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.
Ahmad (Turan) Naimey, Research Undergraduate Student Accordion Closed
I am a senior pursuing a degree in Applied Computer Science and a minor in Mathematics. At PMI, I work as undergraduate research software engineer at the Caporaso Lab where I contribute primarily to the development, maintenance and documentation of QIIME 2 under the supervision of Evan Bolyen, Matthew Dillon and Dr. Caporaso. During my time at the Caporaso Lab, I have worked on a Google Sheets Add-On called Survey Sync which automates the process of downloading and validating data from Survey123 platforms to Google Sheets. Some of my other projects include creating a convenience pipeline in q2-phylogeny plugin of QIIME 2 for fasttree-based tree building and optimizing q2cli’s import/export API. Working at PMI has allowed me to learn the significance of multidisciplinary teamwork. The best thing about working at PMI is knowing that the code I write might be used by scientists who are trying to answer some of the most difficult research questions. The skills I have gained from working in this position will be valuable to me once I transition to the software industry.
Alden Miller, Research Undergraduate Student Accordion Closed
I am currently pursuing a Biomedical Science degree with a minor in Chemistry. I am a premed student with an interest in forensic pathology. Under the direction of Dr. Jason Sahl, my current research project focuses on the organism Clostridium difficile (C. diff) , which is a pathogenic bacterium that causes gastrointestinal symptoms and is most commonly a hospital acquired infection. This project utilizes
amplicon sequencing of C.diff DNA extracted directly from fecal samples as a cheaper and faster alternative to standard sequencing methods such as whole genome sequencing (WGS). Using this methodology, we can theoretically identify mixtures, characterize, and determine antimicrobial resistance profiles within C.diff patient samples. A better understanding of C. diff transmission and antimicrobial resistance will help focus intervention and treatment strategies to control the spread of C. difficile infection (CDI). My current career goals are to attend medical school and pursue a medical degree and specialize as a forensic pathologist.
Allen Clarke, Research Undergraduate Student Accordion Closed
Amalee Nunnally, Research Undergraduate Student Accordion Closed
– Graduated December 2018
My name is Amalee Nunnally and I am working toward a degree in Microbiology with minors in chemistry and sociology. I have been working under Heidie Hornstra O’Neill and Nathan Stone here at PMI for the past two and a half years. Our research is aimed at understanding reservoirs of Clostridium difficile, or C. diff, one of the leading causes of hospital-acquired infections worldwide. We are trying to detect C. diff in soil, healthy dogs, and acutely ill patients in Flagstaff and compare the bacteria from different sources. We are utilizing whole genome sequencing in order to do this, which allows us to see and analyze the entire genome, something that cannot be done with other types of genotyping. In addition, I also play a part in a large project aimed at developing a diagnostic assay for the disease melioidosis. This disease is caused by Burkholderia pseudomallei and is endemic to Australia and Southeast Asia. This tool will identify antigens in human blood produced as a consequence of the infection and will be able to accurately predict aspects of a patient’s disease. This work has inspired a love of science in me, and I plan to continue doing research in infectious disease as a career.
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, Research Undergraduate Student 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, Research Undergraduate Student 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, Research Undergraduate Student 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, Research Undergraduate Student 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.
Emily Borsom, Research Undergraduate Student Accordion Closed
– Graduated December 2018
I am a senior at NAU pursuing a Bachelor’s degree in Biology. I work as an undergraduate researcher at PMI in Dr. Emily Cope’s lab. My research consists of working with various strains of mice in different disease states and characterizing their microbiome composition using 16S rRNA sequencing and quantifying immune gene expression using qPCR. The project I am currently working on is investigating the effects of prebiotic manipulation of the gut microbiome for inflammatory diseases. My next project will longitudinally analyze the gut microbiome composition in transgenic mice that develop Alzheimer’s Disease (AD) pathology. Additionally, we will evaluate the effects of microbiome composition on the development of AD pathology. After finishing my Master’s in Biology at NAU, I would like to continue exploring clinical research through either a PhD program or medical school. Working at PMI has allowed me to apply the information I have learned from science courses to projects that could potentially contribute to improved medical care for patients.
Gabrielle Orsini, Research Undergraduate Student Accordion Closed
I am currently a senior at NAU pursuing a Bachelor’s Degree in Biology and minors in Chemistry and Anthropology. I work in Emily Cope’s laboratory studying the human microbiome and whether prebiotic manipulation of the gut microbiome can reduce certain types of inflammation. We are measuring inflammatory gene expression and sequencing the microbiome of mice fed a Western Diet with and without a prebiotic supplement. Because of my experience at PMI and as a member of the Cope group, I have found a second home and a continued fascination for research. Upon graduating, I plan to pursue a Doctorate in Veterinary Medicine and become an Army Veterinarian. My dream is to be both a Veterinary Pathologist, fueling my passion to understand disease at the microscopic level, and a Behavior Specialist.
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.
Jacqueline Lyman, Research Undergraduate Student Accordion Closed
I am a junior undergraduate pursuing degrees in Biology and Spanish with a minor in Chemistry. As a member of the NAU School of Forestry Bat Ecology and Genetics Lab, I use noninvasive genetics to inform habitat requirements of the endangered New Mexico jumping mouse. Through my work I helped identify herbaceous materials composing jumping mouse nests and added 80 new DNA barcodes for native plants of the Southwest to the Barcode of Life Database (BOLD), a global repository for genetic biodiversity. Adding new barcodes to BOLD helps catalog the diversity of native Southwestern flora and improves our ability to identify diet items of the New Mexico jumping mouse. I am currently designing an assay to detect jumping mouse DNA from water using environmental DNA techniques. This method would be a quick and effective way for managers to monitor for species presence. Upon completion of my undergraduate degrees, I will pursue a PhD in molecular genetics. I intend to apply my degree in Spanish to perform international research on gene variants and rare genetic disease.
Jared Phillips, Research Undergraduate Student Accordion Closed
– Graduated December 2018
I’m a senior at NAU studying biomedical science with a minor in chemistry and a certificate in biotechnology. I’ve been working with PMI through a collaboration at TGen North since January of 2018. Under the supervision of Krystal Sheridan and Heather Centner, I help in the preparation of both genomic and amplicon DNA by creating indexed libraries for next-generation sequencing. As a member of the sequencing-core, we are responsible for providing sequencing data for the majority of PMI’s ongoing projects. My experience at PMI has provided invaluable insight into the world of biological research and the indispensable utility it can provide. After graduating, I plan on pursuing a physician’s assistant graduate program
Jordyn Upton, Research Undergraduate Student Accordion Closed
I am a junior in NAU’s Honors College and am pursuing a double major in Biology and Spanish. I work for the Bat Ecology and Genetics Lab, conducting research at the Pathogen and Microbiome Institute on the southern-hairy nosed wombat. This is a long-lived (>30 years) burrowing marsupial that was recently listed as Near-Threatened (IUCN Red List). In a follow up study to Dr. Faith Walker’s Ph.D. work, I am molecularly tracking this burrowing marsupial through time by applying microsatellite analysis to hair DNA. In so doing, I will determine whether the same individuals are still alive, how their use of space differs from 17 years ago, and whether population size has changed after episodes of drought and mange. I also move forward my team’s ‘Species from Feces’ genetic services. I plan to pursue a Ph.D. in Molecular Biology after obtaining my two undergraduate degrees.
Kaitlyn Parra, Research Undergraduate Student 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, Research Undergraduate Student 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.
Kelly Fulbright, Research Undergraduate Student Accordion Closed
I currently am a junior at NAU pursuing Bachelor’s degrees in Biomedical Science and Chemistry. As an undergraduate research assistant at the Pathogen and Microbiome Institute, I work under the supervision of Shari Kyman and Dr. Talima Pearson in the Microbiome Center. The major project I am currently working on is studying the transmission of Staphylococcus aureus within different ethnic groups in Yuma, Arizona. Our project aims to identify how different social relationships can contribute to the transmission of S. aureus, as well as how similar or dissimilar these individuals’ bacterial microbiomes are from one another based off of these relationships. S. aureus is commonly carried asymptomatically by approximately thirty percent of the population. However, S. aureus is an opportunistic pathogen, that can cause several ailments including cellulitis and various abscesses if given the opportunity to. These opportunities include weakened immune systems and altered microbiota. Understanding the transmission of S. aureus and other bacteria in relation to relationships, can help us better prevent transmission. During my time at PMI, I have acquired crucial critical thinking skills in regards to experimental design, set up and execution. Working at PMI has motivated me to pursue a career in research post-graduation.
Kristen Kyger, Research Undergraduate Student 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.
Kyle Headley, Research Undergraduate Student Accordion Closed
– Graduated December 2018
My major includes a Bachelors in Microbiology with a minor in Chemistry. I have been an employee at PMI since May 2016. I have been working on developing a serodiagnostic assays to detect Burkholderia pseudomallei, a lethal disease that is endemic to Northern Australia and Southeast Asia. This project has been a team effort at PMI and it involves an international collaboration with a clinical partner in at The Royal Darwin Hospital and the Menzies School of Health Research in Northern Australia. My role in the project includes cloning the targeted antigens, sequence verifying the expression plasmids, growing bacteria and inducing expression, final protein purity estimates, and final purified protein concentration determination. My role in the project is expanding as I begin doing diagnostic assay development, which includes antigen bead-conjugations, conjugations-validations. I have also started quantifying products by qPCR for next-generation sequencing. Our goal is to identify bacterial targets for diagnostic assay development with the hope of developing an assay that can diagnosis B. pseudomallei infected patients. I really love my research project since I am helping towards a larger cause. I have always wanted to help save people from different types of infectious diseases and I am very thankful for the opportunity PMI has given me. My overall, career goal has changed since I began working here, since it has shown me what it takes to do research. Through career development classes offered at PMI and interactions with the staff, I have realized that you need to have many career paths in case something doesn’t work out. My dream job currently is to become a Pilot in the Navy; if this does not work out I will try to perform research or diagnostics in Hospital Labs or biotech. My job at PMI has given me so many opportunities to find out my interests and who I am as a person. I am taking a detour from a career in my degree field in pursuit of a big dream of mine that I did not know was possible until a year ago. I thank PMI for being supportive of my decisions and continuing to be one of my biggest support systems at NAU.
Madison Martz, Research Undergraduate Student 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.
Mimi Mbegbu, Research Undergraduate Student Accordion Closed
– Graduated December 2018
My name is Mimi Mbegbu and I am a Biomedical Science, Chemistry, and Psychology major graduating in December 2018. I joined PMI during the second semester of my sophomore year under the supervision of Dr. Jinhee Yi. My research is based in the field of proteomics and immunology and my main focus is to analyze the antigenic proteins of a bacterium called Burkholderia pseudomallei, the causative agent of Melioidosis in Northern Australia and South East Asia. My responsibilities include expressing and purifying antigenic proteins for use in diagnostic assays and antibiotics resistance. I am also responsible for optimizing ELISA assays for another diagnostic assay. The data our team collects can be used to determine more efficient diagnostic techniques to combat the outbreak of the pathogen. My career goal is to attend an accredited medical school and focus on either medical research or anesthesiology. I love working in a research facility that helps expand my knowledge about the scientific world and offers me experience that I can use after graduation. Knowing that I am helping make a difference through my research motivates me to keep pushing forward.
Nicole Bratsch, Research Undergraduate Student Accordion Closed
Currently I am working toward a Bachelor of Science in Biology with a minor in Chemistry with a Bachelor of Arts in Spanish at NAU. The projects that I have worked on at PMI have predominantly been focused on the causative agent of plague, Yersinia pestis, and the causative agent of the disease melioidosis, Burkholderia pseudomallei. Yersinia pestis is a flea borne pathogen that has been responsible for millions of deaths throughout history and continues to thrive in rodent populations in Flagstaff. I use MLVA, a fragment analysis procedure, to look at how Y. pestis has mutated as it has moved through Northern Arizona. Burkholderia pseudomallei, although not a common organism in the United States, is found frequently in tropical areas including Southeast Asia. Using soil culturing techniques and polymerase chain reaction (PCR), I work to detect B. pseudomallei in soil samples collected from the Caribbean. Working at PMI allows me to enhance my technical microbiology skills, work to solve problems with critical thinking, and be a part of a community that works to improve our world through science.
Oliver Kask, Research Undergraduate Student Accordion Closed
My name is Oliver Kask and I am a Senior Biochemistry major here at NAU. I have been an undergraduate researcher at PMI since November 2017. My research is focused on understanding how the composition of the airway microbiome is affected by environmental and genetic factors. My current project is looking at the relationship between the nasal/oral microbiome and polymorphisms in the Lactoferrin gene which encodes for an antimicrobial protein that is expressed in saliva as well as other mucosal surfaces. I am also finishing up a project where we compared the nasal microbiomes of athletes that were consistently exposed to chlorine and not exposed to chlorine at all. We found that there were no statistically significant differences between these two group’s nasal microbiomes indicating nasal microbiome stability. Once I graduate I plan to attend graduate school to receive my PhD in Immunology. I am very interested in studying immuno-oncology and one day starting my own pharmaceutical company.
Pooja Patel, Research Undergraduate Student Accordion Closed
My name is Pooja Patel and I am a senior at NAU. I am majoring in Biomedical Sciences with a minor in Chemistry and Religious Studies. I am a research assistant at PMI under the supervision of Dr. Dave Wagner and Carina Hall. In my time as a research assistant at PMI I have learned various skills pertaining to microbiology and molecular detection. I work directly with Burkholderia species which are close relatives to the pathogen B. pseudomallei. B. pseudomallei is the causative agent of the disease melioidosis, which is endemic in Northern Australia and southeast Asia. I primarily work on characterizing the antibiotic resistance profile of these close relatives for many clinically relevant antibiotics. Upon completion of my Bachelor’s degree at NAU, I plan on attending an accredited medical school to obtain my MD and become a practicing physician. PMI has given me a better insight on the laboratory work and professional development that I can carry on to my future job as a clinician.
Rebekah Turner, Research Undergraduate Student Accordion Closed
I am a senior at NAU majoring in Biomedical Science. I am drawn towards science in an attempt to understand the world. At PMI I have been researching cattle fever ticks (CFTs), which are important vectors of potentially fatal cattle diseases such as babesiosis and anaplasmosis. CFTs and their associated diseases were eradicated from the US in the 1940s, except for a narrow Texas eradication quarantine area (TEQA) established along the Rio Grande border. The TEQA has prevented disease transmission from Mexico, where CFTs and their pathogens are endemic. Recently, CFTs have expanded north of the TEQA, increasing the concern that babesiosis and anaplasmosis may infect US cattle herds. The focus of my research is to understand genetic mechanisms of acaricide resistance that could impair CFT eradication efforts (a project funded by the USDA). After genotyping thousands of ticks, I have found that Mexico populations carry resistant genotypes, some of which have also been found north of the TEQA. I hope to become a co-author on this work after the dataset is finalized. This experience has inspired me to pursue a biology-centered career focused on human diseases.
Ryann Whealy, Research Undergraduate Student Accordion Closed
I am a senior at NAU working toward a Bachelor’s in Biomedical Science with minors in Community Health and Psychology. At PMI, I work on various projects studying the movement, evolution, and prevalence of pathogens under Dr. Crystal Hepp and Dr. Viacheslav Fofanov. In the last six months, I have assisted with the plating and DNA extraction of around 600 oral and nasal bacterial samples to identify Streptococcus mutans, Streptococcus sobrinus, and Staphylococcus aureus in at-risk populations. My undergraduate research project involves identifying methicillin resistance in S. aureus from nasal samples collected in jails. I analyze these samples through detection of resistance-causing genes using polymerase chain reaction. This project will determine if rates of methicillin resistance in S. aureus isolated from this demographic are disproportionate to the general population. In addition, I have amplified both St. Louis Encephalitis Virus and West Nile Virus from mosquito pools collected around the southwestern United States. The projects I have assisted on at PMI have made me even more excited to pursue a Master’s in Medical Microbiology after completing my undergraduate degree at NAU.
Samantha Hershauer, Research Undergraduate Student 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.
Shelby Hutton, Research Undergraduate Student Accordion Closed
– Graduated December 2018
I am a senior at NAU majoring in Biology, minoring in Chemistry and also completing a Certificate in Wildlife Management and Ecology. Most of my work at PMI has been focused on studying vector-borne diseases, such as cattle fever and plague. Plague, caused by the bacterium Yersinia pestis, is a deadly disease that is transmitted primarily by infected fleas. In North America, plague threatens prairie dog colonies which support the critically endangered black-footed ferret. Additionally, transmission of plague to humans is a major concern in areas where prairie dogs are close to urban communities. Monitoring plague outbreaks in prairie dogs, thus, has important applications for conservation and public health. I am part of an effort to detect plague outbreaks in prairie dog populations in the Midwestern United States and inform public health officials of any possible risk to the public. I am also investigating the genetic mechanisms of insecticide resistance in fleas that transmit plague in Madagascar, where an average of 500 human cases of plague occur annually. We plan to develop an assay that scientists in Madagascar can use to screen fleas for insecticide resistance, which will be a useful tool to increase effectiveness of insecticide treatment and therefore, reduce plague transmission. I have also been a part of an ongoing project which focuses on genotyping ticks that transmit cattle fever, a deadly disease in cattle. Because cattle fever ticks are endemic to Mexico, there is a high risk of reintroducing the disease into the US through imported cattle. We collaborate closely with the United States Department of Agriculture (USDA) to better understand the movement of these ticks and the mechanisms of insecticide resistance that hinder control efforts. My research experience has enlightened me about the importance of understanding infectious diseases that affect both animals and humans. My future plans include pursuing a PhD in infectious diseases, primarily focused on zoonotic and emerging diseases.
Vidal Martinez, IT Undergraduate Student Accordion Closed
I am currently a sophomore pursuing an Applied Computer Science degree. 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 PC and Macintosh hardware, setting up workstations, installing required software, and setting up printers. I assist PMI faculty, staff, and students with IT and network issues.
Zane Fink, Research Undergraduate Student 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.