• Title/Summary/Keyword: Multiplex proteins

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Current status on the development of detection methods for genetically modified plants (유전자변형식물의 검정기술 개발 현황)

  • Kim, Jae-Hwan;Kim, Young-Rok;Kim, Hae-Yeong
    • Journal of Plant Biotechnology
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    • v.38 no.2
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    • pp.143-150
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    • 2011
  • Since the first commercial GM plant, the FlavrSavr tomato, authorized in 1994, more than 140 GM plants were authorized for marketing globally. For the authorization and labelling of GM plants, the detection methods for genes introduced and proteins expressed in GM plants were developed qualitatively and quantitatively. This review presented the detection methods, conventional PCR, multiplex PCR and real-time PCR, for soybean, maize, canola and cotton as the dominant GM plants. Also, microarray assay and nanotechnology as new approaches for detection methods for GM plants were investigated.

Microbial Detection and Identification Using Biosensors

  • Kim, Sol
    • Proceedings of the Microbiological Society of Korea Conference
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    • 2008.05a
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    • pp.135-135
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    • 2008
  • Various biosensors were evaluated for identifying and detecting foodborne pathogens in a rapid and effective manner. First, five strains of Escherichia coli and six strains of Salmonella were identified using Fourier transform infrared spectroscopy and a statistical program. For doing this, lipopolysaccharides (LPSs) and outer membrane proteins (OMPs) were extracted from a cell wall of each bacterial strain. As a result, each strain was identifed at the level of 97% for E. coli and 100% for Salmonella. Second, E. coli O157:H7, S. Enteritidis, and Listeria monocytogenes were identified by multiplex PCR products from four specific genes of each bacteria using a capillary electrophoresis (CE). Also, ground beef for E. coli O157:H7, lettuce for S. Enteritidis, and hot dog for L. monocytogenes were used to determine the possibility of detecting pathogens in foods. Foods inoculated with respective pathogen were cultivated for six hours and multiplex PCR products were obtained and assessed. The minimum detection levels of tested bacteria were <10 cells/g, <10 cells/g, and $10^4$ cells/g for E. coli O157:H7, S. Enteritidis, and L. monocytogenes, respectively. Third, it was possible to detect S. Typhimurium in a pure culture and lettuce by a bioluminescence-based detection assay using both recombinant bacteriophage P22::luxI and a bioluminescent bioreporter. In addition, bacteriophage T4 was quantitatively monitored using E. coli including luxCDABE genes.

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A Performance Comparison of Multi-Label Classification Methods for Protein Subcellular Localization Prediction (단백질의 세포내 위치 예측을 위한 다중레이블 분류 방법의 성능 비교)

  • Chi, Sang-Mun
    • Journal of the Korea Institute of Information and Communication Engineering
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    • v.18 no.4
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    • pp.992-999
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    • 2014
  • This paper presents an extensive experimental comparison of a variety of multi-label learning methods for the accurate prediction of subcellular localization of proteins which simultaneously exist at multiple subcellular locations. We compared several methods from three categories of multi-label classification algorithms: algorithm adaptation, problem transformation, and meta learning. Experimental results are analyzed using 12 multi-label evaluation measures to assess the behavior of the methods from a variety of view-points. We also use a new summarization measure to find the best performing method. Experimental results show that the best performing methods are power-set method pruning a infrequently occurring subsets of labels and classifier chains modeling relevant labels with an additional feature. futhermore, ensembles of many classifiers of these methods enhance the performance further. The recommendation from this study is that the correlation of subcellular locations is an effective clue for classification, this is because the subcellular locations of proteins performing certain biological function are not independent but correlated.

Noble Metal Nanowire Based SERS Sensor

  • Gang, Tae-Jun
    • Proceedings of the Korean Vacuum Society Conference
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    • 2013.08a
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    • pp.87-87
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    • 2013
  • The interface between nanomaterials and biosystems is emerging as one of the broadest and most dynamic areas of science and technology, bringing together biology, chemistry, physics and many areas of engineering, biomedicine. The combination of these diverse areas of research promised to yield revolutionary advances in healthcare, medicine, and life science. For example, the creation of new and powerful nanosensors that enable direct, sensitive, and rapid analysis of biological and chemical species can advance the diagnosis and treatment of disease, discovery and screening of new drug molecules. Nanowire based sensors are emerging as a powerful and general platform for ultrasensitive and multiplex detection of biological and chemical species. Here, we present the studies about noble metal nanowire sensors that can be used for sensitive detection of a wide-range of biological and chemical species including nucleic acids, proteins, and toxic metal ions. Moreover, the optical and electrochemical applications of noble metal nanowires are introduced. Noble metal nanowires are successfully used as plasmonic antennas and nanoelectrodes, thereby provide a pathway for a single molecule sensor, in vivo neural recording, and molecular injection and detection in a single living cell.

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Simultaneous Detection of Seven Phosphoproteins in a Single Lysate Sample during Oocyte Maturation Process (난자성숙 과정의 단일 시료에서 일곱 가지 인산화 단백질의 동시 분석 방법)

  • Yoon, Se-Jin;Kim, Yun-Sun;Kim, Kyeoung-Hwa;Yoon, Tae-Ki;Lee, Woo-Sik;Lee, Kyung-Ah
    • Clinical and Experimental Reproductive Medicine
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    • v.36 no.3
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    • pp.187-197
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    • 2009
  • Objective: Phosphorylation and dephosphorylation of proteins are important in regulating cellular signaling pathways. Bead-based multiplex phosphorylation assay was conducted to detect the phosphorylation of seven proteins to maximize the information obtained from a single lysate of stage-specific mouse oocytes at a time. Methods: Cumulus-oocyte complexes (COCs) were cultured for 2 h, 8 h, and 16 h, respectively to address phosphorylation status of seven target proteins during oocyte maturation process. We analyzed the changes in phosphorylation at germinal vesicle (GV, 0 h), germinal vesicle breakdown (GVBD, 2 h), metaphase I (MI, 8 h), and metaphase II (MII, 16 h in vitro or in vivo) mouse oocytes by using Bio-Plex phosphoprotein assay system. We chose seven target proteins, namely, three mitogen-activated protein kinases (MAPKs), ERK1/2, JNK, and p38 MAPK, and other 4 well known signaling molecules, Akt, GSK-$3{\alpha}/{\beta}$, $I{\kappa}B{\alpha}$, and STAT3 to measure their phosphorylation status. Western blot analysis and kinase inhibitor treatment for ERK1/2, JNK, and Akt during in vitro maturation of oocytes were conducted for the confirmation. Results: Phosphorylation of ERK1/2, JNK, p38 MAPK and STAT3 was increased over 3 folds up to 20 folds, while phosphorylation of the other three signal molecules, Akt, GSK-$3{\alpha}/{\beta}$, and $I{\kapa}B{\alpha}$ was less than 3 folds. All of these results except for Akt were statistically significant (p<0.05). Conclusion: This is the first report on the new and valuable method measuring many phosphoproteins simultaneously in one minute sample such as oocyte lysates. All of the three MAPKs, ERK1/2, JNK, and p38 MAPK are involved in the process of mouse oocyte maturation. In addition, STAT3 might be important regulator of oocyte maturation, while Akt phosphorylation at Serine 473 may not be involved in the regulation of oocyte maturation.

A Research and Application of Polyhydroxyalkanoates in Biosensor Chip (생분해성 고분자, 폴리하이드록시알카노에이트를 이용한 바이오센서 칩 연구와 그 응용)

  • Park, T.J.;Lee, S.Y.
    • KSBB Journal
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    • v.22 no.6
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    • pp.371-377
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    • 2007
  • Polyhydroxyalkanoates (PHAs) are a family of microbial polyesters that can be produced by fermentation from renewable resources. PHAs can be used as completely biodegradable plastics or elastomers. In this paper, novel applications of PHAs in biosensor are described. A general platform technology was developed by using the substrate binding domain (SBD) of PHA depolymerase as a fusion partner to immobilize proteins of interest on PHA surface. It could be shown that the proteins fused to the SBD of PHA depolymerase could be specifically immobilized onto PHA film, PHA microbead, and microcontact printed PHA surface. We review the results obtained for monitoring the specific interaction between the SBO and PHA by using enhanced green fluorescent protein, red fluorescent protein, single chain antibody against hepatitis B virus preS2 surface protein and severe acute respiratory syndrome coronavirus surface antigen as model proteins. Thus, this system can be efficiently used for studying protein-protein and possibly protein-biomolecule interactions for various biotechnological applications.

Conservation of cis-Regulatory Element Controlling Timely Translation in the 3'-UTR of Selected Mammalian Maternal Transcripts

  • Lee, Hyun-Joo;Lim, Yoon-Ki;Chang, Sang-Ho;Min, Kwan-Sik;Han, Ching-Tack;Hwang, Sue-Yun
    • Genomics & Informatics
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    • v.5 no.4
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    • pp.174-178
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    • 2007
  • The earliest stages of mammalian embryogenesis are governed by the activity of maternally inherited transcripts and proteins. Cytoplasmic polyadenylation of selected maternal mRNA has been reported to be a major control mechanism of delayed translation during preimplantation embryogenesis in mice. The presence of cis-elements required for cytoplasmic polyadenylation (e.g., CPE) can serve as a useful tag in the screening of maternal genes partaking in key functions in the transcriptionally dormant egg and early embryo. However, due to its relative simplicity, UA-rich sequences satisfying the canonical rule of known CPE consensus sequences are often found in the 3'-UTR of maternal transcripts that do not actually undergo cytoplasmic polyadenylation. In this study, we developed a method to confirm the validity of candidate CPE sequences in a given gene by a multiplex comparison of 3'-UTR sequences between mammalian homologs. We found that genes undergoing cytoplasmic polyadenylation tend to create a conserved block around the CPE, while CPE-like sequences in the 3'-UTR of genes lacking cytoplasmic polyadenylation do not exhibit such conservation between species. Through this cross-species comparison, we also identified an alternative CPE in the 3'-UTR of tissue-type plasminogen activator (tPA), which is more likely to serve as a functional element. We suggest that verification of CPEs based on sequence conservation can provide a convenient tool for mass screening of factors governing the earliest processes of mammalian embryogenesis.

Characterization of a Novel cry1-Type Gene from Bacillus thuringiensis subsp. alesti Strain LY-99

  • Qi, Xu Feng;Li, Ming Shun;Choi, Jae-Young;Roh, Jong-Yul;Song, Ji Zhen;Wang, Yong;Jin, Byung-Rae;Je, Yeon-Ho;Li, Jian Hong
    • International Journal of Industrial Entomology and Biomaterials
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    • v.18 no.1
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    • pp.18-27
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    • 2009
  • B. thuringiensis strain LY-99 belonging to subsp. alesti (H3a3c), was isolated from Chinese tobacco warehouse and showed significantly high toxicity to Plutella xylostella. For the identification of the cry1-type genes from B. thuringiensis LY-99, an extended multiplex PCRrestriction fragment length polymorphism (PCRRFLP) method was established by using two pairs of universal primers based on the conserved regions of the cry1-type genes to amplify around 2.4 kb cry1-type gene fragments. Then the DNA fragment was cloned into pGEM-T Easy vector and digested with EcoRI and EcoRV enzymes. Through this method, a known cry1-type gene was successfully identified from the reference strain, B. thuringiensis subsp. alesti. In addition, the RFLP patterns revealed that B. thuringiensis LY-99 included a novel cry1A-type gene in addition to cry1Aa, cry1Ac, cry1Be and cry1Ea genes. The novel cry1A-type gene was designated cry1Ah2 (Genbank accession No DQ269474). An inverse PCR method was used to amplify the flank regions of cry1Ah2 gene. Finally, 3143 bp HindIII fragment from B. thuringiensis LY-99 plasmid DNA including 5' region and partial ORF was amplified, and sequence analysis revealed that cry1Ah2 gene from LY-99 showed 89.31% of maximum sequence similarity with cry1Ac1 crystal protein gene. In addition, the deduced amino acid sequence of Cry1Ah2 protein shared 87.80% of maximum identity with that of Cry1Ac2. This protein therefore belongs to a new class of B. thuringiensis crystal proteins.

Characterization, detection and identification of transgenic chili pepper harboring coat protein gene that enhances resistance to cucumber mosaic virus

  • Seo, Sang-Gyu;Kim, Ji-Seong;Jeon, Seo-Bum;Shin, Mi-Rae;Kang, Seung-Won;Lee, Gung-Pyo;Hong, Jin-Sung;Harn, Chee-Hark;Ryu, Ki-Hyun;Park, Tae-Sung;Kim, Sun-Hyung
    • Journal of Plant Biotechnology
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    • v.36 no.4
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    • pp.384-391
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    • 2009
  • Previously, two events (H15 and B20) of transgenic pepper (Capsicum annuum L.) that enhanced resistance to Cucumber mosaic virus (CMV) by the introduction of CMV coat protein (CP) gene were constructed. Presently, a single copy number of the CP gene was revealed in H15 and B20 by Southern blot. To predict possible unintended effects due to transgene insertion in an endogenous gene, we carried out sequencing of the 5'-flanking region of the CP gene and a Blastbased search. The results revealed that insertion of the transgene into genes encoding putative proteins may occur in the H15 and B20 transgenic event. Mutiplex polymerase chain reaction (PCR) for simultaneous detection and identification of transgenic pepper was conducted with a set of nine primers. Both transgenic event were differentiated from non-transgenic event by the presence of 267 bp and 430 bp PCR products indicative of CP gene specific primer pairs and primer pairs targeting the CP gene and 35S promoter. H15 and B20 uniquely possessed a 390 bp and 596 bp PCR product, respectively. The presence of a 1115 bp product corresponding to intrinsic pepper actin gene confirmed the use of pepper DNA as the PCR template. The primer set and PCR conditions used presently may allow the accurate and simple identification of CMV resistant transgenic pepper.