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Research Projects Available for Students for Summer 2007
These include projects with biology professors as well as biology-related projects with professors from other HMC departments.
Biochemical Characterization of Arabidopsis SAC9 protein
Advisor: Prof. Williams (Biology)Phosphoinositides (PIs) are membrane-associated phospholipids that play key regulatory roles in eukaryotic cells, primarily through their interactions with proteins. PI accumulation is regulated in part by the action of PI phosphatases such as Sac-domain proteins. My lab studies SAC9, a Sac-domain protein found only in plants and green algae. Plant and algal SAC9 proteins have many conserved differences from the other Sac-domain proteins. The goal of this project is to characterize the activity and cellular localization of AtSAC9 through in vitro and in vivo expression studies, and to generate deleted proteins to identify the functional motifs of the protein. Methods will include expression of AtSAC9 in yeast cells and expression of AtSAC9/GFP fusion proteins in transgenic Arabidopsis plants.
Required Background: Prior molecular biology experience is preferred but not essential.
No. of positions: 2
Cloning and Characterization of SAC9 from Green Algae
Advisor: Prof. Williams (Biology)This position will focus on the newly discovered SAC9 proteins from two green algal species: Chlamydomonas rheinhardtii and Ostreococcus lucimarinus. These proteins resemble the plant SAC9 proteins at the N-terminus, but differ from it (and from each other) at the C-terminus. The goal of this project is to characterize the activities of CrSAC9 and OlSAC9 through in vitro and in vivo expression studies. Methods will include cloning of the coding sequences, and expression of the proteins in yeast cells and in sac9 mutant plants to determine whether they can substitute for the plant SAC9 protein.
Required Background: Prior molecular biology experience is preferred but not essential.
No. of positions: 1-2
DNA Repair in Chromatin
Advisor: Prof. Haushalter (Chemistry & Biology)Researchers in my lab use biochemical techniques to study the mechanism employed by DNA glycosylases, a class of DNA repair enzymes that recognize and excise damaged bases from the genome. DNA glycosylases employ a "base-flipping" mechanism in which the Watson-Crick structure is locally distorted and the damaged base is inserted into an extrahelical pocket in the DNA glycosylase active site. While the base-flipping mechanism for DNA glycosylases acting on naked DNA has been well established, it is not known how the need to base-flip the DNA is reconciled with the structure of DNA assembled into nucleosomes, the fundamental repeating unit of chromatin. Kinetic and structural studies of DNA glycosylases acting on chromatin substrates will increase our understanding of how the structure of the nucleosome modulates DNA repair.
Required Background: Preference for students who have taken Molecular Biology Laboratory (Bio 111) or have other molecular biology experience.
No. of positions: 1
Dynein Gene Expression
Advisor: Prof. Asai (Biology)Dynein is a molecular motor that travels along microtubules, carrying a cargo to the proximal or (-) end of the microtubule track. Depending on the cellular context, dynein usually functions as a complex of approximately 10-12 protein subunits, including one, two, or three heavy chains and several light, light-intermediate, and intermediate chains. An important problem is to determine the subunit composition of specific dynein complexes and to determine the role of each subunit in the overall activity of dynein. The ciliated protozoan Tetrahymena thermophila presents a unique opportunity for us to (i) search the genome for the genes encoding light, light-intermediate, and intermediate chains, (ii) determine the extent of expression of each gene, and (iii) ultimately modify (e.g., delete) each gene to determine the effect on the biology of the cell.
This summer, students will design and build DNA constructs that will disrupt specific genes to determine the role of the targeted dynein subunit in the cell. The effects of the gene disruptions will be determined by a combination of several assays, including swimming behavior, cell division rate, phagocytosis, and the organization of the cytoskeleton as evaluated by fluorescence microscopy. Some of the subunits of interest are: Light Chain-1 (LC1), which is thought to regulate dynein motor activity; LC4, which may confer sensitivity to calcium ions; LC8, of which Tetrahymena expresses six different orthologues; and the light-intermediate chains, which are thought to mediate the binding of the dynein to its molecular cargo. Another protein of interest is EB1, which binds the ends of microtubules and regulates their stability.Required Background: Biology 52 required; Molecular Biology laboratory (Bio 111) recommended.
No. of positions: up to 4
Morphology and Performance of Lizards
Advisors: Prof. Adolph and C. Buckley (Biology)This project involves field work to collect several species of lizards at nearby desert and mountain study sites, and then measuring morphology and sprint performance in the laboratory. (Note: Christine Buckley is a Ph.D. student at the University of Massachusetts-Amherst who works in Prof. Adolph's lab in the summer.)
Required Background: Preference for students who have taken Ecology (Bio 108) or Evolution (Bio 109); ability to provide tender loving care to lizards and lizard eggs; willingness to work in the field.
No. of positions: 1-2
Statistical Estimation of Performance
Advisor: Prof. Adolph (Biology)This project involves estimating how fast animals can run, how far they can jump, etc. based on small sample sizes for each individual. We use data sets obtained by previous students in my laboratory, then use computer sampling experiments to investigate the statistical effects of intraindividual variability and to develop efficient and unbiased ways to estimate performance parameters (maximum performance, correlations between performance traits). We may also obtain some more data using lizards in the lab.
Required Background: Preference for students who want to learn about resampling and simulations in statistics; willingness to do simple programming in MATLAB.
No. of positions: 1-2
Molecular Systematics of Octocorals
Advisor: Prof. McFadden (Biology)Our lab uses molecular tools (primarily DNA sequencing) to study the evolutionary relationships among octocorals, a poorly known group of marine invertebrates that includes 2000+ species of soft corals, sea fans and sea pens. Projects planned for the 2007 summer include sequencing two large nuclear ribosomal genes (18S and 28S rDNA, totaling ~5.5 kB) to construct a phylogeny (i.e., an evolutionary tree) for all known families of octocorals. In addition, we hope to sequence the rapidly evolving ribosomal internal transcribed spacer (ITS) genes in order to identify species boundaries and determine how many genetically different but morphologically similar species belong to a new genus of soft corals from New Zealand. As new nuclear gene markers are being developed by our collaborators at Duke University, we may also screen new genetic loci to determine their sequence variability and utility for phylogenetic reconstruction.
Required Background: Bio 109 (Evolutionary Biology) recommended. Some prior molecular biology experience is preferred but not essential.
No. of positions: 2-3
Conserved Regulatory Elements in the Telomerase Promoter in Primates
Advisor: Prof. Drewell (Biology)Telomeres are the repetitive non-coding DNA that cap most eukaryotic chromosomes. They serve a number of roles including protecting the chromosome ends from DNA damage and degradation. A normal consequence of DNA replication in human cells is that the telomeres shorten with each successive cell division. Eventually, telomere shortening is thought to lead to the onset of cellular senescence in normal cells, as they lack the mechanisms required to counter the continued cycle of telomere shortening. In human cells, telomerase reverse transcriptase (TERT) is the rate-limiting factor for assembly of an active telomerase complex. The expression of the hTERT protein is known to be primarily regulated at the transcriptional level, but our understanding of the control mechanisms for this gene remain superficial. The goal of this project is to characterize the TERT promoter regions in primate species closely related to humans using molecular biology approaches. Comparison of the DNA sequence at these promoters with bioinformatic techniques will reveal if there are evolutionarily conserved motifs in the TERT regulatory regions. Conservation of DNA sequence between species is often indicative of a functional regulatory activity. Ultimately, we will test the role of any identified conserved regions in the regulation of hTERT expression in cell transfection assays.
No. of Positions: Up to 4
Gene Expression in Corneal Cells in a Tissue-Engineered Corneal Model
Advisor: Prof. Orwin (Engineering & Biology)The overall goal of this project is to understand the relationship between corneal cell behavior and transparency in a tissue-engineered cornea model. Prior to the advent of cDNA microarray technology our understanding of the biologic processes that regulate cornea cell behavior at the molecular level has been limited to studying only a few select gene products. Our specific aim in this proposal is to utilize cDNA microarrays to map changes in global gene expression patterns between normal healthy cornea cells and cornea cells exhibiting the wound healing phenotype. Our long term goal is to understand how cornea cells can be regulated to generate transparent corneal tissue in a tissue-engineered model. The application of cDNA microarray technology to studying global gene expression in cells has shown biologists that we are only beginning to learn how gene products function and coordinate to support normal cell function, along with how trauma alters gene expression patterns in damaged tissue. Cell signaling involves the coordinated activities of multiple proteins leading to a directional amplification and modulation of cellular responses to external stimuli. By understanding the functional relationships of proteins comprising these signal cascade networks, as well as the genes that are modulated through these networks; we can gain a better understanding of normal cell physiology and a molecular elucidation of the alterations in these pathways leading to disease and tissue damage.
Effect of Bioreactor Culture on the Optical Properties of a Tissue-Engineered Cornea
Advisor: Prof. Orwin (Engineering & Biology)Corneal keratocytes alter their expressed phenotype in response to wound healing. It has been shown that these phenotypic changes have an effect on the transparency of the tissue. Cells expressing a smooth muscle actin are present during wound healing while the cornea is hazy, while normal keratocytes in the cornea express high levels of two soluble proteins: transketolase (TKT) and aldehyde dehydrogenase 1 (ALDH 1). RT-PCR, Western blots and immunohistology will be used to assess levels of these three proteins in cells grown under applied stress in our corneal bioreactor.
Characterization of Growth Factor Transport Through Novel Matrices
Advisors: Profs. Lape (Engineering) and Orwin (Engineering & Biology)Our overall project focuses on a cell delivery system to treat traumatic brain injury using novel scaffold materials and human adult stem cell populations. Our approach is novel in that we propose to differentiate human adult stem cell populations in three-dimensional culture in a scaffold specifically designed to recreate the natural microenvironment of neural cells. The cells will be delivered in high density attached to scaffolds optimized for cellular growth and differentiation. A component of the research will optimize the structure and nature of polymeric materials with anti bacterial and anti inflammatory ability to optimize graft success. We will include growth factors in the three-dimensional scaffold to support the bone marrow derived stem cells (MSCs), to enhance neuronal differentiation, and to stimulate neurite outgrowth. The effect of growth factors on stem cells is time and concentration dependent. Thus it is crucial to understand the kinetics of growth factor release from our scaffold.
The Barrier Behavior of Skin: Effects of Varying Hydration
Advisor: Prof. Lape (Engineering)Human skin provides a two-way barrier which prevents potentially harmful chemicals or diseases from entering the body while slowing water as it exits the body. These barrier effects are mainly due to the skin's flake-filled structure. The outer-most layer of skin, called the stratum corneum (SC), presents the dominant resistance to transport. The SC is composed of many corneocyte "flakes" in a lipid bilayer continuum; in order to reach the bloodstream, any molecule on the surface of the skin must pass through the SC. Although levels of skin hydration can alter the transdermal transport of toxins and drugs by a factor of 6 or more, possibly by altering transport pathways, current methods for in vitro testing do not account for effects of variable skin hydration. We are investigating the effects of hydration on overall transport rate and transport pathways for both hydrophilic and hydrophobic (lipophilic) molecules. We aim to produce a predictive model for the effects of hydration on transport and to elucidate the transport pathways for hydrophilic versus hydrophobic molecules. To do so, we will run a series of experiments for each target molecule in which the water activity is altered via the addition of a salt (most likely lithium chloride). This induced variation in activity has the same thermodynamic effect as a change in relative humidity.
No. of positions: 2
Life History Evolution in Fish
Advisors: Profs. Adolph (Biology) and Reznick (UC Riverside)Have you ever wondered why some species such as deer have two offspring at a time while others such as Atlantic Cod have thousands? In addition to wondering why species are different in these so called life history traits you may also wonder what specific adaptations allow them to exhibit such differences. These are just some of the questions that we are attempting to answer as part of our ongoing research on life history evolution. Poeciliid fish are a diverse yet closely related family of fish that give birth to live offspring and are found throughout the tropical and subtropical regions of the world. As a family, Poeciliids possess a broad range of reproductive strategies with some giving birth to as many as 300 small offspring at a time while others give birth to as few as one. What environmental differences between these species are responsible for the evolution of these diverse reproductive strategies? In addition to attempting to understand the ultimate, evolutionary factors that cause diversification of reproductive traits among this group of fishes, we are also interested in understanding how specific morphological and physiological adaptations allow species to exhibit such differences. All Poeciliids give birth to live young, some do so by simply retaining eggs in the female body until they hatch while others have evolved a more elaborate method. Many species in the family have evolved a placenta, similar but not identical to placentas that occur in mammals, that they can use to provision their offspring during development.
We are seeking 2 undergraduate students to assist in the laboratory component of this research at the University of California in Riverside this summer. Students will work closely with senior scientists, graduate students and research staff and will gain experience in care of live fish, design of experiments that test predictions of evolutionary hypotheses, measurement of morphological characters, fish dissection and lab techniques to quantify lipid content. Outstanding students may be encouraged to design and conduct an independent research project. This is a great opportunity for those students that are considering a career in biological research, especially those interested in evolutionary ecology and physiology. No previous experience in these areas is necessary and all students are encouraged to apply, however preference will be given to those that display outstanding academic achievement and interest in pursuing a career in research. To apply please send a resume with GPA and a cover letter highlighting your past experiences and achievements, future goals, your interest in the project and how you believe your participation in the project will help you to reach these goals to rbass001@ucr.edu or to david.reznick@ucr.edu .
No. of positions: 2
Life History Evolution in Fish
Advisors: Profs. Adolph (Biology) and Altshuler (UC Riverside)One of the most remarkable adaptations in animals is the ability to fly. Birds, bats and insects are among the most successful of terrestrial organisms, and their colonization of diverse habitats and ecological roles provides a rich context for studies of animal behavior and ecology. The study of how animals fly is an intrinsically multidisciplinary field that involves aspects of aerodynamics, physiology, and neuroscience. Although most flight research concerns either mechanisms or ecological interactions, flight behavior provides a powerful yet experimentally tractable system with which to merge reductionist and comparative approaches to understand how complex locomotion is accomplished, and how variation in locomotor performance influences higher-order behaviors. The goal of our laboratory is to apply techniques from biomechanics and neurophysiology to study flight behavior and evolution. Our current research focuses on hummingbirds because they are easy to train to perform complex flight maneuvers in laboratory settings.
We have openings for two students to spend this summer at our laboratory at UC Riverside and we encourage applicants with interests in biology and skill sets in programming and/or electronics. The ideal candidates will have experience in MATLAB and/or LabView, and have some familiarity with electronics such as oscilloscopes, analog circuits, etc. Students will work closely with senior scientists, graduate students and research staff and will gain experience in biomechanics, neuroethology, experimental design, and data analysis. Summer stipends for each student will be $4000. For more information, please email douga@ucr.edu.
No. of positions: 2
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