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NSF Undergrad Summer Program

NSF logoNSF FUNDED SUMMER RESEARCH PROGRAM IN MOLECULAR BIOSCIENCES:

FROM MOLECULES TO CELLS TO ORGANISMS

 


Program Overview

This REU program at the University of Kansas in Lawrence Kansas provides an intensive 10-week summer research experience for curious and motivated undergraduates who are considering a PhD in molecular biology or related discipline. The program will provide students with exciting and doable research projects and experiences that build self-confidence and encourage critical and independent thinking. Fifteen faculty mentors from the Department of Molecular Biosciences, with strong records of undergraduate mentoring and collegiality will participate in the program. Our faculty mentors conduct state-of-the-art research at three levels of investigation: Molecules, Cells and Organisms. Areas of research interests range from studies on protein folding and protein design, to investigations of mechanisms of cell-cell communication, cell division and cell migration, to studies on the genetics of complex traits, tissue development, and host-parasite interactions. In addition to conducting research, the students will attend enrichment seminars and workshops including; faculty and peer presentations on how to become a research scientist; workshops on applying to graduate school and; workshops on the development of effective communication skills. The program will include several opportunities for the students to present their work and will conclude with a campus-wide mini symposium and a written final report. The program is especially interested in training students who do not have the opportunity to conduct summer research at their home institutions and/or are from underrepresented and minority groups.

Program Activities and Stipends
  • Participants conduct full-time, hands-on research in the molecular biosciences.
  • An overview of faculty research programs can be found here,
  • Enrichment activities include weekly seminars and workshops on graduate school and career opportunities, and on how do develop oral and written presentation skills. At the end of the summer, students write a research report and present their findings in a campus-wide poster session.
  • Program lasts for 10 weeks (May 27–August 1, 2014).
  • Participants receive a $5000 stipend plus free room and board
  • Travel costs up to $500/student are paid by the program.
  • Social activities include an introductory picnic, and an end-of-summer banquet.
Eligibility

The program is intended for undergraduates who:

  • Have completed at least two years of college
  • Will be returning for at least one year of undergraduate study before graduation
  • Are seriously considering pursuing graduate school and a career in biological research
  • Are United States citizens or permanent residents
  • Prior research experience is NOT a requirement

This program seeks to increase diversity in the biological sciences. Minority and/or disadvantaged students (economically or first in family to attend college) are especially encouraged to apply, as are students whose home institutions do not provide summer research opportunities.

Project Descriptions

Brian Ackley (Assistant Professor)
Ph.D. Northwestern University Institute for Neuroscience

Project: Genetic analysis of synapse development

Synapses are the gateways of communication in the nervous system. How synapse form and develop and whether they are maintained or lost, profoundly affect our cognitive functions. What we remember, how we behave and what we feel all come from the function of our synapses. To understand how synapses form and undergo functional modifications we study synapses in Caenorhabditis elegans. These animals are amenable to genetic analysis of synaptogenesis, and because they are transparent, we can observe synapses in living organisms. Our work has profound implications for understanding diseases of the synapse including epilepsy and muscular dystrophy. We hope that by understanding the molecular events that can go awry in these conditions we can help to identify therapies that can intervene in functioning nervous systems.

Matthew Buechner (Associate Professor)
Ph.D., University of Wisconsin – Madison; Postdoc, The Johns Hopkins University

Project:  Genetics of Tube Formation and MaintenanceBuechner REU Graphic

The ability of narrow biological tubes to regulate their diameter is essential for proper function of many tissues, including blood vessels and glial cells.  In the roundworm C. elegans, two long tubular canals maintain water content of the animal.  We study how the movement of small membrane-bound vesicles interacts with cytoskeletal proteins to maintain the narrow diameter of these tubes as the animal bends and grows.  The genes involved encode proteins well-conserved in animals from protozoa to humans, including intermediate filaments and membrane-trafficking GTPases.  Our lab is now measuring and investigating the movement of vesicles in wild-type and mutant worms.  This summer, we will also be carrying out a project to identify other proteins that likely interact with our genes through the use of RNAi screening.  The REU student will play an essential role in these projects, and work together with all the other lab members while learning the use of fluorescent and confocal microscopy, as well as molecular biological and genetic techniques.

Roberto N. De Guzman (Associate Professor)
Ph.D., University of Maryland Baltimore County; Postdoc, Scripps Research Institute, La Jolla, CA

Project: NMR studies of bacterial needle and tip proteins

Our major research project is focused on understanding the assembly of bacterial needles of the so-called type III secretion system. These needles are nanoscale syringe-like protein injection machinery used by bacteria to inject bacterial proteins into animals and plants. We focus on a model organism, Salmonella typhimurium, and use biophysical methods such as NMR, CD and fluorescence spectroscopy plus biological assays to dissect in atomic detail how bacterial needles are assembled. REU students will follow the pattern set by other undergraduate researchers in this lab, performing protein expression and purification, biological assays and analyzing biophysical data. Undergraduate researchers are treated as full lab members with the attendant duties and responsibilities. They are expected to read the literature, perform experiments, and present results in our weekly group meetings.

Susan Egan (Professor)
Ph.D., Cornell University; Postdoc, Johns Hopkins University

Project: Allosteric Regulation of AraC Family Transcriptional Activators.

The majority of sequenced bacterial genomes encode one or more (up to ~70) proteins belonging to the AraC family of transcriptional activators. These proteins are required to activate expression of genes involved in carbon metabolism, stress responses and virulence – but only when the cell is in the appropriate environment. The activity of many AraC family activators can be switched between on and off states by small molecule effectors that bind to one protein domain and allosterically regulate the activity of the otherdomain. The goal of one REU project will be to identify residues involved in the allosteric signaling in AraC family proteins. This will involve genetic and biochemical approaches, such as the construction of mutant proteins, protein purification and assay of protein-DNA interactions. The student will have the opportunity to interact with the P.I., postdocs, graduate students and undergraduate students in the laboratory, and will participate in weekly lab meetings.

T. Chris Gamblin (Associate Professor)
Ph.D., Vanderbilt University; Postdoc, Northwestern University

Project: Modeling conformational changes in unfolded proteins.

Tau protein functions critically in neuronal pathfinding through its role in stabilizing microtubules. Tau belongs to an important family of natively unfolded proteins that gain biological activity following a poorly understood disorder-order transition. Our lab is interested in identifying domains within Tau that initiate this transition. One REU project would involve the construction of a Tau protein variant and determining its ability to initiate folding using light scattering and other biophysical techniques that can detect regions of order within an otherwise unfolded protein. The student will learn several molecular biology and protein biochemistry techniques and a number of important concepts in the field of protein folding and function. They will learn to keep a daily record of their research and make weekly presentations of their progress to the laboratory.

Lynn E. Hancock (Associate Professor)
Ph.D., University of Oklahoma Health Sciences Center; Postdoc, The Scripps Research Institute

Project: Biofilm development and lysozyme resistance in Enterococcus faecalis

Enterococcus faecalis has emerged in recent decades as a successful pathogen in hospital-associated infections, due in part to its ability to colonize biotic and abiotic surfaces as microbial biofilms.  It also is remarkably resistant to the important innate immune effector, lysozyme, which is found at many tissue sites, and is a component of killing arsenal that phagocytic cells use to kill bacteria.  A student interested in working in the lab would have the option of pursuing research in biofilm development by creating targeted gene deletions in candidate gene targets and analyzing those mutants for defects or alterations in biofilm development.  The other project entails understanding how the bacterium senses lysozyme stress to alter gene expression resulting in phenotype changes that allow the bacteria to resist lysozyme.  We know some major components of the sensing pathway, and the potential REU student would assist in the identification of other gene products (proteins) that assist in this process through development of genetic screens, and targeted gene deletions to examine the effect of these mutations on lysozyme resistance.  Students working in the lab develop skills in molecular biology applications to investigate these problems using a variety of techniques from PCR and molecular cloning to qRT-PCR and western immunoblot analysis. 

Wonpil Im (Associate Professor)
Ph.D., Weill Cornell Medical School; Postdoc, The Scripps Research Institute

Project: Modeling the dynamics of transmembrane protein domains.

Most cellular processes, including growth, division, migration and death, respond to extracellular signals that are transmitted to the cell via transmembrane receptor proteins. While it has long been appreciated that the binding of a ligand to a receptor's extracellular domain triggers conformational changes in the receptor's intracellular domain that allow it to interact with downstream effectors, little is known about the role of the transmembrane domain in linking these events to each other. My lab uses computational biophysics, including dynamic simulations, to address this problem. An REU student in my lab will build their own simulation systems using the Membrane Builder module at the CHARMM-GUI website (www.charmm-gui.org), which my lab has helped to create. The REU student will learn UNIX (OS), Emacs (text editing), PyMol (visualization), CHARMM (simulation), Python (programming) systems, and gain a general background in the use of computer simulations to tackle important biological problems. The student will be expected to keep a detailed notebook of his or her activities and attend our weekly lab meetings.

John Karanicolas (Assistant Professor)
Ph.D., The Scripps Research Institute; Postdoc, University of Washington

Project: Building allosteric control into enzymes.

In recent years chemical biology has been used to engineer small-molecule dependent function into a variety of biomolecules. Members of our lab have developed a new strategy for coupling protein function to the presence of an activating ligand. A student engaged in an REU project will generate a gene corresponding to one such redesigned enzyme, overexpress it in E. coli, purify it, and set up a functional assay. The student will then test whether enzyme activity is dependent on the presence of the intended (designed) activator. Through the course of this research, the student will learn aspects of protein purification, enzymology, and protein engineering. Further, the student will be part of a dynamic research group that will provide assistance and collegiality over the course of the project, and will present results at weekly lab meetings.

Audrey Lamb (Associate Professor)
Ph.D., Vanderbilt University; Postdoc, Northwestern University

Project: Mechanistic enzymology and structural biology of siderophore production.

Bacteria require iron for survival and have developed elaborate iron-scavenging mechanisms. Our goal is to understand the enzymes that produce small molecules called siderophores – one type of iron-scavenging mechanism of these bacteria. A student completing an REU project may clone the gene of an enzyme in the siderophore biosynthetic pathway for overexpression in E. coli, purify the enzyme, and work to develop a crystallization protocol for the enzyme. If time permits, the student may establish an assay to detect enzymatic activity and conduct steady-state analyses of the enzyme. The student will learn protein purification, enzyme analysis and structure, and be part of a dynamic group of research associates, graduate students and undergraduates. As such, the student will share in the responsibility of general lab duties and present progress at weekly group meetings.

Stuart Macdonald (Associate Professor)
Ph.D., University of Oxford; Postdoc, University of California, Irvine.

Project: Genetics of complex traits.

Complex traits such as susceptibility to diabetes, mental illness and other diseases are influenced by a number of genetic loci and environmental factors. Our lab has developed a unique resource for high-resolution genetic analysis of complex trait variation in Drosophila and have used it to identify a large set of QTL (quantitative trait loci) underlying variation in traits of biomedical and evolutionary importance. In one REU project, a student will employ existing sets of mutant strains to refine these QTL intervals, and find the causative genes controlling trait variation. In a 10-week period a motivated student can drive this experiment to completion, and help answer a fundamental question in biology: How is phenotypic variation controlled? The work will reinforce basic genetic concepts, since the experimental design is an extension of techniques most students will be familiar with from introductory genetics classes. In addition, since the data collected must be interpreted via statistical analyses, the student will get hands-on training in widely-used biological data analysis techniques. The student will be included in all lab activities, including weekly lab meetings, and be a valuable and respected member of the group.

Kristi Neufeld (Associate Professor)
Ph.D., University of Utah; Postdoc, University of Utah

Project: Genetic analysis of nuclear APC functions.

Tissue homeostasis is maintained by a series of signaling pathways that control cell proliferation, differentiation and death. Loss of tissue homeostasis is an early step in the development of most cancers. Although tumor suppressor protein APC plays a particularly critical role in maintaining cellular homeostasis of intestinal epithelium, specific functions of nuclear APC are only beginning to be understood. To analyze nuclear functions of APC in intestinal tissue, our lab has generated a mouse model in which the Apc nuclear localization signals (NLS) have been mutated leading to reduced levels of nuclear Apc. The REU student will analyze intestinal differentiation and apoptosis in these mice using histological and molecular biology techniques. The student will learn basic mouse genotyping, RNA and genomic DNA isolation, RT-PCR, tissue preservation, sectioning and protein staining techniques, as well as cell lysis and quantitative protein analysis. The student will also participate in weekly lab meetings and journal clubs to allow full integration into the research team.

Lisa Timmons (Associate Professor)
Ph.D., Johns Hopkins University; Postdoc, Carnegie Institution of Washington

Role of ABC transporters in RNA interference.

ABC transporters are conserved trans-membrane proteins that function as ATP-dependent pumps in the trafficking of small molecules across membrane bilayers. Some ABC transporters can export drugs or heavy metals, which allows cells to survive in harsh chemical environments. An unanticipated consequence of this role is drug resistance in cancer or virus infected cells, which is often due to up-regulation of some ABC transporter genes. ABC transporters also maintain proper homeostasis of essential substances, providing intracellular trafficking roles for biosynthesis, and routes for export when in excess in order to prevent toxicity. (Heme is a good example of such a substance.) RNA interference mechanisms are activated by non-coding RNAs that are transcribed by, or artificially delivered into, eukaryotic cells. RNAi mechanisms rely on the sequence information encoded in the ncRNAs to direct them to a specific mRNA and/or chromatin sequence. RNAi mechanisms commonly interfere with complete gene function by preventing translation of mRNAs, degrading mRNAs, or inhibiting transcription of chromatin. RNAi mechanisms are found in the nucleus and cytoplasm: RNAi mechanisms in the cytoplasm can protect cells against virus infection; RNAi mechanisms in the nucleus maintain heterochromatin states, which is another anti-foreign genome responses that keeps transposons from mobilizing and also allows for centromeres to function properly. We have found that some ABC transporter genes are required for efficient functioning of those RNAi mechanisms that act in the nucleus. Understanding how ABC transporter and RNAi mechanisms are interconnected will impact our understanding of the etiology of aggressive, drug-resistant cancers as well as the potential for small molecules, derived from the environment or from cellular biosynthesis, to contribute to the differentiation of stem cells.

Robert Ward (Associate Professor)
Ph.D., Duke University; Postdoc, University of Utah

Project: Genetics of tissue-specific growth.

Animal development requires the coordinated growth of organs and tissues. To elucidate the underlying mechanisms of coordinated tissue growth, my lab studies two genes that when mutated alter the growth rate of the Drosophila tracheal system relative to the growth rate of other organs. In one REU project, the student will determine whether these genes regulate tracheal growth throughout the development of this organ, or just during one or two critical phases. To this end, the student will measure tracheal growth in wild type and mutant larvae at defined intervals throughout larval development. In a second possible REU project, the student will use genetic mosaic analyses to determine whether these genes effect tracheal growth in a cell autonomous or non-autonomous fashion. Both projects are straightforward and will provide the REU student experience in fly husbandry and genetics, cell biology, microscopy, and statistical analysis. The REU student will also participate in our weekly lab meetings and have the opportunity to interact with senior lab personnel on a daily basis.

Liang Xu (Associate Professor)
Ph.D., Fourth Military Medical University; Postdoc, Stanford University, Georgetown University

Project: Molecular cancer therapy targeting cancer stem cells.

Cancer stem cells (CSCs) are a subpopulation of cancer cells capable of self-renewal and differentiation, and have been identified in a variety of tumors. CSCs are resistant to current cancer therapy and are responsible for tumor recurrence and metastasis. To be maximally effective, cancer therapy must be directed against both the resting CSCs and the proliferating cancer cells. Our goal is to employ a contemporary, structure-based, multidisciplinary and integrated drug discovery approach to discover and design novel drugs that inhibit the CSCs via blocking the cell signaling pathways involved in CSC function. We have recently identified several promising lead compounds to be further developed as novel chemical probes and eventually an entire new class of molecularly targeted anti-cancer drugs. With supervision of the PI and direction from post-docs in the lab, the REU student will examine the activity of the lead compounds, validate the target, and delineate the mechanism of action in CSCs. The student will learn basic molecular biology and cell biology assays, as well as new techniques for CSC analysis. The student will also participate in weekly lab meetings and journal clubs to allow full integration into the research team.

 

How to Apply

Your complete application includes:

  1. The online application form (click here to apply).
    Application deadline is March 15, 2014.
  2. A copy of your undergraduate transcript mailed to the Program Administrator, John Connolly, at the address below:
    John Connolly
    University of Kansas
    Department of Molecular Biosciences
    1200 Sunnyside Ave
    Lawrence, KS 66047
  3. Two letters of recommendation on official letterhead. Recommenders should address the applicant's intellectual abilities, level of motivation, ability to work with others, and career interests (e.g., research, teaching, medical school, etc.). Please ask your recommenders to email their letters to jconnolly@ku.edu. If this is not possible, they may be sent via regular mail to John Connolly.
Contact Information

Program Director (PI)
Robert Ward
University of Kansas
Department of Molecular Biosciences
1200 Sunnyside Ave
Lawrence, KS 66045
robward@ku.edu
785-864-5235

Co-Director
Kristi Neufeld
University of Kansas
Department of Molecular Biosciences
1200 Sunnyside Ave
Lawrence, KS 66045
klneuf@ku.edu
785-864-5079

Program Administrator
John Connolly
University of Kansas
Department of Molecular Biosciences
1200 Sunnyside Ave
Lawrence, KS 66047
jconnolly@ku.edu
785-864-4311

 


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Amber Smith (graduate student, Xu lab) presented a poster entitled “Characterization of Small Molecules Bound to Oncogenic Protein, Musashi-1 using Nuclear Magnetic Resonance” at Seventh Great Plains Regional Annual Symposium on Protein and Biomolecular NMR at the University of Kansas, on October 17. http://psf.cobre.ku.edu/graspnmr2014
2014 GRASP NMR | Center of Biomedical Research Excellence
in Protein Structure & Function
«» 2014 Great Plains Regional Annual Symposium on Protein and Biomolecular NMR We invite you to join us on Friday, October 17 and Saturday, October 18, 2014 to present your research at the Seventh Great Plains Regional Annual Symposium on Protein and Biomolecular NMR. The symposium will be held in L…