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BIOL 2004 - Special Projects

These projects will require approximately the same amount of work as the regular BIOL 2004 project, but will allow you to develop somewhat different skills and explore different kinds of questions in a small group setting. Students will be matched with a project that interests them through an online application and interviews. You must have successfully completed BIOL 2002 by the end of fall 2013 to be eligible for this section.

For descriptions of the research projects, see below. Please contact the appropriate postdoc if you want to know more about a particular project.

If you'd like to participate in this special section, please complete the application form here. For more information about enrollment or other general questions, contact Catherine Kirkpatrick (cakirkpa@umn.edu).

 

Do childhood illnesses warp you for life? How about if you're a cricket?

Having and using an immune system is costly - if it weren’t, there would be no such thing as disease. In this project, you’ll use the common pet store cricket (Acheta domesticus) to investigate how the costs of responding to an immune challenge at different points in an individual’s life affect its physiology and behavior as an adult. As part of the project, you’ll learn various ways to challenge an insect’s immune system; as well as how to perform behavioral experiments, quantify behavioral observations, and record and analyze acoustic signals. You’ll work with three other students and one postdoctoral fellow. This project relates to ongoing research in Dr. Marlene Zuk’s lab, in the Ecology, Evolution, and Behavior Department. For more information about Dr. Zuk and her work, please visit her lab website.

Why crickets? Insects encounter many of the same immune challenges as mammals and other vertebrates; including bacteria, viruses, fungi, and other pathogens. They also encounter some challenges rare in the vertebrate world, such as flies and wasps who deposit their larvae in unsuspecting hosts, after which the larvae gradually devour the hosts from the inside out. Insects have evolved impressive abilities to deal with many of these challenges, despite lacking the adaptive immune system typical of vertebrates. That means no MHC locus, no T cells, no B cells, and no antibodies!

Insects are an ideal model for studying the immune response from an evolutionary perspective. Their immune system is highly sophisticated, but its mechanisms of action are often quite different from those of the vertebrate immune system. These differences may help us to parse out which “failures” of the immune response in humans and other vertebrates are mechanism-specific vs. which ones result from the fundamental costs of evolving, maintaining, and using an immune system at all.

For more information about this project, please feel free to contact Beth Bastiaans (ebastiaa@umn.edu).

 

Germs

Our bodies are covered inside and out with bacteria, which outnumber our own cells by 10-to-1. Recent research shows that the human microbiome can impact our health, from causing obesity to changing behavior. If you join my research project, you will focus on understanding the relationship between the human microbiome and cancer.

Working in small groups, you will develop research questions and devise ways to answer them using large databases, such as The Cancer Genome Atlas and the Human Microbiome Project. In doing your project, you will learn how human and bacterial genomes are sequenced, basic bioinformatics, and how to manipulate “big data.” The research work will be almost entirely computer-based as opposed to “wet-lab” based, so students will be able to perform much of the work from anywhere that has a computer and an Internet connection. The skills you will develop are currently in high demand among researchers in academia and industry. In addition, several large medical centers, such as the Mayo Clinic, are moving forward with clinical trials that involve sequencing patient genomes (example list). You will be at a distinct advantage if you not only understand how this sequencing is performed, but have actually worked with patient sequence data as an undergraduate researcher.

To learn more, check out the Blekhman Lab website or contact Michael Burns at burn0230@umn.edu.

 

Growth and Physiology of the Vibrionaceae

Have you ever played with bacteria that live in squid and glow in the dark? If not, here is your chance! The Vibrionaceae is a diverse family of marine bacteria, which includes bioluminescent members such as Vibrio fischeri, V. harveyi, and Photobacterium species. The Vibrionaceae have a free-living phase during part of their ecology. They are also able to colonize some eukaryotic hosts, such as squid. Most evolutionary work has focused on the relationship of the Vibrionaceae with their hosts, with little regard for the evolutionary impact of the free-living phase on those interactions. We have evidence that evolution during the free-living phase may actually be more important than the interactions these bacteria have with their host. How members of this bacterial family respond to abiotic factors and pollutants in their ocean environment is surprisingly poorly understood.

The Vibrionaceae have the potential to serve as indicator organisms for evaluating environmental health of the world’s oceans, so understanding their physiology outside their hosts is imperative. This work also has applications to human health and medical microbiology, as members of the Vibrionaceae such as Vibrio cholerae, V. vulnificus, and V.parahaemolyticus (close relatives of the bacteria we will be studying) are serious human pathogens. For example, recent work suggests that ocean temperatures and salinities can accurately predict the threat of future outbreaks of V. cholerae.

In this project you’ll work with numerous species of Vibrionaceae using microbiological methods to study various environmental factors and gain a deeper understanding of this bacterial family. You will also learn how to use the NCBI database of published DNA sequences. You will gain an appreciation for bacterial metabolic diversity, microbial evolution, and microbial ecology. This project relates to ongoing work in Mike Travisano’s lab in the department of Ecology, Evolution and Behavior.

For more information, please see the Travisano lab website or contact Will Soto at wsoto@umn.edu.

 

The environmental impact on obesity in zebrafish

Did you know that our environment could make us fat? Why is this and what are the factors involved? It is thought that by the year 2030, over 50% of Americans will be obese (Trust for America’s Health and the Robert Wood Johnson Foundation, 2012). Furthermore, obesity has tripled in the last 30 years to 20% of 6-19 year olds (Center for Disease Control). Obesity is associated with diseases such as high blood pressure, type II diabetes, cardiovascular disease and asthma. Current investigations are underway to determine the cause of obesity and develop new drugs to combat it.

In this project, you will have an opportunity to explore how conditions in our environment can contribute to obesity. You will add to the current knowledge on this topic and you may even discover new treatment strategies. How will you do this? Did you know that zebrafish share almost 80% of their genes with humans? In your research, you will learn to manipulate zebrafish embryos, use microscopy, assess development by using angle measurements and observe behavior as you formulate and answer your own questions about nutritional or environmental factors that can impact obesity and diabetes. You may even learn to stain fat cells. Yes, fish can get fat!

For a live look at zebrafish development see http://youtu.be/moL5C8SjeJU.

For more information about this project, contact Bao Vang at vang0280@umn.edu.

 

Discover your own drug; solve antibiotic resistance

Aspiring med students and people interested in solving disease, pay attention! This project is for you.

We have all seen the headlines on newspapers and TV: new superbugs resistant to antibiotics are popping up everywhere, posing an increasingly greater threat to public health. The recent emergence of strains resistant to entire classes of antibiotics has given rise to the frightening possibility that common diseases such as tuberculosis and gonorrhea may soon become untreatable. I say let's go do something about it. Let's go and discover the new antibiotics that will replace the old ones.

The University of Minnesota has recently generated a metagenome library consisting of thousands of bacteria sampled from the Mississippi River. This library more or less takes all the DNA from each water sample, fragments it, and puts each fragment into an E. coli cell so each cell contains around three to four genes. Luckily for you, this library has already been screened for resistance to four antibiotics and several hundred strains have been discovered as resistant. The objective of my project is to test a wide range of herbal extracts against these resistant bacteria to see which extracts can overcome the resistances. When an extract kills a resistant strain, we know it contains some chemical that is overcoming the resistance. Each student in my project will be able to choose his/her own herb to work with so it will be YOUR project and YOUR discovery. And if you're lucky, someday it might be your drug.

For more information about this project, please contact Justin Fendos at jfendos@aya.yale.edu.

 

Engineer bacteria to clean the environment.

Heavy metals like cadmium, nickel, and copper are toxic when released into the environment in large quantities. Industrial waste, exhaust from power plants and cars, and mining practices are some of the largest contributors of heavy metal contamination. Isolated water can often be purified of these metals rather easily with filters or chemistry but what about more complex and larger systems such as lakes or rivers? Obviously we can’t attach a filter to Hoover Dam so the tools at our disposal are limited if we want to do a larger-scale cleanup.

Enter Dr. Renu Kumar, professor at Minneapolis Community and Technical College (MCTC). She has recently isolated a few strains of unidentified bacteria from the wild that exhibit strong resistances to copper or zinc. Wouldn’t it be interesting to see if these bacteria can be engineered to absorb toxic metals and remove them from the environment? The ideal bacteria for this purpose would be resistant to heavy metals in addition to being good at absorbing them. A strong resistance would allow the bacteria to survive while internalizing high quantities of toxic metal, sequestering them from the environment. My project is designed to characterize the resistance of Dr. Kumar’s strains to heavy metals such as nickel and cadmium. Each student will be given one strain to work with and test the strain’s resistance against a panel of toxic metals. After the screen, students will have the opportunity to devise and implement strategies to determine what protein might be conferring the resistance, allowing us to identify the source of the resistance for bioengineering.

For more information about this project, please contact Justin Fendos at jfendos@aya.yale.edu..