapping was performed to show expression pattern of biosynthesis genes related in flavonoid, isoflavonoid, flavons and anthocyanin biopathway. DroughtDB (http://pgsb.helmholtz-muenchen.de/droughtdb/) was used for detection of DEGs to explain that physiological and molecular drought avoidance by drought tolerance mechanisms. Drought response pathway, such as ABA signaling, water and ion channels, detoxification signaling, enzymes of osmolyte biosynthesis, phospholipid metabolism, signal transduction, and transcription factors related DEGs were selected to explain response mechanism under water deficit condition. Anthocyanin, phenol compound, and DPPH radical scavenging activity were measured and antioxidant activity enzyme assays were conducted to show biochemical adaptation under water deficit condition. Several MYB and bHLH transcription factors were up-regulated in both ABA and PEG treated condition, which means highly expressed MYB and bHLH transcription factors enhanced the expression of genes related in the biosynthesis pathways of flavonoids, such as anthocyanin and dihydroflavonols in colored wheat seedlings. Subsequently, the accumulation of total anthocyanin and phenol contents were observed in colored wheat seedlings, and antioxidant capacity was promoted by upregulation of genes involved in maintaining redox state and activation of antioxidant scavengers, such as CAT, APX, POD, and SOD in colored wheat seedlings under water deficit condition. This work may provide valuable and basic information for further investigation of the molecular responses of colored-grain wheat to water deficit stress and for further gene-based studies.

• Proceedings of the Korean Society of Plant Biotechnology Conference
• /
• 2005.11a
• /
• pp.95-105
• /
• 2005

Transposon-mediated insertional mutagenesis provides one of the most powerful tools for functional studies of genes in higher plants. This project has been performed to develop a large population of insertional mutations, and to construct databases of molecular information on Ds insertion sites in rice. Ultimate goals are to supply genetic materials and information to analyze gene function and to identify and utilize agronomically important genes for breeding purpose. Two strategies have been employed to generate the large scale of transposon population in a Japonica type rice, Dongjin Byeo; 1) genetic crosses between Ac and Ds lines and 2) plant regeneration from seeds carrying Ac and Ds. Our study showed that over 70% of regenerated plants generally carried independent Ds elements and high activity of transposition was detected only during regeneration period. Ds-flanking DNA amplified from leaf tissues of F2 and T1 (or T2) plants have been amplified via TAIL-PCR and directly sequenced. So far, over 65,000 Ds lines have been generated and over 9,500 Ds loci have been mapped on chromosomes by sequence analysis. Database of molecular information on Ds insertion sites has been constructed, and has been opened to the public and will be updated soon at http://www.niab.go.kr. Detailed functional analysis of more than 30 rice mutants has been performed. Several Ds-tagged rice genes that have been selected for functional analysis will be briefly introduced. We expect that a great deal of information and genetic resources of Ds lines would be obtained during the course of this project, which will be shared with domestic and international rice researchers. In addition to the Japonica rice, we have established the tagging system in an rice line of indica genetic background, MGRI079. MGRI079 (Indica/Japonica) was transformed with Agrobacteria carrying Ac and Ds T-DNA vectors. Among transgenic lines, we successfully identified single-copy Ds and Ac lines in MGR1079. These lines were served as ‘starter lines’ to mutagenize Indica genetic background. To achieve rapid, large scale generation of Ds transposant lines, MGR1079 transformants carrying homozygous Ac were crossed with ones with homozygous Ds, and $F_2$seeds were used for plant regeneration. In this year, over 2,000 regeneration plants were grown in the field. We are able to evaluate the tagging efficiency in the Indica genetic background in the fall.

• Korean Journal of Clinical Laboratory Science
• /
• v.52 no.3
• /
• pp.229-236
• /
• 2020

Sixty-five molds isolated from clinical specimens were included in this study. All the isolates were molds that could be identified morphologically, strains that are difficult to identify because of morphological similarities, and strains that require species-level identification. PCR and direct sequencing were performed to target the internal transcribed spacer (ITS) region, the D1/D2 region, and the β-tubulin gene. Comparative sequence analysis using the GenBank database was performed using the basic local alignment search tool (BLAST) algorithm. The fungi identified morphologically to the genus level were 67%. Sequencing analysis was performed on 62 genera and species level of the 65 strains. Discrepancies were 14 (21.5%) of the 65 strains between the results of phenotypic and molecular identification. B. dermatitidis, T. marneffei, and G. argillacea were identified for the first time in Korea using the DNA sequencing method. Morphological identification is a very useful method in terms of the reporting time and costs in cases of frequently isolated and rapid growth, such as Aspergillus. When molecular methods are employed, the cost and clinical significance should be considered. On the other hand, the molecular identification of molds can provide fast and accurate results.