NSF Undergrad Summer Program
NSF FUNDED SUMMER RESEARCH PROGRAM IN MOLECULAR BIOSCIENCES:
FROM MOLECULES TO CELLS TO ORGANISMS
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 20-July 26, 2013).
- 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.
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.
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.
Mizuki Azuma (Assistant Professor)
Ph.D. Osaka University; Postdoc, National Institutes of Health
Project: The role of the EWS gene in the development of the zebrafish cranium.
Ewing sarcoma, the most common form of childhood bone cancer, is thought to be initiated by a chromosomal translocation that fuses the 5' end of the Ewing Sarcoma gene (EWS) to the 3' end of the FLI1 gene or to other genes that contain an ETS-family DNA binding motif. We are using a Zebrafish model to study the role of the endogenous EWS gene, which we and others have shown is required for faithful development of the embryonic cranium. One project for an REU student is to characterize more precisely the skeletal defects of EWS deficient zebrafish. To this end the student will use TUNEL and BrdU assays in combination with in situ hybridization to examine programmed cell death and cell division in the developing cranium. The project will provide the student an opportunity to work with the Zebrafish model and to learn important concepts underlying organogenesis and tumorigenesis. The student will also have frequent informal opportunities to interact with senior lab personnel and more formal opportunities at our weekly journal and data meetings.
Yoshiaki Azuma (Associate Professor)
Ph.D., Kyushu University; Postdoc, National Institute of Health
Project: Biochemical and cell biological analyses of cell cycle progression.
Regulated progression through the cell cycle is fundamental to development, tissue homeostasis and disease. Our lab is interested in the role of post-translational modification, especially SUMOylation, in the regulation of cell cycle progression. We have developed methods that allow us to knockdown the SUMOylation of specific subsets of proteins in synchronized cultured cells and in Xenopus Egg Extracts (XEEs). In one REU project, the student will use immunoblotting and immunofluorescence staining techniques to identify and characterize the expression patterns of novel proteins that are targeted for SUMOylation in a cell-cycle dependent fashion. During the course of this project, the student will learn basic concepts in cell cycle control and a variety of molecular biology and cell culture techniques. The student will participate in all lab activities, including weekly journal club and lab meetings and will have multiple informal opportunities to discuss his or her work with other members of the lab.
Robert Cohen (Professor, PI)
Ph.D. University of Southern California; Postdoc, Harvard University
Project: Molecular genetics of stem cell cross-talk.
Many adult tissues and organs are maintained by two or more stem cell populations, but little is known about the mechanisms that coordinate the division, growth, and behaviors of those stem cell populations. To address this problem, we use the Drosophila ovary, which contains germline stem cells and two populations of somatic stem cells. One REU project involves the analysis of somatic stem cell division rates in response to genetic and dietary manipulations that are known to affect germline stem cell division rates. This project is straightforward in execution, yet will expose the student to important concepts in stem cell biology and give him or her experience in working with genetic model systems, fluorescence microscopy, and statistical analysis of data. The student will also have the opportunity to interact with senior lab personnel on a regular basis and will attend our weekly lab meeting and journal club.
David Davido (Associate Professor)
Ph.D., Washington University, Postdoc, University of Pennsylvania, and Harvard Medical School
Project: Function and organization of nuclear domain 10s (ND10s).
ND10s are subnuclear organelles that play important roles in differentiation, proliferation, and antiviral defenses. Understanding how ND10s are formed and altered during the course of disease will provide insights into how they regulate various cellular processes. Preliminary studies from our laboratory and others suggest that selected ND10 constituents organize the interactions and localization of other ND10-associated proteins. Consequently, one REU project for a student in my laboratory will involve using RNA interference (RNAi) technology to deplete specific ND10-associated proteins and knock-in mutant forms of one or more of these proteins to ask: What domains or motifs of a given ND10-associated protein are required for the morphology, organization, and biological activities of ND10s? The student working on this project will become familiar with cellular and molecular biology techniques and develop his/her skills as a scientist by analyzing his or her data and presenting these results in regularly scheduled laboratory meetings.
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.
P. Scott Hefty (Associate Professor)
Ph.D., University of Oklahoma Health Sciences Center; Postdoc, University of California, Berkeley
Project: Regulation of the chlamydial developmental cycle.
Chlamydia are phylogenetically distinct bacteria that are maintained and propagated through a characteristic bi-phasic developmental cycle. Our goal is to better understand how this developmental cycle is regulated at the transcriptional level and what critical mechanisms are employed. A student participating in an REU project may focus on the analysis of a transcription factor or other regulatory component hypothesized to play a role in the developmental cycle of Chlamydia. The student will learn a broad range of theoretical and technical aspects within biochemistry, cell biology, and microbiology. Students will attend and participate in weekly laboratory meetings, and other group activities.
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.
Erik Lundquist (Professor)
Ph.D. University of Minnesota; Post-doc, University of California, San Francisco
Project: Molecular genetics of neuronal cell migration.
An ongoing effort in the lab is to identify and characterize genes important for neuronal migration. An undergraduate in the lab, Megan Razak, has conducted a forward genetic screen using EMS mutagenesis and has identified ~40 new mutations that affect migration of the Q neuroblast descendants AQR and PQR in C. elegans. We are in the process of categorizing these new mutations as to their exact effects on AQR and PQR, and have successfully used next generation sequencing to re-sequence the genomes of the new mutants to identify the affected genes. A potential REU project in the lab would involve phenotypic characterization of one or more of the new mutants using fluorescence microscopy, and identifying the lesion in the gene responsible by next generation sequencing. This project would involve cutting edge use of fluorescence microscopy combined with next generation sequencing, and would provide an undergraduate participant with the most up-to-date methodologies of analysis of gene function in C. elegans. The student will also participate in weekly lab and group meetings, and will be involved in aspects of data analysis and presentation.
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.
Berl Oakley (Irving Johnson Distinguished Professor)
Ph.D., University of London; Postdoc, University of British Columbia, York University
Project: Fungal secondary metabolites (SM) as a rich source of medically and agriculturally important compounds.
Fungal genome projects have revealed that fungi have many SM gene clusters that are not expressed under normal lab conditions, and that common fungi are potential sources of useful new compounds. We are using the power of Aspergillus nidulans molecular genetics to express SM genes from Aspergillus terreus, a fungus with many SM gene clusters but a poor molecular genetic system. Building on our current work the REU student will develop a system for expression, in A. nidulans, of non-ribosomal peptide synthases, an important class of SM biosynthetic genes, from A. terreus. The student will interact with the lab chief and other lab personnel daily, will learn gene annotation, SM profile analysis, fusion PCR and transformation techniques, will participate in normal lab activities (e.g. media and solution making) and will participate in and present his or her work at weekly lab meetings.
Liang Tang (Associate Professor)
Ph.D., Institute of Biophysics, the Chinese Academy of Sciences; Postdoc, the Scripps Research Institute
Project: Genome packaging in viruses
Genome packaging is a crucial process in virus lifecycles, and is essential for assembly of infectious virus particles. In herpesviruses and many double-stranded DNA (dsDNA) bacterial viruses, genome packaging is fulfilled in a precisely coordinated molecular synergy involving a powerful molecular device that pumps viral DNA into a preformed protein shell called procapsid. The viral DNA packaging device consists of a portal protein and a two-component enzyme complex called terminase. This project is aimed at understanding the assembly, function and regulation of the viral DNA packaging molecular device at atomic or near-atomic detail. The student will have opportunities to learn about protein/virus preparation and characterization and advanced technologies such as X-ray crystallography and electron microscopy, and will be working with post-doctoral research associates and other students in a highly collaborative environment in this laboratory. Lab website: carbon.bio.ku.edu
Lisa Timmons (Associate Professor)
Ph.D., Johns Hopkins University; Postdoc, Carnegie Institution of Washington
Project: Role of cyclic nucleotides in abiotic stress responses.
Cells harbor a number of different pathways that respond to environmental stress, pathways that can also influence longevity, metabolism, and reproductive fitness. Our goal is to understand how cyclic nucleotides affect abiotic stress response pathways. We are currently using Caenorhabditis elegans due to the wealth of genetics resources available. Undergraduate researchers in my lab have already played a central role in uncovering aberrant stress responses in adenylyl cyclase and phosphodiesterase mutants. Incoming REU students will learn cell biology and genetics techniques and will assist with biochemical analyses of the enzymes. Training of undergraduates will be overseen by graduate students, technicians, and the lab PI. The students will have the opportunity to participate in weekly lab meetings that will include Skype participation from our collaborators at the Medical School of Hannover, Germany. REU students will update the project poster at the end of the program, and may present the poster in an undergraduate research symposium held here at KU at the end of summer.
Ilya Vakser (Professor)
Ph.D. Moscow State University; Postdoc, Washington University, and Rockefeller University
Project: Knowledge-based prediction of protein complexes.
Protein-protein interactions are a key element of life processes. Thus a better understanding of these interactions, coupled with our ability to model them, is essential for the fundamental knowledge of their biology. Computational modeling of protein-protein complexes (protein docking) produces multiple candidate matches of the participating proteins. The scoring/ranking of these matches is essential for choosing the correct structures. Machine-learning techniques have been shown to significantly improve the scoring. To distinguish between near-native and false-positive matches, a student will use machine-learning approach and a comprehensive set of protein recognition characteristics. A computer model will be built to evaluate residue-residue contacts from 3D structures and to score protein-protein matches. The student will learn the advanced techniques of computational structural biology, in an important project that should significant improve our ability to model protein interactions.
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.
How to Apply
Your complete application includes:
- The application deadline was March 1, 2013. The deadline has passed, and we will not be accepting any more applications.
- A copy of your undergraduate transcript mailed to the Program Administrator, John Connolly, at the address below.
- 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 email@example.com. If this is not possible, they may be sent via regular mail to John Connolly.
Program Director (PI)
University of Kansas
Department of Molecular Biosciences
1200 Sunnyside Ave
Lawrence, KS 66047
University of Kansas
Department of Molecular Biosciences
1200 Sunnyside Ave
Lawrence, KS 66047
University of Kansas
Department of Molecular Biosciences
1200 Sunnyside Ave
Lawrence, KS 66047