2013-2014 Research Cohort

The following are abstracts of previous Bridges Students who completed their research projects. 

Pipeline Scripting for the Parallel Alignment of Genomic Short Sequence Reads

Adam Bradley, Kevin Drees, Paul Keim, Jeffrey Foster

The alignment procedure compares the complete reference genome (provided by whole genome sequencing) from an organism to samples. Recent alignment methods required a user to stop and restart with a new piece of software every time an alignment was processed. The procedure was not taking advantage of the computer processing available. The pipeline project was organized to link several alignment programs together. A Python script was created to execute piped commands through a Unix Secure Shell. Python was chosen because it is a ‘more object’ oriented programming language, users find a relative ease of understanding the Python code, and the writing and distributing of Python scripts is growing in popularity in science. Piping several alignment processes together in a Python script result in a complex, but flexible alignment program. Additional commands will be added to the script to remove temporary files providing optimal memory space. Furthermore, the pipeline must be modified to run multiple alignment processes at the same time. 

Cloning the Soluble Guanylate Cyclase α1 N-terminus into Yeast-Two-Hybrid Expression Vector

Amber R. Laughter, Candice V. Benally, Matthew J. Gage

Nitric oxide (NO) regulates physiological functions such as vasodilation, neurotransmission and platelet aggregation for soluble guanylate cylase (sGC) the primary receptor for NO (Derbyshire  and Marletta, 2012).  NO diffuses across cell membranes or is made endogenously and activates sGC. sGC catalyzes the conversion of guanosine triphosphate (GTP) to cyclic guanosine monophosphate (cGMP). cGMP’s downstream cellular targets include  phosphodiestreases, ion-gated channels and other cGMP regulated  kinases. Dysfunctional sGC is implicated in several diseases, such as arthrosclerosis, heart disease, and possibly even cancer. sGC regulates angiogenesis and has been implicated to contribute to the pre-cancerous stage of neoplastic development (Hanahan  and Weinberg, 2011).

The Role of MicroRNA Variation in Prostate Cancer Progression Within Native American Populations

Denise Brown, Dr. Jason Wilder, Virginia Ware, River Black

Within Native American populations, Prostate Cancer is the leading cause of cancer mortality. MicroRNAs are 21 to 24 nucleotide long single-stranded, non-coding RNAs. They regulate gene expression at a post-transcriptional level. MicroRNAs bind to the 3’ UTR of target mRNAs, resulting in decreased expression.  Single Nucleotide Polymorphisms (SNPs) within microRNAs are known to be oncogenic by affecting the interaction between microRNAs and target mRNAs. Phosphotase Tensin Homolog (PTEN) is a tumor suppressor gene down regulated in a number of cancers including prostate, bladder, lung, breast, and kidney. Characterizing variation within microRNAs known to target PTEN in Native American populations is a key component in understanding prostate cancer progression and susceptibility.

Qualitative Research in Healthcare Projects

Monique C. Tsosie, Alejandra Flores, Lisa Hardy, & Cruz Begay

The Health Resilience among American Indians in Arizona project is part of the Center for American Indian Resilience- CAIR directed by Dr. Priscilla Sanderson and Dr. Nicolette Teufel-Shone.

The vision of CAIR is to have strong, healthy and resilient American Indian communities. Their mission is to work with the American Indian communities so that they can promote health and resilience.

Dr. Hardy and Dr. Begay are the lead researchers for the NAU pilot project and have as main goal the identification of the knowledge, beliefs, and behaviors that Native Americans have when working towards a healthy lifestyle. Researchers also want to learn how resilience affects people’s lives and overall wellness. The research team has conducted interviews in Flagstaff to collect data, and is now analyzing the results. Dr. Hardy and Dr. Begay hope to make policy and procedural recommendations to health care providers that will improve the relationship between doctors, health professionals, and community members.

This poster is about how qualitative research can have an impact in health care projects. During this summer I learned what has to be done to  perform qualitative research, and some of the methods that you can follow to get the data you need for your project. I interned with an Anthropology project, created a survey and analyzed the mock data presented in this poster.

Promoting Health Against Chronic Disease and Tobacco Use

Eleanor Miller, Theresa Kulpinski, Marty Eckrem

The  main goals of the Arizona  Nutrition Network (AzNN)  include: promoting health and  nutrition, shaping food consumption  in a positive way and to reduce disease among the Arizona population. The Tobacco and Chronic Disease Prevention  mission is to enable the community to  live  healthier, reduce the risk factors of  chronic disease, and  educate about policies regarding tobacco use. Both programs aim to provide resources to encourage healthy eating habits, increasing physical activity, and promoting healthy lifestyles.

Analysis of heat-labile sites generated by reactions of depleted uranium and ascorbate in plasmid DNA.

Wilson J, Young A, Civitello ER, Stearns DM.

The goal of this study was to characterize how depleted uranium (DU) causes DNA damage. Procedures were developed to assess the ability of organic and inorganic DNA adducts to convert to single-strand breaks (SSB) in pBR322 plasmid DNA in the presence of heat or piperidine. DNA adducts formed by methyl methanesulfonate, cisplatin, and chromic chloride were compared with those formed by reaction of uranyl acetate and ascorbate. Uranyl ion in the presence of ascorbate produced U-DNA adducts that converted to SSB on heating. Piperidine, which acted on DNA methylated by methyl methanesulfonate to convert methyl-DNA adducts to SSB, served in the opposite fashion as U-DNA adducts by decreasing the level of SSB. The observation that piperidine also decreased the gel shift for metal-DNA adducts formed by monofunctional cisplatin and chromic chloride was interpreted to suggest that piperidine served to remove U-DNA adducts. Radical scavengers did not affect the formation of uranium-induced SSB, suggesting that SSB arose from the presence of U-DNA adducts and not from the presence of free radicals. A model is proposed to predict how U-DNA adducts may serve as initial lesions that convert to SSB or AP sites. The results suggest that DU can act as a chemical genotoxin that does not require radiation for its mode of action. Characterizing the DNA lesions formed by DU is necessary to assess the relative importance of different DNA lesions in the formation of DU-induced mutations. Understanding the mechanisms of formation of DU-induced mutations may contribute to identification of biomarkers of DU exposure in humans.

Cultural Competency in Cancer Education and Prevention for the Navajo Nation

Amber Howard,  Heather Eastman,  Dr. Octaviana Trujillo

Cultural competency is a set of congruent behaviors, attitudes, and policies that come together in a system, agency, or among professionals that enables effective work in cross-cultural situations. The Office of Minority Health (OMH) recognizes the importance of developing innovative activities like core cultural competencies for health care professionals at all levels of education in a language the patient understands and that honors the values and beliefs for respectful care (Beamon et al., 2006). Conducting literature reviews, community outreach, interviews, and attending cancer conferences confirmed the importance of cultural competency in Native American cancer prevention. However, there is limited empirical data available to address the issue of cultural competency training that is tribal specific. 

Quantification of Uranium in Sheep Meat and Soft Tissue

Crystal Yazzie, Lucio Sanchez Andee Lister, Marsha Bitsui, Tommy Rock & Jani Ingram (PI)

On the Navajo Reservation, located in Arizona, Utah and New Mexico, there are more than 500 abandoned uranium mines. The uranium mine operations started in the 1940’s and continued until the late1980’s. When the mines were abandoned minimal effort was made to treat the remnants. During this time period the Cold War has begun which sparked a necessity for uranium for power plants, weapons, and armor. In nature, uranium is found as uranium-238, uranium-235, and a very small amount of uranium-234. The natural form of uranium cannot be absorbed through the skin; humans are exposed to uranium by inhalation of dust and/or ingestion of contaminated water and food. The goal of this research is to quantify uranium concentrations in specific organs and muscles in the sheep to identify high-risk exposure. We collected sheep from Cameron and Leupp, AZ. Cameron has over 100 abandoned uranium mines. Leupp has no known abandoned mines, and is our control. The Navajo that reside in Cameron and in Leupp use sheep as a traditional food source. In Cameron, the sheep graze in areas of the abandoned uranium mines. For this study we collected samples of sheep meat and soft tissue. Acid digestion will be done to solubilize the samples. An inductively coupled plasma mass spectrometer will be utilized for analysis of uranium concentrations. If concentrations exceed the natural background levels of 3-5 micrograms per gram of uranium will have a major health risk to the communities.