Nucleic acid based in-vitro diagnostic device

Download
index.pdf
2018
Balcı, Oğuz
Show full item record
108
views
76
downloads
Commonly used nucleic acid based in-vitro diagnostic systems utilize either quantitative PCR (polymerase chain reaction) or conventional PCR. Quantitative PCR is a fast and reliable method; however, the prices of quantitative PCR devices are relatively expensive due to the cost of highly sensitive sensors. Equipment using conventional PCR is lower in price but have several disadvantages such as long analysis periods, contamination risk, false positivity risk, and usage of carcinogenic chemicals. The purpose of the study is to design, manufacture, and validate a nucleic acid based in-vitro diagnostic device operating with a novel microparticle based method. In this microparticle based method, PCR is performed with the presence of microparticles and oligonucleotide probes. Oligonucleotide probes that are unused in PCR adsorb onto the microparticles; however, fluorophore molecules released with the exo-nuclease activity of Taq. DNA polymerase does not adsorb onto microparticles. By this way, background fluorescence is reduced and the need for sensitive sensors for detecting the fluorescence difference disappears. For this purpose, a prototype device including a LED light source, two filter sliders, two excitation band-pass filters, a 24 sample carousel, two emission band-pass filters, and a CCD camera was designed and manufactured. Microparticle batch equilibrium analysis was performed and using DNA eluates from 105 HBV negative-diagnosed and 187 HBV positive-diagnosed samples, prototype device validation study including cutoff score, analytical sensitivity, analytical specificity, linear range, precision, robustness, diagnostic sensitivity, and diagnostic specificity was conducted. The findings suggest that low-cost prototype device combines high sensitivity, specificity, reproducibility and accuracy for HBV DNA quantitation in a high linear range.
Diagnostic imaging, Biotechnology., Imaging systems in medicine
http://etd.lib.metu.edu.tr/upload/12621847/index.pdf
https://hdl.handle.net/11511/27106
Graduate School of Natural and Applied Sciences, Thesis

Suggestions

Role of the cmcH-ccaR intergenic region and ccaR overexpression in cephamycin C biosynthesis in Streptomyces clavuligerus
Kurt, Aslihan; Alvarez-Alvarez, Ruben; Liras, Paloma; Özcengiz, Gülay (Springer Science and Business Media LLC, 2013-07-01)
The effect of the CcaR regulatory protein on expression of the cephamycin C gene cluster is studied. Quantitative reverse transcription PCR (qRT-PCR) expression analysis of the cephamycin biosynthesis genes in the ccaR-disrupted strain, S. clavuligerus ccaR::aph, revealed that in the absence of CcaR, the lat and cmcI genes expression was reduced 2,200-and 1,087-fold compared with the wild type. Expression of pcbAB-pcbC-cefD-cefE-cmcJ-cmcH and blp was 225- to 359-fold lower, while expression of pcbR-pbpA-bla...
Regulatory effects of alanine-group amino acids on serine alkaline protease production by recombinant Bacillus licheniformis
Çalık, Pınar; Ozdamar, TH (Wiley, 2003-04-01)
Influences of the concentration and addition time of alanine-group amino acids, i.e. alanine, leucine and valine, on serine alkaline protease (SAP) synthesis were investigated by Bacillus licheniformis (DSM 1969) carrying pHV1431::subC in a defined medium to identify the amino acids creating intracellular reaction-rate limitation in SAP production. While the precursors of alanine-group amino acids, pyruvate and alanine, did not affect SAP production considerably within the range 0-15 mM, the addition of leu...
PCR with degenerate primers amplifies a subgenomic DNA fragment from the endoglucanase gene(s) of Torula thermophila, a thermophilic fungus
Ozturk, ZN; Ögel, Zümrüt Begüm (Springer Science and Business Media LLC, 2000-10-01)
The aim of this study was to enable the polymerase chain reaction (PCR) amplification of DNA fragments within endoglucanase gene(s) of Torula thermophila, by using degenerate primers so that the amplified fragment(s) could be used as homologous probe(s) for cloning of full-length endoglucanase gene(s). The design of the degenerate PCR primers was mainly based on the endoglucanase sequences of other fungi. The endoglucanase gene sequence of Humicola insolens was the only sequence from a thermophilic fungus p...
Influence of oxygen transfer on benzaldehyde lyase production by recombinant Escherichia coli BL21(DE3) pLySs
Angardi, Vahideh; Çalık, Pınar; Department of Chemical Engineering (2007)
In this study, the effects of oxygen transfer conditions on the synthesis of the enzyme benzaldehyde lyase as intracellular in recombinant E. coli BL21 (DE3) pLysS was investigated sistematically and a comprehensive model was developed to determine benzaldehyde lyase activity. For this purpose, the research program was carried out in mainly two parts. In the first part of study, the effects of oxygen transfer together with the mass transfer coefficient (KLa), enhancement factor E (=KLa/KLao), volumetric oxy...
A medical image processing and analysis framework
Çevik, Alper; Eyüboğlu, Behçet Murat; Oğuz, Kader Karlı; Department of Biomedical Engineering (2011)
Medical image analysis is one of the most critical studies in field of medicine, since results gained by the analysis guide radiologists for diagnosis, treatment planning, and verification of administered treatment. Therefore, accuracy in analysis of medical images is at least as important as accuracy in data acquisition processes. Medical images require sequential application of several image post-processing techniques in order to be used for quantification and analysis of intended features. Main objective...
Citation Formats
O. Balcı, “Nucleic acid based in-vitro diagnostic device,” Ph.D. - Doctoral Program, Middle East Technical University, 2018.
METU IIS - Integrated Information Service open@metu.edu.tr