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Coronaviruses are a significant group of viruses that cause enteric and respiratory infections in a variety of animals, including humans. Outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle Eastern Respiratory Syndrome (MERS) in the past 15 years has increased research into coronaviruses to gain an understanding of their structure and function so one day therapies and vaccines may be produced. These viruses have four main structural proteins: the spike, nucleocapsid, envelope, and membrane proteins. The envelope (E) protein is an integral membrane protein in the viral envelope that acts as a viroporin for transport of cations and plays an important role in pathogenesis and viral assembly. E contains a hydrophobic transmembrane domain with polar residues that is conserved across coronavirus species and may be significant to its function. This experiment looks at the possible role of one polar residue in assembly, the 15th residue glutamine, in the Mouse Hepatitis Virus (MHV) E protein. The glutamine 15 residue was mutated into positively charged residues lysine or arginine. Plasmids with these mutations were co-expressed with the membrane protein (M) gene to produce virus-like particles (VLPs). VLPs are produced when E and M are co-expressed together and model assembly of the coronavirus envelope, but they are not infectious as they do not contain the viral genome. Observing their production with the mutated E protein gives insight into the role the glutamine residue plays in assembly. The experiment showed that a changing glutamine 15 to positive charges does not appear to significantly affect the assembly of the VLPs, indicating that this specific residue may not have a large impact on viral assembly.
ContributorsHaller, Sarah S. (Author) / Hogue, Brenda (Thesis director) / Liu, Wei (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor) / Biodesign Institute (Contributor)
Created2017-05
Description
Productivity in the construction industry is an essential measure of production efficiency and economic progress, quantified by craft laborers' time spent directly adding value to a project. In order to better understand craft labor productivity as an aspect of lean construction, an activity analysis was conducted at the Arizona State University Palo Verde Main engineering dormitory construction site in December of 2016. The objective of this analysis on craft labor productivity in construction projects was to gather data regarding the efficiency of craft labor workers, make conclusions about the effects of time of day and other site-specific factors on labor productivity, as well as suggest improvements to implement in the construction process. Analysis suggests that supporting tasks, such as traveling or materials handling, constitute the majority of craft labors' efforts on the job site with the highest percentages occurring at the beginning and end of the work day. Direct work and delays were approximately equal at about 20% each hour with the highest peak occurring at lunchtime between 10:00 am and 11:00 am. The top suggestion to improve construction productivity would be to perform an extensive site utilization analysis due to the confined nature of this job site. Despite the limitations of an activity analysis to provide a complete prospective of all the factors that can affect craft labor productivity as well as the small number of days of data acquisition, this analysis provides a basic overview of the productivity at the Palo Verde Main construction site. Through this research, construction managers can more effectively generate site plans and schedules to increase labor productivity.
ContributorsFord, Emily Lucile (Author) / Grau, David (Thesis director) / Chong, Oswald (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The overall energy consumption around the United States has not been reduced even with the advancement of technology over the past decades. Deficiencies exist between design and actual energy performances. Energy Infrastructure Systems (EIS) are impacted when the amount of energy production cannot be accurately and efficiently forecasted. Inaccurate engineering assumptions can result when there is a lack of understanding on how energy systems can operate in real-world applications. Energy systems are complex, which results in unknown system behaviors, due to an unknown structural system model. Currently, there exists a lack of data mining techniques in reverse engineering, which are needed to develop efficient structural system models. In this project, a new type of reverse engineering algorithm has been applied to a year's worth of energy data collected from an ASU research building called MacroTechnology Works, to identify the structural system model. Developing and understanding structural system models is the first step in creating accurate predictive analytics for energy production. The associative network of the building's data will be highlighted to accurately depict the structural model. This structural model will enhance energy infrastructure systems' energy efficiency, reduce energy waste, and narrow the gaps between energy infrastructure design, planning, operation and management (DPOM).
ContributorsCamarena, Raquel Jimenez (Author) / Chong, Oswald (Thesis director) / Ye, Nong (Committee member) / Industrial, Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
With the rising data output and falling costs of Next Generation Sequencing technologies, research into data compression is crucial to maintaining storage efficiency and costs. High throughput sequencers such as the HiSeqX Ten can produce up to 1.8 terabases of data per run, and such large storage demands are even more important to consider for institutions that rely on their own servers rather than large data centers (cloud storage)1. Compression algorithms aim to reduce the amount of space taken up by large genomic datasets by encoding the most frequently occurring symbols with the shortest bit codewords and by changing the order of the data to make it easier to encode. Depending on the probability distribution of the symbols in the dataset or the structure of the data, choosing the wrong algorithm could result in a compressed file larger than the original or a poorly compressed file that results in a waste of time and space2. To test efficiency among compression algorithms for each file type, 37 open-source compression algorithms were used to compress six types of genomic datasets (FASTA, VCF, BCF, GFF, GTF, and SAM) and evaluated on compression speed, decompression speed, compression ratio, and file size using the benchmark test lzbench. Compressors that outpreformed the popular bioinformatics compressor Gzip (zlib -6) were evaluated against one another by ratio and speed for each file type and across the geometric means of all file types. Compressors that exhibited fast compression and decompression speeds were also evaluated by transmission time through variable speed internet pipes in scenarios where the file was compressed only once or compressed multiple times.
ContributorsHowell, Abigail (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Taylor, Jay (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Many bacteria actively import environmental DNA and incorporate it into their genomes. This behavior, referred to as transformation, has been described in many species from diverse taxonomic backgrounds. Transformation is expected to carry some selective advantages similar to those postulated for meiotic sex in eukaryotes. However, the accumulation of loss-of-function alleles at transformation loci and an increased mutational load from recombining with DNA from dead cells create additional costs to transformation. These costs have been shown to outweigh many of the benefits of recombination under a variety of likely parameters. We investigate an additional proposed benefit of sexual recombination, the Red Queen hypothesis, as it relates to bacterial transformation. Here we describe a computational model showing that host-pathogen coevolution may provide a large selective benefit to transformation and allow transforming cells to invade an environment dominated by otherwise equal non-transformers. Furthermore, we observe that host-pathogen dynamics cause the selection pressure on transformation to vary extensively in time, explaining the tight regulation and wide variety of rates observed in naturally competent bacteria. Host-pathogen dynamics may explain the evolution and maintenance of natural competence despite its associated costs.
ContributorsPalmer, Nathan David (Author) / Cartwright, Reed (Thesis director) / Wang, Xuan (Committee member) / Sievert, Chris (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Mammary gland development in humans during puberty involves the enlargement of breast tissue, but this is not true in non-human primates. To identify potential causes of this difference, I examined variation in substitution rates across genes related to mammary development. Genes undergoing purifying selection show slower-than-average substitution rates, while genes undergoing positive selection show faster rates. These may be related to the difference between humans and other primates. Three genes were found to be accelerated were FOXF1, IGFBP5, and ATP2B2, but only the latter one was found in humans and it seems unlikely that it would be related to the differences between mammary gland development at puberty between humans and non-human primates.
ContributorsArroyo, Diana (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Schwartz, Rachel (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Building construction, design and maintenance is a sector of engineering where improved efficiency will have immense impacts on resource consumption and environmental health. This research closely examines the Leadership in Environment and Energy Design (LEED) rating system and the International Green Construction Code (IgCC). The IgCC is a model code, written with the same structure as many building codes. It is a standard that can be enforced if a city's government decides to adopt it. When IgCC is enforced, the buildings either meet all of the requirements set forth in the document or it fails to meet the code standards. The LEED Rating System, on the other hand, is not a building code. LEED certified buildings are built according to the standards of their local jurisdiction and in addition to that, building owners can chose to pursue a LEED certification. This is a rating system that awards points based on the sustainable measures achieved by a building. A comparison of these green building systems highlights their accomplishments in terms of reduced electricity usage, usage of low-impact materials, indoor environmental quality and other innovative features. It was determined that in general IgCC is more holistic, stringent approach to green building. At the same time the LEED rating system a wider variety of green building options. In addition, building data from LEED certified buildings was complied and analyzed to understand important trends. Both of these methods are progressing towards low-impact, efficient infrastructure and a side-by-side comparison, as done in this research, shed light on the strengths and weaknesses of each method, allowing for future improvements.
ContributorsCampbell, Kaleigh Ruth (Author) / Chong, Oswald (Thesis director) / Parrish, Kristen (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
This paper describes the research done to quantify the relationship between external air temperature and energy consumption and internal air temperature and energy consumption. The study was conducted on a LEED Gold certified building, College Avenue Commons, located on Arizona State University's Tempe campus. It includes information on the background of previous studies in the area, some that agree with the research hypotheses and some that take a different path. Real-time data was collected hourly for energy consumption and external air temperature. Intermittent internal air temperature was collected by undergraduate researcher, Charles Banke. Regression analysis was used to prove two research hypotheses. The authors found no correlation between external air temperature and energy consumption, nor did they find a relationship between internal air temperature and energy consumption. This paper also includes recommendations for future work to improve the study.
ContributorsBanke, Charles Michael (Author) / Chong, Oswald (Thesis director) / Parrish, Kristen (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The Chinese Construction Industry has grown to be one of the largest construction markets in the world within the last 10 years. The size of the Chinese Construction Industry is on par with many developed nations, despite it being a developing country. Despite its rapid growth, the productivity and profitability of the Chinese Construction Industry is low compared to similar sized construction industries (United States, United Kingdom, etc.). In addition to the low efficiency of the Chinese Construction Industry, there is minimal documentation available showing the performance of the Chinese Construction Industry (projects completed on time, on budget, and customer satisfaction ratings).
The purpose of this research is to investigate potential solutions that could address the poor efficiency and performance of the Chinese Construction Industry. This research is divided into three phases; first, a literature review to identify countries that have similar construction industries to the Chinese Construction Industry. The second phase is to compare the risks and identify solutions that are proposed to increase the performance of similar construction industries and the Chinese Construction Industry. The third phase is to create a survey from the literature-based information to validate the concepts with the Chinese Construction Industry professionals and stakeholders.
The purpose of this research is to investigate potential solutions that could address the poor efficiency and performance of the Chinese Construction Industry. This research is divided into three phases; first, a literature review to identify countries that have similar construction industries to the Chinese Construction Industry. The second phase is to compare the risks and identify solutions that are proposed to increase the performance of similar construction industries and the Chinese Construction Industry. The third phase is to create a survey from the literature-based information to validate the concepts with the Chinese Construction Industry professionals and stakeholders.
ContributorsChen, Yutian (Author) / Chong, Oswald (Thesis advisor) / Kashiwagi, Dean T. (Committee member) / Badger, Willliam (Committee member) / Arizona State University (Publisher)
Created2020
Description
Although Saudi Arabia is moving towards a sustainable future, Existing residential buildings in the country are extremely unsustainable. Therefore, there is a necessity for greening the existing residential building. Mostadam green rating systems was developed by the Saudi ministry of housing in 2019 to address the long-term sustainability vision in residential buildings in the country. By setting Mostadam requirements as an objective of the retrofit process, it will ensure that the building achieve sustainability. However, Mostadam is new and there is a lack of knowledge of implementing its requirements on existing buildings. The aim of this research is to develop a framework to green existing residential buildings in Saudi Arabia to achieve Mostadam energy and water minimum requirements. The framework was developed based on an extensive keyword-based search and an analysis of 92 relevant research. The process starts with assessing the building against the minimum requirements of energy and water of Mostadam. After that, optimization phase is conducted. Building information modelling is used in the optimization phase. Energy and water efficiency optimization measures are identified from the analysed literature. Revit is used in the base model authoring and Green building studio cloud is used to simulate the energy and water efficiency measures. Then, payback period is calculated for all the efficiency measured to assess the decision making. A case study of a villa in Riyadh, Saudi Arabia is provided. result shows that the implemented efficiency measures led to an increment of 37.5% in annual energy savings and 26.1% in the annual water savings. Results shows that the application of the proposed framework supports evaluating energy and water efficiency measures to implement it on the buildings to achieve Mostadam minimum energy and water requirements. Recommendations were made for future work to bridge the knowledge gap.
ContributorsMohamed, Sara Murad (Author) / Sullivan, Kenneth (Thesis advisor) / Chong, Oswald (Committee member) / Hurtado, Kristen (Committee member) / Arizona State University (Publisher)
Created2022