• Radiation Oncology Journal
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• v.23 no.1
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• pp.43-50
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• 2005

Purpose : A number of genes and their products are Induced early or late following exposure of cells to ionizing radiation. These radiation-Induced genes have various effects on irradiated cells and tissues. Suppression subtractive hybridization (SSH) based on PCR was used to Identify the differentially expressed genes by radiation in cervix carcinoma cells. Materials and Methods : Total RNA and poly $(A)^+$ mRNA were Isolated from Irradiated and non-irradiated HeLa cells. Forward- and reverse-subtracted cDNA libraries were constructed using SSH. Eighty-eight clones of each were used to randomly select differentially expressed genes using reverse Northern blotting (dot blot analysis). Northern blotting was used to verify the screened genes. Results : Of the 17t clones, 10 genes in the forward-subtracted library and 9 genes In the reverse-subtracted library were identified as differentially expressed radiation-induced genes by PCR-select differential screening. Three clones from the forward-subtracted library were confirmed by Northern blotting, and showed increased expression in a dose-dependent manner, including a telomerase catalytic subunit and sodium channel-like protein gene, and an ESTs (expressed sequence tags) gene. Conclusion : We Identified differentially expressed radiation-induced genes with low-abundance genes with SSH, but further characterization of theses genes are necessary to clarify the biological functions of them.

• Journal of Plant Biology
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• v.39 no.3
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• pp.189-195
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• 1996

The major cuticular components have been shown to be synthesized in the epidermis. Therefore, cloning of epidermis-specific genes could yield information to be used to isolate and characterize the enzymes involved in the cuticle biosynthesis. A subtractive cDNA library was prepared from Senecio odorus in which epidermis-specific cDNAs were enriched. Differential screening of the library using epidermal and non-epidermal probes revealed two cDNAs. One of them designated epi425 was identified, based on the sequence homology, as a member of a new class in the LTP gene family and the other clone designated epi23 as a gene encoding an aldehyde decarbonylase. Northern blot analyses showed that epi425 and epi23 cDNAs hybridized with a transcript of about 600 and 2, 100 nucleotides, respectively, from the epidermis but not from the non-epidermal tissues. Further characterization of these clones will provide more information on the mechanism of the cuticle biosynthesis.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.256-263
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• 2006

In the model legume Medicago truncatula, two mutants, sickle and sunn, exhibit morphologically and genetically distinct hypernodulation phenotypes. However, efforts to isolate the single recessive and single semidominant genes for sickle and sunn, respectively, by map-based cloning have so far been unsuccessful, partly due to the absence of clones that enable walks from linked marker positions. To help resolve these difficulties, a new bacterial artificial chromosome (BAC) library was constructed using BamHI-digested genomic fragments. A total of 23,808 clones were collected from ligation mixtures prepared with double-size-selected high-molecular-weight DNA. The average insert size was 116 kb based on an analysis of 88 randomly selected clones using NotI digestion and pulsed-field gel electrophoresis. About 18.5% of the library clones lacked inserts. The frequency of the BAC clones carrying chloroplast or mitochondrial DNA was 0.98% and 0.03%, respectively. The library represented approximately 4.9 haploid M. truncatula genomes. Hybridization of the BAC clone filters with a $C_{0}t-l$ DNA probe revealed that approximately 37% of the clones likely carried repetitive sequence-enriched DNA. An ordered array of pooled BAC DNA was screened by polymerase chain reactions using 13 sequence-characterized molecular markers that belonged to the eight linkage groups. Except for two markers, one to five positive BAC clones were obtained per marker. Accordingly, the sickle- and sunn-linked BAC clones identified herein will be useful for the isolation of these biotechnologically important genes. The new library will also provide clones that fill the gaps between preexisting BAC contigs, facilitating the physical mapping and genome sequencing of M. truncatula.

• Journal of Microbiology and Biotechnology
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• v.11 no.4
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• pp.592-597
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• 2001

The pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate with the formation of $CO_2$, acetyl-CoA, NADH, and H+. This complex contains multiple copies of three catalytic components including pyruvate dehydrogenase(E1), dihydrolipoamide acetyltransferase(E2), and dihydrolipoamide dehydrogenase (E3). Two regulatory components (E1-kinase and phospho-E1 phosphatase) and functionally less-understood protein (protein X, E3BP) are also involved in the formation of the complex. In this study, cloning and characterization of a gene for human E3BP have been carried out. A cDNA encoding the human E3BP was isolated by database search and cDNA library screening. The primary structure of E3BP has some similar characteristics with that of E2 in the lipoyl domain and the carboxyl-terminal domain, based on the nucleotide sequence and the deduced amino acid sequence. However, the conserved amino acid moiety including the histidine residue for acetyltransferase activity in E2 is not conserved in the case of human E3BP. The human E3BP was expressed and purified in E. coli. The molecular weight of the protein, excluding the mitochondrial target sequence, was about 50 kDa as determined by SDS-PAGE. Cloning of human E3BP and expression of the recombinant E3BP will facilitate the understanding of the role(s) of E3BP in mammalian PDC.

• The korean journal of orthodontics
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• v.51 no.5
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• pp.337-345
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• 2021

Objective: To investigate the phenotypes and predominant skeletodental pattern in pre-adolescent patients with Pierre-Robin sequence (PRS). Methods: The samples consisted of 26 Korean pre-adolescent PRS patients (11 boys and 15 girls; mean age at the investigation, 9.20 years) treated at the Department of Orthodontics, Seoul National University Dental Hospital between 1998 and 2019. Dental phenotypes, oral manifestation, cephalometric variables, and associated anomalies were investigated and statistically analyzed. Results: Congenitally missing teeth (CMT) were found in 34.6% of the patients (n = 9/26, 20 teeth, 2.22 teeth per patient) with 55.5% (n = 5/9) exhibiting bilaterally symmetric missing pattern. The mandibular incisors were the most common CMT (n = 11/20). Predominant skeletodental patterns included Class II relationship (57.7%), posteriorly positioned maxilla (76.9%) and mandible (92.3%), hyper-divergent pattern (92.3%), high gonial angle (65.4%), small mandibular body length to anterior cranial base ratio (65.4%), linguoversion of the maxillary incisors (76.9%), and linguoversion of the mandibular incisors (80.8%). Incomplete cleft palate (CP) of hard palate with complete CP of soft palate (61.5%) was the most frequently observed, followed by complete CP of hard and soft palate (19.2%) and CP of soft palate (19.2%) (p < 0.05). However, CP severity did not show a significant correlation with any cephalometric variables except incisor mandibular plane angle (p < 0.05). Five craniofacial and 15 extra-craniofacial anomalies were observed (53.8% patients); this implicated the need of routine screening. Conclusions: The results might provide primary data for individualized diagnosis and treatment planning for pre-adolescent PRS patients despite a single institution-based data.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.81-85
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• 2002

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Stenotrophomonas, but were not included in these genera. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium. We attempted to screening of bioactive compounds from oligotrophs which was isolated from forest soil. The active compounds were analyzed by mass and NMR spectrum, one of them identified as crisamicin A. Another one designated as SAPH is a new compound. The results indicate that there were possibilities for finding new compounds from the rare microorganisms such as oligotrophs.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.250-256
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• 2009

Acinetobacter strain $KNF2022^T$ was isolated from tobacco plant roots during the screening of antiviral substances having inhibitory effects on Tobacco mosaic virus (TMV) and examined by phenotypic, chemotaxonomic, and genetic characterization. It was a nonmotile, Gram-negative bacterium. This strain contained Q-9 as the main respiratory quinone. The major cellular fatty acids of the isolate were 16:0, 18:1 w9c, and 16:1 w7c/15 iso 2OH. The DNA base composition was 44 mol%. Phylogenetic analysis based on the 16S rRNA sequence revealed that the isolate formed an evolutionary lineage distinct from other Acinetobacter species. Based on the evaluation of morphologic, physiologic, and chemotaxonomic characteristics, DNA-DNA hybridization values, and 16S rRNA sequence comparison, we propose the new species Acinetobacter antiviralis sp. nov., the type strain of which is $KNF2022^T$ (=KCTC $0699BP^T$).

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1386-1392
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• 2010

A bacterial strain designated GR5$^T$, previously isolated from a freshwater culture pond in Taiwan while screening for bacteria for antimicrobial compounds, was characterized using a polyphasic taxonomic approach. Strain GR5$^T$ was found to be Gram-negative, aerobic, greenish-yellow colored, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at $10-40^{\circ}C$ (optimum, $35^{\circ}C$), pH 7.0-8.0 (optimum pH 8.0), and with 0-2.0% NaCl (optimum, 0.5-1.0%). The major fatty acids were $C_{16:1}{\omega}7c$(36.3%), $C_{16:0}$(16.6%), $C_{12:0}$ 3-OH (12.5%), and $C_{18:1}{\omega}7c$(9.1%). The major respiratory quinone was Q-8, and the DNA G+C content of the genomic DNA was 51.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GR5$^T$ belongs to the genus Rheinheimera, where its most closely related neighbors are Rheinheimera texasensis A62-14B$^T$ and Rheinheimera tangshanensis JA3-B52$^T$ with sequence similarities of 98.1% and 97.5%, respectively, and the sequence similarities to any other recognized species within Gammaproteobacteria are less than 96.5%. The mean level of DNA-DNA relatedness between strain GR5$^T$ and R. texasensis A62-14B$^T$, the strain most closely related to the isolate, was $26.5{\pm}7.6%$. Therefore, based on the phylogenetic and phenotypic data, strain GR5$^T$ should be classified as a novel species, for which the name Rheinheimera aquatica sp. nov. is proposed. The type strain is GR5$^T$ (=BCRC 80081$^T$=LMG 25379$^T$).

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.316-327
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• 2007

In this study, a Korean native cattle strain (Hanwoo) evidencing high performance in terms of both meat quality and quantity was employed in the generation of 150,000 BAC clones with an average insert size of 140 kb, and corresponding to about a 6X coverage of bovine chromosomal DNA. The BAC clones were pooled in a mini-scale via three rounds of a pooling protocol, and the efficiency of this pooling protocol was evaluated by testing the accuracy of accessibility to the positive clones, via a PCR-based screening method. Two sets of primers designed from each of two known genes were tested, and each yielded 2 or 3 positive clones for each gene, thereby indicating that the BAC library pooling system was appropriate with regard to the accession of the target BAC clones. Analyses of $3.3{\times}10^6$ base pairs obtained from the 7,090 BAC end sequence (BES) showed that 34.88% of the DNA sequence harbored the repetition sequence. Analysis of the 7,090 BES to the $1^{st}$ and $2^{nd}$ generation radiation hybrid map of the cattle genome, using the COMPASS program designed for the construction of a cattle-human comparative mapping, resulted in the localization of a total of 1,374 clones proximal to 339 $1^{st}$ generation markers, and 1,721 clones proximal to 664 $2^{nd}$ generation markers. Collectively, the BAC library and pooling system of the BAC clones from the Korean cattle, coupled with the chromosome-localized BAC clones, will provide us with novel tools for the excavation of desired clones for genome mapping and sequencing, and will also furnish us with additional information regarding breed differences in cattle.