Matching Items (161)
Description
Filtration for microfluidic sample-collection devices is desirable for sample selection, concentration, preprocessing, and downstream manipulation, but microfabricating the required sub-micrometer filtration structure is an elaborate process. This thesis presents a simple method to fabricate polydimethylsiloxane (PDMS) devices with an integrated membrane filter that will sample, lyse, and extract the DNA from microorganisms in aqueous environments. An off-the-shelf membrane filter disc was embedded in a PDMS layer and sequentially bound with other PDMS channel layers. No leakage was observed during filtration. This device was validated by concentrating a large amount of cyanobacterium Synechocystis in simulated sample water with consistent performance across devices. After accumulating sufficient biomass on the filter, a sequential electrochemical lysing process was performed by applying 5VDC across the filter. This device was further evaluated by delivering several samples of differing concentrations of cyanobacterium Synechocystis then quantifying the DNA using real-time PCR. Lastly, an environmental sample was run through the device and the amount of photosynthetic microorganisms present in the water was determined. The major breakthroughs in this design are low energy demand, cheap materials, simple design, straightforward fabrication, and robust performance, together enabling wide-utility of similar chip-based devices for field-deployable operations in environmental micro-biotechnology.
ContributorsLecluse, Aurelie (Author) / Meldrum, Deirdre (Thesis advisor) / Chao, Joseph (Thesis advisor) / Westerhoff, Paul (Committee member) / Arizona State University (Publisher)
Created2011
Description
The goal of this project was to design and create a genetic construct that would allow for <br/>tumor growth to be induced in the center of the wing imaginal disc of Drosophila larvae, the <br/>R85E08 domain, using a heat shock. The resulting transgene would be combined with other <br/>transgenes in a single fly that would allow for simultaneous expression of the oncogene and, in <br/>the surrounding cells, other genes of interest. This system would help establish Drosophila as a <br/>more versatile and reliable model organism for cancer research. Furthermore, pilot studies were <br/>performed, using elements of the final proposed system, to determine if tumor growth is possible <br/>in the center of the disc, which oncogene produces the best results, and if oncogene expression <br/>induced later in development causes tumor growth. Three different candidate genes were <br/>investigated: RasV12, PvrACT, and Avli.
ContributorsSt Peter, John Daniel (Author) / Harris, Rob (Thesis director) / Varsani, Arvind (Committee member) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Single cell phenotypic heterogeneity studies reveal more information about the pathogenesis process than conventional bulk methods. Furthermore, investigation of the individual cellular response mechanism during rapid environmental changes can only be achieved at single cell level. By enabling the study of cellular morphology, a single cell three-dimensional (3D) imaging system can be used to diagnose fatal diseases, such as cancer, at an early stage. One proven method, CellCT, accomplishes 3D imaging by rotating a single cell around a fixed axis. However, some existing cell rotating mechanisms require either intricate microfabrication, and some fail to provide a suitable environment for living cells. This thesis develops a microvorterx chamber that allows living cells to be rotated by hydrodynamic alone while facilitating imaging access. In this thesis work, 1) the new chamber design was developed through numerical simulation. Simulations revealed that in order to form a microvortex in the side chamber, the ratio of the chamber opening to the channel width must be smaller than one. After comparing different chamber designs, the trapezoidal side chamber was selected because it demonstrated controllable circulation and met the imaging requirements. Microvortex properties were not sensitive to the chambers with interface angles ranging from 0.32 to 0.64. A similar trend was observed when chamber heights were larger than chamber opening. 2) Micro-particle image velocimetry was used to characterize microvortices and validate simulation results. Agreement between experimentation and simulation confirmed that numerical simulation was an effective method for chamber design. 3) Finally, cell rotation experiments were performed in the trapezoidal side chamber. The experimental results demonstrated cell rotational rates ranging from 12 to 29 rpm for regular cells. With a volumetric flow rate of 0.5 µL/s, an irregular cell rotated at a mean rate of 97 ± 3 rpm. Rotational rates can be changed by altering inlet flow rates.
ContributorsZhang, Wenjie (Author) / Frakes, David (Thesis advisor) / Meldrum, Deirdre (Thesis advisor) / Chao, Shih-hui (Committee member) / Wang, Xiao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Food system and health characteristics were evaluated across the last Waorani hunter-gatherer group in Amazonian Ecuador and a remote neighboring Kichwa indigenous subsistence agriculture community. Hunter-gatherer food systems like the Waorani foragers may not only be nutritionally, but also pharmaceutically beneficial because of high dietary intake of varied plant phytochemical compounds. A modern diet that reduces these dietary plant defense phytochemicals below levels typical in human evolutionary history may leave humans vulnerable to diseases that were controlled through a foraging diet. Few studies consider the health impact of the recent drastic reduction of plant phytochemical content in the modern global food system, which has eliminated essential components of food because they are not considered "nutrients". The antimicrobial and anti-inflammatory nature of the food system may not only regulate infectious pathogens and inflammatory disease, but also support beneficial microbes in human hosts, reducing vulnerability to chronic diseases. Waorani foragers seem immune to certain infections with very low rates of chronic disease. Does returning to certain characteristics of a foraging food system begin to restore the human body microbe balance and inflammatory response to evolutionary norms, and if so, what implication does this have for the treatment of disease? Several years of data on dietary and health differences across the foragers and the farmers was gathered. There were major differences in health outcomes across the board. In the Waorani forager group there were no signs of infection in serious wounds such as 3rd degree burns and spear wounds. The foragers had one-degree lower body temperature than the farmers. The Waorani had an absence of signs of chronic diseases including vision and blood pressure that did not change markedly with age while Kichwa farmers suffered from both chronic diseases and physiological indicators of aging. In the Waorani forager population, there was an absence of many common regional infectious diseases, from helminthes to staphylococcus. Study design helped control for confounders (exercise, environment, genetic factors, non-phytochemical dietary intake). This study provides evidence of the major role total phytochemical dietary intake plays in human health, often not considered by policymakers and nutritional and agricultural scientists.
ContributorsLondon, Douglas (Author) / Tsuda, Takeyuki (Thesis advisor) / Beezhold, Bonnie L (Committee member) / Hruschka, Daniel (Committee member) / Eder, James (Committee member) / Arizona State University (Publisher)
Created2012
Description
Laboratory automation systems have seen a lot of technological advances in recent times. As a result, the software that is written for them are becoming increasingly sophisticated. Existing software architectures and standards are targeted to a wider domain of software development and need to be customized in order to use them for developing software for laboratory automation systems. This thesis proposes an architecture that is based on existing software architectural paradigms and is specifically tailored to developing software for a laboratory automation system. The architecture is based on fairly autonomous software components that can be distributed across multiple computers. The components in the architecture make use of asynchronous communication methodologies that are facilitated by passing messages between one another. The architecture can be used to develop software that is distributed, responsive and thread-safe. The thesis also proposes a framework that has been developed to implement the ideas proposed by the architecture. The framework is used to develop software that is scalable, distributed, responsive and thread-safe. The framework currently has components to control very commonly used laboratory automation devices such as mechanical stages, cameras, and also to do common laboratory automation functionalities such as imaging.
ContributorsKuppuswamy, Venkataramanan (Author) / Meldrum, Deirdre (Thesis advisor) / Collofello, James (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Johnson, Roger (Committee member) / Arizona State University (Publisher)
Created2012
Description
This dissertation is intended to tie together a body of work which utilizes a variety of methods to study applied mathematical models involving heterogeneity often omitted with classical modeling techniques. I posit three cogent classifications of heterogeneity: physiological, behavioral, and local (specifically connectivity in this work). I consider physiological heterogeneity using the method of transport equations to study heterogeneous susceptibility to diseases in open populations (those with births and deaths). I then present three separate models of behavioral heterogeneity. An SIS/SAS model of gonorrhea transmission in a population of highly active men-who-have-sex-with-men (MSM) is presented to study the impact of safe behavior (prevention and self-awareness) on the prevalence of this endemic disease. Behavior is modeled in this examples via static parameters describing consistent condom use and frequency of STD testing. In an example of behavioral heterogeneity, in the absence of underlying dynamics, I present a generalization to ``test theory without an answer key" (also known as cultural consensus modeling or CCM). CCM is commonly used to study the distribution of cultural knowledge within a population. The generalized framework presented allows for selecting the best model among various extensions of CCM: multiple subcultures, estimating the degree to which individuals guess yes, and making competence homogenous in the population. This permits model selection based on the principle of information criteria. The third behaviorally heterogeneous model studies adaptive behavioral response based on epidemiological-economic theory within an $SIR$ epidemic setting. Theorems used to analyze the stability of such models with a generalized, non-linear incidence structure are adapted and applied to the case of standard incidence and adaptive incidence. As an example of study in spatial heterogeneity I provide an explicit solution to a generalization of the continuous time approximation of the Albert-Barabasi scale-free network algorithm. The solution is found by recursively solving the differential equations via integrating factors, identifying a pattern for the coefficients and then proving this observed pattern is consistent using induction. An application to disease dynamics on such evolving structures is then studied.
ContributorsMorin, Benjamin (Author) / Castillo-Chavez, Carlos (Thesis advisor) / Hiebeler, David (Thesis advisor) / Hruschka, Daniel (Committee member) / Suslov, Sergei (Committee member) / Arizona State University (Publisher)
Created2012
Description
Single cell analysis has become increasingly important in understanding disease onset, progression, treatment and prognosis, especially when applied to cancer where cellular responses are highly heterogeneous. Through the advent of single cell computerized tomography (Cell-CT), researchers and clinicians now have the ability to obtain high resolution three-dimensional (3D) reconstructions of single cells. Yet to date, no live-cell compatible version of the technology exists. In this thesis, a microfluidic chip with the ability to rotate live single cells in hydrodynamic microvortices about an axis parallel to the optical focal plane has been demonstrated. The chip utilizes a novel 3D microchamber design arranged beneath a main channel creating flow detachment into the chamber, producing recirculating flow conditions. Single cells are flowed through the main channel, held in the center of the microvortex by an optical trap, and rotated by the forces induced by the recirculating fluid flow. Computational fluid dynamics (CFD) was employed to optimize the geometry of the microchamber. Two methods for the fabrication of the 3D microchamber were devised: anisotropic etching of silicon and backside diffuser photolithography (BDPL). First, the optimization of the silicon etching conditions was demonstrated through design of experiment (DOE). In addition, a non-conventional method of soft-lithography was demonstrated which incorporates the use of two positive molds, one of the main channel and the other of the microchambers, compressed together during replication to produce a single ultra-thin (<200 µm) negative used for device assembly. Second, methods for using thick negative photoresists such as SU-8 with BDPL have been developed which include a new simple and effective method for promoting the adhesion of SU-8 to glass. An assembly method that bonds two individual ultra-thin (<100 µm) replications of the channel and the microfeatures has also been demonstrated. Finally, a pressure driven pumping system with nanoliter per minute flow rate regulation, sub-second response times, and < 3% flow variability has been designed and characterized. The fabrication and assembly of this device is inexpensive and utilizes simple variants of conventional microfluidic fabrication techniques, making it easily accessible to the single cell analysis community.
ContributorsMyers, Jakrey R (Author) / Meldrum, Deirdre (Thesis advisor) / Johnson, Roger (Committee member) / Frakes, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Due to persistent undernutrition in India and the increased demands placed on a woman’s body during childbearing and lactation, the Indian government has implemented a program to provide supplemental nutrition packets to women in rural India. This study examines the factors influencing uptake of nutritional packets by lactating mothers in southern, rural Rajasthan. Women were recruited from 65 villages in Rajasthan, India (n=149, minimum of 2 per village) to evaluate the relationship of nutrition packet uptake and two factors--education levels and distance to the health center.
Level of education had little impact on whether or not women received the nutrition packet. Of those women with no education, 63.1% received the packet. Of those with any education, 63.9% got the packet.
In contrast, distance was strongly correlated with whether or not women received the packet. For example, of the women living within 200 meters of the health center, 93.2% received a nutrition packet. Of the women living between 250 meters and one kilometer of the health center, 68.4% received a nutrition packet. Of the women living over one kilometer from the health center, only 25% received a nutrition packet. The relationship between uptake of packets and women’s perception of distance to the health center was also explored. Out of 50 women who did not receive the packet, all of the women who said there was no health center in their village did live more than one kilometer from a health center. Of the women who lived between 250 meters and one kilometer from the health center, 40% felt it was too far. Of the women who lived more than a kilometer from the health center, 66.7% felt it was too far and 29.6% said there was no health center in their village. Again, it does not appear that ‘too far’ is just a default reason for women, but that actual distance, more so than education, is a major contributing factor in their ability to take the nutrition packet. These findings suggest that improving access to supplemental nutrition packets at the village level may increase uptake by the women.
Level of education had little impact on whether or not women received the nutrition packet. Of those women with no education, 63.1% received the packet. Of those with any education, 63.9% got the packet.
In contrast, distance was strongly correlated with whether or not women received the packet. For example, of the women living within 200 meters of the health center, 93.2% received a nutrition packet. Of the women living between 250 meters and one kilometer of the health center, 68.4% received a nutrition packet. Of the women living over one kilometer from the health center, only 25% received a nutrition packet. The relationship between uptake of packets and women’s perception of distance to the health center was also explored. Out of 50 women who did not receive the packet, all of the women who said there was no health center in their village did live more than one kilometer from a health center. Of the women who lived between 250 meters and one kilometer from the health center, 40% felt it was too far. Of the women who lived more than a kilometer from the health center, 66.7% felt it was too far and 29.6% said there was no health center in their village. Again, it does not appear that ‘too far’ is just a default reason for women, but that actual distance, more so than education, is a major contributing factor in their ability to take the nutrition packet. These findings suggest that improving access to supplemental nutrition packets at the village level may increase uptake by the women.
ContributorsJeffers, Eva Marie (Author) / Hruschka, Daniel (Thesis director) / Maupin, Jonathan (Committee member) / Cook, Jeffrey (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05
Description
Background: Human papillomavirus (HPV) is the cause of 99.7% of cervical cancers. Research of cervical cancer has made this disease mostly curable in the developing world. Head and neck cancer, which is increasingly caused by HPV, still is associated with a mortality rate of 50,000 in the US annually. This study proposed to evaluate the biology of HPV-16 in head and neck tumors by using RT-qPCR to measure the RNA expression and its relation to physical status of the virus. Methods: This study was to develop an assay that uses RT-qPCR to determine the quantitative expression of HPV-16 RNA coding for proteins E1, E2, E4, E5, E6, and E7 in tumor samples. The assay development started with creation of primers. It went on to test the primers on template DNA through traditional PCR and then on DNA from HPV-16 positive cell lines, SiHa and CaSki, using RT-qPCR. This paper also describes the troubleshooting methods taken for the PCR reaction. Once the primers are verified, the RT-qPCR process can be carried out on RNA purified from tumor samples. Results: No primer sets have been confirmed to produce a product through PCR or RT-qPCR. The primer sequences match up correctly with known sequences for HPV-16 E1, E2, E4, E5, E6, and E7. RT-qPCR showed results consistent with the hypothesis. Conclusion: The RT-qPCR protocol must be optimized to confirm the primer sequences work as desired. Then primers will be used to study physical status and RNA expression in HPV-positive and HPV-negative head and neck tumor samples. This assay can help shed light on which proteins are expressed most in tumors of the head and neck and will aid in the development of future screening and treatment options.
ContributorsKhazanovich, Jakob (Author) / Anderson, Karen (Thesis director) / Mangone, Marco (Committee member) / Sundaresan, Sri Krishna (Committee member) / Barrett, The Honors College (Contributor)
Created2015-05
Description
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disease characterized by progressive muscle loss and weakness. This disease arises from a mutation that occurs on a gene that encodes for dystrophin, which results in observable muscle death and inflammation; however, the genetic changes that result from dystrophin's dysfunctionality remain unknown. Current DMD research uses mdx mice as a model, and while very useful, does not allow the study of cell-autonomous transcriptome changes during the progression of DMD due to the strong inflammatory response, perhaps hiding important therapeutic targets. C. elegans, which has a very weak inflammatory response compared to mdx mice and humans, has been used in the past to study DMD with some success. The worm ortholog of the dystrophin gene has been identified as dys-1 since its mutation phenocopies the progression of the disease and a portion of the human dystrophin gene alleviates symptoms. Importantly, the extracted RNA transcriptome from dys-1 worms showed significant change in gene expression, which needs to be further investigated with the development of a more robust model. Our lab previously published a method to isolate high-quality muscle-specific RNA from worms, which could be used to study such changes at higher resolution. We crossed the dys-1 worms with our muscle-specific strain and demonstrated that the chimeric strain exhibits similar behavioral symptoms as DMD patients as characterized by a shortened lifespan, difficulty in movement, and a decrease in speed. The presence of dys-1 and other members of the dystrophin complex in the body muscle were supported by the development of a resulting phenotype due to RNAi knockdown of each component in the body muscle; however, further experimentation is needed to reinforce this conclusion. Thus, the constructed chimeric C. elegans strain possesses unique characteristics that will allow the study of genetic changes, such as transcriptome rearrangements and dysregulation of miRNA, and how they affect the progression of DMD.
ContributorsNguyen, Thuy-Duyen Cao (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Duchaine, Thomas (Committee member) / School of Social Transformation (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05