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Chemistry and Biochemistry
University of California
230 Physical Sciences Bldg.
Santa Cruz, CA 95064
Phone: (831) 459-4002
Fax: (831) 459-2935
Email
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Summer Undergraduate Research Fellowship (SURF) Program
Dates: June 22nd - August 29, 2009
Application Deadline: Monday, January 19th, 2009
THE FELLOWSHIP PROGRAM
As an NSF "SURF" Fellow you will join a UCSC research team and will take part in a research effort under close faculty supervision. The first step will be to formulate the research problem, then learn the necessary techniques or strategies to vigorously pursue
the problem during the summer's work. Ideally, significant results will be obtained that COULD be included in a research publication.
We believe that students who participate in this program will mature considerably in their scientific
outlook. Fellowships of $3,750.00 plus on-campus housing will be awarded.
THE UNIVERSITY OF CALIFORNIA AT SANTA CRUZ
The Santa Cruz campus is unique within the University of California in that
it maintains outstanding graduate programs in the sciences and a special commitment to undergraduate programs. The Campus Academic Plan and even its physical layout of ten residential colleges are designed to
serve the diverse needs of motivated undergraduates and graduate students in the most imaginative ways possible.
The Chemistry Department's twenty-nine faculty and approximately 120 graduate students and postdoctoral
fellows have moved to a brand new state-of-the-art building with an award-winning science library and
excellent instrumentation and computational facilities. Research group meetings and seminars provide rich
student-faculty interaction at the frontiers of chemistry/biochemistry and contact with many distinguished visiting
scientists. Based on frequency of citation of published papers, UC Santa Cruz is among the highest-ranked
universities for physical sciences in the country.
APPLICANT ELIGIBILITY
- Full-time chemistry or biochemistry undergraduates who will have completed their junior year, but will not have graduated as a senior, are eligible.
- Applications from women, ethnic minorities, and persons with disabilities are actively encouraged.
- Students at institutions with limited opportunities for research involvement are welcome.
- Applicants must be citizens or permanent residents of the United States and it's possessions.
TO APPLY
Complete application forms are available to download in Word format. Hard copies are available from the Chemistry Department office. Your application should include preferred research advisors, a completed two-page information sheet, an official academic transcript, and two reference letters. The application deadline is Monday, January 18, 2009 5:00 PM. Only completed applications will be considered. Applicants will be notified of our decision around February 15, 2009.
Download Application Materials:
Instructions
Participating Laboratories
Application form (This PDF can be filled out electronically and saved only by using Adobe Acrobat Reader 7 or above).
If you have difficulty downloading please send an email to surf@chemistry.ucsc.edu and we will send it to you.
Submit the application materials to:
Lesley-Reid Harrison
SURF Program
Dept. of Chemistry and Biochemistry
UC Santa Cruz
1156 High Street
Santa Cruz, CA 95064
Tel: (831)459-4823
Fax: (831)459-2935
Email: surf@chemistry.ucsc.edu
Disclaimer
Please note that: In order to assess the total number of applicants to REU-chemistry programs nationwide, the various chemistry REU site directors plan to share the names and home institution of all applicants. This information will be used solely to document the widespread interest in Chemistry-REU programs and will be confidential. We will share your information unless you specifically request that your name not be included.
RESEARCH PROJECTS AND FACULTY ADVISORS
The labs of the 14 participating faculty span all of the major areas of chemistry. These include: Biochemistry, Bioinorganic, Inorganic, Organic & Bioorganic, Physical, & Physical Biochemistry. The UCSC faculty Web site should be consulted for more information beyond the short sketches below.
RESEARCH CLUSTER A: BIOCHEMISTRY & BIOPHYSICS
Prof. Ted Holman --- "The Role of Iron in Lipoxygenase Oxidation of 1,4-Diene Substrates"
A goal of this project is to understand the structure and function of lipoxygenase, a critical enzyme in both mammalian and plant biology. Specifically, we wish to define how the enzyme utilizes an atom of iron to perform the oxygenation of the 1,4-diene substrate. A number of interesting site-specific mutants of the active site iron coordination are in hand which modify the enzyme’s spectroscopic and enzymatic properties. In this manner, we will correlate structural changes of the iron coordination with mechanistic changes. The SURF student will potentially work on three crucial aspects of the lipoxygenase project. First, a student could generate mutants of lipoxygenase and purify the enzyme. This entails the learning of molecular biology to mutate the enzyme by modifying the genetic sequence and biochemistry to express and purify the enzyme. Second, the student could study the enzymatic mechanism of the enzyme by kinetic measurements. This could be done on either the mutants generated by the student or on any of the twenty mutants I have generated. Third, the student could investigate the structural changes at the iron site of the mutants with Electron Paramagnetic Resonance. By monitoring the changes in the EPR signal, the student would compare the structural changes of various mutants with their corresponding kinetic changes to explain the experimental results.
Prof. David S. Kliger --- "Nanosecond Time-Resolved Spectroscopic Studies of Protein Function and Folding"
The SURF student will participate in using nanosecond time-resolved spectroscopy to study heme protein function, early events in protein folding, or activation mechanisms of visual pigments, depending on the talents and interests of the student. We have been using time-resolved absorption, CD, and MCD spectroscopy to understand a wide variety of such processes. Various studies underway involve studies of ligand binding to heme proteins such as hemoglobin and myoglobin, investigations of photolysis intermediates of visual pigments and phytochromes, intermediates involved in the function of cytochrome c oxidase, and folding of cytochrome c. Most of these projects involve the use of time-resolved polarization spectroscopies as well as time-resolved absorption spectroscopies. The SURF students will concentrate on time-resolved absorption studies since these techniques are more easily understood by undergraduates with limited physical chemistry experience and the apparatus for carrying out nanosecond time-resolved spectral studies in our lab is very straightforward to run. Students will be exposed to more complex polarization spectroscopies, however, through discussions at regular research group meetings and group research talks. Which project a given student would work on will depend on the status of experiments being carried out at the time the SURF student would join the research group as well as specific interests of the students. In each case, however, the student would be exposed to sample preparation, spectroscopic measurements, and global analysis techniques for analyzing time-resolved spectral data. The student would initially work closely with a postdoc from the laboratory and gradually work more independently in the various techniques required for the work.
Prof. Glenn L. Millhauser --- "Structure Determination of Novel Protein Motifs of the Central Nervous System"
Our research on proteins that function in the central nervous system is focused in two directions. The first seeks understanding the normal physiological function of the prion protein. Prions are infectious proteins that produce neurodegenerative diseases. These diseases share in common accumulation of a misfolded form of the endogenous prion protein. The properly folded form of the prion protein is found in healthy tissues of the central nervous system and periphery of all mammals. What remains unknown, however, is its normal physiological function. Research now suggests that the prion protein participates in the regulation of the micronutrient copper. Our lab, as part of a wide-ranging collaboration, determined the first accurate structure of the copper binding sites in the prion protein. This work is helping to establish feasible models for prion protein function and is leading to new theories to explain neurodegeneration in prion and related neurological diseases. We are especially interested in the signaling molecule called the Agouti-Related Protein (AgRP). Our experiments use peptide and protein synthesis and advanced magnetic resonance techniques. SURF students will be involved at all levels. In the past we have found that bright undergraduate researchers are able to learn the basics of peptide synthesis in a few weeks. Thus, SURF students will be able to synthesize their own constructs relevant to our studies. In addition, they will perform both NMR and EPR experiments.
Asst. Prof. Seth M. Rubin --- "Biochemical Mechanisms of Cell Cycle Regulation and Cancer"
Our research focuses on understanding the biochemical mechanisms that regulate cell growth and division and how defects in these mechanisms result in diseases such as cancer. The cell cycle is coordinated by a shifting network of protein-protein interactions. We develop and use a number of structural and biophysical techniques, particularly x-ray crystallography and nuclear magnetic resonance (NMR), to characterize these interactions at atomic resolution and use molecular biology and biochemical methods to understand their relevance in the cell. We currently study two protein families that control the G1 to S phase transition of the eukaryotic cell cycle and potentially play a critical role in tumorigenesis. Members of the E2F family of transcription factors activate genes required for DNA synthesis and other processes towards cell division. The retinoblastoma (Rb) and related “pocket proteins” bind and inhibit E2F until the cell is ready to begin S phase. At this point, Rb is phosphorylated by cyclin-dependent kinase (Cdk)-Cyclin complexes and E2F is activated through its release. While this simple model for the biological role of Rb as a growth regulator is clear, the biochemical mechanisms underlying Rb function remain unexplained. Our goal is to understand in molecular detail the interactions of Rb with E2F and other regulatory proteins and how these interactions are affected by phosphorylation.
RESEARCH CLUSTER B: INORGANIC CHEMISTRY
Prof. Scott Oliver --- "Synthesis of new inorganic substances of relevance to materials science"
The Oliver group studies several different research projects in the area of materials science using multiple characterization techniques to probe or further understand our systems. One main focus is the synthesis of cationic inorganic materials. Despite the enormous industrial importance of layered (2D) and microporous (3D) inorganic materials for catalysis and environmental processes, almost all are anionic or neutral in charge. Therefore, only cationic or neutral species can reside in the pores. We are working towards new highly stable cationic hosts with anions in the pores. A recent milestone discovery is the second known cationic inorganic material that can undergo anion-exchange, and this is the seed for additional advances that can involve SURF students. Other projects focus on devising thin films or membranes. One study involves organic self-assembled monolayers for fabricating electronic devices. Another looks at using polymers and their surface modification for protecting light-weight air batteries. Another project looks at swollen organic polymer matrices as a scaffold for the construction of meso- and macrostructured inorganic materials.
Prof. Pradip Mascharak --- "Synthesis and Study of Bioinorganic Systems"
Synthesis of designed Photoactive Metal Nitrosyls The recent discovery of the roles of Nitric oxide (NO) in blood pressure control, neurotransmission, immune response, and cell apoptosis has raised interest in the isolation of compounds that deliver NO at biological targets under strict control. In my laboratory, one subgroup is involved in synthesizing metal nitrosyls (metal complexes with one or more NO as ligands) that release NO upon exposure to light. We intend to utilize these compounds as NO-donors in phototherapy against malignancy and in local control of blood pressure. A SURF student in my lab will have the opportunity to work on (a) the organic synthesis of the designed ligands, (b) isolation of the metal complexes derived from such ligands and NO, (c) their spectroscopic and structural characterization, and (d) finally their application to either inhibit specific enzyme(s) or induce programmed cell death (apoptosis) in malignant locales. Research in this area will not only allow the student to acquire synthetic and spectroscopic skills but also provide insight into enzyme kinetics and drug design. In most cases, The SURF student will begin work under the supervision of a senior graduate student. Once experience (and confidence) has been gained the student will be encouraged to take up independent, related project(s) to move the research further toward the desired goal. Work in this project will offer the SURF student a lot of insight in the inorganic chemistry and biochemistry of NO-drugs.
RESEARCH CLUSTER C: ORGANIC & BIOORGANIC CHEMISTRY
Assoc. Prof. Rebecca Braslau --- "Synthesis of Nitroxides for 'Living' Free Radical Polymerization"
Our lab has developed a class of alpha-hydrogen containing nitroxides, which are effective mediators of “living” polymerization. Using these nitroxides, we prepare designed polymers bearing the nitroxide on the polymer terminus. We have found that the nitroxide is very tolerant of functionality on the t-butyl group. In close analogy to our standard synthetic protocol (carried out regularly by undergraduates), the SURF student will prepare new nitroxides bearing a remote ketone group, which will allow selective post-polymer modification at the polymer terminus. Standard organic methods will be employed. These will include reaction planning, monitoring reaction progress by TLC or GC, chromatographic separation, and spectroscopic analysis of the resulting products. The SURF student will receive direct guidance from the faculty member, and will also have in-lab supervision by an advanced graduate student.
Prof. Phillip Crews --- "Studies in Marine Natural Products Chemistry"
The SURF student will participate in our ongoing program in marine natural products chemistry. The long-term focus is to expand fundamental knowledge about the novel structures and the bioactivity of marine natural products. Tropical sponges are the primary marine taxa being studied in a highly collaborative program with other academic and cooperate scientists. The strategy of bioassay guided isolation enables the discovery of novel compounds that are active against a variety of human diseases. The goal will be to have the SURF student join in on an ongoing projects involving cytotoxic alkaloids such as fascaplysins (1) or the mixed ketide-amino acids headed by milnamide A (2). SURF student participants in our research will learn the state of the art in analytical organic chemistry and organic structure analysis. Students will begin research with material taken from our organism repository. They will initiate the project by completing standard extraction schemes. Next the SURF student will execute our standard separation techniques including liquid-liquid extraction, column chromatography (sephadex, silica gel) and HPLC to isolate the compounds of interest. Once a pure compound is in hand they will be able to carry out structure elucidation using state-of-the-art methods of organic structure analysis, i.e., 2-D NMR pulse sequences such as gHSQC and gHMBC, g-COSYand ESIMS at our in-house spectroscopy facilities.
Prof. Joseph Konopelski --- "Development of New Synthetic Methodologies and Total Synthesis"
The focus of our research effort is the development of new synthetic methodologies and their application to the total synthesis of complex organic molecules. The demands of developing a project for a ten-week summer session are somewhat unique, and we have been successful with different types of projects. One has been to integrate a summer student directly into the project of a graduate student or postdoctoral fellow, with the focus on preparation of important compounds needed for further study. Our current program has as its main focus the total synthesis of three natural products. Diazonamide A is a marine natural product with excellent cytotoxicity toward cancer cells. N-Methylwelwitindolinone C isothiocyanate is a terrestrial natural product with established multidrug resistance reversal activity. Psymberin is a cytotoxic compound isolated by our colleague Professof Phil Crews that has selective solid tumor activity. Several smaller projects derive from this larger program, and these have been the focus of our undergraduate coworkers.
Assist. Prof. Roger Linington --- "Marine Natural Products Research; The Development of Drugs for Neglected Diseases"
Research in our lab is centered upon i) the exploration of the chemical diversity of marine microbes as sources for new drug leads and ii) the development of these leads as chemical probes for exploring contemporary questions in infectious disease biochemistry. In particular our research program is interested in identifying lead compounds for the treatment of orphan diseases including malaria, leishmaniasis, Chagas disease and dengue fever. Students in my group are members of a highly collaborative research effort who gain the opportunity to interact with researchers in such diverse disciplines as parasitology, molecular biology, microbial ecology and environmental toxicology. SURF students joining this program will be involved in the preparation of microbial extracts, screening these extracts chemically by HPLC-MS and NMR and biologically in conjunction with the UCSC Chemical Screening Center, and following up on lead hits using a variety of modern chromatographic techniques. It is anticipated that students will have the opportunity to learn about structure determination techniques including high field NMR analysis as a component of the lead identification process.
Assist. Prof. Scott Lokey --- "High-Throughput Assays of Sponge Extracts for DNA-Damage Cell Cycle Checkpoint"
Research in my lab spans several areas in chemical and cell biology. We use a combination of combinatorial synthesis and high-throughput screening to discover compounds with novel biological activity. We are working closely with the Crews lab to perform high-throughput purification of marine sponge extracts and format the resulting fractions for input into our cell-based assays. An ideal SURF research project would be to format a series of sponge extracts into 384-well plates and run the resulting library through one of our high-throughput assays. One of our primary screening platforms is to identify compounds that are selectively toxic to yeast deletion mutants. Any "hits" that are found can be followed up by studying their effects in secondary screens. Purifying the compound and determining its structure using high field NMR and mass spectrometry constitutes follow up on those with promising activity.
RESEARCH CLUSTER D: PHYSICAL CHEMISTRY
Assoc. Prof. Shaowei Chen --- "Photo-Gated Charge Transfer of Quantum Dot Organized Assemblies"
This research is focused on understanding the molecular mechanism of electron transfer at nanoscale interfaces. One project involves electrochemical and spectroscopic measurements of the electronic conductivity properties of thin films of semiconductor nanoparticles (quantum dots, or QDs). As these QDs are photoactive, their electron transfer properties can be sensitively manipulated by photoexcitation, a fundamental process in photovoltaic applications. Our goal is to establish a correlation between the QD structures and the photo-gated charge transfer properties. In this research project, synthesis of stable QD materials will be a key starting point. A SURF student will have a unique opportunity in making contributions to these varied areas of research. This includes: (i) synthesis and processing of new QD materials, (ii) spectroscopic characterizations (including transmission electron microscopic and optical measurements), and (iii) preparation and photoelectrochemical measurements of QD organized assemblies. Ideally the student will participate in all these activities for a complete and systematic appreciation of the project. Nonetheless, depending on the background and capability, the student can also choose to focus on a specific aspect and collaborate with co-workers to complete the project.
Asst. Prof. Yat Li --- "Semiconductor nanowire heterostructures for photovoltaic"
This project focuses on the development of novel semiconductor nanowires and nanowire heterostructures that can be used to address the fundamental questions in photovoltaic. The project consists of the following three interrelated sub-programs: 1) Rational synthesis of novel nanowire heterostructures, in which the composition and/or doping can be modulated down to the atomic level in axial or radial direction, using CVD and MOCVD techniques. Particular emphasis will be placed on semiconductors such as III-V and II-VI materials due to their outstanding optical and electrical properties. 2) The investigation of structural, optical and electronic properties of these nanomaterials. It involves electrical transport measurements, a variety of spectroscopic and advanced electron microscopic techniques. We want to understand the correlation between the nanomaterial properties and structures, and ultimately to tune their properties by controlled synthetic variation of structure. 3) The development of nanowire photovoltaic devices. The cell efficiency will be studied and compare to bulk materials. The unique 1D nanostructure could open up new opportunities in addressing the critical scientific issues in photovoltaic. The SURF student will participate in all these steps, including nanowire synthesis using CVD and MOCVD, characterization of nanomaterials, nanoscale device fabrication and measurements.
Prof. Jin Z. Zhang --- "Semiconductor and Metal Nanomaterials and Applications in Cancer Biomarker Detection"
Our major research focus is on the design, synthesis, characterization, and application of novel semiconductor and metal nanomaterials. The synthesis is based on colloidal chemistry techniques and the characterization employs a combination of microscopy, spectroscopy, x-ray, electrochemistry, and ultrafast laser techniques. We are interested in: (i) effects of surface, size, and shape on electron transfer and electron-hole recombination in quantum-confined semiconductor quantum dots; (ii) effects of interface, size and shape on hot electron relaxation and SERS (surface-enhanced raman scattering) activities in metal nanoparticles; (iii) use of photoluminescence of semiconductor quantum dots and SERS of metal nanoparticles for detection of cancer biomarkers such as antibodies. The SURF student will joint a short-term project involving the preparation of semiconductor and metal nanoparticles. This will involve characterization of their optical and interfacial electron dynamics using conventional spectroscopy and modern femtosecond laser techniques. There will be an opportunity to learn how to conjugate nanoparticles to proteins for cancer biomarker detection applications.
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