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형광 Differential Display법에 의한 파리지옥풀 포충잎트랩 특이발현 유전자 탐색 (Molecular Cloning of Differentially Expressed Genes in First Trap Leaf of Dionaea muscipula by Fluorescent Differential Display)

  • 강권규;이근향;박진희;홍경의
    • Journal of Plant Biotechnology
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    • 제30권4호
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    • pp.307-313
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    • 2003
  • 파리지옥풀 first trap leaf에만 발현하는 유전자군을 탐색하기 위하여 기내배양 식물체와 포충능력을 가진 3년생 실생주을 이용하여 각각의 포충잎 (leaf base), 꽃조직 (flower tissue) 및 포충잎트랩 (first trap leaf)으로부터 분리한 RNA로 Fluorescent differential display (FDD)를 실시하였다. First trap leaf특이발현 유전자 15개를 screening하여 염기서열을 분석하였다. 분리된 DNA들은 protease inhibitor (Pl), myo-inositol-1-phosphate synthase 및 lipocalin-type prostaglandin D syn-thase 유전자들과 매우 유사하였다. 또한 Northern blot분석 결과, 이들 유전자들이 first trap leaf에 특이적으로 발현하고 있는 것을 확인하였다 FDD방법은 세포, 조직 및 기관에 특이적으로 발현하고 있는 유전자들을 선발하는데 매우 유용한 수단으로 사용될 수 있다.

아까바네 바이러스의 분리 및 RT-PCR 진단법에 관한 연구 (Isolation of akabane virus and its molecular diagnosis by reverse transcription polymerase chain reaction)

  • 조재진;이정길;박봉균;장정호;정정원;조인수;안수환
    • 대한수의학회지
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    • 제40권1호
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    • pp.42-48
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    • 2000
  • Akabane disease is transmitted through mosquitoes in cattle, sheep and goats. It shows congenital abnormalities including encephalomyetitis, hydranencephaly, neurogenic arthrogryposis, and deformed neonatal calves. Akabane viruses, 93FMX and K-9 strain, were isolated from fetal matrix of aborted cow and blood of healthy cow, respectively. S gene sequences of 93FMX and K-9 showed 100% homology with that of OBE-1 strain isolated in Japan. Based upon our sequencing data, we synthesized specific primers for PCR diagnosis. Using these primers, we were able to amplify the S gene of Akabane virus not only from the culture fluid of Vero cells but also from the brain tissue of suckling mouse inoculated with, Akabane virus. These PCR products were confirmed by Southern blot hybridization. Not only the sensitivity of PCR test was high enough to detect the viruses of $10^{1.0}TCID_{50}/ml$, but also the time for diagnosis was significantly shorter than that of the virus isolation by tissue culture method. This method was also effective for the detection of Akabane virus in the cerebrum of fetus. RT-PCR method may be used for a useful diagnostic test of the clinical cases of Akabane disease.

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Homogeneity of XEN Cells Is Critical for Generation of Chemically Induced Pluripotent Stem Cells

  • Dahee Jeong;Yukyeong Lee;Seung-Won Lee;Seokbeom Ham;Minseong Lee;Na Young Choi;Guangming Wu;Hans R. Scholer;Kinarm Ko
    • Molecules and Cells
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    • 제46권4호
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    • pp.209-218
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    • 2023
  • In induced pluripotent stem cells (iPSCs), pluripotency is induced artificially by introducing the transcription factors Oct4, Sox2, Klf4, and c-Myc. When a transgene is introduced using a viral vector, the transgene may be integrated into the host genome and cause a mutation and cancer. No integration occurs when an episomal vector is used, but this method has a limitation in that remnants of the virus or vector remain in the cell, which limits the use of such iPSCs in therapeutic applications. Chemical reprogramming, which relies on treatment with small-molecule compounds to induce pluripotency, can overcome this problem. In this method, reprogramming is induced according to the gene expression pattern of extra-embryonic endoderm (XEN) cells, which are used as an intermediate stage in pluripotency induction. Therefore, iPSCs can be induced only from established XEN cells. We induced XEN cells using small molecules that modulate a signaling pathway and affect epigenetic modifications, and devised a culture method which can produce homogeneous XEN cells. At least 4 passages were required to establish morphologically homogeneous chemically induced XEN (CiXEN) cells, whose properties were similar to those of XEN cells, as revealed through cellular and molecular characterization. Chemically iPSCs derived from CiXEN cells showed characteristics similar to those of mouse embryonic stem cells. Our results show that the homogeneity of CiXEN cells is critical for the efficient induction of pluripotency by chemicals.

국어 낭독체 발화의 운율경계 예측 (Prediction of Break Indices in Korean Read Speech)

  • 김효숙;김정원;김선주;김선철;김삼진;권철홍
    • 대한음성학회지:말소리
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    • 제43호
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    • pp.1-9
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    • 2002
  • This study aims to model Korean prosodic phrasing using CART(classification and regression tree) method. Our data are limited to Korean read speech. We used 400 sentences made up of editorials, essays, novels and news scripts. Professional radio actress read 400sentences for about two hours. We used K-ToBI transcription system. For technical reason, original break indices 1,2 are merged into AP. Differ from original K-ToBI, we have three break index Zero, AP and IP. Linguistic information selected for this study is as follows: the number of syllables in ‘Eojeol’, the location of ‘Eojeol’ in sentence and part-of-speech(POS) of adjacent ‘Eojeol’s. We trained CART tree using above information as variables. Average accuracy of predicting NonIP(Zero and AP) and IP was 90.4% in training data and 88.5% in test data. Average prediction accuracy of Zero and AP was 79.7% in training data and 78.7% in test data.

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대어휘 연속음성인식을 위한 서브네트워크 기반의 1-패스 세미다이나믹 네트워크 디코딩 (1-Pass Semi-Dynamic Network Decoding Using a Subnetwork-Based Representation for Large Vocabulary Continuous Speech Recognition)

  • 정민화;안동훈
    • 대한음성학회지:말소리
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    • 제50호
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    • pp.51-69
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    • 2004
  • In this paper, we present a one-pass semi-dynamic network decoding framework that inherits both advantages of fast decoding speed from static network decoders and memory efficiency from dynamic network decoders. Our method is based on the novel language model network representation that is essentially of finite state machine (FSM). The static network derived from the language model network [1][2] is partitioned into smaller subnetworks which are static by nature or self-structured. The whole network is dynamically managed so that those subnetworks required for decoding are cached in memory. The network is near-minimized by applying the tail-sharing algorithm. Our decoder is evaluated on the 25k-word Korean broadcast news transcription task. In case of the search network itself, the network is reduced by 73.4% from the tail-sharing algorithm. Compared with the equivalent static network decoder, the semi-dynamic network decoder has increased at most 6% in decoding time while it can be flexibly adapted to the various memory configurations, giving the minimal usage of 37.6% of the complete network size.

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Identification of differentially expressed genes in the developmental stages from olive flounder Paralichthys olivaceus using an annealing control primer system

  • Kim, Young-Ok;Park, Eun-Mi;Nam, Bo-Hye;Kong, Hee-Jeong;Kim, Woo-Jin;Noh, Jae-Koo;Lee, Sang-Jun;Kim, Kyung-Kil
    • Animal cells and systems
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    • 제14권1호
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    • pp.25-30
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    • 2010
  • We employed a new and improved differential display reverse transcription-polymerase chain reaction (DDRT-PCR) method, which involves annealing control primers (ACPs), to identify the genes that are specifically or prominently expressed in olive flounder (Paralichthys olivaceus) juveniles (35 days post-hatch; dph) compared to larval-stage (dph 21) flounder. Using 60 ACPs, we identified eight differentially expressed genes (DEGs) and basic local alignment search tool (BLAST) searches revealed eight known genes. Gene expression levels were confirmed by RT-PCR. Phosphoglucose isomerase (PGI) was highly expressed at 21 dph, while nephrosin, myosin light chain (MLC), myosin heavy chain (MHC), carboxypeptidase A, chymotrypsin B, fish-egg protein, and matrix protein were expressed at 35 dph. PGI, MLC, and MHC expression was further analyzed by RT-PCR. The differentially expressed genes identified in this study may provide insights into the molecular basis of development in olive flounder.

A New Reporter Vector System Based on Flow-Cytometry to Detect Promoter Activity

  • Jung, Sun-Do;Choi, Ji-Hye;Hong, Chang-Wan;Lee, Hyun-Ji;Park, Yoon-Kyung;Shin, Jung-Hoon;Park, Jae-Won;Park, Se-Ho
    • IMMUNE NETWORK
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    • 제9권6호
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    • pp.243-247
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    • 2009
  • In this study, we report the development of a new dual reporter vector system for the analysis of promoter activity. This system employs green fluorescence emitting protein, EGFP, as a reporter, and uses red fluorescence emitting protein, DsRed, as a transfection control in a single vector. The expression of those two proteins can be readily detected via flow cytometry in a single analysis, with no need for any further manipulation after transfection. As this system allows for the simultaneous detection of both the control and reporter proteins in the same cells, only transfected cells which express the control protein, DsRed, can be subjected to promoter activity analysis, via the gating out of all un-transfected cells. This results in a dramatic increase in the promoter activity detection sensitivity. This novel reporter vector system should prove to be a simple and efficient method for the analysis of promoter activity.

Cellular zinc deficiency inhibits the mineralized nodule formation and downregulates bone-specific gene expression in osteoblastic MC3T3-E1 cells

  • Cho, Young-Eun;Kwun, In-Sook
    • Journal of Nutrition and Health
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    • 제51권5호
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    • pp.379-385
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    • 2018
  • Purpose: Zinc (Zn) is an essential trace element for bone mineralization and osteoblast function. We examined the effects of Zn deficiency on osteoblast differentiation and mineralization in MC3T3-E1 cells. Methods: Osteoblastic MC3T3-E1 cells were cultured at concentration of 1 to $15{\mu}M$ $ZnCl_2$ (Zn- or Zn+) for 5, 15 and 25 days up to the calcification period. Extracellular matrix mineralization was detected by staining Ca and P deposits using Alizarin Red and von Kossa stain respectively, and alkaline phosphatase (ALP) activity was detected by ALP staining and colorimetric method. Results: Extracellular matrix mineralization was decreased in Zn deficiency over 5, 15, and 25 days. Similarly, staining of ALP activity as the sign of an osteoblast differentiation, was also decreased by Zn deficiency over the same period. Interestingly, the gene expression of bone-related markers (ALP, PTHR; parathyroid hormone receptor, OPN; osteopontin, OC; osteocalcin and COLI; collagen type I), and bone-specific transcription factor Runx2 were downregulated by Zn deficiency for 5 or 15 days, however, this was restored at 25 days. Conclusion: Our data suggests that Zn deficiency inhibits osteoblast differentiation by retarding bone marker gene expression and also inhibits bone mineralization by decreasing Ca/P deposition as well as ALP activity.

Quantification of the galactose-operon mRNAs 5 bases different in their 5'-ends

  • Ji, Sang-Chun;Wang, Xun;Jeon, Heung-Jin;Yun, Sang-Hoon;Lee, Hee-Jung;Lim, Heon-M.
    • BMB Reports
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    • 제43권7호
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    • pp.474-479
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    • 2010
  • Three assay methods for quantification of the two galactose-operon mRNAs that only differ by 5 bases in their 5'-end are presented. The 5' ends of each mRNA were extended by ligating the 3'-end of the abundant 5S rRNA. This ligation extends the 5' ends of the two gal mRNAs long enough to be distinguished by the specific PCR primers in the following quantification reactions. Quantification of the corresponding cDNAs was performed either by primer extension assay or real-time qPCR. To circumvent the problem of the RNA ligation reaction (i.e. very low ligation efficiency), we devised a new method that employs real-time qPCR directly for the quantification of the gal transcripts which differ by 5 bases in their 5'-ends.

TFSCAN 검색 프로그램 TFSCAN의 개발

  • 이병욱;박기정;김기봉;박완;박용하
    • 한국미생물·생명공학회지
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    • 제24권3호
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    • pp.371-375
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    • 1996
  • TFD is a transcription factor database which consists of short functional DNA sequences called as signals and their references. SIGNAL SCAN, developed by Dan S. Prestridge, is used to determine what signals of TFD may exist in a DNA sequence. This program searches TFD database by using a simple algorithm for character string comparison. We developed TFSCAN that aims at searching for signals in an input DNA sequence more efficently than SIGNAL SCAN. Our algorithms consist of two parts, one constructs an automata by scanning sequences of rFD, the other searches for signals through this automata. Searching for signal-related references is radically improved in time by using an indexing method. Usage of TFSCAN is very simple and its output is obvious. We developed and installed a TFSCAN input form and a CGI program in GINet Web server, to use TFSCAN. The algorithm applying automata showed drastical results in improvement of computing time. This approach may apply to recognizing several biological patterns. We have been developing our algorithm to optimize the automata and to search more sensitively for signals.

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