Browsing by Subject "DNA"
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Item A Connection Of Quantum Computation And Dna Computation Using The Bloch Sphere(2011) Inkoom, Patrick K.; Stojkovic, Vojislav; Lupton, William; Computer Science and Bioinformatics Program; Master of ScienceQuantum and DNA computing are distributing and parallel types of computing. They are useful for solving problems which require high complexity computations and (or) massive data set computations such as searching, sorting, merging, pattern recognition, image processing, encryption, etc. Quantum and DNA algorithms cannot be efficiently simulated on classical computers because classical computers cannot efficiently deal with the parallelism. The quantum circuit model is adequate to describe quantum algorithms whereas DNA circuit model is adequate to describe DNA algorithms. This thesis establishes the relationship between a quantum qubit and a DNA string using the Bloch sphere. The Bloch sphere is a convenient graphical representation of a qubit in a 3-dimensional space. The model used in this thesis presents one-to-one mapping between qubits, DNA strings, and points on the Bloch sphere. The model is implemented at the real computer - von Neumann machine, therefore, there are restrictions related to the precision of qubits value, the length of DNA strings, and the precisions of coordinates values. The Bloch sphere and the relations between qubits, DNA strings and points are implemented as "Quantum and DNA Computation Simulation Programming System". Quantum and DNA Computation Simulation Programming System is implemented in the Java programming language. This system is a modified and upgraded interactive Quantum Computation applet developed at the Johns Hopkins Center for Educational Resources. The modifications include connecting (a) DNA strings and the Bloch sphere and (b) DNA strings and qubits. There are many researches in Quantum Computing and DNA Computing as independent study fields, but this is the first research which tries to connect Quantum and DNA Computing together using the Bloch sphere.Item Development and Evaluation of Microwave-Accelerated and Metal-Enhanced Fluorescence Assays for Detection of Bacterial Pathogens(2016-01-01) Melendez, Johan Humberto; Geddes, Chris D.; Chemistry & Biochemistry; ChemistryInfectious diseases with high mortality rate or serious complications require rapid and accurate diagnosis. In order to develop rapid and sensitive assays for detection of bacterial pathogens, microwave-accelerated processes have been investigated to extract and fragment the bacterial DNA, followed by Microwave-Accelerated Metal-Enhanced Fluorescence (MAMEF)-based DNA detection. MAMEF combines the benefits of low-power microwave-acceleration (MA) with those of Metal-Enhanced Fluorescence (MEF) to aid in the development of ultra-fast and sensitive bioassays. The first part of this research explored the use of microwaves and highly-focused microwaves to rapidly extract and fragment DNA. Two different, but complementary approaches were investigated - the efficiency of microwaves for microbial lysing in comparison to conventional heating, and the effect of microwave-focusing metal structures on microbial lysing and DNA isolation/fragmentation. Using microwave irradiation, Neisseria gonorrhoeae was lysed and the DNA fragmented in as little as 30 seconds. Furthermore, the incorporation of microwave-focusing bowtie structures during the irradiation process enhanced the rate of cellular lysis and DNA fragmentation. The conditions used for the lysis of N. gonorrhoeae cannot be used to lyse other bacteria with different cell wall structure, such as the gram-positive Listeria monocytogenes. The second part of the research was devoted to the development and testing of MAMEF assays for the detection of the sexually transmitted infections chlamydia and gonorrhea and Salmonella infections. The chlamydia MAMEF assay which targets the cryptic plasmid proved to be more sensitive than the assay targeting the 16S rRNA gene. Additionally, both assays proved to have moderate sensitivity for detection of chlamydia directly from vaginal swabs. The gonorrhea MAMEF assay showed low sensitivity, and a new assay targeting a multi-copy gene has been developed. MAMEF-based detection of Salmonella from white blood cells-spiked samples and stool was also achieved. However, further work is necessary to develop a robust and reproducible assay. Lastly, proof-of-concept experiments were carried out to determine if a surface plasmon resonance (SPR) approach can be used to detect genetic modifications associated with antimicrobial resistance in gonorrhea. No reproducible results were obtained using a portable SPR instrument. In summary, the use of microwave-accelerated processes for detection of bacterial pathogens was demonstrated including the clinical validation of the chlamydia MAMEF assay.Item The Test(Originally published by: Urbanite Magazine, 2008-04-01) Rudacille, Deborah; EnglishItem What is the Shape of Water?Moren, Lisa; BACHVAROFF, TSETSOThe audience enters a pitch black room with thousands of invisible organisms floating above their heads in a skylight aquarium. They’re invited to speak, and if they do their voice drops to a chant-like rumbling sound that excites the bioluminescent dinoflagellates into illuminating. Their blue glow mimics the shape of the sound waves in the water. Therefore, if you ask “what’s the shape of water?”, the dinoflagellates will tell you.Item Widespread distribution of a lexA‐regulated DNA damage‐inducible multiple gene cassette in the Proteobacteria phylum(Wiley, 2004-08-03) Abella, Marc; Erill, Ivan; Jara, Mónica; Mazón, Gerard; Campoy, Susana; Barbé, JordiThe SOS response comprises a set of cellular functions aimed at preserving bacterial cell viability in front of DNA injuries. The SOS network, negatively regulated by the LexA protein, is found in many bacterial species that have not suffered major reductions in their gene contents, but presents distinctly divergent LexA‐binding sites across the Bacteria domain. In this article, we report the identification and characterization of an imported multiple gene cassette in the Gamma Proteobacterium Pseudomonas putida that encodes a LexA protein, an inhibitor of cell division (SulA), an error‐prone polymerase (DinP) and the alpha subunit of DNA polymerase III (DnaE). We also demonstrate that these genes constitute a DNA damage‐inducible operon that is regulated by its own encoded LexA protein, and we establish that the latter is a direct derivative of the Gram‐positive LexA protein. In addition, in silico analyses reveal that this multiple gene cassette is also present in many Proteobacteria families, and that both its gene content and LexA‐binding sequence have evolved over time, ultimately giving rise to the lexA lineage of extant Gamma Proteobacteria.