• Title/Summary/Keyword: Sequence Selection

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Targeted Therapies and Radiation for the Treatment of Head and Neck Cancer (두경부 암의 표적 지향적 방사선 치료)

  • Kim, Gwi-Eon
    • Radiation Oncology Journal
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    • v.22 no.2
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    • pp.77-90
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    • 2004
  • Purpose: The purpose of this review Is to provide an update on novel radiation treatments for head and neck cancer Recent Findings: Despite the remarkable advances In chemotherapy and radiotherapy techniques, the management of advanced head and neck cancer remains challenging. Epidermal growth factor receptor (EGFR) Is an appealing target for novel therapies In head and neck cancer because not only EGFR activation stimulates many important signaling pathways associated with cancer development and progression, and importantly, resistance to radiation. Furthermore, EGFR overexpression Is known to be portended for a worse outcome in patients with advanced head and neck cancer. Two categories of compounds designed to abrogate EGFR signaling, such as monoclonal antibodies (Cetuxlmab) and tyrosine kinase inhibitors (ZD1839 and 051-774) have been assessed and have been most extensively studied In preclinical models and clinical trials. Additional TKIs In clinical trials include a reversible agent, Cl-1033, which blocks activation of all erbB receptors. Encouraging preclinical data for head and neck cancers resulted In rapid translation Into the clinic. Results from Initial clinical trials show rather surprisingly that only minority of patients benefited from EGFR inhibition as monotherapy or In combination with chemotherapy. In this review, we begin with a brief summary of erbB- mediated signal transduction. Subsequently, we present data on prognostic-predictive value of erbB receptor expression in HNC followed by preclinlcal and clinical data on the role of EGFR antagonists alone or in combination with radiation In the treatment of HNC. Finally, we discuss the emerging thoughts on resistance to EGFR biockade and efforts In the development of multiple-targeted therapy for combination with chemotherapy or radiation. Current challenges for investigators are to determine (1 ) who will benefit from targeted agents and which agents are most appropriate to combine with radiation and/or chemotherapy, (2) how to sequence these agents with radiation and/or cytotoxlc compounds, (3) reliable markers for patient selection and verification of effective blockade of signaling in vivo, and (4) mechanisms behind intrinsic or acquired resistance to targeted agents to facilitate rational development of multi-targeted therapy, Other molecuiar-targeted approaches In head and neck cancer were briefly described, Including angloenesis Inhibitors, farnesyl transferase inhibitors, cell cycle regulators, and gene therapy Summary: Novel targeted theraples are highly appealing in advanced head and neck cancer, and the most premising strategy to use them Is a matter of intense Investigation.

Single Nucleotide Polymorphisms (SNPs) Discovery in GHSR Gene and Their Association Analysis with Economic Traits in Korean Native Chickens (GHSR 유전자 내 유전변이의 탐색과 한국재래계의 성장 및 산란 특성에 미치는 연관성 분석)

  • Choi, So-Young;Hong, Min-Wook;Yang, Song-Yi;Kim, Chong-Dae;Jeong, Dong Kee;Hong, Yeong Ho;Lee, Sung-Jin
    • Korean Journal of Poultry Science
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    • v.43 no.4
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    • pp.273-279
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    • 2016
  • Recently, it was reported that certain polymorphisms in the growth hormone secretagogue receptor gene (GHSR) are associated with the growth of chickens. However, the correlation between GHSR polymorphisms and economic traits has not been investigated in Korean native chickens (KNCs). Therefore, the objective of this study was to confirm the suitability of the GHSR gene as a candidate for genomic selection and identify a genetic marker for KNCs. A total of 220 KNCs from six breeds raised at the National Institute of Animal Science were genotyped for the c.739+726 SNP in the GHSR gene using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP), and the sequence for a subset of 30 birds was analyzed using direct sequencing. The association between the SNP genotypes and the economic traits of the KNCs was analyzed using the statistical package for the social science (SPSS) software program. The association analysis between the c.739+726T>C SNP and economic traits revealed that the SNP was significantly associated with body weight at 150 and 270 days (BW150 and BW270, respectively) in all KNCs (p<0.01), BW150 in KNC (Gary) (p<0.05), and egg production number in KNC (White, p<0.05). In addition, the SNPs discovered using direct sequencing (513A>G, 517A>T) had a significant effect on the body weight and egg production traits (p<0.05). In conclusion, these results might be useful as a basis for studies on the improvement of KNC breeds. Furthermore, these results suggest that the SNPs (c.739+726T>C, 513A>G, and 517A>T) located in the GHSR gene could be useful molecular genetic markers for KNCs.

Amino Acid Biosynthesis and Gene Regulation in Seed (종자내 아미노산 합성 조절 유전자에 관한 연구)

  • ;;;;;Fumio Takaiwa
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Current Status of Cattle Genome Sequencing and Analysis using Next Generation Sequencing (차세대유전체해독 기법을 이용한 소 유전체 해독 연구현황)

  • Choi, Jung-Woo;Chai, Han-Ha;Yu, Dayeong;Lee, Kyung-Tai;Cho, Yong-Min;Lim, Dajeong
    • Journal of Life Science
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    • v.25 no.3
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    • pp.349-356
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    • 2015
  • Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds.

Molecular Characterization and Phylogenetic Analysis of Season Influenza Virus Isolated in Busan during the 2006-2008 Seasons (부산지역에서 유행한 계절인플루엔자바이러스의 유전자 특성 및 계통분석('06-'08 절기))

  • Park, Yon-Koung;Kim, Nam-Ho;Choi, Seung-Hwa;Lee, Mi-Oak;Min, Sang-Kee;Kim, Seong-Joon;Cho, Kyung-Soon;Na, Young-Nan
    • Journal of Life Science
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    • v.20 no.3
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    • pp.365-373
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    • 2010
  • To monitor newly emerged influenza virus variants and to investigate the prevalence pattern, our laboratory performed isolation of the viruses from surveillance sentinel hospitals. In the present study, we analysed influenza A/H1N1, A/H3N2, B viruses isolated in Busan during the 2006/07 and 2007/08 seasons by sequence analysis of the hemagglutinin (HA1 subunit) and neuraminidase (NA) genes. The isolates studied here were selected by the stratified random sample method from a total of 277 isolates, in which 15 were A/H1N1, 16 were A/H3N2 and 29 were B. Based on the phylogenetic tree, the HA1 gene showed that A/H1N1 isolates had a 96.7% to 97.7% homology with the A/Brisbane/59/2007, A/H3N2 isolates had a 98.4% to 99.7% homology with the A/Brisbane/10/2007, and B isolates had a 96.5% to 99.7% homology with the B/Florida/4/2006(Yamagata lineage), which are all the vaccine strains for the Northern Hemisphere in 2008~2009 season. In the case of the NA gene, A/H1N1 isolates had 97.8% to 98.5% homologies, A/H3N2 isolates had 98.9% to 99.4% homologies, and B isolates had 98.9% to 100% homologies with each vaccine strain in the 2008~2009 season, respectively. Characterization of the hemagglutinin gene revealed that amino acids at the receptor-binding site and N-linked glycosylation site were highly conserved. These results provide useful information for the control of influenza viruses in Busan and for a better understanding of vaccine strain selection.

Development of highly uniform variety for processing using SSR markers in radish (Raphanus sativus L) (분자표지를 활용한 고품질 가공용 고순도 무 품종 육성)

  • Jung, Un-Hwa;Oh, Jong-Hyuck;Kim, Young-Gyu;Ahn, Chun-Hee;Lee, Kwang-Sik;Choi, Su-Ryun;Lim, Yong-Pyo;Park, Su-Hyoung;Choi, Ki-Young;Lee, Yong-Beom
    • Journal of Plant Biotechnology
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    • v.41 no.1
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    • pp.56-63
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    • 2014
  • Using commercial radish varieties for processing, about 30% of radish was discarded due to the root shape and low purity. To raise the processing ability, we tried to develop a new variety producing H-shaped root. As another characteristic required in variety for processing is high purity, we tried to raise purity using simple sequence repeats (SSR) markers for testing seed purity in every segregating generation. To develop Male-sterile (MS) seeding parent, we crossed commercial variety of 'Gwan dong spring' and 'Gyeo ryong spring'. One elite inbred was selected as recurrent parent for the MS plant. The major horticultural traits of selected inbred line were disease resistance, late bolting, heat resistance and bright green root top color. To develop pollen parent, we crossed commercial variety of 'Tae sang king' and 'Seoul spring'. We used individual selection method to develop H-shaped hard root and disease resistant inbred. In each segregating generation, we selected one plant based on phenotype and the uniformity of selected plant was tested by SSR markers using self-pollinated seeds. In the first segregating generation, 64.6% of sib plants shared the same band in PCR amplification using ACMP-490 primer and 66.7% using cnu-316 primer. The uniformity of segregating generations using ACMP-490 and cnu-316 raised in second generation to 68.8%, 70.8%, respectively; in third generation to 93.8%, 100%; in fourth generation to 93.8%, 100%; in fifth generation to 95.8%, 100%; in sixth generation to 100%, 100%. A novel cross was made using selected MS parent and pollen parent. When we checker the horticultural traits using autumn cultivation, the novel cross variety produced H-shaped root comparing other commercial varieties and produced highly uniform radish. Thus we registered this novel cross variety as 'YR ORE' at 2013 (Registration No. 4550).

Development of SNP Molecular Markers Related to Seed-hair Characteristic Based on EST Sequences in Carrot (당근 EST 염기서열을 이용한 종자모 형질 관련 SNP 분자표지 개발)

  • Oh, Gyu-Dong;Shim, Eun-Jo;Jun, Sang-Jin;Park, Young-Doo
    • Horticultural Science & Technology
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    • v.31 no.1
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    • pp.80-88
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    • 2013
  • Carrot (Daucus carota L. var. sativa) is one of the most extensively used vegetable crops in the world and a significant source of nutrient because of its high content of ${\beta}$-carotene, well known as the precursor of vitamin A carotenoid. However, seed-hairs generated and elongated from the epidermal cell of seeds inhibit absorption and germination by various factors such as carotol and so on. Accordingly, mechanical hair removal process is essential before commercialization of carrot seeds. Because of this process, producers will have additional losses such as time consuming, manpower, capital and so on. Furthermore, physical damage of seeds causes irregular germination rate. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed and studies for molecular markers related to seed-hair characteristic is needed for a new breeding program. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-SMR 616 OP 659-1 line, hairy-seed phenotype CT-SMR 616 OP 677-14 line and short-hair seed phenotype CT-ATR 615 OP 666-13 line, hairy-seed phenotype CT-ATR 615 OP 671-9 were constructed, respectively. Furthermore, 1,248 ESTs in each line, total 4,992 ESTs were sequenced. As a result, 19 SNP sites and 14 SNP sites in each of 2 combinations were confirmed by analyzing these EST sequences from short-hair and hairy-seed lines. Then we designed SNP primer sets from EST sequences of SNP sites for high resolution melting (HRM) analysis. Designed HRM primers were analyzed using hairy seed phenotype CT-SMR 616 OP 1040 line and short-hair seed phenotype CT-SMR 616 OP 1024, 1025, 1026 lines. One set of HRM primers showed specific difference between the melting curves of hairy and short-hair seed phenotype lines. Based on this result, allele-specific (AS) PCR primers were designed for easier selection between hairy-seed carrot and hairless seed carrot. These results of HRM and AS-PCR are expected to be useful in breeding of hairless seed carrot cultivar as a molecular marker.

A Study on the Preference Analysis of the Traditional Design Elements Emerging in the Contemporary City Park of China - with Special Reference to Beijing Olympic Forest Park - (중국 현대 도시공원에 나타난 전통원림 요소에 대한 선호도 분석 - 베이징 올림픽산림공원을 사례로 -)

  • Liu, Il-Hong;Cho, Se-Hwan
    • Journal of the Korean Institute of Traditional Landscape Architecture
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    • v.28 no.2
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    • pp.109-117
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    • 2010
  • This study conducts a case analysis based on the Olympic Forest Park in Beijing, which is specially designed for the 2008 Beijing Olympic Games. The construction of the Olympic Forest Park not only comprises the design philosophy of city parks and forest parks, but also applies Chinese traditional design elements. This study, first, researches on the design concepts of city parks in the context of traditional landscape architecture elements from both physical and cultural perspectives. The author studies the related materials including the"General Introduction of the Beijing Olympic Forest Park Landscape Plan", and employs the approaches of site investigation and user survey and interview, to analyze the cognition and preference degree of the various traditional design elements displayed in the Olympic Forest Park. To quantize the survey data on the Olympic Forest Park, this study uses the spss(v17.0) software to run a frequency analysis and presents detailed demographic, frequencies and means analyses. The author then reaches the conclusion on the preference degree of the various Chinese traditional design elements in the Olympic Forest Park. According to the analysis result, the elements that appear with the highest frequencies are mountains and waters, traditional garden plants and artistic conception. The most favorable elements are in sequence traditional garden architecture, traditional garden philosophical thinking and artistic conception. The Olympic Forest Park in Beijing is constructed on the basis of multiple design elements, comprising Chinese traditional design elements and the historical axis. As an exemplification of contemporary city park that reflects the variation of age and development of society, the Olympic Forest Park offers the reference for the selection of traditional design elements in the future schemes of city parks. However, due to the difficulty in gathering materials about the Forest Park and the limitations on the location and time constrain of the survey, there exists lack of sufficiency that could be improved in the future.

Analysis of Variation for Parallel Test between Reagent Lots in in-vitro Laboratory of Nuclear Medicine Department (핵의학 체외검사실에서 시약 lot간 parallel test 시 변이 분석)

  • Chae, Hong Joo;Cheon, Jun Hong;Lee, Sun Ho;Yoo, So Yeon;Yoo, Seon Hee;Park, Ji Hye;Lim, Soo Yeon
    • The Korean Journal of Nuclear Medicine Technology
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    • v.23 no.2
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    • pp.51-58
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    • 2019
  • Purpose In in-vitro laboratories of nuclear medicine department, when the reagent lot or reagent lot changes Comparability test or parallel test is performed to determine whether the results between lots are reliable. The most commonly used standard domestic laboratories is to obtain %difference from the difference in results between two lots of reagents, and then many laboratories are set the standard to less than 20% at low concentrations and less than 10% at medium and high concentrations. If the range is deviated from the standard, the test is considered failed and it is repeated until the result falls within the standard range. In this study, several tests are selected that are performed in nuclear medicine in-vitro laboratories to analyze parallel test results and to establish criteria for customized percent difference for each test. Materials and Methods From January to November 2018, the result of parallel test for reagent lot change is analyzed for 7 items including thyroid-stimulating hormone (TSH), free thyroxine (FT4), carcinoembryonic antigen (CEA), CA-125, prostate-specific antigen (PSA), HBs-Ab and Insulin. The RIA-MAT 280 system which adopted the principle of IRMA is used for TSH, FT4, CEA, CA-125 and PSA. TECAN automated dispensing equipment and GAMMA-10 is used to measure insulin test. For the test of HBs-Ab, HAMILTON automated dispensing equipment and Cobra Gamma ray measuring instrument are used. Separate reagent, customized calibrator and quality control materials are used in this experiment. Results 1. TSH [%diffrence Max / Mean / Median] (P-value by t-test > 0.05) C-1(low concentration) [14.8 / 4.4 / 3.7 / 0.0 ] C-2(middle concentration) [10.1 / 4.2 / 3.7 / 0.0] 2. FT4 [%diffrence Max / Mean / Median] (P-value by t-test > 0.05) C-1(low concentration) [10.0 / 4.2 / 3.9 / 0.0] C-2(high concentration) [9.6 / 3.3 / 3.1 / 0.0 ] 3. CA-125 [%diffrence Max / Mean / Median] (P-value by t-test > 0.05) C-1(middle concentration) [9.6 / 4.3 / 4.3 / 0.3] C-2(high concentration) [6.5 / 3.5 / 4.3 / 0.4] 4. CEA [%diffrence Max / Mean / median] (P-value by t-test > 0.05) C-1(low concentration) [9.8 / 4.2 / 3.0 / 0.0] C-2(middle concentration) [8.7 / 3.7 / 2.3 / 0.3] 5. PSA [%diffrence Max / Mean / Median] (P-value by t-test > 0.05) C-1(low concentration) [15.4 / 7.6 / 8.2 / 0.0] C-2(middle concentration) [8.8 / 4.5 / 4.8 / 0.9] 6. HBs-Ab [%diffrence Max / Mean / Median] (P-value by t-test > 0.05) C-1(middle concentration) [9.6 / 3.7 / 2.7 / 0.2] C-2(high concentration) [8.9 / 4.1 / 3.6 / 0.3] 7. Insulin [%diffrence Max / Mean / Median] (P-value by t-test > 0.05) C-1(middle concentration) [8.7 / 3.1 / 2.4 / 0.9] C-2(high concentration) [8.3 / 3.2 / 1.5 / 0.1] In some low concentration measurements, the percent difference is found above 10 to nearly 15 percent in result of target value calculated at a lower concentration. In addition, when the value is measured after Standard level 6, which is the highest value of reagents in the dispensing sequence, the result would have been affected by a hook effect. Overall, there was no significant difference in lot change of quality control material (p-value>0.05). Conclusion Variations between reagent lots are not large in immunoradiometric assays. It is likely that this is due to the selection of items that have relatively high detection rate in the immunoradiometric method and several remeasurements. In most test results, the difference was less than 10 percent, which was within the standard range. TSH control level 1 and PSA control level 1, which have low concentration target value, exceeded 10 percent more than twice, but it did not result in a value that was near 20 percent. As a result, it is required to perform a longer period of observation for more homogenized average results and to obtain laboratory-specific acceptance criteria for each item. Also, it is advised to study observations considering various variables.