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Introduction: "Do Not Try to Remember": Pedagogy in Transition
Get PDFThis introductory session was part of the 2020 Schools of Thought Conference hosted by the Christopher C. Gibbs College of Architecture at the University of Oklahoma.This introductory section of the "Do Not Try to Remember": Pedagogy in Transition portion of the Schools of Thought proceedings contains an overview of the session's chairs, its themes, and included papers.N
Community Engagement and Service-Learning Reciprocity
Get PDFThis paper was presented at the 2020 Schools of Thought Conference hosted by the Christopher C. Gibbs College of Architecture at the University of Oklahoma.As part of the University of Oklahoma’s Christopher C. Gibbs College of Architecture, the Urban Design Studio prepares graduate students from diverse backgrounds in its Master of Urban Design program to practice as urban design professionals. The studio uses a reciprocal community engagement and service-learning approach that benefits cities and residents of Oklahoma and provides students with meaningful educational experiences. Four case studies of studio projects are considered here. Each case study focuses on a different type of project, including creative urban design practice, participatory action research, community-based planning, and real-life, real-time placemaking. The studio regularly collaborates with communities on urban design studies and interventions. One such project focused on the revitalization of a three-mile stretch of Route 66 running through the heart of Tulsa. Participatory action research is represented by Tulsa Photovoice, an example of how studio faculty and students collaborate with communities to discover knowledge. Working in a more traditional framework, studio students led a community-based planning process for the downtown plan of the city of Muskogee, Oklahoma, entitled a Landscape of Hope. Finally, placemaking activities like the one for the Chapman Green illustrate how students learn by making. Each case study explains how the project was initiated, what community engagement techniques were used, and how students participated. Project outcomes are also summarized.Ye
Evaluating Languages for Bioinformatics: Performance, Expressiveness and Energy
Get PDFOne of the fastest growing concerns in the technology sector is the increased demand for power in the world's data centers. Global data center electricity use in 2021 was estimated as between 220 and 320 terawatt-hours (TWh), as much as 1.3% of global electricity demand. As the data center industry continues to expand, so too will power usage, and therefore the need for increased energy efficiency in software development.
This thesis introduces a methodology that evaluates a set of programming languages based on three key metrics: performance, expressiveness, and energy use, demonstrating a fair consideration of each language's strengths and weaknesses. The framework presented creates a collection of string-matching algorithms used on DNA sequences to demonstrate the capabilities of each language, and draw out their distinctiveness.
DNA sequencing was chosen due to its growing uses and applications as technology evolves and makes such sequencing faster and less expensive. This in turn has lead to a growing percentage of compute-time being spent on this field. Using the methodology presented here it will be shown that using a newer language, like Rust, has advantages that help it balance speed, ease of use, and power consumption when used for advanced scientific computing.
A key part of this work introduces a novel approximate-matching algorithm to aid in this evaluation process. This new algorithm differs from current algorithms in use, in its ability to hold the gap between nucleotides to a specific maximum while allowing other gaps to exist. It will offer an alternative technique to other current approximate-matching algorithms and hopes to offer researchers another tool to consider for sequence-matching problems.
The expectation is that this research will show how testing and evaluating via performance, expressiveness and energy use metrics allows for rating and ranking programming languages in a consistent and reproducible manner. This will enable developers to make educated choices when selecting a language for a project. The methods described here will be applicable to other languages as well, given similar data to work with. This research will benefit the programming field by providing methods and techniques that can be used in the language selection process, particularly when energy efficiency is as important as overall performance
Protein engineering of Cas9 for safer genome tools, and phylogenetic analysis of Coronavirus spike protein for efficient antiviral targets
No full textClustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins are adaptive immune systems that protect bacteria and archaea from mobile genetic elements. These systems have been repurposed for gene editing biotechnologies. CRISPR-Cas9-based gene therapies are in clinical trials, but a safety concern is that Streptococcus pyogenes Cas9 can trigger non-specific DNA damage when not bound to guide RNA (gRNA). Such gRNA-free damage to genomic DNA in human nuclei was reported recently with Streptococcus pyogenes Cas9 (SpyCas9) in human cells transfected with plasmids carrying the Cas9 but devoid of a gRNA, signifying the prevalence of such promiscuous DNA damage under cellular conditions. To eliminate these non-specific cleavage activities, SpyCas9 variants are being developed through our research. One mutation that successfully removes Mn2+-dependent gRNA-free DNA cleavage is SpyCas9H982A. Elucidating the fidelity-increasing DNA cleavage mechanisms of SpyCas9H982A will advance the development of safe Cas9-based gene therapies.
Another safety concern is the finding that SpyCas9 cuts the DNA at unintended sites that partially hybridize to the guide RNA. Effects of such off-targeting include increased risks of cancer and other health problems. The SpyCas9 L64P/K65P substitution variant has been shown to have higher selectivity such that it is less likely to cleave DNA when there is a mismatch to the guide RNA. In this research, a SpyCas9 L64A/K65A variant was constructed and assayed for RNA-guided DNA cleavage to determine whether the loss of intra-protein interactions or compromised structure of the helix containing L64/K65 has the primary role in eliciting this increase in specificity. In vitro DNA cleavage assays showed that the compromised helical structure causes the increase in selectivity for on-target as opposed to PAM-proximal mismatched DNA cleavage in terms of linearization efficiency.
A novel coronavirus outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) occurred in December 2019, and variants of the virus have been emerging and causing surges in cases, hospitalizations, deaths, and societal disruptions over the past few years. Vaccines have been developed, but research on a variety of vaccines and potentially antiviral targets for small-molecule drugs is helpful for preventing infections from future variants. Initial contact between human cells and SARS-CoV-2 is mediated by the viral Spike (S) protein. The objective of this research is to identify antiviral target sites in S protein and categorize them into sites that are highly evolving and that are highly conserved in a range of human-infecting coronaviruses. The rationale is that targeted drug discovery to these two types of sites will enable better preparedness in tackling coronavirus as it continues to evolve. S protein sequence conservation was analyzed among severe disease causing human coronaviral strains (including MERS, SARS-CoV, and SARS-CoV-2), along with molecular docking of the S protein receptor binding domain with a compound library. Our results identified four pockets and six compounds that are promising for rational drug development