• Parasites, Hosts and Diseases
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• 제46권4호
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• pp.209-216
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• 2008

A monoclonal antibody against Toxoplasma gondii of Tg556 clone (Tg556) blotted a 29 kDa protein, which was localized in the dense granules of tachyzoites and secreted into the parasitophorous vacuolar membrane (PVM) after infection to host cells. A cDNA fragment encoding the protein was obtained by screening a T. gondii cDNA expression library with Tg556, and the full-length was completed by 5'-RACE of 2,086 bp containing an open reading frame (ORF) of 669 bp. The ORF encoded a polypeptide of 222 amino acids homologous to the revised GRA3 but not to the first reported one. The polypeptide has 3 hydrophobic moieties of an N-terminal stop transfer sequence and 2 transmembrane domains (TMD) in posterior half of the sequence, a cytoplasmic localization motif after the second TMD and an endoplasmic reticulum (ER) retrival motif in the C-terminal end, which suggests GRA3 as a type III transmembrane protein. With the ORF of GRA3, yeast two-hybrid assay was performed in HeLa cDNA expression library, which resulted in the interaction of GRA3 with calcium modulating ligand (CAMLG), a type II transmembrane protein of ER. The specific binding of GRA3 and CAMLG was confirmed by glutathione S-transferase (GST) pull-down and immunoprecipitation assays. The localities of fluorescence transfectionally expressed from GRA3 and CAMLG plasmids were overlapped completely in HeLa cell cytoplasm. In immunofluorescence assay, GRA3 and CAMLG were shown to be co-localized in the PVM of host cells. Structural binding of PVM-inserted GRA3 to CAMLG of ER suggested the receptor-ligand of ER recruitment to PVM during the parasitism of T. gondii.

• Fisheries and Aquatic Sciences
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• 제19권8호
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• pp.33.1-33.7
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• 2016

Antifreeze proteins (AFPs) lower the freezing point but not the melting point of aqueous solutions by inhibiting the growth of ice crystals via an adsorption-inhibition mechanism. However, the function of type IV AFP (AFP IV) is questionable, as its antifreeze activity is on the verge of detectable limits, its physiological concentration in adult fish blood is too low to function as a biological antifreeze, and its homologues are present even in fish from tropic oceans as well as freshwater. Therefore, we speculated that AFP IV may have gained antifreeze activity not by selective pressure but by chance. To test this hypothesis, we cloned, expressed, and assayed AFP IV from cultured subtropical olive flounder (Paralichthys olivaceus), which do not require antifreeze protein for survival. Among the identified expressed sequence tags of the flounder liver sample, a 5'-deleted complementary DNA (cDNA) sequence similar to the afp4 gene of the longhorn sculpin was identified, and its full-length cDNA and genome structure were examined. The deduced amino acid sequence of flounder AFP IV shared 55, 53, 52, and 49 % identity with those of Pleuragramma antarcticum, Myoxocephalus octodecemspinosus, Myoxocephalus scorpius, and Notothenia coriiceps, respectively. Furthermore, the genomic structure of this gene was conserved with those of other known AFP IVs. Notably, the recombinant AFP IV showed a weak but distinct thermal hysteresis of $0.07{\pm}0.01^{\circ}C$ at the concentration of 0.5 mg/mL, and ice crystals in an AFP IV solution grew star-shaped, which are very similar to those obtained from other polar AFP IVs. Taken together, our results do not support the hypothesis of evolution of AFP IV by selective pressure, suggesting that the antifreeze activity of AFP IV may have been gained by chance.

• Mycobiology
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• 제37권3호
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• pp.183-188
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• 2009

The molecular phylogeny in nine different commercial cultivated strains of Pleurotus nebrodensis was studied based on their internal transcribed spacer (ITS) region and RAPD. In the sequence of ITS region of selected strains, it was revealed that the total length ranged from 592 to 614 bp. The size of ITS1 and ITS2 regions varied among the strains from 219 to 228 bp and 211 to 229 bp, respectively. The sequence of ITS2 was more variable than ITS1 and the region of 5.8S sequences were identical. Phylogenetic tree of the ITS region sequences indicated that selected strains were classified into five clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by RAPD with 20 arbitrary primers. Twelve primers were efficient to applying amplification of the genomic DNA. The sizes of the polymorphic fragments obtained were in the range of 200 to 2000 bp. RAPD and ITS analysis techniques were able to detect genetic variation among the tested strains. Experimental results suggested that IUM-1381, IUM-3914, IUM-1495 and AY-581431 strains were genetically very similar. Therefore, all IUM and NCBI gene bank strains of P. nebrodensis were genetically same with some variations.

• Journal of Ginseng Research
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• 제37권2호
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• pp.227-247
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• 2013

MicroRNAs (miRNAs) are a class of recently discovered non-coding small RNA molecules, on average approximately 21 nucleotides in length, which underlie numerous important biological roles in gene regulation in various organisms. The miRNA database (release 18) has 18,226 miRNAs, which have been deposited from different species. Although miRNAs have been identified and validated in many plant species, no studies have been reported on discovering miRNAs in Panax ginseng Meyer, which is a traditionally known medicinal plant in oriental medicine, also known as Korean ginseng. It has triterpene ginseng saponins called ginsenosides, which are responsible for its various pharmacological activities. Predicting conserved miRNAs by homology-based analysis with available expressed sequence tag (EST) sequences can be powerful, if the species lacks whole genome sequence information. In this study by using the EST based computational approach, 69 conserved miRNAs belonging to 44 miRNA families were identified in Korean ginseng. The digital gene expression patterns of predicted conserved miRNAs were analyzed by deep sequencing using small RNA sequences of flower buds, leaves, and lateral roots. We have found that many of the identified miRNAs showed tissue specific expressions. Using the insilico method, 346 potential targets were identified for the predicted 69 conserved miRNAs by searching the ginseng EST database, and the predicted targets were mainly involved in secondary metabolic processes, responses to biotic and abiotic stress, and transcription regulator activities, as well as a variety of other metabolic processes.

• BMB Reports
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• 제35권2호
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• pp.213-219
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• 2002

Malonyl-CoA decarboxylase (E.C.4.1.1.9) catalyzes the conversion of malonyl-CoA to acetyl-CoA. Although the metabolic role of this enzyme has not been fully defined, it has been reported that its deficiency is associated with mild mental retardation, seizures, hypotonia, cadiomyopathy, developmental delay, vomiting, hypoglycemia, metabolic acidosis, and malonic aciduria. Here, we isolated a cDNA clone for malonyl CoA decarboxylase from a rat brain cDNA library, expressed it in E. coli, and characterized its biochemical properties. The full-length cDNA contained a single open-reading frame that encoded 491 amino acid residues with a calculated molecular weight of 54, 762 Da. Its deduced amino acid sequence revealed a 65.6% identity to that from the goose uropigial gland. The sequence of the first 38 amino acids represents a putative mitochondrial targeting sequence, and the last 3 amino acid sequences (SKL) represent peroxisomal targeting ones. The expression of malonyl CoA decarboxylase was observed over a wide range of tissues as a single transcript of 2.0 kb in size. The recombinant protein that was expressed in E. coli was used to characterize the biochemical properties, which showed a typical Michaelis-Menten substrate saturation pattern. The $K_m$ and $V_{max}$ were calculated to be $68\;{\mu}M$ and $42.6\;{\mu}mol/min/mg$, respectively.

• Journal of Ginseng Research
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• 제29권4호
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• pp.167-175
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• 2005

The $Ca^{2+}-activated$ chloride channel (CLCA) was activated by ginseng total saponin (GTS) in Xenopus oocytes. The reverse transcription PCR (RT-PCR) method was performed with gene specific primers on oocytes. The gene specific primers were deduced from spleen cDNA in expressed sequence tags (EST) database showing high homology to the mouse CLCA. Full length of cDNA sequence was completed by linkage of several 5' and 3'-half cDNA fragments have been sequenced. We named the full cDNA to oCLCA transiently. The oCLCA gene encodes a protein of 911 amino acids with $48.9\%$ identity overall to that of mouse CLCA (mCLCA4). A predicted oCLCA amino acids sequence shows the molecular weight of 108 kDa and has four or more transmembrane domains, and also the one hydrophobic C­terminal domain. oCLCA gene was expressed ubiquitously in various tissues included oocytes, also interfered in oocytes by siRNA for oCLCA. Here, we suggest that oCLCA is a endogenous chloride channel gene in oocytes. We are studying for the identification of oCLCA gene and further physiological research.

• Journal of Communications and Networks
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• 제18권2호
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• pp.218-226
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• 2016

Coordination among users is an inevitable but time-consuming operation in wireless networks. It severely limit the system performance when the data rate is high. We present FC-MAC, a novel MAC protocol that can complete a contention within one contention slot over a joint frequency-code domain. When a node takes part in the contention, it generates randomly a contention vector (CV), which is a binary sequence of length equal to the number of available orthogonal frequency division multiplexing (OFDM) subcarriers. In FC-MAC, different user is assigned with a distinct signature (i.e., PN sequence). A node sends the signature at specific subcarriers and uses the sequence of the ON/OFF states of all subcarriers to indicate the chosen CV. Meanwhile, every node uses the redundant antennas to detect the CVs of other nodes. The node with the minimum CV becomes the winner. The experimental results show that, the collision probability of FC-MAC is as low as 0.05% when the network has 100 nodes. In comparison with IEEE 802.11, contention time is reduced by 50-80% and the throughput gain is up to 200%.

• 한국정보과학회논문지:데이타베이스
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• 제28권3호
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• pp.344-356
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• 2001

본 논문에서는 시퀀스 데이터베이스에서 시간왜곡 변환(time warping)을 지원하는 서브시퀀스 탐색 문제를 다룬다. 서브시퀀스 탐색은 데이터 시퀀스의 평균 길이의 이차 함수로 성능이 저하된다. 이러한 문제를 해결하기 위하여 본 논문에서는 세그먼트 기반 서브시퀀스 탐색 기법(Segment-Based Approach for Subsequence Searches : SBASS)을 제안한다. SBASS는 데이터와 질의 시퀀스를 연속된 세그먼트들로 분할하여 다음의 두가지 조건을 만족하는 모든 데이터 시퀀스를 검색한다. (1) 세그먼트의 개수가 질의 시퀀스의 세그먼트 개수와 같다. (2) 모든 세그먼트 쌍 간의 거리가 주어진 오차 한도 이내이다. 제안된 세그먼트 분할 기법에서는 세그먼트가 서로 다른 길이를 갖도록 허용하며, 세그먼트 쌀간의 유사성의 척도로서 시간왜곡 변환 거리를 이용한다. 효율적인 유사 서브시퀀스 탐색을 위하여, 각 데이터 세그먼트로부터 요서 값들이 단조적으로 변화하는 특성을 이용하여 특성 벡터를 추출하고, 추출된 특성 벡터를 이용하여 공간 인덱스를 생성한다. 질의는 이 인덱스를 이용하여 (1) R-트리 여과, (2) 특성 여과, (3) 순서 여과, (4) 후처리의 네 단계로 처리된다. 다양한 실험을 통하여 제안된 기법의 효율성을 입증한다.

• Parasites, Hosts and Diseases
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• 제45권2호
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• pp.87-94
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• 2007

In this study, we describe Korean isolates of Trichomonas vaginalis infected with double-stranded (ds) RNA virus (TVV). One T. vaginalis isolate infected with TVV IH-2 evidenced weak pathogenicity in the mouse assay coupled with the persistent presence of a dsRNA, thereby indicating a hypovirulence effect of dsRNA in T. vaginalis. Cloning and sequence analysis results revealed that the genomic dsRNA of TVV IH-2 was 4,647 bp in length and evidenced a sequence identity of 80% with the previously-described TVV 1-1 and 1-5, but only a 42% identity with TVV 2-1 and 3 isolates. It harbored 2 overlapping open reading frames of the putative capsid protein and dsRNA-dependent RNA polymerase (RdRp). As previously observed in the TVV isolates 1-1 and 1-5, a conserved ribosomal slip-page heptamer (CCUUUUU) and its surrounding sequence context within the consensus 14-nt overlap implied the gene expression of a capsid protein-RdRp fusion protein, occurring as the result of a potential ribosomal frameshift event. The phylogenetic analysis of RdRp showed that the Korean TVV If-2 isolate formed a compact group with TVV 1-1 and 1-5 isolates, which was divergent from TVV 2-1, 3 and other viral isolates classified as members of the Giardiavirus genus.

• 한국해양바이오학회지
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• 제1권2호
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• pp.119-125
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• 2006

어류의 insulin-like growth factor-I (IGF-I)의 생화학적 작용기작을 연구하기 위하여 한국산 조피볼락의 IGF-I cDNA 유전자 cloning을 행하였다. 완전한 cDNA 유전자 염기서열은 PCR과 RACE 방법을 통하여 얻어진 DNA로부터 결과를 얻을수 있었다. 결정된 IGF-I의 염기서열은 flounder, chinook salmon, human IGF-I의 염기서열과 비교한 결과 각각 93.6%, 90.7%, 85.4%의 높은 상동성을 보였다. 생화학적으로 활성이 있는 재조합 IGF-I을 얻기 위하여 IGF-I의 B-C-A-D domain 부분을 PCR로 얻은 뒤 E. coli BL21(DE3)에 넣어 overexpression 시켰다. Ni-NTA colummn을 사용하여 순수한 재조합 단백질을 정제할수 있었다. 정제된 단백질은 SDS-PAGE 상에서 7 kDa의 단일 band를 보여 주었으며 [$^3H$]-thymidine 결합정도를 측정하는 방법으로 활성을 가지고 있음을 확인할수 있었다.