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,
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
The Role of MicroRNA
Variation in Prostate Cancer Progression Within Native American Populations
Denise Brown, Dr. Jason Wilder, Virginia
Ware, River Black
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.
Research in Healthcare Projects
C. Tsosie, Alejandra Flores, Lisa Hardy, & Cruz Begay
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.
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.
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.
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
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.
in Cancer Education and Prevention for the Navajo Nation
Howard, Heather Eastman, Dr. Octaviana Trujillo
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
Lucio Sanchez Andee Lister, Marsha Bitsui, Tommy Rock & Jani Ingram (PI)
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