Development of diagnostic platforms for single nucleotide polymorphism detection

Akça, Oya
In this study, we report the results of different simple and cost effective approaches and platforms which were used to improve single nucleotide mismatch discrimination ability and investigation of the applicability of various materials and environments for the system. As the solid support of the array platform both customly functionalized epoxy and amine combination and commercially purchased poly-L-lysine modified materials were used. Surface-probe interactions and immobilization efficiencies were investigated and affirmative results are gained with heterobifunctional cross linker mediated immobilization of polyethyleneglycol spacer functionalized surface probes. Glass capillary tubes were also used to develop a partially solution based approach that can detect single nucleotide polymorphisms (SNPs) through the Oligonucleotide Ligation Reaction. The established sytem was capable of discriminating mistmatches at single nucleotide level by using unlabeled targets. Mesoporous silica nanoparticles and nitrocellulose membrane strips were also used to develop a novel platform for SNP detection. Controlled release of chromogen molecules inside the pores of the silica nanoparticles were achieved related with the specific complementary probe hybridization events. Use of unmodified target sequences in sandwich hybridization format permitted the usage of different detection signal probes throughout the study. Signal probes modified with 6-carboxyfluorescein or biotin at 3’ ends were successfully used to visualize the experimental results by using simple UV illumination and of color formation. This enables the platform to be followed by unaided eyes which makes it an ideal candidate for point of care detection purposes.


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Tokdemir Demirel, Elif; Enginarlar, Hüsnü; Department of English Language Teaching (2009)
This study aimed at developing a complementary peer-teacher feedback model, in which students and teachers share the responsibility of providing feedback in a systematic way and testing its effectiveness. The effectiveness of the developed feedback model on improving students’ writing ability was tested in the context of a multiple draft writing course which followed a process approach with 57 preparatory class students at Karadeniz Technical University, Department of English Language and Literature for a p...
A Methodology for Resolution Mapping for Cross-Resolution Simulation using Event-B
Kara, Ahmet; Oğuztüzün, Mehmet Halit S.; Alpdemir, M. Nedim (2015-11-01)
This paper proposes a software engineering solution for implementing simulations via the composition of models at different resolution levels with the help of formal methods. Our solution provides a systematic methodology that offers a well-defined sequence of stages to obtain executable converters for entity resolution mapping, given the types of entity attributes that are exchanged at model interfaces and the mapping specifications. Our methodology uses Event-B as the formal specification language and Dis...
Development of sensitive analytical methods for the determination of thallium at trace levels by slotted quartz tube flame atomic absorption spectrometry
Ari, Betul; BAKIRDERE, Sezgin; Ataman, Osman Yavuz (Elsevier BV, 2020-09-01)
A simple, sensitive and economical technique is needed for the determination of thallium and this study demonstrates the different analytical strategies were developed using atomic absorption spectrometry (AAS). In order to improve the sensitivity of flame atomic absorption spectrometry (FAAS), a basic slotted quartz tube (SQT) was used for the thallium determination. In the first strategy, mixing propanol (100 mu L) and Tl standard solution (500 mu L) under the optimum conditions, namely solvent assisted S...
Development of a software for determination of kinetic parameters in thermal analysis
Ertunç, Göker; Kök, Mustafa Verşan; Department of Petroleum and Natural Gas Engineering (2011)
In this thesis, a new software, THERA-Kinetics was developed for the evaluation of kinetic parameters using non-isothermal data. Different computational methods, available in the software, were applied to a set of experimental and simulated data distributed in the ICTAC (International Confederation for Thermal Analysis and Calorimetry) Kinetics Project. The reliability of the software was verified by comparing the kinetic results, which were in good agreement, with those obtained by the participants of the ...
Development of a quadtree based agglomeration method for a multigrid viscous flow solver on unstructured grids
Mahmutyazicioglu, Emel; Tuncer, İsmail Hakkı; Aksel, Haluk (null; 2010-12-13)
In this study, a new cell agglomeration technique is developed and applied to 1st and 2nd order inviscid/viscous multigrid flow solutions on unstructured/hybrid grids. The grid coarsening required by the multigrid scheme is achieved by agglomerating the unstructured/hybrid cells based on their distribution on a quadtree data structure. The paper presents the coarsening strategy and the multigrid adaptation on inviscid/viscous 2D solutions over a NACA 0012 airfoil section. It is shown that, the quadtree base...
Citation Formats
O. Akça, “Development of diagnostic platforms for single nucleotide polymorphism detection,” Ph.D. - Doctoral Program, Middle East Technical University, 2014.