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Probing the Functional Motifs of Escherichia coli 5S rRNA in Relation to 16S rRNA Using a SELEX Experiment

  • 고재형;조봉래;안정근;이용훈;박인원
    • Bulletin of the Korean Chemical Society
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    • v.20 no.11
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    • pp.1335-1339
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    • 1999
  • The function of 5S rRNA, a constituent of a large subunit of ribosome, is not clearly known yet. To identify RNA motifs interacting with 5S rRNA, and thereby to get an insight into the function of 5S rRNA in the ribosome, a SELEX (Systematic Evolution of Ligands by Exponential Enrichment) experiment was performed. RNA molecules binding to Escherichia coli 5S rRNA were selected from a 48-mer random sequence library through 12 rounds of selection, cloned, and sequenced. Two groups of the selected RNA molecules had the consensus sequences GCGG and GUGAAA, respectively, which are present in the segment, G688 through A696, of E. coli 16S rRNA. The gel mobility shift assay showed that 5S rRNA interacted with the 16S rRNA fragment containing the GCGG and GUGAAA sequences. The enzymatic protection experiment shows that the A29CCUGA34 and G51AAGUG56 sequences of 5S rRNA and the C680AGG683 and G688CGG691 sequences of the 16S rRNA fragment are involved in the interaction between the two RNA molecules. On the basis of this observation, we suggest that 5S rRNA and 16S rRNA play a role for the association of two ribosomal subunits.

Population Ecology of Squalidus japonicus coreanus (Cyprinidae) in the Namhan River, Korea (남한강에 서식하는 몰개 Squalidus japonicus coreanus (Cyprinidae)의 개체군 생태)

  • Byeon, Hwa-Kun
    • Korean Journal of Environment and Ecology
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    • v.26 no.3
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    • pp.367-373
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    • 2012
  • Population ecology (Ecological characteristics) of Squalidus japonicus coreanus from the Namhan River(Yangpyeong-gun Yangpyeong-eup Changde-ri), Gyeonggi-do, Korea were investigated from January to December 2011. Short barbel gudgeon inhabits habitats run of the lower river. The stream bed was mostly covered sand. Their current velocities were 0.14~1.38m/sec and depths were 80~120cm. The sex ratio of female to male was 1 : 0.82. It is presumed that the spawning season is from June to July and water temperatures were $18.5{\sim}24.3^{\circ}C$. Sexually matured individuals appeared over the two year of age. Frequency analysis of total length indicated that the group with 34~50mm in total length was one year old, the 51~74mm was two years old, and the group over 75mm was three years old. The average number of eggs in the ovaries was estimated as 1,871 per matured female. Stomach content of S. japonicus coreanus were Cyanophyta, Chlorophyta, Bacillariophyta, Rotatoria, Crustaceae, Copepoda, Ephemeroptera, Diptera, and Nematoda. omnivorous, mainly feeds on benthic invertebrates such as chironomidae larvae.

A Study on DNA Sequences and Mutation of Integrase Region of Korean-type Bovine Leukemia Virus (BLV) pol Gene

  • Kwon, Oh-Sik;Kang, Jung-Soon;Park, Hyun-Jin;Yoo, Min
    • Biomedical Science Letters
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    • v.10 no.1
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    • pp.55-63
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    • 2004
  • Bovine leukemia virus (BLV) is a causative agent for lymphoma disease in cattle including cows worldwide. BLV shares similar virion structure and characteristics with other retroviruses. The pol gene of the BLV genome produced reverse transcriptase (RT) and integrase (IN) for important roles for BLV genome integration into host cell chromosomes that is known to be coded in the 3' side of the BLV pol gene (one third portion). In this study, we have sequenced 978 bp in the 3' side of the BLV pol gene from BLV 10C3 in order to determine the BLV IN region of it. And we compared it to the nucleotide sequences of an Australian BLV isolate. As a result, nucleotide sequences of the IN region of the Korean-type BLV pol gene were mutated at a rate of 3.7%. We can confirm that the typical mutations are such as Arg (AGG) $\rightarrow$ Lys (AAG), Thr (ACG) $\rightarrow$ Met (ATG), Ile (ATT) $\rightarrow$ Val (GTT), Asn (ACC) $\rightarrow$ His (CAC), Phe (TTT) $\rightarrow$ Leu (TTG) and Asn (ACC) $\rightarrow$ Asp (GAC). From the analysis of the sequencing data, we were able to determine the zinc-finger-like "HHCC" motif in the amino terminus of BLV IN, that was H-$X_3$-H-$X_{25}-C-X_2$-C. It was also found the DD35E motif in the IN catalytic domain as D-$X_{56}$-D-$X_{35}$-E. It fits very well to the consensus sequences of retroviral IN as well as HHCC motif.

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High-level Production of Recombinant Human IFN-$\alpha2a$ with Co-expression of $tRNA^{Arg(AFF/AGA)}$ in High-cell-density Cultures of Escherichia coli

  • Shin, Chul-Soo;Hong, Min-Seon;Shin, Hang-Chel;Lee, Jeewon
    • Biotechnology and Bioprocess Engineering:BBE
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    • v.6 no.4
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    • pp.301-305
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    • 2001
  • The co-expression of the arg U gene in a double-vector expression system of recombi-nant Escherichia coli BL22(DE3)[pET-IEN2a+pAC-argU] significantly enhanced the production level of reconminant human interferon -$\alpha$2a(rhIFN-$\alpha$2a) in high cell density cultures, compared to a recombinant E. coli culture containing only the single expression vector, pET-IEN2a. The dry cell mass concentration increased to almost 100 g/L, and more than 4 g/L of rhIFN-$\alpha$2a was accumu-lated in the culture broth. Evidently, the synthesis of rhIFN-$\alpha$2a was strongly dependent on the pre-induction growtih rate and more efficient at a higher specific growth rate. The additional sup-ply of tRN $A^{Arg(AGG/AGA)}$ enhanced the expression level of the rhIFN-$\alpha$2a gene in the early stage of the post-induction phase, yet thereafter the specific production rate of rhIFN-$\alpha$2a rapidly de-creased due to severe segregational instability of plasmid vector pET-IEN2a. It would appear that the plasmid instability with only occurred to pET-IEN2a in the double vector system, was re-lated to the effect of translational stress due to the over expression of rhIFN-$\alpha$2a.

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Development of a One-Step PCR Assay with Nine Primer Pairs for the Detection of Five Diarrheagenic Escherichia coli Types

  • Oh, Kyung-Hwan;Kim, Soo-Bok;Park, Mi-Sun;Cho, Seung-Hak
    • Journal of Microbiology and Biotechnology
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    • v.24 no.6
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    • pp.862-868
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    • 2014
  • Certain Escherichia coli (E. coli) strains have the ability to cause diarrheal disease. Five types of diarrheagenic E. coli have been identified, including EHEC, ETEC, EPEC, EAEC, and EIEC. To detect these five diarrheagenic types rapidly, we developed a one-step multiplex PCR (MP-PCR) assay using nine primer pairs to amplify nine virulence genes specific to the different virotypes, with each group being represented (i.e., stx1 and stx2 for EHEC, lt, sth, and stp for ETEC, eaeA and bfpA for EPEC, aggR for EAEC, and ipaH for EIEC). The PCR primers were constructed using MultAlin. The sensitivity and specificity of the constructed multiplex PCR primers were measured using DNA isolated from diarrheagenic E. coli strains representing each group. The limits of detection were as follows: $5{\times}10^1CFU/ml$ for EHEC, $5{\times}10^3CFU/ml$ for ETEC expressing lt and sth, $5{\times}10^4CFU/ml$ for ETEC expressing stp, $5{\times}10^2CFU/ml$ for EPEC, $5{\times}10^4CFU/ml$ for EAEC, and $5{\times}10^2CFU/ml$ for EIEC. To confirm the specificity, C. jejuni, C. perfringens, S. Typhimurium, V. parahaemolyticus, L. monocytogenes, Y. enterocolitica, B. cereus, and S. aureus were used as negative controls, and no amplification was obtained for these. Moreover, this kit was validated using 100 fecal samples from patients with diarrhea and 150 diarrheagenic E. coli strains isolated in Korea. In conclusion, the multiplex PCR assay developed in this study is very useful for the rapid and specific detection of five diarrheagenic E. coli types. This single-step assay will be useful as a rapid and economical method, as it reduces the cost and time required for the identification of diarrheagenic E. coli.

$UO_2-5wt%CeO_2$분말에서 소결온도, 소결분위기 및 $Li_2O$ 첨가에 따른 소결성 변화

  • 김시형;정창용;김한수;나상호;이영우
    • Proceedings of the Korean Nuclear Society Conference
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    • 1998.05b
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    • pp.186-191
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    • 1998
  • $UO_2$-5wt%CeO$_2$ 분말에서 소결온도(1600, 1$700^{\circ}C$), 소결분위기(H$_2$, $N_2$-7vol.%H$_2$) 및 Li$_2$O 첨가량(0.05-2wt%)에 따른 소결성의 변화를 관찰하였다. $UO_2$-5wt%CeO$_2$를 attrition mill에서 2 시간까지 분쇄한 후, 1$700^{\circ}C$에서 H$_2$, N2-7vol.%H$_2$ 분위기에서 소결하면 소결밀도가 각각 10.46, 10.36 g/㎤이지만, 각 분위기에서 소결체내의 결경립크기가 일정하지 않고 Ce agg1omerate도 소결체내의 여러 곳에 분포되어 있어 분말처리만으로 소결성을 개선하는데는 한계가 있었다. 반면에, $UO_2$-5wt%CeO$_2$에 0.lwt%Li$_2$O를 첨가하여 1 시간동안 분쇄란 후, 1$600^{\circ}C$에서 H$_2$$N_2$-7vol.%H$_2$ 분위기로 소결하면 밀도는 각각 10.51, 10.48 g/㎤이었고, 결정립크기는 각각 8.9, 42.1 $\mu\textrm{m}$이었다. 즉, Li$_2$O의 첨가에 의해 밀도와 결정립크기가 모두 증가했으며, H$_2$ 분위기보다는 $N_2$-7vol.%H$_2$ 분위기에서 결정립이 더 크게 성장하였고, 1$700^{\circ}C$에서도 유사한 경향을 나타내었다. $UO_2$-5wt%CeO$_2$와 이 조성에 0.lwt%Li$_2$O를 첨가한 분말들을 H$_2$$N_2$-7vol.%H$_2$ 분위기에서 소결하여 기공크기 및 기공부피의 변화를 관찰한 결과, H2 분위기에서 소결하였을 때는 Li$_2$O의 첨가에 의해 치밀화가 주로 일어났고, 반면에 $N_2$-7vol.%H$_2$ 분위기에서 소결하면 Li$_2$O의 첨가에 의해 작은 기공은 소멸되고 큰 기공이 생성되었다.

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Chondrogenic Differentiation of Porcine Skin-Derived Stem Cells with Different Characteristics of Spontaneous Adipocyte Formation

  • Bae, Hyo-Kyung;Jung, Bae-Dong;Lee, Seunghyung;Park, Choon-Keun;Yang, Boo-Keun;Cheong, Hee-Tae
    • Journal of Embryo Transfer
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    • v.32 no.3
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    • pp.193-200
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    • 2017
  • The purpose of this study is to confirm whether spontaneous adipocyte generation during chondrogenic induction culture affects the chondrogenic differentiation of porcine skin-derived stem cells (pSSCs). For this purpose, chondrogenic differentiation characteristics and specific marker gene expression were analyzed using cell lines showing different characteristics of spontaneous adipocyte formation. Of the four different lines of pSSCs, the pSSCs-IV line showed higher Oil red O (ORO) and glycosaminoglycan (GAG) extraction levels. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the levels of adipogenic markers peroxisome proliferator-activated receptor gamma 2 ($PPAR{\gamma}2$) and adipocyte Protein 2 (aP2) mRNAs were significantly higher in pSSCs-IV than those of the other pSSC lines (P<0.05). Among three chondrogenic markers, collagen type II (Col II) and sex determining region Y-box (Sox9) mRNAs were strongly expressed in pSSCs-IV (P<0.05), but not in aggrecan (Agg), which was significantly higher in pSSCs-II (P<0.05). These results demonstrate that the spontaneous adipocyte generation during chondrogenic differentiation has a positive effect on the chondrogenesis of pSSCs. More research is needed on the correlation between adipocyte generation and cartilage formation.

Genetic Relationship of Mono-cotyledonous Model Plant by Ionizing Irradiation (단자엽 모델 식물의 방사선원 별 처리에 따른 유전적 다형성 분석)

  • Song, Mira;Kim, Sun-Hee;Jang, Duk-Soo;Kang, Si-Yong;Kim, Jin-Baek;Kim, Sang Hoon;Ha, Bo-Keun;Kim, Dong Sub
    • Journal of Radiation Industry
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    • v.6 no.1
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    • pp.23-29
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    • 2012
  • In this study, we investigated the genetic variation in the general of monocot model plant (rice) in response to various ionizing irradiations including gamma-ray, ion beam and cosmic-ray. The non-irradiated and three irradiated (200 Gy of gamma-ray and 40 Gy of ion beam and cosmic-ray) plants were analyzed by AFLP technique using capillary electrophoresis with ABI3130xl genetic analyzer. The 29 primer combinations tested produced polymorphism results showing a total of 2,238 bands with fragments sizes ranged from 30 bp to 600 bp. The number of polymorphism generated by each primer combinations was varied significantly, ranging from 2 (M-CAC/E-ACG) to 158 (M-CAT/E-AGG) with an average of 77 bands. Polymorphic peaks were detected as 1,269 with an average of 44 per primer combinations. By UPGMA (Unweighted Pair Group Method using Arithmetic clustering) analysis method, the clusters were divided into non-irradiated sample and three irradiated samples at a similarity coefficient of 0.41 and three irradiation samples was subdivided into cosmic-ray and two irradiation samples (200 Gy of gamma-ray and 40 Gy of ion beam) at similarity coefficient of 0.48. Similarity coefficient values ranged from 0.41 to 0.55.

Development of SCAR Markers for Korean Wheat Cultivars Identification

  • Son, Jae-Han;Kim, Kyeong-Hoon;Shin, Sanghyun;Choi, Induk;Kim, Hag-Sin;Cheong, Young-Keun;Lee, Choon-Ki;Lee, Sung-Il;Choi, Ji-Yeong;Park, Kwang-Geun;Kang, Chon-Sik
    • Plant Breeding and Biotechnology
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    • v.2 no.3
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    • pp.224-230
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    • 2014
  • Amplified fragment length polymorphism (AFLP) is a molecular marker technique based on DNA and is extremely useful in detection of high polymorphism between closely related genotypes like Korean wheat cultivars. Six sequence characterized amplified regions (SCARs) have been developed from inter simple sequence repeat (ISSR) analysis which enabled the identification and differentiation of 13 Korean wheat cultivars from the other cultivars. We used six combinations of primer sets in our AFLP analysis for developing additional cultivar-specific markers in Korean wheat. Fifty-eight of the AFLP bands were isolated from EA-ACG/MA-CAC, EA-AGC/MA-CTG and EA-AGG/MA-CTA primer combinations. Of which 40 bands were selected to design SCAR primer pairs for Korean wheat cultivar identification. Three of 58 amplified primer pairs, KWSM006, KWSM007 and JkSP, enabled wheat cultivar identification. Consequently, 23 of 32 Korean wheat cultivars were classified by eight SCAR marker sets.

Psychological Characteristics of Psychiatric outpatients with High Suicide Risk : Using MMPI-2-RF (정신건강의학과 외래 환자 중 자살 고위험 집단의 심리적 특성 : MMPI-2-RF를 이용하여)

  • Nam, Jisoo;Kim, Daeho;Kim, Eunkyeong
    • Korean Journal of Psychosomatic Medicine
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    • v.28 no.1
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    • pp.8-19
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    • 2020
  • Objectives : The purpose of this study was to examine whether the MMPI-2-RF serves as a useful tool to differentiate between the subtypes of high risk of suicide among psychiatric outpatients. Methods : Patients were recruited from the department of psychiatry of university hospital. Participants were diagnosed using DSM-5 criteria by board certified psychiatrists. Their medical records were reviewed retrospectively. And participants were put into 4 groups (Suicide ideation, Suicide attempt, Non-suicidal self-injury, and general psychiatric diagnosis as a control group). For statistical comparison, the MANCOVA with gender as a covariate was used. Results : The results indicated that as previous research with non-clinical sample suggested, psychiatric outpatients with high suicide risk also have significantly higher Emotional/Internalizing Dysfunction, Helplessness/Hopelessness, Suicidal/Death Ideation, Demoralization, Cognitive complaints, Cynicism, Dysfunctional negative thoughts than general psychiatric patients group. But group differences within the high suicide risk patients have not been observed. However, suicide attempt group and NSSI group has higher Behavioral/Externalizing Dysfunction, RC4, AGG than general psychiatric patients group. But there was no difference between suicidal idea group and general psychiatric patients group. Conclusions : There was no group difference observed between all three subtypes, which mean the MMPI2-RF may not be the useful diagnostic tool to navigate high suicide risk subtypes. Even though there was no difference observed in the suicide ideation group, suicide attempt group and NSSI group have higher aggression and externalization. So those indexes could serve as a useful marker to investigate riskiness of suicide related symptoms.