Welcome to the Pathogen and Microbiome Institute (PMI) undergraduate research program webpage. Students in our program work on exciting biological research projects under the careful mentorship from faculty (professors) and staff scientists (see students’ research statements). Students are the frontline data generators, responsible for a large share of data production and analysis at PMI. Their contributions are integral to the success of our research institute. Students present their work in professional conferences and are given co-authorships on publications of manuscripts in recognition for their contribution. Our PMI undergrad research program provides students opportunities to build their professional value through acquiring professional skills (technical, communication, leadership, and organizational) and professional networks. The professional experiences and credentials gained through PMI’s undergrad research program make our graduates highly competitive for advance professional degrees within the scientific research field and outside of research. Many of our graduates go on to receive advanced degrees in medicine, pharmacy, public health, education, and business.
Allen Clarke, Undergraduate Research Assistant Accordion Closed
Benjamin Graziano, Undergraduate Office Assistant Accordion Closed
I am a junior currently working toward a Visual Communications degree with an emphasis in Graphic Design. At PMI, I work under the direction of Alyssa Barrett and Debbie Martin in the Finance and Business Operations Core (FBO), the administrative department at PMI. My work involves supporting all of PMI’s research teams with ordering lab supplies from a multitude of scientific vendors. By navigating NAU’s PeopleSoft Financial system and the PMI order board, I routinely create, update, and receive orders on a daily basis. Along with receiving incoming orders and notifying PMI research teams of order arrivals, I manage returning orders and/or contacting suppliers when we receive faulty products. My role also requires me to manage all filing of PMI documents related to grants and contracts, personnel, and invoices. I work to keep PMI databases up-to-date and ensure that invoices and packing slips are in an easy-to-find, easy-to-read format. Alongside these daily office tasks and other tasks such as office upkeep and receiving visitors, I design and create the “PMI Quarterly,” a quarterly newsletter for the department that highlights the ongoing research of many scientific teams at PMI. This newsletter is disseminated to roughly over 500 people.
Bryce Schmidt, Undergraduate Research Assistant Accordion Closed
My research at PMI focuses on the southern cattle tick (Rhiphicephalus microplus), which is a vector for a potentially lethal disease in cattle called cattle fever. These ticks are endemic to Mexico, from where we import over 1 million cattle into the US every year. The United States Department of Agriculture (USDA) implemented a rigorous monitoring program of ticks at the border in order to avoid disease reintroduction. However, tick infestations continue to emerge on cattle ranches in southern Texas, increasing the risk that cattle fever could impact the modern US livestock and agriculture industry. We collaborate with the USDA to genotype ticks from Texas and Mexico at various genomic markers. Specifically, we look for single-nucleotide polymorphisms (SNPs) that are known to confer insecticide resistance, reducing the effectiveness of insecticides on tick populations. We also use species-specific markers to identify cattle fever pathogens within the ticks collected from Mexico and southern Texas. Understanding the prevalence of insecticide resistance and pathogenicity in cattle fever ticks assists the USDA in effectively assessing and reducing the risk of disease reemergence within the states. Overall, my experience at PMI has made me a more confident and competent researcher and has inspired me to pursue a career in molecular biology.
Chris Keefe, Undergraduate Research Assistant Accordion Closed
I am a dual major in Computer Science and Biology, interested in building software tools that provide insights into biological and ecological systems. Working in the Caporaso lab, I am a developer of QIIME 2, a leading microbiome bioinformatics platform. In addition, I am involved with longitudinal and interventional studies on correlations between gut microbiome and the onset and severity of symptoms in mouse models of Alzheimer’s Disease. My role in these studies will be bioinformatics analysis and custom software development in support of those analyses. I’m looking forward to a career built on study and practice, in which the principles and processes of software engineering and biological science support productive development.
Colin Wood, Undergraduate Research Assistant Accordion Closed
My name is Colin Wood, and I am in my second year here at Northern Arizona University. I’m working towards a Bachelor of Science, with a major in biology, and a minor in chemistry. Under the direction of Shari Kyman and Dr. Talima Pearson, I have been helping to extract, amplify, and sequence the DNA of strains of the bacterium Stahpylococcus aureus that were isolated in Yuma, Arizona. This bacterium is a well-known causative agent of many less severe but prevalent illnesses such as skin infections, but can also be to blame for much more serious conditions like bacteremia. S. aureus is also often a cause of food-poisoning. The purpose of our project is to map and understand the transmittance of S. aureus from one person to another in conjunction with the relationship these persons share, and with regard to ethnicity. This information will allow us to understand the types of relationships that are most likely to result in transmission, and will help to prevent recurring infections.
Daryn Erickson, Undergraduate Research Assistant Accordion Closed
My name is Daryn Erickson and I am pursuing a B.S. in Microbiology with a minor in Chemistry. I have been an undergraduate researcher at PMI since June 2017 working under Dr. Crystal Hepp and Dr. Viacheslav Fofanov. In their labs, I am able to work with and study, various pathogens such as, West Nile Virus (WNV), Staphylococcus aureus, Streptococcus mutans, and Streptococcus sobrinus. Our goal when working with these pathogens is to understand their prevalence and movement throughout different populations. For my undergraduate project, I will be examining the Aedes aegypti mosquito population in Maricopa County, AZ. Along with Dr. Hepp, I will determine what types of arboviruses, if any, are circulating within this mosquito population. I will also be testing for insecticide resistance within the same mosquito population. After NAU I plan to pursue a PhD to further study pathogens and pathogen genetics. My dream is to work for the CDC or NIH. I love working in the research field because there is always something new to learn. I love being a part of such a progressive field; a field in which I know I can keep learning and never get bored.
Holland Hoogstad, Undergraduate Office Assistant Accordion Closed
I am a student pursuing a degree in Music Education with an emphasis in Instrumental instruction. At PMI, I work under the direction of Alyssa Barrett and Debbie Martin in the Finance and Business Operations Core (FBO), the administrative department at PMI. My work involves supporting all of PMI’s research teams with ordering lab supplies from a multitude of scientific vendors. By navigating NAU’s PeopleSoft Financial system and the PMI order board, I routinely create, update, and receive orders on a daily basis. Along with receiving incoming orders and notifying PMI research teams of order arrivals, I manage returning orders and/or contacting suppliers when we receive faulty products. My role also requires me to manage all filing of PMI documents related to grants and contracts, personnel, and invoices. I work to keep PMI databases up-to-date and ensure that invoices and packing slips are in an easy-to-find, easy-to-read format. Alongside these daily office tasks and other tasks such as office upkeep and receiving visitors, I am responsible for placing orders using a department business credit card which requires weekly reconciling of all credit card transactions. I also pay over 50 invoices a week for the department, a task which requires me to be detail orientated, have financial/accounting knowledge, and knowledge of NAU’s extensive PeopleSoft Financials system.
Kaitlyn Parra, Undergraduate Research Assistant Accordion Closed
I am currently a sophomore at NAU pursuing a Bachelor’s in Microbiology and a minor in Chemistry. After my undergraduate years, I plan on matriculating into a PhD program focused on infectious disease research. I work under Dr. Bridget Barker who is a lead researcher in Coccidioides spp, which are dimorphic soil-dwelling fungi responsible for Valley fever. My primary job is to help run the Valley Fever PAWS project, which looks at Valley fever in canines though a citizen-science approach. The project goal is to identify how the host’s genome is a factor in the rate of disease. Currently, the project is studying canine breeds to understand how their genetic architecture plays a role in disease susceptibility. My project and time at PMI has been the best part about my college experience. I participate in research and develop professionally as a scientist all while still being an undergraduate student!
Karisma Kocos, Undergraduate Research Assistant Accordion Closed
My name is Karisma Kocos, and I am working towards a degree in Biomedical Science with a minor in Chemistry. I work on a variety of projects here at PMI, but am currently focusing on comparing two methodologies to determine antibiotic resistance, antibiotic microdilutions and E-Tests, on three different antibiotics for Burkholderia near neighbors. By determining the minimum inhibitory concentration necessary to inhibit the bacteria’s growth, and comparing these values in both techniques, I can discuss which method would be best suited for determining antibiotic resistance in a clinical setting. In addition, the results of this study will provide depth in understanding the antibiotic resistance of Burkholderia species, which can cause devastating human diseases such as Glander’s and Melioidosis. As an aspiring Physician Assistant, my research in antibiotic resistance is directly translatable to my professional goals. The research I conduct at PMI fuels my passion to work in the medical field through ground-breaking research and providing the groundwork for me to learn about pathogens and diseases that affect the human body.
Kristen Kyger, Undergraduate Research Assistant Accordion Closed
I am a sophomore at NAU currently pursuing a Bachelor of Science in Biology with a minor in Chemistry. I have worked at PMI since July 2018 under the supervision of Dr. Jason Sahl and Adam Vazquez. During the short time I have been at PMI, my research has been centered around the analysis and classification of E. coli through our E.coli AmpSeq project. The goal of this project is to create better methods to identify co-infections and track E.coli in urinary tract infections, which allows us to determine strain relationships, antibiotic resistance patterns, and to focus antibiotic therapy. This has lead to an overall better understanding of where these strains are coming from and how to classify them. I would like to take my knowledge and skills obtained at PMI and pursue a career in research, ultimately working for the Centers for Disease Control and Prevention.
Madison Martz, Undergraduate Research Assistant Accordion Closed
I am currently working towards a degree in Biomedical Science with minors in Chemistry and Psychology. Since August 2018, I have worked as an Undergraduate Research Assistant at PMI under the supervision of Dr. David Wagner and Carina Hall. At PMI, my research is primarily centered on the infectious agent of Melioidosis, Burkholderia pseudomallei. Melioidosis is a disease endemic to tropical regions that is difficult to diagnose and treat. B. pseudomallei is naturally found in the environment and has an intrinsic resistance to various clinically relevant antibiotics. Due to this, I have been assisting in a project that is focused on identifying the antimicrobial resistance across various Burkholderia spp. and B. pseudomallei strains. My main goal is to determine mechanisms of antimicrobial resistance through transcriptomic analysis. This will ultimately be beneficial in determining proper treatment of clinical infections of B. pseudomallei and near-neighbor species. My research here at PMI has helped me to learn about and greater understand infectious diseases and the research methods surrounding them. Upon completion of my undergraduate studies, I plan to attend medical school and pursue a career as a physician.
Samantha Hershauer, Undergraduate Research Assistant Accordion Closed
I am currently a Junior at NAU majoring in biology and minoring in chemistry. As a member of the Ancient DNA Core, my projects start in the Ancient DNA Lab, where I handle and extract DNA from sensitive samples, and finish at the Pathogen and Microbiome Institute (PMI), where I amplify gene targets of interest. My main project uses ancient DNA genetic techniques to determine when key species arrived into Alaskan ecosystems. In the Ancient DNA Lab, I handle and extract DNA from samples taken along Alaskan lake sediment cores. I then bring my work to PMI to PCR-amplify and sequence gene targets of interest so I can determine which organisms left behind their DNA. This line of work is relatively new and is developing into a significant tool for understanding past ecological communities. In addition, I perform Species from Feces genetic assays with the Bat Ecology and Genetics Lab. The aim of Species from Feces is to serve as a noninvasive method of tracking bats for conservation and management purposes by genetically identifying species that use roosts through DNA in their guano. I plan to continue research in genetics through graduate school and a PhD program.
Vidal Martinez, Undergraduate IT Assistant Accordion Closed
I am currently in my third year pursuing a degree in Computer Science. My work at PMI is focused around computer maintenance, working with the PMI network domain, and IT support. I am responsible for maintaining hardware inventory, installing operating systems on new and used computer hardware, setting up workstations and printers, and installing needed software. I assist PMI faculty, staff, and students with IT and network issues.
Zane Fink, Undergraduate Research Assistant Accordion Closed
I am currently a junior pursuing a Bachelor’s degree in Computer Science. My research with Dr. Jason Ladner involves designing algorithms and software for the creation of synthetic oligonucleotide (oligo) pools. These oligos will ultimately be used to conduct high-throughput serological assays, which will be used to elucidate an individual’s viral exposure history by probing for antiviral antibodies in peripheral blood samples. Because the dataset of all sequenced proteins from viruses known to infect humans is so large, we have developed a pipeline that allows for efficient, multi-stage clustering of viral protein sequences, where each cluster is then processed as an instance of the weighted set-cover problem. The goal of this software is to find the minimum number of oligos that cover up to 100% of the input data’s component epitopes. As a Computer Science student, bioinformatics research is interesting because the large datasets require you to think about optimization and algorithmic efficiency. After graduation, I plan to continue my education and research in a computer science graduate program.