The faculty members listed below will host REU students in their laboratories in Summer 2015.
Ph.D., University of Wisconsin – Madison; Postdoc, The Johns Hopkins University
Project: Molecular Genetics of the formation and regulation of epithelial tubes
Why are capillaries small while the aorta is large? My laboratory investigates a series of mutations that affect the diameter of a narrow tube, the excretory canal of the roundworm C. elegans. “exc” mutations cause the canal to swell into fluid-filled cysts. The genes involved all encode proteins well conserved in humans, including proteins implicated in conditions from muscular dystrophy to inflammatory bowel disease. We are now looking for the ways in which these proteins interact with each other, through genetic, cell biological, and biochemical assays. One summer project will be to screen for mutants that alter or restore canal shape inexc mutants. Such a mutation would identify interactors in the signaling pathway involved in maintaining the narrow diameter of the excretory canal. A second project will allow the student to investigate the motion of fluorescently labelled subcellular compartments in the tubule; the movement of such vesicles appears to be critical in constantly remodeling the tubule to maintain its shape as the animal grows and moves. These projects will expose the undergraduate to multiple techniques in molecular biology, genetics, and cell biology, and have been used successfully by former REU students.
Ph.D., University of Minnesota; Postdoc, University of Iowa
Many bacteria communicate with dedicated chemical or peptide signaling molecules. Such communication systems are widespread and found in bacteria, animals, plants and even insects. Our lab is particularly interested in a type of communication in bacteria called quorum sensing. Quorum sensing systems are cell density dependent and thought to be important for cooperative or group activities. Many quorum sensing systems are used by bacteria to control production of antibiotics and factors that may be important for antibiotic resistance, which may be important for bacteria during competition for limited space or nutrients. The REU student will participate in projects to understand the importance of quorum sensing during competition and the mechanism of the factors controlled. As part of these projects they will learn many standard laboratory techniques and have the opportunity to interact with the P.I., postdocs, graduate students and other undergraduates in the laboratory and participate in weekly lab meetings.
Roberto N. De Guzman
Ph.D., University of Maryland Baltimore County; Postdoc, Scripps Research Institute, La Jolla, CA
Project: NMR studies of bacterial needle and tip proteins
The major goal of the De Guzman lab is to understand in atomic detail the molecular interactions involved in the assembly of bacterial nanoinjectors. Many bacterial assemble a protein delivery nanomachinery known as the type III secretion system (T3SS) to inject bacterial proteins directly into host cells to modulate host cell biology. Bacterial nanoinjectors are assembled from over 20 different proteins and part of the nanoinjector consists of an external needle and a tip complex. Our goal is to determine the protein-protein interactions involved in the assembly of the needle and the tip complex. The methods used are nuclear magnetic resonance (NMR) spectroscopy, crystallography and computational approaches, followed by mutagenesis and cell-based assays. Salmonella typhimurium was chosen as a model organism to study the T3SS assembly because of established genetics for this organism, which is needed to correlate the biophysical results with biology. tings.
Ph.D., Cornell University; Postdoc, The 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 in most cases, only when the cell is in the appropriate environment. The environmental signals that switch AraC family activators between off and on states are most often small molecule effectors that bind to one protein domain and allosterically regulate the activity of the other domain. The goal of one REU project will be to identify mechanisms 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., graduate students and undergraduate students in the laboratory, and will participate in weekly lab meetings.
Lynn E. Hancock
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.
P. Scott Hefty
Ph.D., University of Oklahoma Health Sciences Center; Postdoc, University of California, Berkeley
Project: Cellular and developmental processes of Chlamydia.
Chlamydia are obligate intracellular bacteria that are maintained through a developmental cycle that is unique among bacteria. One form (elementary body) is needed to obtain entry into a eukaryotic cell and the other (reticulate body) is needed for replication and formation of the infectious form. Throughout the developmental cycle, these bacteria manipulate host eukaryotic cells. Our group seeks to understand how these developmental processes occur and are regulated. A student engaged in an REU project will be challenged with progressing a specific scientific question such as what does the bacteria sense to begin converting into infectious forms, what is the role of specific transcription factors in controlling the developmental cycle, how do these bacteria replicate with a paucity of known cell division components? Over a ten-week period, student will learn some aspects of biochemistry, microbiology, and cell biology during their experience. They will also have the opportunity to learn about other projects ongoing in the laboratory and interact with current undergraduates, graduate students and post-doctoral scientists.
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.
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.
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 iron-scavenging mechanism of these bacteria. A student completing an NSF-REU project will chose a siderophore biosynthetic enzyme to clone for overexpression in E. coli, develop an overproduction and purification strategy for the enzyme, and design a crystallization protocol for the enzyme. Upon crystallization, the student will assist in remote diffraction data collection at the Stanford Synchrotron Radiation Light Source and work toward structure solution. The student will 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 determination, and be part of a dynamic group of research associates, graduate students and undergraduates. As such, the student will be expected to present progress at weekly group meetings and to share in the responsibility of general lab duties.
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 Adenomatous polyposis coli 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 mouse phenotypes relating to intestinal cell differentiation, apoptosis, stem cell maintenance, and asymmetric cell division 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.
Ph.D., University of Pennsylvania; Postdoc, Stockholm University.
Project: Folding of outer membrane proteins.
Our lab studies how outer membrane proteins fold for the purpose of developing cancer therapeutics, novel vaccines, and methods of environmental remediation. Outer membrane proteins are the proteins found in the outer membrane of bacteria, mitochondria and chloroplasts. There are thousands of outer membrane proteins reported in genomic databases with 2–3% of the genes in gram-negative bacteria encoding these proteins. These proteins have a wide variety of biological functions including active and passive transport, cell adhesion, catalysis and structural anchoring. The question of how these membrane proteins insert into the membrane and how they fold into secondary, tertiary, and quaternary structure is relevant to basic science and pharmaceutical development. Our lab probes this question using both computational and experimental approaches. The student will be able to choose a project that is either computational or experimental and will present his or her results at weekly lab meetings.
Ph.D., University of Michigan; Postdoc, Rice University and M.D. Anderson.
Project: Analysis of Scale Transitions in Genetic and Metabolic Networks.
Understanding the principles of biological organization is an important problem in its infancy whole solution is a key factor needed to handle emerging global health crises including cancer and antibiotic-resistant infectious disease. This field represents a great opportunity to fundamentally advance our scientific knowledge by thinking about biology in a new way. A particularly important property underlying many living systems is transition points where molecular events drive the way entire populations of cells respond to stress, grow, and evolve. The REU student will join an integrated team of computational biologists and experimental microbiologists, with opportunities to learn mathematical tools and quantitative single-cell analysis that will be necessary for the next generation of biology. Examples of ongoing projects include understanding the paradox noisy information transfer in bacterial cells by characterizing emergent effects on cellular and population fitness using synthetic biology, and understanding the effects of noise in enzyme gene expression driving heterogeneous population growth. The REU student will be expected to contribute to one of three areas: (i) learning about and developing mathematical models of biological networks, (ii) driving an important experimental component of a project in collaboration with other experimentalists, or (iii) using computational methods to do quantitative data analysis of single-cell measurements taken in time-lapse microscopy and flow cytometry.
Ph.D., The Johns Hopkins University; Postdoc, The 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.
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.
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.