FINAL ABSTRACT with Short Paper.150115 Targeted Genes Variations Detection/Monitoring Systems Using Structural/Genetic Detectors Sarayoot Piboonnithikasem* Medical Mycology and parasitology Group, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, 11000, THAILAND. *Corresponding Author e-mail address: [email protected] ------------------------- Abstract ----------------------- Targeted Genes Variations Detection/Monitoring Systems Using Structural/Genetic Detectors Sarayoot Piboonnithikasem* Medical Mycology and parasitology Group, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, 11000, THAILAND. Emerging virulent traits and its consequence, emerging fungal infection, can be caused of biological variations. Risk of changing of virulent traits can be examined by detection and monitoring of those variations in biological information. The Structural/Genetic variation detection and monitoring system were established using its RMSD and PCR as tools for our purposes. RMSD were computed from homology model comparison and PCR systems were design from genetic information in its differences of primary structure. Homology models of tested proteins were constructed. There were overall structural differences among tested proteins located in tertiary structure compared with both reference CaSAPs phylogenetic tree and the published CaSAP phylogenetic tree reconstruction. Moreover, its secondary and primary strucutures also contained major differences among each other that can be detected by RMSD. Its genetic information encoded major structural different segment differed among tested proteins. The major structural differences can be assigned as probe to detect, compare, and monitor the structural difference among genes in family. PCR detection system of genetic differences inside major structural segments can be designed from its primary structure. Keywords: Structural/Genetic variation, Detection/Monitoring system, Emerging Virulent Factors and Traits and Fungal infection. *Corresponding Author e-mail address: [email protected] ------------------------- Abstract ----------------------- ------------------------ Short Paper --------------------- Short Paper 1. Introduction Novel targeted genes as putative virulent factors for fungal infection may be discovered from fungal genome monitoring systems. Targeted genes variations detection/monitoring systems can be applied for identification and characterization of both genetic and structural biological variations in order to assessed emerging virulent traits and its consequence, an emerging fungal infection. Moreover, risk of changing of virulent traits can be examined by those variations in its biological information. This investigation, Targeted genes variations detection/monitoring systems were established using major structural and its genetic information differences by its RMSD and PCR as detector tools. 2. Research Investigation Reference CaSAPs phylogenetic tree was reconstructed to use for comparing with structural and genetic variations from established systems. CaSAPs homology models were constructed then, structural comparisons were performed to identify major structural differences. It will be used for assigned both structural and genetic detectors. In the comparison, RMSD were calculated and genetic information of its primary structures will be used for primers design in order that the structural and genetic comparison can be performed, respectively. 3. Result and Discussion Homology models of tested proteins were constructed and model qualities were estimated (Table 1). There were overall structural differences among tested proteins located in tertiary structure compared with both reference CaSAPs phylogenetic tree and the published CaSAP phylogenetic tree reconstruction (Figure 1). ------------------------------------------------------------ Table 1. The homology models and its qualities Reference CaSAPs homology models were constructed on SWISS-MODEL server against reference structures. The homology model qualities were validated on QMEAN Model Quality Estimation Server. ------------------------------------------------------------ Moreover, its secondary and primary structures also contained major differences among each other that can be detected by RMSD(Figure 2). Major structural differences were used to set structural Detectors. CaSAP5 and CaSAP3 were assigned to be structural detectors as probe to detect the differences among CaSAP1,2 and 3 and CaSAP4,5 and 6, respectively. The RMSD of CaSAP1,2 and 3 against CaSAP5 and were 1.44 A, 1.42 A and 1.54 A and for CaSAP4,5 and 6 against CaSAP3 were 0.81, 1.52 and 0.81, respectively. Major structural differences with its molecular surface among CaSAP4,5 and 6 were compared against reference Candida albicans phylogenetic tree reconstruction. According to figure 2 there were different in secondary structure made its tertiary structure were differed too. The structural detector with its RMSD demostrated the overall difference and its relation corresponded both reference CaSAPs phylogenetic tree and the publised CaSAP phylogenetic tree reconstruction. Its genetic information encoded major structural different segment differed among tested protein (Table 2.). Its genetic information in primary structure of the major structural differences were used for primer design to amplify/sequencing by PCR. To assess CaSAP1 using CaSAP5 as structural detectors, Two major structural difference segments, targeted segment 1 APLSYANGQPYPKCQ (Chain A, Secreted Aspartic Proteinase (Sap) 1 From C. albicans 100% 1e-06 100% 2QZW_A) and targeted segment 2 SVTCDKPRPGQSADFC(Chain A, Secreted Aspartic Proteinase (Sap) 1 From C. albicans 00% 2e-07 100% 2QZW_A), were applied for primer design to perform PCR/sequencing. ------------------------------------------------------------ Figure 1. Reference CaSAPs Phylogenetic Tree Reconstruction. Reference CaSAPs biological information were used phylogenetic tree reconstruction with 10000 replicates boostraped analysis compared with published CaSAP phylogenetic tree reconstruction by Naglik JR. et al.2003. DOI: 10.1128/MMBR.67.3.400–428. ------------------------------------------------------------ According to Figure 2, Two genetic information in primary structure of the major structural differences (Table 2a) of CaSAP1 against CaSAP5 as structural detector were used to design primers/probe and performed In silico PCR(Table 2b). The putative In silico Amplicons containing genetic information in primary structure of the major structural differences and its putative amplicon product sizes were shown. ------------------------------------------------------------ Figure 2. Structural Detector with its RMSD Major structural differences were used to set Structural Detectors. CaSAP5 and CaSAP3 were assigned to be structural detectors as probe to detect the differences among CaSAP1,2 and 3 and CaSAP4,5 and 6, respectively. ------------------------------------------------------------ The major structural differences can be assigned as probe to detect, compare, and monitor the structural difference among genes in family. PCR detection system of genetic differences inside major structural segments can be designed from its primary structure. Thus, the Structural/Genetic detection and monitoring system can be established using its Biological information in Central Dogma for both genetic information, as nucleic acid both DNA and RNA, and protein information and its structures, primary, secondary and tertiary structures. ------------------------------------------------------------ Table 2. Primers and PCR Systems Two genetic information in primary structure of the major structural differences (Table 2a) of CaSAP1 against CaSAP5 as structural detector were used to design primers/probe and performed In silico PCR(Table 2b). The putative In silico amplicons containing genetic information in primary structure of the major structural differences and its putative amplicon product sizes were shown. ------------------------------------------------------------ 4. Conclusion The variation detection and monitoring system have been established using major structural and its genetic information differences as detector by its RMSD and PCR as tools. The RMSD can be assessed the evolutional relationship comparing with reference phylogenetic tree reconstruction. Moreover In silico PCR can be described the details of genetic differences of major structural segments. 5. Acknowledgements 1. Biozentrum University of Basel, and SIB Swiss Institute of Bioinformatics, Basel, Switzerland for SWISS- MODEL homology-modelling server and QMEAN Server for Model Quality Estimation. 2. Department of Medical Sciences, Ministry of Public Health for Computational Facility. 6. References 1. Jones T. et al.2004.The diploid genome sequence of Candida albicans. PNAS.101(19):7329-7334. 2. Biasini M. et al.2014.SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.NAR.42(W1): W252-W258; doi: 10.1093/nar/gku340. 3. Benkert P. et al.2009.QMEAN Server for Protein Model Quality Estimation.NAR.37.W510-4. ------------------------ Short Paper --------------------- --------------------------------------------- บทคัดย่อ ------------------------------------------------ บทคัดย่อ ระบบตรวจตรวจหาและติดตามความผันแปรของยีนเป้าหมาย ด้วยการใช้ ตัวติดตามเชิงโครงสร้างและตัวติดตามเชิงพันธุกรรม สรายุทธ พิบูลนิธิเกษม* กลุ่มเชื้อราวิทยาและพาราสิตวิทยา สถาบันวิจัยวิทยาศาสตร์สาธารณสุข กรมวิทยาศาสตร์การแพทย์ กระทรวงสาธารณสุข ปัจจัยก่อโรค ลักษณะที่ก่อโรค และการติดเชื้อราอุบัติใหม่ เป็นภัยคุกคามที่เกิดขึ้นได้จากความผันแปรทางชีวภาพ ความเสี่ยงอันเกิดจากสิ่งเหล่านี้ สามารถตรวจจับและติดตามได้จากสารพันธุกรรมของปัจจัยก่อโรคเป้าหมายนั้น ๆ ในการนี้จึงพัฒนาระบบตรวจจับและติดตาม ความผันแปรเชิงโครงสร้างและพันธุกรรมขึ้น โดยใช้ค่า RMSD และ PCR primer เป็นเครื่องมือในการตรวจจับและติดตาม โดย RMSD จะคำนวณจากการเปรียบเทียบโครงสร้างสามมิติที่จำลองขึ้น และ PCR primer จะออกแบบจากลำดับสารพันธุกรรมที่เป็นรหัสของโครงสร้างปฐมภูมิ โดยจะสร้างแบบจำลองโครงสร้างสามมิติขึ้น แล้วเปรียบเทียบความแตกต่างทั้งโครงสร้างตติยภูมิ ทุติยภูมิ และปฐมภูมิ เทียบกับความสัมพันธ์เชิงวิวัฒนาการ ยิ่งไปกว่านั้น ในโครงสร้างทุติยภูมิ และปฐมภูมิ จะพบความแตกต่างหลักระหว่างกลุ่มโครงสร้างโปรตีนซึ่งสามารถนำมาใช้เป็นตัวติดตามเชิงโครงสร้างและตัวติดตามเชิงพันธุกรรม เพื่อเป็นเครื่องมือในการตรวจจับและติดตามความผันแปรทางชีวภาพได้ ส่วนลำดับสารพันธุกรรมในโครงสร้างปฐมภูมิจะนำมาใช้ในการออกแบบไพร์เมอร์เพื่อนใช้ตรวจจับและติดตามความผันแปรในสารพันธุกรรมของปัจจัยก่อโรคเป้าหมาย ในการวิจัยครั้งนี้สามารถเตรียม ตัวติดตามเชิงโครงสร้างและตัวติดตามเชิงพันธุกรรมต้นแบบ เพื่อใช้เป็นแนวทางในการพัฒนาตัวติดตามต่อ ๆ ไป โดยอาศัย ค่า RMSD และ PCR primer จากข้อมูลในโครงสร้างของโปรตีนและลำดับสารพันธุกรรมที่กำหนดรหัสโครงสร้างปฐมภูมิซึ่งเป็นส่วนของความแตกต่างหลักระหว่างกลุ่มโครงสร้างโปรตีน คำสำคัญ ความผันแปรเชิงโครงสร้างและพันธุกรรม, ระบบตรวจสอบและติดตาม, ปัจจัยก่อโรค ลักษณะที่ก่อโรค และการติดเชื้อราอุบัติใหม่ *Corresponding Author e-mail address: [email protected] --------------------------------------------- บทคัดย่อ ------------------------------------------------
Posted on: Thu, 15 Jan 2015 02:25:05 +0000
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