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Welcome!» Summer Research Opportunities for Undergraduates» Research Labs & Application Process


Summer Research Labs and Application Process

See also: REU participants in summer 2013 | REU participants in summer of 2012 | REU participants in summer 2011 | REU participants in summer of 2010

Award No. DBI-1156744  

“Sensing and Signaling” Reseach Experience for Undergrads
May 25 through August 1, 2014

The BCMB Department at UTK will once again offer a special summer program for undergraduates interested in research. The aim of this Research Experience for Undergraduates (REU) is to provide hands-on research opportunities for undergraduate students majoring in the sciences, with an introduction to cutting-edge research in the broad area of “Sensing and Signaling”. The team of REU investigators represents a multidisciplinary ensemble of Cell Biologists, Geneticists, Biochemists, and Biophysicists who are taking modern approaches to the analysis of how signals are perceived and transduced in myriad biological systems.

We especially encourage rising sophmore and junior undergraduate science majors to apply. Underrepresented minorities, women, and first-generation college students are strongly encouraged to apply. Applicants must be a US citizen or a permanent resident.

To Apply: REU Fellowships will be awarded to qualified students on a competitive basis. Each Fellowship will include a $5,000 stipend as well as an allowance for cost of living, travel (up to $500), and research supplies. To be considered, applicants should complete the APPLICATION by February 28 and email the completed form (as a PDF) to: bcmbreu@utk.edu. In addition, each applicant should arrange to have two letters of recommendation and a college transcript emailed to the same address.

Available topics include:

 

 

 

 

 

 

 

 

 

 


Decriptions of BCMB REU Projects in “Sensing and Signaling”

 

Sensing and Processing in the Six-protein "Brain" of Bacteria
Gladys Alexandre

Motile bacteria are capable of navigating in gradients of various physicochemical cues by constantly monitoring their surroundings using dedicated chemoreceptors. The ability to sense the environment using these chemoreceptors is essential as it allows these motile bacteria to modulate their swimming behavior to reach niches that are optimal for growth and survival. Our laboratory has recently uncovered a complex sensing and signaling between chemoreceptors and chemotaxis-like pathways, that ultimately modulate the swimming motility response (chemotaxis) as well as other cellular behaviors. We are currently analyzing the dynamic subcellular localization of chemoreceptors and putative chemotaxis-like protein targets using a combination of fluorescent tagging and imaging of chemoreceptors and chemotaxis-like proteins, biochemistry and molecular biology  techniques. Several projects focusing on a subset of these proteins  are available and suitable for undergraduate summer research experience.
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Dividing Cells in Time and Space
Josh Bembenek

Multicellular organisms rely on the most basic process of cell division to develop from a single cell, the fertilized egg, into an adult animal with an extraordinary diversity of cell type, shape, fate and behavior that collectively function for survival and reproduction. We are studying the basic mechanics of how cells divide with a special emphasis of how this process occurs within a developing embryo to produce a viable organism. This unique view has led us to uncover new mechanisms that regulate the myriad of events during cell division, and also revealed surprising insights into how cell division mechanisms can regulate developmental events. At the heart of cell division is the accurate duplication and segregation of the chromosomes, which contain all the genes within a cell and must be carefully maintained. One key effort in our lab is to better understand how various cytoplasmic organelles such as membrane compartments are divided together with the chromosomes. We have found surprising cross-talk between core chromosome segregation regulatory genes and membrane trafficking pathways, which is crucial for the very first developmental events in a fertilized oocyte. These studies will lead to a deeper understanding of how cells organize a variety of events during the division process, and how these basic cellular mechanisms can impact the development of an organism.
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Ethylene Signaling: What a gas!
Brad Binder

This lab studies ethylene signal transduction with a focus on understanding ethylene receptor function. Ethylene is a simple, unsaturated hydrocarbon that is a plant hormone that affects diverse processes throughout the lifetime of a plant including seed germination, growth, senescence, fruit ripening, abscission, gravitropism, and responses to various stresses. While this work is aimed primarily at understanding ethylene signaling at the molecular level, the lab correlates observations at the biochemical level with time-lapse imaging of growing seedlings to provide links between events at the molecular level with those at the organ level. This use of multiple scales of investigation is critical to provide a broader framework to understand how organisms grow and develop. Recently, research in the lab has expanded to include cyanobacteria that contain putative ethylene receptors. The function of these proteins in cyanobacteria remains unexplored but preliminary results suggest that ethylene affects phototaxis through these proteins. More information can be found at the lab website: http://www.bio.utk.edu/binderlab/
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How are Membrane-Cytoskeletal Interactions Established?
Maitreyi Das

Cell growth and division involve important cellular events such as endocytosis (a process by which the cell engulfs molecules) and cytokinesis (a process by which the cell divides into two). Defects in these cellular events have been shown to be associated with cancer development and progression. Central to cytokinesis and endocytosis is actin cytoskeleton associated cell membrane remodeling. Membrane remodeling is a complex process involving several players the details of which are poorly defined. The lab is focused on understanding how membrane-actin cytoskeletal events are established. Recent results from this lab have shown that the major cell growth regulator Cdc42 promotes membrane-actin cytoskeletal events. Several projects are available for students to study how Cdc42 regulates membrane-cytoskeletal events. Students will be trained in fission yeast genetics and cell biology approaches, and particularly in fluorescent confocal microscopy.
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Water and a Primitive Enzyme
Liz Howell

Research in the Howell lab has focused on characterization of R67 dihydrofolate reductase (DHFR) as a good model for a primitive enzyme. One surprising result associated with this enzyme is weaker binding of substrate (dihydrofolate, DHF) in the presence of small molecules called osmolytes. This result is unusual as binding of most ligands is tighter in solutions with low water activity. In other words, binding is usually accompanied by release of water from the interaction surfaces and when the water concentration is low, binding is enabled. Our model to understand the unusual result for DHF is that it is a sticky molecule and that it interacts with the osmolytes. These interactions must be stronger than those with water, so the osmolytes act as inhibitors to the binding process with the DHFR enzyme. To test this hypothesis, we are examining the binding of various redox states of folate to other folate utilizing enzymes, which should also show weaker binding. We are addressing this hypothesis using purified proteins as well as with genetic selections.

While water is ubiquitous & occurs at high concentration, it is often ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular environment. Thus our hypothesis of osmolyte interaction with folate/DHF is novel. High osmolyte concentrations can exist in the mammalian kidney, some plants, cartilaginous fish & coelacanths, bacteria, etc), and our model predicts varying osmolyte concentration will impact function. We propose that weak interactions are unavoidable in the cell due to intracellular crowding. In other words, our studies address the basic question of whether the in vitro behavior of folate and its derivatives accurately reflects their behavior in vivo.
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Dynamic Dance of the Enzymes
Nitin Jain

Cytochrome P450s are a class of heme-containing enzymes that catalyze chemical reactions in various lifeforms, such as biosynthesis of steroid hormones and hydroxylated fatty acids, metabolism of an extensive variety of xenobiotic compounds, including a high percentage of drugs produced by the pharmaceutical industry. They are also of high relevance to the chemical industry due to their potential in catalyzing difficult monooxygenation reactions that may be necessary in chemical synthesis, refinement of petroleum products and degradation of pollutants. The catalytic cycle of these enzymes entail many steps during which they bind specific substrate molecules, add an oxygen atom to them in a series of oxidation and reduction reactions, and form product with high regio- and stereo-selectivity. Structural studies on several P450s have thus far revealed that they have highly conserved structural features. Given this fact, it is likely that diversity of substrate binding and catalysis observed in various P450s is regulated by intrinsic characteristics of the protein that are not observable in static representations of their structures. One such factor is the dynamic flexibility inherent in the active site and the substrate binding regions for these P450s that allows them to sense multitude of substrates and monooxyenate them at a variety of positions. It is being increasingly observed that there is a varying degree of plasticity within these regions in all P450s and such dynamic motions have become a topic of intense research inquiry, both in drug metabolizing enzymes and bacterial enzymes of importance in chemical synthesis. Of the techniques currently available to observe dynamic effects in proteins, spectroscopic techniques in concert with molecular dynamic simulations are most useful in investigating dynamics on timescales spanning from picoseconds to seconds. Our lab has been instrumental in application of these techniques to characterize dynamic motions in individual amino acids and to assess the degree to which they are correlated to the functional dynamics of the molecule as a whole on all relevant timescales. Several projects are available within the lab in this regard to study the effect of dynamic movements on substrate binding and catalysis by various P450s. Characterizing these in-step movements or the dynamic dance of these enzymes can potentially be exploited in the creation of improved, more efficient pharmaceutical and chemical products.
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"Neuropeptides in Stress and Alcohol-related Behavior"
Jae Park

Neuropeptides, as produced by neurosecretory cells and inter-neurons in the central nervous system, are major physiological regulators in insects and mammals.  One of the research goals in this lab is to elucidate biological functions of the neuropeptides using Drosophila as a premier genetic model system.  Using available mutants lacking neuropeptides or their receptors, students are involved in the characterization of phenotypes associated with the responses to various stresses.  Further molecular analysis will highlight the mechanisms underlying neuropeptide-regulated stress responses.  Another project studies the effects of ethanol on the neuronal degeneration.  Ethanol consumption is a major factor that influences human behaviors and ethanol-triggered behavioral and neurological changes are remarkably similar in invertebrates.  To understand the impact of alcohol on the neuronal degeneration, studies will investigate how ethanol influences development of the peptidergic neurons in fruit flies.
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"Waging War on Antibiotic Resistance"
Engin Serpersu

The Serpersu lab uses biophysical and biochemical techniques to study interactions of aminoglycoside antibiotics with several enzymes that modify these antibiotics and cause resistance to their action against bacteria. Projects involve studies of aminoglycoside-enzyme interactions by kinetic and spectroscopic methods including fluorescence, EPR and NMR spectroscopy to determine effects of aminoglycoside binding on structure and dynamics of these enzymes. In addition, these studies require the use of chromatographic methods to purify either enzymes or, in some cases, aminoglycosides and their analogs. Other approaches include culturing cells in isotopically enriched media, computational work to determine relaxation rates of nuclei, and analysis and interpretation of spectral data. Projects involve a wide assortment of techniques starting from molecular biology to highly sophisticated spectroscopic techniques within the framework of a biological problem.
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Cell to Cell Communications During Plant Development
Elena Shpak

This lab is interested in the mechanisms regulating coordinated growth and differentiation in plants. Currently the research is focused on a particular signal transduction pathway that determines size and shape of plant organs and regulates cell differentiation during development. This pathway facilitates communications between cells; one type of cell secretes small proteins that are recognized by plasma membrane receptors located on other cells.  The receptors belong to the ERECTA family of Ser/Thr kinases and they activate a downstream signaling cascade by still an unknown mechanism. In the model organism Arabidopsis, loss of these receptors leads to severe dwarfism, infertility, and changes in epidermis development. The goal of the summer project is to identify and characterize novel components of this signaling pathway using forward genetics. The project will involve phenotypic analysis of plants by microscopy and use of molecular biology techniques.
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Biosensors for Cellular Signaling Events Based on Real-Time in vivo Luminescence Imaging
Albrecht von Arnim

Climatologists rely on satellites, neuroscientists have electrodes and magnetic resonance imaging, behavioral biologists peek through binoculars, but how about cell biologists? How does one observe the inner workings of living cells in real time? Biosensors are tools designed to visualize one specific cog of the cellular machinery in real time. One of these, the green fluorescent protein, has taken the community by storm; indeed, modern cell biology would be unthinkable without it. The von Arnim lab is developing a class of biosensors based on a fluorescent protein that is paired with a luciferase, a protein that converts chemical energy into light. Biologists love a pretty picture, yet luciferases are notoriously difficult to image. Until recently, simultaneous microscopy of two different luciferases was not for the faint-of-heart. An NSF funded project to develop a bioluminescence ratio-imaging microscope is beginning to change that. Undergraduate researchers have already been involved in optimization of this advanced imaging technique and future opportunities exist for undergraduate researchers to participate in this project.
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