Summer Research Labs and Application Process
See also: REU participants in summer 2011 | REU participants in summer of 2010
Award No. DBI-1156744
“Sensing and Signaling” Reseach Experience for Undergrads
May 28 through August 3, 2012
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. Available topic areas
include:
- Sensing and Signaling in the Six-Protein "Brain" of Bacteria. Gladys Alexandre
- Ethylene Signaling: What a gas! Brad Binder
- How do Plant Cells Talk to Each Other? Tessa Burch-Smith
- Water and a Primitive Enzyme. Liz Howell
- Keeping Nano-scale Motors Under Control. Andreas Nebenführ
- "Disorder, Disorder in the Court!” Cynthia Peterson
- "Waging War on Antibiotic Resistance". Engin Serpersu
- Signaling by Receptor Kinases. Elena Shpak
- Biosensors for Cellular
Signaling Events Based on Real-Time in vivo Luminescence Imaging. Albrecht von Arnim
This opportunity is available to Sophomore and Junior undergraduate science majors, with preference for Juniors. Applicants must be a US citizen or a permanent resident. 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, and research supplies. To be considered, applicants should complete the APPLICATION and email the completed form to cbpeters@utk.edu.
Applications will be reviewed as they are received but should be completed and submitted by March 30, 2012.
In addition to the application, each applicant should arrange to have two letters of recommendation and a college transcript sent to:
Dr. Cynthia B. Peterson
Professor
Department of Biochemistry and Cellular and Molecular Biology
M407 Walters Life Sciences
The University of Tennessee
Knoxville, TN 37996
FAX: 1-865-974-6306
cbpeters@utk.edu
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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Recognition by the TOC Translocon by Phosphorylation.
Barry
Bruce
It has been reported that both the transit peptide associated with a chloroplast destined precursor and its import receptor can be phosphorylated in vivo (1). This phosphorylation can modulate the binding between the transit peptide and the receptor GTPases, Toc34 and Toc159. In the case of the transit peptide to Rubisco Small Subunit it is the S34 that has been shown to increase affinity with Toc34 upon phosphorylation. However, this is based on in vitro biochemical assays such as Surface Plasmon Resonance (SPR) and immunological pull down assays using synthetic peptides. Efforts to test the effect of this phosphoserine residue in vivo have challenged the physiological significance of this interaction by using site-specific mutagenesis (2) and in vivo GFP targeting assays. Reconciliation of these competing results may be the result of the propensity of transit peptides to be serine rich (>25%) which may enable one or more of these Ser to may undergo compensatory phosphorylation in vivo.
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 do Plant Cells Talk to Each Other?
Tessa Burch-Smith
One of the most important processes in multicellular organisms is communication between cells. In animals, this is accomplished by direct contact between adjacent cells, the movement of cells or the secretion of small molecules through the circulatory system. However, plant cells are bound by their cellulose cell walls, precluding the direct contact of cell membranes and preventing cell migration. Plant cells have therefore developed plasma membrane-lined, cytoplasmic channels that allow the direct transport of molecules between neighboring cells. These channels, called plasmodesmata, transport not only water and small solutes like sugars but also macromolecules including proteins, small RNAs and viruses. The Burch-Smith lab aims to understand how cells regulate the movement of these molecules through plasmodesmata. We also seek to understand how plasmodesmata form and how their structures change as plant tissues mature. We use cell and molecular biology techniques, microscopy and reverse genetics to address these questions, and there are several projects available to undergraduate researchers in the laboratory.
Molecular Basis for the Regulation of Genes, Development
and Metabolism
Elias Fernandez
Through decades of awe-inspiring research it is now known that
DNA, the genetic blueprint, stores information for the maturity
and behavior of most living organisms. This information is released
in response to signals that various organisms receive. The receptors
for these signals belong to a class of molecules called nuclear
receptors. This signaling process controls virtually all aspects
of human physiology, including development, metabolism and even
emotional response. Malfunction of these signaling processes lead
to diseases such as obesity, cancer, heart ailments and premature
aging. Ours is a research laboratory funded by the National Institutes
of Health with a focus towards understanding the basis of the signaling
mechanism that regulates such receptors. We utilize techniques
based in physics, chemistry and molecular biology to study these
critically important processes.
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Effect of xenobiotics (foreign chemicals) on gene expression
Ranjan Ganguly
Insects cause a lot of economic damage by destroying agricultural
products in the fields and storages, and by infecting livestock
and humans with deadly germs. To control these insects, more
than million metric tons of insecticides are sprayed every year. Unfortunately,
at the end the insects win and develop resistance to most insecticides. One
of the mechanisms that confer insecticide resistance is mediated
by a family of enzymes called cytochrome P450 monooxygenase or
CYPs. These enzymes are found in all living organism from
bacteria to man. Besides their normal metabolic functions,
CYPs detoxify hundreds of xenobiotic compounds that we all ingest
everyday via food, water and air. In insects, CYPs are known
to be involved in conferring resistance to different insecticides
such as DDT, Malathion etc. In various insect species, the
resistant strains produce higher amounts of multiple CYP enzymes
by overexpressing the respective CYP genes. However, the
mechanism of CYP gene overexpression is not known. To understand
the molecular and genetic basis of overexpression of insect CYP
genes, my laboratory uses fruit fly or Drosophila melanogaster as
a model insect and Cyp6a8 as a prototype gene that shows
overexpression in DDT resistant strains. We have discovered
that this gene is induced in adult flies and Drosophila cells in
culture by three xenobiotic compounds: caffeine, DDT and phenobarbital. Using
transgenic technology and reporter gene assay we have identified
a 200 base pair regulatory DNA that can sense caffeine signaling. We
have also found that caffeine signaling is mediated via cyclic
AMP pathway. Current goals of our research are to identify the
exact sequence of the regulatory DNA and proteins that interact
with the regulatory DNA for caffeine signaling. Site-directed
mutagenesis and DNA-protein interaction assays will be used for
these objectives.
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Water and a Primitive Enzyme
Liz Howell
Research in the Howell lab focuses on characterization of R67
dihydrofolate reductase (DHFR) as a good model for a primitive
enzyme. One surprising result associated with this enzyme
is uptake of water upon substrate (dihydrofolate, DHF) binding.
This is unusual as binding of most ligands is accompanied by water
release. One mechanism by which water uptake may occur is
via effects on the free ligand. To test this hypothesis, we are
examining the binding of dihydrofolate to other DHF utilizing enzymes,
which should show water uptake. The mechanism by which this
occurs may be effects of osmolytes (small neutral, typically organic
molecules) on the Kd for dihydrofolate dimerization. This
is just one research avenue available for examination by a REU
student. Another focus area includes directed evolution of
either the R67 gene, a duplicated R67 DHFR gene (that produces
an active protein dimer) or a quadruplicated R67 DHFR gene (that
produces an active monomer).
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Are Chromatin Insulators Epigenetic Landmarks of the Genome
Architecture?
Mariano Labrador
A major challenge in modern Biology is to understand how the organization
of the DNA within the nucleus affects its function. Analysis of
chromatin structure and function have revealed that DNA is capable
of transmitting, through cell divisions, two major levels of information:
The well know level of information residing within the DNA sequence,
and the not so well understood information level that resides in
the peculiar manner in which DNA is packed within the nucleus,
which is known as “epigenetic” level of information.
Epigenetic information is responsible, among other things, of the
differences in expression profiles existing between different stages
of development or between tissues. Most of epigenetic information
is found as chromatin structures associated to local DNA sequences
such as regulatory sequences and promoters, but there is a growing
body of evidence suggesting that higher order chromatin structure,
mediated by long-range interactions within the chromatin fiber
also plays a major role in gene transcription regulation, and may
as well be considered a critical component of the epigenetic identity
of each of the cell lineages occurring in metazoans. Chromatin
insulators are regulatory elements found in Drosophila and in vertebrates
that are considered to have a major role in higher order chromatin
organization based on their capacity to mediate long range interactions
within the chromatin fiber. Chromatin insulators are DNA sequences
that have the ability to block communication between enhancers
and promoters when located between them and to prevent heterochromatin
spreading. It is generally accepted that these properties result
from cis-interactions between insulator proteins, which loop out
the intervening DNA sequences to form functionally independent
chromatin domains, and providing a model that supports their ability
to mediate higher order chromatin organization. The long term goal
of research in my laboratory is to elucidate the role of chromatin
organization during cell differentiation and gene expression regulation
and whether chromatin insulators play a major role mediating the
long-range interactions necessary for the formation of the higher
order chromatin structures that lie at the base of chromosome organization.
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Keeping Nano-scale Motors Under Control
Andreas Nebenführ
Cytoplasmic streaming is the process by which organelles move rapidly through plant cells. Although this remarkable behavior has been described for over two hundred years, its physiological function as well as its integration with other cellular processes is still unknown. Our own observations have revealed that different organelles move with different speeds, suggesting that their movements can be regulated independently. In addition, in some tissues cytoplasmic streaming can be triggered by external signals, e.g. light. We want to understand these regulatory processes better and therefore are studying motor proteins of the myosin family since these are thought to provide the force behind the organelle movements. We have previously shown that the tail end of these myosins can bind to organelles. This attachment of a motor protein to an organelle could be an important regulatory point that determines organelle motility. In other organisms (i.e., fungi and animals), it has been shown that posttranslational modification of myosin tails can regulate organelle binding. In this project, we will investigate whether this is also true for plant myosins. This involves live-cell microscopy with fluorescently labeled myosin proteins that are transiently or permanently expressed in plant cells and application of various inhibitors.
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"Neuropeptides in Stress and Alcohol-related Behavior"
Jae Park
Neuropeptides, as produced by neurosecretory cells and interneurons 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 for 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 behavior. Ethanol consumption is a major factor that influences human behaviors. Such ethanol-triggered behavioral and neurological changes are remarkably similar in invertebrates. Neuropeptides are key neural substances that regulate certain aspects of ethanol-induced brain malfunctions. To understand the impact of alcohol on the brain structure and functions, studies will investigate roles of the neuropeptidergic neuronal system in the ethanol-associated behavior in fruit flies.
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Disorder, Disorder in the Court!
Cynthia Peterson
New research directions in the area of structural biology have revealed a big surprise. That is that large segments of protein sequences are highly disordered! In contrast to the paradigm that dictates the regularly folded structures in proteins yield activity, it is becoming apparent that up to a third of all “sequence space” is occupied by intrinsically unfolded or disordered regions in proteins. Furthermore, many of these disordered sequences function in cell signaling. The research in the Peterson laboratory explores the role of an accessory protein, vitronectin, in regulating the activity of a specific protease inhibitor, plasminogen activator inhibitor-1 (PAI-1). PAI-1 is the primary inhibitor of serine proteases that are active in extracellular spaces to remodel tissues and break down blood clots. Vitronectin binds and stabilizes PAI-1. At least part of the interface between these two proteins comes from an intrinsically disordered region. Furthermore, the key structural element in PAI-1 that is responsible for regulating proteases is itself disordered. This laboratory is harnessing a suite of tools to study the role of disorder in protein structure and function. These include using fluorescence probes, spin-labels and even neutrons. Small angle neutron scattering can provide insights into the disorder-to-order transition that is hypothesized to occur when these two protein partners form a complex. Such SANS studies are possible due to the close proximity of state-of-the-art neutron facilities at Oak Ridge National Laboratory (ORNL).
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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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ssDNA damage response: assemble the checkpoint assembly
Tongye Shen
Dr. Yan, a colleague at UNC-Charlotte is studying ssDNA assembly. Using
ssDNA 'fishing' for the damage response, he found that if using
ssDNA length > 150 nt, the assembly will be formed, but < 100
nt, no assembly is formed, most players in the assembly are known,
but there is lacking a physical model of putting all the response
proteins together to form the assembly. The summer student will
investigate and get as high res as possible all involved protein's
geometry and physical properties from papers and simple modeling,
and try to build a model of the assembly, or at least exclude some
models based on the experimental data and modeling.
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Signaling by Receptor Kinases
Elena Shpak
This lab is interested in the cellular mechanisms of growth and differentiation in plants. Currently the research is focused on ERECTA-mediated signaling, a pathway that determines size and shape of aboveground plant organs and differentiation of cells in epidermis. ERECTA is a receptor-like kinase (RLK) with an extracellular leucine-rich repeat domain, a single transmembrane domain, and a cytoplasmic Ser/Thr kinase domain. Two functional paralogs of ERECTA, ERL1 and ERL2, are redundant with ERECTA in part of the signaling pathway. Loss of the entire ERECTA family in Arabidopsis leads to dwarfism, a decrease in lateral organ size, abnormal flower development and changes in stomatal patterning. The goal is to identify novel downstream components of the signaling pathway and to investigate the mechanism of receptor function. In addition, using the ERECTA gene we examine intron mediated enhancement of gene expression, as introns are essential for expression of ERECTA protein.
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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.
Other potential mentors include Barry Bruce (regulation of chloroplast protein import), Elias Fernandez (nuclear receptor signaling), Ranjan Ganguly (insect pesticide resistance), and Tongye Shen (stability of biomolecular structures). From the above summaries it can be seen that REU students will have diverse and interesting projects from which to choose. Fifteen faculty mentors participated in the summer BCMB programs over the past two summers. We anticipate that there will be a similar number of mentors in upcoming years.