DNA benefits from a system of self-maintenance, containing genes that code for the repair of its damage. The base-excision repair pathway serves as the primary means of preventing mutations attributed to oxidative stress, such as 8-oxoguanine (8-oxoG), within both the nuclear and mitochondrial DNA. Initiated by the 8-oxogunine DNA glycosylase (OGG1), the removal of 8-oxoG is known to prevent genomic instability and neoplasia. The current study presents new data indicating a role for OGG1 in the maintenance of energy homeostasis at both cellular and whole-body levels. Oxidative stress introduced via high-fat diet (HFD) yielded increased adiposity and hepatic steatosis within the OGG1 knockout (OGG1-/-) mouse model. The HFD-fed OGG1-/- mice were also prone to increased levels of plasma insulin and impaired glucose tolerance. The same mice exhibited a higher resting VCO₂, indicating a preference for carbohydrate metabolism versus fat oxidation. Analysis of expression levels in the livers of OGG1-/- mice revealed significant downregulation of the metabolism-regulating transcriptional coactivator PGC1 and other genes integral to fatty acid oxidation. Consistent with a reduction in PGC1a, multiple genes involved in the TCA cycle were significantly downregulated. Also noted was a reduction in glycogen stores within the OGG1-/- livers, and fasting plasma ketones were significantly reduced. We conclude that OGG1 deficiency alters cellular substrate metabolism, fosters a fat-sparing phenotype, and renders the OGG1-/- mouse highly susceptible to obesity and related diseases. An understanding of OGG1 and its role in energy homeostasis will contribute to the direction of research within the realm of disease initiation due to oxidative stress.

Current network frameworks that are in widespread use today are insufficient for protecting sensitive data, and cybercrime activities are continuing to rise at alarming rates. By adopting new network framework designs into current computing infrastructure, we need to offer users a more safe and secure infrastructure by which to handle sensitive information and data, while not limiting their ability to be productive. For this purpose, we show how a private cloud can be highly assured by integrating the current network infrastructure with the High Assurance Platform (HAP) framework. The National Security Agency proposed the HAP framework in order to provide a high security environment in which to conduct day-to-day computing activities by utilizing a mix of commercially available virtualization and network security technologies. By integrating a private cloud for an academic computing environment with the HAP framework, we can demonstrate how a high assurance private cloud can be designed and implemented. We plan to create a private cloud in a university computer lab using computing resources that are currently in use or available to the general public. This high assurance private cloud allows students to conduct day-to-day academic activities in the freedom of a low assurance environment, by offering low restriction access to common resources such as email, web browsing, and file sharing across an internal network. At the same time, students will have access to a high assurance environment in order to reference confidential or sensitive information. Through the use of virtualization technology and network security technology, sensitive information can be better protected than what is commonly seen today in our academic computing environment and students still have the freedom to perform daily computing activities quickly and efficiently.

Information technology is changing at an exponential rate. The advent of cloud computing allows small businesses to take advantages of technological services that reduce the cost of their capital expenses. The Software as a Service (SaaS), which is the top layer of cloud computing, is taking the helm in this technology era for small businesses that cannot afford initial capital expenses for their businesses. Now software can be rented as a service instead of being purchased as an application package. The first purpose of our research is to demonstrate how cloud computing can be beneficial to the small businesses: we discover a need for photographers who are small business owners and have limited revenue for the commercialization of their products and services. To sell their photos via the internet, photographers are using other storefronts to sell. Our cloud based shopping cart allows photographers to create their accounts and sell their own photos; thereby, saving on cost and expenses. The second purpose of our research is to demonstrate how an agile software development methodology, Scrum, can be beneficial to the SaaS providers: we as the service providers manage the cloud-based shopping cart development project for photographers by using Scrum. The use of the agile methodology helps us to timely respond the changes of user requirements and the deliveries of the service components in a cloud environment.

Using the Internet is leaving tremendous amount of the identity information about the person who accessed. Perhaps it may not be an issue if this information were not used against this person. However, this is a wrong impression of anonymity of the online users who have formed by the users themselves trying to achieve Internet anonymity to ensure privacy. Most of the time the users are not aware of two types of information that can be gathered online: the information that software is gathering from the users and the information that every person leaves about himself, or herself. My research includes reviewing of the United States and Washington state cyber-crime law, developing a new model of cyber-crime investigation procedure and suspect’s profiling, mapping modern techniques of revealing the Internet identity, and developing a prototype of a software application Cyber Bounty Hunter with usage of Python and C++ programming languages. I created Cyber Bounty Hunter as all-in-one tool for tracing suspects via IP-address, HTTP cookies, flash cookies, tracking bugs, HTTP referrer, TCP protocol, browser plugins, search engine's queries, social networks and so on. All of these tools and options can be used in cyber-crime scene investigation applying to tracking of suspects and fugitives, analysis of crime profiler and suspects’ identity. Cyber technologies opened up new possibilities in tracking. Generally, Cyber Bounty Hunter application software deploys cyber-espionage techniques and is capable of tracking and profiling suspects such as professional hackers, thefts, cyber-stalkers, cyber pedophiles, electronic terrorists and vandals.

The world of computing has made major migrations into cloud computing. More and more enterprises, both big and small, begin to rapidly relocate their infrastructure to the cloud both internally, and externally. Virtualization has also become a key component to this migration and is often times inseparable from a particular application of a cloud computing solution. This major jump can be readily seen from major technology industry heavyweights such as Microsoft, Google, and Amazon. It is important to note that this migration to cloud computing is not only taking place externally as companies seek to provide cloud services for clients and consumers, but also taking place as companies and organizations move their internal infrastructure operations to the cloud, particularly, with a virtualized infrastructure as a service (VIaaS). Deploying a VIaaS provides cost effective and convenient solutions to companies and organizations that do not desire the rigors of managing and maintaining their infrastructure by way of physical locations. However, with the utilization of VIaaS, comes a host of concerns from an information assurance standpoint.We propose a scenario in which a simulated small business has moved their infrastructure to the cloud through a VIaaS. Specifically, two common servers in a given network, web and email, are used for testing and evaluation process in which an iterated approach is used after initial installation and configuration. Based upon our experiments using VIaaS, we will address and analyze the configuration and security issues that arise when employing a VIaaS. Since VIaaS can be different for each business, general best practice guidelines are proposed for developing the infrastructure.

Beginning level programmers have learned basic programming concepts and skills without considering security at the beginning. However, the broad adoption of the Internet technologies allowed more software applications to be connected and vulnerable to attacks. It has become more important for beginning level programmers to learn coding with a security perspective in order to avoid bad coding habits. For this purpose, we introduce threat model to beginning level programmers, while they are studying programming fundamentals and examine how the threat model can create a paradigm of higher assurance when the beginning level programmers develop programs with the threat model. We conduct two programming assignments in a course for beginning level programmers without or with the threat models, respectively. Through the threat modeling, we create Data Flow Diagrams to check security trust boundaries and analyze the diagrams to countermeasure vulnerabilities of the programs. The number of vulnerabilities in the source code and the time for implementing the threat modeling are compared and analyzed. Regardless of the longer time for the threat modeling implementation, the early adoption of the threat model allows the beginning level programmers to discuss and expand ideas from the data flow diagram, help them to understand security trust boundaries better, categorize threats with computer security threat classifications, and make their code more secure.

The purpose of this research is to develop a user-friendly interface for rapid deployment of virtual machines in the academic industry utilizing an agile development methodology and the Model-View-Controller framework. Virtualization technologies have allowed many enterprises to modify the traditional client server model. While virtualization technologies have many benefits, they are not always easy or cost effective to manage with existing tools. In order to manage changing requirements and reduce maintenance cost associated with tight coupling among software components; this development project follows the agile development methodology of Scrum to produce a web application using the Microsoft ASP.NET Model-View-Controller 3.0 framework. The application developed improves the manageability of virtual machines used by information technology instructors who currently employ Microsoft Hyper-V in the classroom. It allows for the rapid configuration and deployment of virtual machines by instructors for use by students. The product will be of benefit outside higher education, for system administrators who regularly deploy large numbers of virtual machines images.

Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes gastroenteritis. Components of the outer and inner membrane, characteristic of Gram-negative bacteria, contribute to Salmonella’s mechanisms to avoid detection and killing by the host immune system. The anionic bacterial cell surface is disrupted by cationic antimicrobial proteins (CAMP) that increase outer membrane (OM) permeability and access to the inner membrane. To resist CAMP killing Salmonella activates the PhoPQ two-component system, which is essential for pathogenesis. Because many PhoPQ-regulated enzymes are dispensable during infection, we conducted a forward genetic screen that identified new components of the PhoPQ regulon involved in maintaining the OM permeability barrier. Sequencing revealed mutations in genes encoding a variety of membrane proteins including transporters, phospholipid and lipopolysaccharide biosynthetic enzymes and efflux pumps, as well as regulatory proteins. Amongst the results, yejM mutants expressed the highest levels of membrane damage. YejM is an inner membrane protein with a periplasmic enzymatic domain that is critically involved in maintaining the OM permeability barrier. Structural alignments suggest that YejM is a member of the alkaline phosphatase superfamily. Attempts at full length deletions of yejM were unsuccessful suggesting the transmembrane domain is essential for viability, whereas periplasmic deletion mutants were viable but expressed varied levels of OM damage. Complementation with periplasmic deletion mutants and plasmids carrying the periplasmic domain rescued the OM permeability defect. Using structural models generated by a Protein Homolog/analogy Recognition Engine (PHYRE), we located putative metal binding sites involved in catalysis. To investigate the enzymatic mechanism, specific metal-binding residues were mutated via Polymerase Chain Reaction. We aim to determine if these residues contribute to the OM permeability defect of the yejM mutant Salmonella.

Organic photovoltaics (OPVs) are a promising low-cost option in developing renewable energies. OPVs are solar cells made from organic semiconductors instead of the more traditionally used inorganic semiconductors such as silicon. OPVs have several advantages including: low cost, ease of processing, physical flexibility, and highly tunable properties. Therefore, if the efficiency of OPVs can be increased, they could become a major, inexpensive renewable energy source. Electron-accepting materials used in OPVs have traditionally been fullerene-based due to their high electron mobility. However, fullerenes contribute little to light harvesting in an OPV as they have negligible absorption in the solar spectrum. Thus, our goal was to develop new electron-accepting materials for OPVs that absorb significantly in the solar spectrum as a means to increase light harvesting and therefore OPV efficiency. A series of novel oligomers with an oligothiophene-naphthalene diimide (NDI) structure was synthesized. All oligomers exhibited absorption in the visible region with band gaps ranging from 1.39 eV to 2.06 eV, and could therefore contribute to light harvesting in an OPV. Solution-processed solar cells using the new oligomers as the electron-acceptors showed power conversion efficiencies up to 1.5%. Overall, these new materials exhibited that non-fullerenes can function as the electron-accepting material in OPVs while contributing to light harvesting. This approach therefore shows promise for increasing OPV efficiency to make OPVs a viable, cost-effective renewable energy source.