2008 Internship Booklet - To download the pdf file click here

SCIENTIFIC ABSTRACTS & PERSONAL STATEMENTS

Laura Aguirre

UNDERGRADUATE INSTITUTION 
   Solano Community College
   Major: Biology
CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Kit Lam, M.D., Ph.D., Professor of Internal Medicine,
                     Division of Hematology/Oncology, School of Medicine, 
                     UC Davis Cancer Center, Sacramento, CA
   Secondary Mentors: Urvashi Bhardwaj and Hyounggee Baek
   Laboratory: Center for Neuroscience, UC Davis, Davis, CA and   
                 Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

SCREENING ONE BEAD TWO COMPOUNDS

Laura Aguirre, Urvashi Bhardwaj, Hyounggee Baek, Kit Lam

The Blood-brain barrier (BBB) serves to significantly restrict the passage of soluble and cellular elements between the brain and circulation.This poses a big challenge to deliver drugs and other chemicals to the brain cells.The goal of this research is to identify small molecules, or peptides, that can cross the blood brain barrier to deliver drugs or DNA to the brain. In order to accomplish this goal we used One Bead Two Compound combinatorial technology. We synthesized millions of random X6 and X10 peptide beads, with each 130µm hydrogel bilayer bead expressing unique peptide. We have used two peptides on one bead in our library.The first random peptide/targeting peptide were cleavable and the second peptide acts as a ligand that promotes cell binding to the bead.These libraries were screened with Chinese hamster Ovary (CHO) cell line as well as murine microvascular endothelial cells.The cleavable targeting peptide was tagged with Streptavidin Quantum Dot via biotin to obtain a fluorescent signal. Each cell line was screened with approximately 75,000 compounds to identify molecules/peptides that can penetrate brain microvascular endothelial cells as well as CHO cells.The beads with fluorescence in the cells were considered positive and were picked up and sequenced to identify the peptide that could enter in the cell.These peptides will be further tested on endothelial cells lined with another layer of brain cells to identify the peptides that can cross BBB.This in turn would help us to use these transporter peptides to deliver drugs and DNA across BBB.

Personal Statement

Words cannot begin to explain how thankful I am to CBST for giving me the opportunity to be a part of this great summer internship. I had heard great things about it from previous interns who attended my community college, and I knew that I wanted to apply. Being able to work in Dr. Kit Lam’s lab was truly a privilege. He is really interested in what we are learning and always wants to make sure that we have all the resources we need. My secondary mentor Urvashi was just amazing and really took the time to teach me all the lab skills that I needed to know for example how to work in the tissue culture room, which I had never done before. Not to mention that everyone else in the lab is more than friendly and willing to answer any of my questions, and take the time to show me where things are. Another great part of this internship is all the AMAZING interns that you get to meet. I have made some new friends that I know I will keep in touch with. The first week intensive was really fun and truly set the ground work for our group bonding. The Lake Tahoe retreat really allowed us to become a closer group thanks in big part to all the great activities and seminars that we got to attend. Having all of this hands on experience has only further encouraged me to continue my education and reach my ultimate goal of obtaining a Ph.D.

Matthew Auyoung 

UNDERGRADUATE INSTITUTION 
   University of California, Davis
   Major: Biology
CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Ting Guo Ph.D., Associate Professor, 
                     Analytical and Physical Chemistry
   Secondary Mentors:  Yongquan Qu and Neal Cheng
   Laboratory: Department of Chemistry, UC Davis

Scientific Abstract

Gold nanoparticles (AuNPs) can be detected through conventional optical means and pose several advantages over optical labels and probes that are in current use. AuNPs exhibit strong, resonant light scattering in the visible and near-infrared range, facilitating their ease of visualization. By comparison, chemical fluorophores are much dimmer and have the drawback of photobleaching. Additionally, gold’s low cytotoxicity enables AuNPs to be used in cell labeling applications. For example, conjugating antibodies to AuNPs allows for functionality similar to antibody-conjugated quantum dots, while circumventing the cell toxicity issues associated with semi-conductor quantum dots.The primary interest of this project is to investigate whether AuNPs situated within a cell can be detected and visualized. Light scattering by AuNPs is detectable when the particles are roughly 30-nm or greater in diameter. For this reason we will make use of 35-nm particles, prepared through the citrate reduction of HAuCl4.To prevent the aggregation of the AuNPs in solution, poly(ethylene) glycol (PEG) is added. Incubation with cells will allow for an uptake of AuNPs into cell cytoplasm, after which confocal microscopy will be employed to visualize the spatial distribution of the nanoparticles within the cells. As of now, synthesis of 35-nm AuNPs with minimal aggregation has been accomplished.Three sizes of PEG (400, 1K, and 2K Daltons) have been separately added to AuNPs and imaged with transmission electron microscopy (TEM) – the resulting micrographs suggest that an increase in PEG size accompanies a decrease in overall AuNP aggregation. Information regarding AuNP distribution in the cell environment will allow us to better assess the utility of gold nanoparticles as probes and labels. 
 
Personal Statement

My CBST summer internship has been highly rewarding and I would not hesitate to recommend the program to any of my peers. Being assigned a project and working closely with supportive mentors has afforded me valuable insight on both laboratory practice and the thought processes underlying research. The supplementary seminars and lectures have been diverse and engaging, broaching topics that range from bioimaging techniques to navigating career paths. A great feature of the CBST program has been the opportunity to network with students and experts in the field of biophotonics, which is now at the interface of many scientific disciplines - the diversity of viewpoints represented at such events as the Annual Retreat have been a real eye-opener on how collaborative science is conducted. Above all, the people that have made this internship possible are friendly and highly motivated, both staff members and students alike.

Namrata Barbhaiya

UNDERGRADUATE INSTITUTION 
   Evergreen Valley College
   Major: Molecular and Cell Biology
CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Kit Lam, M.D., Ph.D., Professor of Internal Medicine,
                   Division of Hematology/Oncology, School of Medicine, 
                   UC Davis Cancer Center, Sacramento, CA
   Secondary Mentor: Pappanaicken Kumaresan, PhD
   Laboratory: Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

Namrata Barbhaiya, Sheng Qin, Yan Wang, Yoshiko Maeda, Inderjeet Kaur, Pappanaicken Kumaresan, Kit S. Lam

Personal Statement

The CBST summer internship was a wonderful experience. The first week intensive and other activities like the bowling night, and various workshops brought all the interns together as a group. It was a unique experience to work with interns not only from different academic backgrounds, but also from different walks of life with similar goals. Working in the lab was an invaluable experience. Dr. Kumar and Dr. Lam were always excited to answer my questions and guide me. Overall, it was a great learning experience and it was an honor to be a part of CBST again after the winter internship.

Sabrina Bedell

UNDERGRADUATE INSTITUTION 
   University of California, Davis
   Major: Biochemistry
CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Kit Lam, M.D., Ph.D., Professor of Internal Medicine,
                     Division of Hematology/Oncology, School of Medicine, 
                     UC Davis Cancer Center, Sacramento, CA
   Secondary Mentor: Jared Townsend
   Laboratory: Center for Neuroscience, UC Davis, Davis, CA and   
               Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

The one-bead-one-compound (OBOC) combinatorial library method is a powerful tool for basic research and drug discovery. Diverse peptide and small molecule libraries are synthesized by the split-mix method, such that each 90-micron bead contains one compound. Beads are then screened for binding with proteins or whole cells. Methods currently exist that screen such vast libraries under one condition or with one analyte. At present, it is impossible to screen the same library multiple times with different analytes and track the response of every compound-bead. To achieve this, we have developed a method of immobilizing the library beads on a microscope slide.The entire slide can be scanned after each screening experiment and the beads can be tracked through multiple screenings before sequencing.This enables us to determine the binding profile of every compound-bead with a number of different analytes. Only beads with a desirable profile will be isolated for microsequencing or chemical decoding. In this method, library beads are manually spread onto an array of wells and then transferred to a microscope slide covered with a vacuum-spun layer of urethane glue. Adhesives were tested for strength, water resistance, transparency, and cell-interactions.The current method has been tested with LLP2A beads and random OBOC peptide libraries using an enzyme-linked colorimetric assay and a whole cell binding assay. We used Jurkat T- lymphoma cells, MOLT-4 T-lymphoma cells, MDM-MB-231 breast cancer cells, and αvα3 transfected K562 cells in our whole-cell binding studies. We are also exploring the screening of photoswitchable libraries with this new method. 
 
Personal Statement

This summer has been such an incredible experience—not to say that every moment was a happy one—many times I found my self frustrated, exasperated, and exhausted. But these times are just as valuable to me as the times I spent laughing and jumping for joy (literally, ask my lab mates!). One of the most important things I learned this summer is that just like life, science is not perfect. You often run into problems in the lab that you must work to overcome, and it may be hard to do, but the feeling of accomplishment is worth it. I gained so much more than just lab experience from this internship. The weekly workshops helped with different aspects of getting a job (and keeping it) like resumes, interviews, how to dress, and problem solving skills. We also had a panel of scientists from different backgrounds come in which was very informative and helped tremendously with that nagging question “what am I going to do for the rest of my life?” The friendships I’ve made with the other interns are invaluable to me. It is such a privilege to have spent my summer with this intelligent and fun group of people that I almost feel like I should have paid for the summer instead of getting paid (like summer camp). The CBST team is amazing and has done an awesome job making this internship successful. Everything is well-organized, balanced between work and play and interns are genuinely cared for. This experience enabled me to mature into a better person and I am grateful to all because of that.

Bryan Brandon

UNDERGRADUATE INSTITUTION 
   Cal Poly, San Luis Obispo
   Major: Biomedical Engineering

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Bruce Lyeth, Ph.D., Professor of Neurological Surgery, 
                     Neurological Surgery, School of Medicine, UC Davis. 
   Secondary Mentors: Paul Mello, Gene Gurkoff 
   Laboratory: Center for Neuroscience, UC Davis, Davis, CA and   
                 Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

Traumatic brain injury (TBI) is the main cause of death and disability in the pediatric population. Both in-vivo and in-vitro experiments have determined that excessive post- injury neuronal activation is correlated with an increase in neuronal dysfunction and death. Specifically, concentrations of excitatory amino acids, such as glutamate, become elevated to pathophysiologic levels causing excessive neuronal activation and significant increases in levels of intracellular calcium.This increase in intracellular calcium concentration is thought to be directly related to neuronal dysfunction and death. We hypothesize that by increasing extracellular potassium we will reduce post TBI neuronal activation, and increase viability. Increasing extracellular potassium levels will reduce the normal ion gradient necessary for neurons to repolarize following an action potential.This ultimately will cause sodium channels to remain deactivated for longer periods of time and decreases the rate at which a neuron can depolarize. Utilizing the ratiometric sodium binding dye, SBFI-AM, mixed neuronal and astrocyte cultures, and a mechanical strain model, we intend to measure changes in intracellular sodium concentrations over a 15 minute time period post injury in the presence of varying potassium concentrations (3, 30, 65, and 90 mM). If sodium channels are prevented from reactivating by increasing extracellular potassium levels, we will expect to see decreased sodium and calcium accumulations and increasing cell viability. By better understanding the post-traumatic pathophysiologic changes in the extracellular space, we hope to design better therapies to treat TBI. 

Personal Statement

I am very grateful to have been able to participate in this internship for two consecutive summers. While my first summer in the CBST internship exposed me to new things seemingly every day, my second year has really helped prepare me for the next step in my life. I was able to continue working in the same lab in the UC Davis Center of Neuroscience and this way I was able to immediately begin working on the project that I helped start the summer before. Even though I worked in the same lab last summer, I found myself constantly learning new things this summer. Ultimately, it is the people you work with that really determine how much you will enjoy your experience. That is what makes this internship so special. Everyone affiliated with CBST is enthusiastic, kind and helpful. They really want to make sure that you get the very most out of this experience, which is made evident through the fun retreat at Lake Tahoe and the numerous interesting and helpful workshops, presentations, and seminars that we participated in. This internship was an invaluable experience that helped me grow in many ways. The people I met and the knowledge I gained this summer will undoubtedly help me achieve both my professional and life goals. I feel both honored and privileged to have been able to participate in this program and I am certain that it will be an experience that I will never forget.

David Brown

UNDERGRADUATE INSTITUTION 
   Brigham Young University, Provo, UT 
   Major: Physics 

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Thomas Huser, Ph.D., Associate Professor, Internal Medicine, 
                   School of Medicine and Center for Biophotonics Science and 
                   Techology, UC Davis
   Secondary Mentors: Jay Bhatt, Sebastian Wachsmann-Hogiu   
   Laboratory: Oak Park Research, UC Davis Cancer Center, Sacramento, CA

A number of systems exist for long-term, dynamic, molecularly-specific imaging of whole live animals, such as magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT) with X-rays, and bioluminescence. Most of these techniques, however, are either very expensive or require high energies, which can lead to tissue damage and are not well suited for long-term imaging. For small animal imaging, optical imaging is typically most suitable, but requires probes that emit in the near-infrared part of the optical spectrum for deep tissue penetration. Non-surgical optical imaging in mice permits long-term monitoring with no trauma to the animal and accurate observation of a drug’s possible side effects. Here, we report the successful design and construction of a multimodal animal imaging system designed with these purposes in mind. This system is centered around a light-tight box measuring 2’x2’x18”with a top-mounted electron- multiplying CCD camera focused on an adjustable stage. A telecentric lens permits motion of the sample along the z-axis with no change in magnification. Multiple LED’s inside the box provide illumination, a laser source induces fluorescence, and a heating pad and exhaust fan insure the well-being of the animal during imaging, where it is kept motionless by injected anesthetics.This multimodal system can operate with a combination of different probes, such as fluorescent organic dyes or quantum dots, bioluminescence, and Raman tags to monitor tumor size and metastasis, angiogenesis, gene expression, and uptake of labeled drugs. The design, construction, and future experiments of our new imaging system will be presented. 

Personal Statement

This summer was perfect.  The CBST internship provided me with a link between my Physics training and my career aspirations that my own university couldn't give to me.  Working in the labs was the "missing link" that my education needed to be complete.  I've been to many medical school interviews since my internship, with many more to go, and everyone has been impressed with the amount of hands-on experience that CBST provides.

Clarissa Calderon-Meza 

UNDERGRADUATE INSTITUTION 
   Mills College
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Susan Spiller Ph.D., Assistant Professor, Biology
   Laboratory: Mills College, Oakland, CA

Scientific Abstract

 
Highlly fluorescent red protein is a tool that is useful for fluorescent microscopy because
red light can report events from deep in mammalian tissue. A green fluorescent protein
(GFP) is currently being used but it does not have this tissue penetrating property.
Certain cyanobacterial genes share sequence homology with plant phytochromes;
therefore, alignments of the gene reveal common features, which describe protein
domains. Our purpose is to isolate a minimal GAF domain from the cyanobacterium
Thermosynechococcus elogatus that will produce a small highly fluorescent red protein
which will be useful as a biological tool similar to Green Fluorescent Protein (GFP). Our
previous work shows that mutation of the tlr0924 gene from T. elongatus produces this red
fluorescent protein.Thermosynechococcus elongatus has five phytochrome-like proteins. My
part of this collaborative project is to work with one of the five T. elongatus genes, tlr0911,
and I am in the process of inserting it into a plasmid vector with intein tag-chitin binding
domain (CBD) for better purification. After successfully ligating our insert, I plan to
transform it into E. coli for expression to later be characterized. Finally, I plan to make the
homologous mutation of cystene to aspartate to produce fluorescence. Our long term goal
is to produce a 160-180 amino acids long red fluorescent probe. We plan to insert it into
mammalian cells without causing an activation or repression of other genes nearby. If we are
successful, our protein will be used as a reporter gene for human systems.

  
Personal Statement

During my internship with CBST, I had one of the best times of my life. Not only did I learn about science, but also about interacting with other people and developing skills for networking. I did my internship at Mills College and my primary mentor was Dr. Susan Spiller. The research I was doing was so amazing to me because it involved creating a protein that could help a lot of people in the long run. Because my research interested me so much, I was very eager to learn as much as I could about my topic so I did a lot of outside research to better my understanding of it. I managed to learn a lot of terminology and facts about chemical processes, as well as learning how to work as a group since there were other two students working on the same subject with me. Patience and communication are definitely key things that will improve interactions with other people.
As far as networking, I spent such a wonderful time with the other interns and graduate students during the annual retreat in Tahoe. We got to exchange ideas and thoughts about our research projects and discuss possible solutions to improve and confirm our results. 
I learned a lot of things during my time with CBST, and I would love to have the opportunity to do it again. I thank all the people at UC Davis that helped me and also my fellow interns who made it more fun.

Lucy Freer 

UNDERGRADUATE INSTITUTION 
   Folsom Lake Community College
   Major: Biochemistry 
CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Delmar Larsen, Ph.D., Assistant Professor
   Secondary Mentors: Arther Thibert, Lu Zhao
   Laboratory: Department of Chemistry, UC Davis

Scientific Abstract

ULTRAFAST DYNAMICS OF THE CYANOBACTERIOCHROMETLR0924 TAKEN FROM THE CYANOBACTERIUM ThERMOSNEchOcOccuS ElONgaTES 

Lucy Freer, Arther Thibert, Lu Zhao, and Delmar Larsen

This summer internship has been a great experience for so many different reasons. The center involves studying a range of subject areas with many novel methods, offering something for every science major. I loved learning about the cutting edge techniques that are furthering our understanding of biological systems. The labs have so much to offer because even the methods of data collection are interesting and fun. There was never a point where I felt that what I was doing was boring or tedious. Everyone within the lab has been extremely helpful. Another benefit of the program is getting to attend the annual retreat. We were privileged to listen to lectures on the latest research on viruses and other subject areas and what role the CBST could potentially play in future research collaborations.  In addition, the workshops and first week intensive provided extra exposure to what a career in science could truly mean. The panel of professionals was particularly eyeopening. It was truly liberating to hear them describe the career changes they have made when their current job didn’t fit with their lifestyle, or they simply became bored. To top it all off, Dr. Corbacho did an excellent job organizing activities with the other interns and making the whole summer fun.

Jamila Gittens

UNDERGRADUATE INSTITUTION 
   George Washington University
   Major: Biomedical Engineering

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Laura Marcu, Ph.D., Associate Professor, 
                     Department of Biomedical Engineering, UC Davis 
   Secondary Mentor: Caitlin McDonnell, Nisa Hatami, Brett Fite, Jennifer Phipps
   Laboratory:  Department of Biomedical Engineering
		   College of Engineering  
                 University of California

Scientific Abstract

Atherosclerosis is a cardiovascular disease which annually causes unexpected deaths of
millions of people, whom may have appeared healthy and had no prior symptoms. The
discovery of the role of vulnerable plaque rupture in these deaths has led to the investigation of in-vivo methods of characterizing plaque composition. The purpose of this study is to quantify atherosclerotic plaque composition and eventually show its correlation to the time-resolved laser-induced fluorescence spectroscopy (tr-LIFS) measurements. Plaque from 65 patients undergoing carotid endarterectomy was measure using tr-LIFS. Histological
stains including SMC actin, picrosirius red, and trichrome, along with circularly polarized
light, and image-analysis software, were used to compare the composition of the plaque
to the 810 flourescence measurements. Components such as collagen, smooth muscle
cell (SMC), and macrophages, play a vital role in determining the atherosclerotic plaques.
Matrix metalloproteinases-2 (MMP-2) and MMP-9, part of a family of enzymes that
degrade collagen, are particularly significant in the pathogenesis of atherosclerosis. MMP-
2 is synthesized in SMCs and is typically associated with more stable plaque higher levels
of collagen. MMP-9 is synthesized in macrophages and is typically associated with an
inflamed plaque with less collagen content. Initial results show that our data supports these
trends. Because the presence or absence of collagen can be measured spectroscopically
and correlated to pathological markers of plaque, it is expected that the tr-LIFS will be a
modality capable of recognizing markers of plaque vulnerability in vivo.


Personal Statement

My internship through the Center for Biophotonics Science and Technology (CBST) was a great experience.  Everything was stimulating, from the people to my everyday lab activities. I also obtained advanced knowledge about how to write an abstract and resume. I was able to assess how all the skills that I have learned in class are actually used on an everyday basis in the lab to solve problems that could potentially help millions of people.  First week intensive truly prepared me for entering the laboratory, easily enabling me to overcome any uneasiness with working in an unfamiliar setting. I was able to work in the Genome and Biomedical Sciences Facility on the University of California at Davis (UCDavis) campus.  My understanding of research processes was conceptually enhanced and I had a lot of hands on experience.  The retreat opened my eyes to research projects being conducted in different laboratories all over the country.  The weekly seminars were a great break from the lab and an excellent way to prepare us for some of our future endeavors.

Brianna Gonzales 

UNDERGRADUATE INSTITUTION 
   Solano Community College
   Major: biotechnology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Kit Lam, M.D., Ph.D., Professor of Internal Medicine,
                     Division of Hematology/Oncology, School of Medicine, 
                     UC Davis Cancer Center, Sacramento, CA
  Secondary Mentor: Chun-Yi Wu
  Laboratory: Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

USING ONE BEAD-ONE COMPOUND METHODTO DISCOVER INTERACTIONS BETWEEN LIGANDS AND CANCEROUS CELL PROTEINS

There is a need to develop capturing agents for the proteome so that a vast number of
proteins can be examined concurrently. Using phage-display protein expression library
derived from cDNA of Jurkat cells to screen one-bead-one-compound (OBOC)
combinatorial small molecule library, Dr. Lam and his colleagues have identified over 93
descrete small molecule ligands against Jurkat cells derived proteins. Jurkat cell is a cell line
derived from a patient with T-cell leukemia. Some of these ligands may have interesting
biological and biochemical effects on Jurkat cells.To facilitate the determination of the
target proteins to which these 93 small molecule ligands bind, we used bead bound ligands
to pan the phage-display protein expression library.The phage display library was first
incubated with ligand-covered beads, thoroughly washed, and the bound phages were
eluted and introduced to log phase E. coli TG 1 for infection. In this way, those phages
displaying Jurkat cell protein with affinity to the ligand are amplified. After three rounds of
amplification and four rounds of panning, several individual E. coli colonies corresponding
to each ligand were isolated. Selected E. coli colonies were then expanded and lysed for
phagemid DNA extraction and sequencing. Based on the DNA sequence, we can search the
public program BLAST to determine the identity of the proteins displayed on the bound
phages. We are still working on obtaining data from the sequencing of the phagemid.
In future research, the properties of the identified small molecules, the binding between
cancerous cell proteins and their corresponding ligands, and the resulted downstream
signaling pathways will be further characterized.

I think the best part of this internship was the people.  All of the interns made the first week intensive a blast from the crazy picture challenge to the difficult laboratory training.  Ana, Marco, and the rest of the people at CBST also made this program exciting for me due to their enthusiasm of science and teaching.  I learned a lot from them and the workshops they put together.  I feel I was able to obtain a better direction for my future education and career goals for grad school and entering industry.   

Working in Dr. Lam’s lab was challenging and intriguing.  The interdisciplinary research being done in the lab surprised me.  I had no idea how much important research is being done in academia.  I enjoyed how I was able to apply my knowledge of biology and biotechnology to Jimmy’s cancer research as well as learn from him.  Everyone I meet in Dr. Lam’s lab was friendly, helpful, and gave good advice about grad school.  This internship definitely made me feel more comfortable about transferring to UC Davis in the future and hopefully going to grad school there.  

Margarita R. Gutierrez 

UNDERGRADUATE INSTITUTION 
   Skyline College
   Major: Biochemistry

CBST 2008 SUMMER INTERNSHIP
   Primary Mentors: Karen Kalanetra Ph.D. 
   Secondary Mentors: Huguette Albrecht, Christine Hegedus, Christophe Morisseau, 
                        and David Rocke
   Laboratory: Oak Park Research, UC Davis Medical Center, Sacramento, CA

Margarita Gutierrez, Karen Kalanetra, Huguette Albrecht, Christine Hegedus, Christophe Morisseau, and David Rocke

Epoxyeicosatrienoic acids (EETs), the products of cytochrome P450 epoxygenase,
contribute to multiple biological functions, including the regulation of renal tubular
transport, vascular tone, and inflammatory processes. In mammalian tissues, EETs are
inactivated by soluble epoxide hydrolase (sEH) by conversion to the corresponding diols-
dihydroxyeicosatrenoic acid (DHET). Recent studies suggest that sEH represent novel drug
discovery targets for regulation of blood pressure and inflammation. In this study a human
keratinocyte cell line (HaCaT) was treated with gamma irradiation to induce inflammation
in order to test if EETs can reduce inflammation and thereby subsequent cellular damage.
Techniques used were cell culture, protein extraction, western blot and mass spectroscopy.
First, HaCat and HeLa cultures were screened for the presence of sEH by western blot
analysis, which indicated that the sEH enzyme, which degrades EETs, is expressed in the
HaCaT cell line. HeLa cells were used as positive control for sEH. Next, HaCat and HeLa
cell cultures were irradiated at 0 and 1Gy. Following irradiation, EETs (0, 0.5, 1uM) was
added and its degradation was analyzed by mass spectroscopy at 6 and 12 hour intervals.
Additionally, irradiation induced inflammatory markers were detected by western blot
analysis. Moving forward, since sEH plays an important role in the regulation of EETs and
its metabolites, further studies of sEH activity may lead to a new class of anti-inflammatory
pharmaceuticals targeting this enzyme.

Personal Statement

My summer internship spent at CBST was a great experience which helped me grow personally and professionally. Working in the lab and networking with scientists made this summer invaluable. One benefit, among many that I had in lab was the ability to learn first hand what it is like to do work independently on a project and overcome the obstacles that come in hand with it. This project was also beneficial because most of it involved biochemistry which is a major I want to pursue. As a community college student I feel that without this internship I would not have had the opportunity to do research in a field I am interested in. This internship also helped me to solidify my goals and guided me in the direction I needed to pursue graduate school. Networking with different scientists both during the internship and at the retreat was a great learning experience. The experiences they shared with me about their careers encouraged me to pursue and finish my own. I am very thankful to have been a participant in this program because it provided me with the foundation for my future career.

Nadine F. Hachouche 

UNDERGRADUATE INSTITUTION 
   Mills College
   Major: 

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Susan Spiller Ph.D., Assistant Professor, Biology
     Laboratory: Mills College, Oakland, CA

Scientific Abstract

ISOLATING CLASS II GAF DOMAINS IN NOSTOC PUNCTIFORME FROMTHE CPH2A1 AND CPH2A2 GENESTO PRODUCE A FLUORESCENT PROTEIN THAT CAN BE USED AS A MOLECULAR PROBE

Phytochromes are photosensory proteins that absorb in the red and far- red region. In cyanobacteria, a protein with a GAF domain homologous to the phytochrome’s GAF is necessary for the processes of binding of the tetrapyrrole chromophore, photoconversion, and signal transduction. Cyanobacterial proteins retaining the conserved GAF with two chromophore binding cysteines have been termed class II cyanobacteriochromes. These absorb blue or green light rather than red and far-red light in canonical phytochromes. We are examining truncated sequences from the Cph2a1 and Cph2a2 genes of Nostoc punctiforme.These cyanobacteria contain some class II GAF domain that may be engineered to produce a small, 160 to 180 amino acids, fluorescent protein, which can be used as a molecular probe. Previous research indicates that C499 of tlr0924 from Thermosynechococcus elongatus is a critical residue that covalently links the bilin chromophore in the blue absorbing form, but breaks in the green absorbing form. Mutation of the C499 to asparate (C499D) ablates blue/ green photoreversbility, resulting in the absorption of red light. By the use of standard molecular cloning techniques: protein purification, PCR of genomic DNA, restriction digest, ligation, transformation into E.coli cells, and protein expression, we sought to isolate the class II GAF domains of the Cph2a1 and Cph2a2 by PCR, followed by aspartate mutation in C499 homologous cysteine.This phytochrome engineering should provide a red fluorescent protein similar that was obtained by the mutation of tlr0924 of T.elongatus.

Personal Statement

The internship with CBST has been a rewarding experience.  The whole staff that worked closely with the interns, especially Ana Corbacho, has been very supportive and encouraging throughout the nine weeks of the internship.  The workshops that were held weekly provided the interns with skills that will only assist and enhance their abilities to finding other opportunities. The workshops included building a resume and a CV, writing an abstract, networking, interviewing, and so much more.  I have personally found these workshops to fine-tune my skills in networking and interviewing by being more confident and aware of how I present myself to people.  Furthermore, my skills in building a resume and a CV have dramatically improved by understanding the differences of each and how to tailor each one to a specific job of interest.
 
My research project on phytochromes has only reinforced subjects I have covered in my previous science courses.  The skills I have learned in Dr. Spiller's lab has forced me to trouble shoot when an experiment did not go according to plan, be proactive in finding information related to my research, and learn how to work with other people in the lab.  All these skills that I have acquired throughout this internship will only assist me in my future endeavors .  My overall experience has been wonderful. 

Victoria Hamscho 

UNDERGRADUATE INSTITUTION 
   University of California, Davis 
   Major: 

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Ting Guo Ph.D., Associate Professor, Analytical and Physical 
                   Chemistry
   Secondary Mentor: Reem Yunis, Yongquan Qu, and Andrew Vaughan.
   Laboratory: Department of Chemistry, UC Davis

Scientific Abstract

SUGAR-FUNCTIONALIZED GOLD NANOPARTICLES IN IONIZING RADIATION THERAPY OF BRAIN CANCER

Victoria Hamscho, Reem Yunis, Yongquan Qu, Andrew Vaughan, and Ting Guo

Radiation therapy is commonly used to treat brain tumors. Radiotherapy uses ionizing
radiation (IR) to destroy cancerous cells mainly by damaging their DNA, and thus leading
to cellular death. Sensitizing cancerous cells to ionizing radiation can increase the efficacy
of radiotherapy. Recent studies have used gold nanoparticles (AuNPs) as radiosensitizers
to increase the level of stand-alone DNA damage and have shown a 200% enhancement
of damage to a DNA molecule conjugated to ten 3 nm AuNPs.The aim of the present
study is to determine the radiosensitizing effect of sugar-functionalized gold nanoparticles
(S-AuNPs) in a human medulloblastoma-derived cell line (DAOY) and a glioblastoma-
derived cell line (U87MG).The cell lines were grown and maintained in EMEM medium
supplemented with 10% fetal bovine serum and incubated in a 37°C atmosphere.The cells
were treated with 0 and 100 µg of S-AuNPs for 8 or 24 hours, washed, and subjected to
different doses of IR (0, 2, 4, 6, 8 Gy). Cell survival was measured by the clonogenic assay
in which cell colonies were counted after fixing the cells in ice-cold methanol and staining
them with 0.1% crystal violet.The cellular death was higher in cells preincubated with
S-AuNPs, suggesting that S-AuNPs could serve as radiosensitizers in brain tumor cells. A
future direction of our study is to investigate the mechanism by which S-AuNPs enhance
the IR effect in brain tumor cells.

Personal Statement

At first I did not know much about the internship. All I knew was that it would be an invaluable academic experience for me, for it would provide me with the opportunity to acquire different laboratory skills and learn about biophotonics in a team-based environment. After working at the laboratory for eight weeks, I am able to say that not only did I learn about biophotonics and its applications, but also about how to conduct and perform scientific research.  

      Working with an interdisciplinary team of physicists, chemists, and biologists taught me that research is not about what I know or am capable of doing, but about how well I am able to combine my knowledge and skills with the expertise of others for a common goal. It was indeed invaluable for me to experience the blending of so many disciplines, as well as to experience and learn about them individually. Yet learning about the different aspects of my project would not have been easy without the unconditional support of my mentor and friend Dr. Guo. His enthusiasm and commitment towards research made it easy for me to feel connected to our project.  

      Regardless of what profession I decide to pursue in life, I know this internship has both enriched and broadened my undergraduate education. I could not have had a better opportunity to take all the knowledge I have gained from textbooks and see it all come together in real life. 

Harliv Hans 

UNDERGRADUATE INSTITUTION 
    University of California, Berkley
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Thomas Huser, Ph.D., Associate Professor, Internal Medicine, 
                   School of Medicine and Center for Biophotonics Science and 
                   Techology, UC Davis
   Secondary Mentor: Samantha fore   
   Laboratory: Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

Cardiovascular disease is the leading cause of death in the United States today. One
symptom of atherosclerotic vascular disease is a “hardening”of the arteries that is caused
by the buildup of fats and cholesterol on artery walls and is promoted by low density
lipoproteins (LDL). High density lipoproteins (HDL) remove cholesterol from artery
walls and transport it to the liver for excretion or reuse. Apolipoprotein A-1 (APOA1) is
the major protein component of high density lipoproteins in plasma. APOA1 is known
to promote cholesterol efflux from various tissues to the liver for excretion. APOA1
interacts with phospholipid bilayers and is known to form phospholipid bilayer nanodiscs.
Dimyristoylphosphatidylcholine (DMPC) is one of the lipids that is found in cell
phospholipid bilayers. Phospholipid bilayer nanodiscs are membrane models that are useful
in studying small-molecule binding to membranes and membrane proteins.
APOA1 was reacted in different concentrations with micromolar concentrations of 100nm
DMPC vesicles. The reaction was monitored for different periods of time and samples
were analyzed through Fluorescence Correlation Spectroscopy (FCS). FCS uses a confocal
microscope to focus light on a sample and measure fluorescence intensity fluctuations.
Fluctuations are caused by diffusion and chemical reactions. The results are analyzed using
temporal autocorrelation and allow us to obtain the diffusion coefficients of molecules in
the reaction. By studying the characteristics of the reaction of APOA1 with phospholipid
vesicles, we can gain a better understanding of the mechanisms of apoliprotein interactions
with lipids, and their potential use for therapeutic application.

Personal Statement

PENDING    

Alfredo Hernandez 

UNDERGRADUATE INSTITUTION 
   Contra Costa Community College
   Major: 

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Min Zhao Ph.D., Professor
   Secondary Mentor: Vu Tran, Lin Cao
   Laboratory: Department of Dermatology

Scientific Abstract

PTEN plays an important role in the regulation of cell division and proliferation. PTEN
prevents cells from dividing out of control by antagonizing pAkt signaling. So PTEN
is important because it prevents tumors from forming. But by inhibiting PTEN in a
controlled way, we can promote cell growth in wounds and thus the increase rate of wound
healing. The focus was to study inhibition of PTEN by testing different concentrations
of the drug, bisperoxovanadium (bpv).The objective was to understand wound healing in
correlation to the PTEN levels in in-vitromonolayer epithelia (HCE). HCE cells were
subcultured in 24 wells until an adhesive monolayer was formed. Using a pippette tip, a
“cut”was made across each HCE monolayer sample.The wound applied to the monolayer
sample was put under a microscope with a camera. The process of proliferation and
migration of the monolayer sample was recorded. Monolayer samples consisted of different
concentration for comparison.The data showed that higher concentrations of drug increased
rate of migration.The ideal amount of drug increased migration by two-fold. Addition of
extra drug resulted in unwanted toxic effects in cells. It showed that low levels of PTEN
increased cell migration, since the drug was inhibiting PTEN. Alternative drugs can be
tested for better PTEN inhibition. testing different varieties of bisperoxovanadium drug
should also be considered.


Personal Statement

CBST internship was a great internship that, believe it or not, has changed my life. I expected to work in a lab all day with a protocol in my hand, and as a shy person I didn’t really mind it. But on the contrary, CBST had plenty of activities for us to connect with the other interns and their helpful staff. The best thing about this program was that it completely submerged me into the scientific community. I learned about things I wasn’t expecting to learn from an internship. In this internship I was given the opportunity to learn about scientists and researchers, the stereotypes were shattered. I also learned about the importance of networking. Near the end of the internship during the CBST annual retreat, I had the opportunity to meet researchers from around the world. I even had the privilege to hold a one -hour conversation with a German researcher who was working in Japan. I also had the opportunity to meet many post graduates and learn about their work. I’m also glad I met Ana Corbacho, our CBST director, a wonderful person I would like to thank for this wonderful experience.

Nicole Hernandez 

UNDERGRADUATE INSTITUTION 
   University of California, Davis
   Major: Biological Science emphasis in Biotechnology and applied Microbiology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Satya Dandekar, Ph.D., Chair of Immunology and 
                     Microbiology of the UC Davis School of Medicine   
   Secondary Mentors: Monica Macal, Irina Grishina
   Laboratory: Department of Medical Microbiology and Immunology,
                 Genome and Biomedical Sciences Facility, UC Davis,

Scientific Abstract

Inflammatory bowel disease (IBD) is an autoimmune disorder where an upward
regulation of CD4+ T-cells is seen in the intestinal tract of patients; in contrast, Human
Immunodeficiency Virus Type 1 (HIV-1) is a disease in which the HIV virus is capable of
infecting CD4+ T cells and via multiple pathways kills these cells. CD4+ T cells are mature
lymphocytes that express the surface protein CD4 and play an important role in immune
function. Due to HIV-1’s ability to infect CD4+ lymphocytes, in an individual who has
IBD, we expect to find an overwhelming number infected CD4+ T cells.This study will
be conducted on formalin-fixed paraffin-embedded intestinal tissue sections from subjects
with HIV-1 and IBD.These specimens will be immunohistochemically stained with CD4+,
CD68, and P24 antibodies to distinguish T cells, macrophages, and HIV-1 infected cells,
respectively, which will then be evaluated using confocal microscopy.The gut-associated
lymphoid tissue (GALT) is the site for early inflammatory response, and by analyzing the
CD4+ T-cell expression and HIV-1 infection of HIV-1 and IBD infected subjects we will
be able to elicit significant evidence about the mechanisms that occur in the GALT with
relationship to these immune response disorders.

Personal Statement

As a CBST Summer Intern, I was fortunate enough to gain a firsthand account of modern-day scientific breakthroughs. Through the hands-on experience and by guidance from my mentors, the post-docs and grad students, I was able to witness the creative side of science that is very rarely exposed. New ideas were highly encouraged and simple linear thinking was dissuaded. From a professional standpoint, the Summer CBST Internship has given me the chance to see science on a different level. I worked in labs prior to this internship, but this experience was definitely on a completely different playing field. It is in these labs that the answers to some of science's most puzzling questions are answered through the development of new technology. To me, this internship was much more than just lab work. This internship was about developing the tools needed to be able to succeed in a scientific field and being part of an innovative scientific research community.

Adrian Lam 

UNDERGRADUATE INSTITUTION 
   University of California, Davis  
   Major: Biomedical Engineering

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Laura Marcu, Ph.D., Associate Professor, 
                   Department of Biomedical Engineering, UC Davis 
   Secondary Mentors: Christopher W. Dunsby, Jesung Park, Yang Sun
   Laboratory:  Department of Biomedical Engineering
		   College of Engineering  
                 University of California, Davis

The medical applications of tissue autofluorescence to diagnose brain cancer, detect oral lesions or characterize atherosclerotic plaques have become popular due to their simple and inexpensive characteristics. However, the wavelengths used for excitation during the photodiagnostic process often lie in the UVA/UVB region and can cause mutagenic DNA damage in cells. With few studies focused toward measuring the extent of damage induced by these processes, our goal was to assess the sensitivities of hamster cheek, palate, tongue, and skin tissue to both pulsed and continuous wave lasers in order to find a threshold at which spectroscopic measurements could be taken safely. Each laser delivered 2-3 different doses (0.5, 1, 5 mJ/mm2) in vivo with fluorescence lifetime data obtained at specific times. Additional exposures were also performed to determine whether higher doses at shorter exposure times were more or less harmful than lower doses at longer exposure times. Biopsy samples taken immediately after and 24 hours after irradiation were fixed in formalin and immunohistochemically stained for p53, a protein transcribed in response to DNA damage, as well as H2A.X, a histone which undergoes phosphorylation upon double strand DNA breaks. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was also used to mark 3’-OH terminal DNA ends to evaluate the fraction of apoptotic cells within each tissue section. Spectroscopic data showed that there was at max 15% photobleaching at radiant exposures less than 5 mJ/mm2. However, further steps are still required to match and analyze lifetime plots to immunohistochemical results.

Personal Statement

“I play with lasers.” Through perhaps a child’s daydream as he fires lasers from a gun, it was my reality through fluorescence spectroscopy, an exciting internship I participated in by CBST this summer. From the beginning to end was a nonstop and tiring process, sometimes even mentally demanding, but it was an experience which school could never offer. The first week intensive I found to introduce and prepare all the interns to the laboratory setting in a creative, yet fun manner, allowing for a very friendly and warm atmosphere. However, as we all split up and went into our respective labs, I found my days to start up slowly, but the pace picked up rapidly and I was fortunate enough to participate in a collaborative experiment with physicians, a professor from London and my principal investigator. Watching minds from different disciplines work together was truly inspiring as I witnessed and took part in the entire process, from idea to actualization. In the future, I definitely plan to continue helping the Marcu Lab to facilitate the paper writing process and look forward to working on other exciting projects with amazing people. Overall, this internship coordinated by Ana through CBST has been absolutely phenomenal from laboratory experience to people met, providing an excellent place for growth as a researcher and person; my deepest thanks and appreciation goes out to CBST for what turned out to be a very memorable summer.

Hanqing Li

UNDERGRADUATE INSTITUTION 
   Sacramento City College
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Min Zhao Ph.D., Professor
   Secondary Mentor:  Brian Reid 
   Laboratory: Department of Dermatology   

USING CHAMBER MEASUREMENTS OF RAT EPITHELIUM AND MDCK CELL MONOLAYERS

Measuring the membrane potential across epithelium is an important and effective way of studying the mechanism of wound healing.  Knowing the potential change across the membrane before and after infliction of a wound may have strong applications clinically.   Our goal was to determine how the voltage, current, and resistance of a piece of epithelium or monolayer of cells changed before and after wound infliction.  To accomplish this, we used a Ussing chamber to measure pieces of rat, and Madin-Darby canine kidney (MDCK) cells before wound infliction and after.  For the MDCK cells, the voltage and current of 60% of the experimental trials decreased after wound infliction, and resistance in 80% of the trials increased after wound infliction.   For the rat skin, the voltage of 67% and current of 50% of the experimental trials increased, while the resistance of 67% of the trials decreased.  From the above data we can see that the effects of wound infliction are different for cell monolayers and epithelium.   Further studies on drug effects on wound healing hopefully will lead to more effective clinical treatment of epithelial wounds. 

    I came into the CBST 2008 summer internship with eagerness and high hopes.  Before this, I had the fortune to participate in the 2008 CBST winter internship for community college students.  I had a great time in that internship and so when I learned I was accepted into the summer internship, I was esctatic.
      As it turned out, my hopes and expectations were fulfilled.  I had as much fun and learned as much in this internship as in the winter one.  I worked in Dr. Min Zhao’s lab at UC Davis.  Dr. Zhao’s lab does work in electrophysiology and I assisted in doing experiments with rat epithelium using a Ussing chamber.  We measured the voltage, current, and resistance across wounded and unwounded rat epithelium.  Along with this, I also learned many other techniques, such as culturing cells.  Dr. Zhao and the other people in the lab were all very friendly and helpful.
      Besides the lab work, there were many activities that the CBST interns did as a group.  During the first week, we participated in many activities together designed for us to learn and to get to know each other better.  After that, we had a group meeting every week where we were taught a multitude of skills, ranging from how to write a resume to how to face an interview.  We also had the chance to participate in the CBST annual retreat at Lake Tahoe.  There, we listened to researchers present the results of their research, met a variety of people affiliated with CBST, enjoyed the many recreational activities the resort and the environment had to offer, and had some great food.  It was all great fun and very educational.
      All in all, I had a fabulous time in this internship.  Dr. Corbacho and everyone at CBST were so encouraging and helpful.  Thanks everyone!

Molly McDevitt 

UNDERGRADUATE INSTITUTION 
   Creighton University
   Major: Biochemistry

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Henning Stahlberg, Ph.D., Associate Professor
   Secondary Mentor: Lisa Yee, and Lenin Dominguez-Ramirez.
   Laboratory: Molecular and Cellular Biology, 
                College of Biological Sciences, UC Davis

As the source of ATP for the cell, mitochondria are essential to cellular life.The
supercomplex responsible for the synthesis and transport of ATP is known as the ATP
synthasome. It consists of ATP synthase in association with the phosphate carrier (PIC)
and adenine nucleotide carrier (ANC). A mutation in any component of the complex may
cause a variety of mitochondrial diseases; some of which are lethal. In order to understand
and perhaps treat these diseases, it is important to determine the native structure of
the ATP synthasome. Because it consists of integral membrane proteins, this has so far
proven difficult. In this laboratory, electron microscopy has been used to procure images
of small inner mitochondrial vesicles of bovine cardiac tissue. However, the higher-order
organization cannot be determined by computer processing because the vesicles are too
small. In theory, concentrations of detergent below the critical micelle concentration (cmc)
will cause fusion of the vesicular membranes while retaining the native structure of the
ATP synthasome. Size of the small inner mitochondrial vesicles can be monitored via
spectroscopic techniques and fusion can be confirmed by electron microscopy. It is the goal
of this experiment to determine optimum conditions for the production of vesicles large
enough for analysis while retaining the proteins’native shape. By obtaining better images,
we hope to gain a greater understanding of the structure of the ATP synthasome within an
environment similar to the one it inhabits within the mitochondrial membrane.

 My summer spent with CBST was nothing short of a wonderful experience. The first week intensive gave me a chance to get to know others in the internship and the subsequent weekly meetings gave me a chance to hear what others were doing.  Being from Iowa, I was a little nervous but I ended up meeting some people that I know I will keep in touch with for many years to come.
      It was great to be able to take ideas I had learned in previous courses and actually apply them in the laboratory. I also learned that many of the skills necessary in the laboratory cannot be learned from a book but must be learned from hands-on experience. This summer I was given the opportunity to get some of that experience. The member’s of the lab were both welcoming and helpful and I feel lucky to have had the chance to spend my summer working in the Dr. Henning Stahlberg at the University of Davis.
      The annual retreat gave me a chance to see applications for biophotonics outside of the research being done in my laboratory. I got a chance to see how biophotonics are being applied to research in both the academic field as well as in industry. It was a great experience all around. Unfortunately, since I am not from the Davis area I will not be able to continue to work in Dr. Stahlberg’s lab but as graduation nears, my experience with CBST will definitely make me think about returning to California for graduate school.

Paul J. Mello

UNDERGRADUATE INSTITUTION 
   Ohlone College
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Bruce Lyeth, Ph.D., Professor of Neurological Surgery, 
                     Neurological Surgery, School of Medicine, UC Davis. 
   Secondary Mentors: Bryan Brandon, Gene Gurkoff, Justin Beller 
   Laboratory: Center for Neuroscience, UC Davis, Davis, CA and   
                Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

DETERMINING HOWTRAUMATIC BRAIN INJURY AFFECTS THE ONTOGENY OF N-METHYL-D- ASPARTATE RECEPTOR (NMDAR) IN MIxED NEURONAL AND ASTROCYTIC CULTURES

Traumatic Brain Injury (TBI) is the foremost cause of death and disability among
children. Additionally it has been reported that 10-20% of front-line soldiers from Iraq
and Afghanistan receive a TBI. It is known that TBI leads to a chemical cascade of events
in which neurotransmitters (and their receptors) are hyper-activated leading to neuronal
dysfunction and death. Previous in vivo studies suggest these TBI-induced chemical
cascades reduce the expression of NR2A, a subunit of the N-Methyl-D-Aspartate receptor
(NMDAR).This is particularly relevant in the developing brain as NMDAR is undergoing
a maturational process where specific expression of the receptor and its subunits is thought
to play a critical role in plasticity. Using mixed neuron-astrocytic cultures, Western-Blot
Analysis, and performing mechanical and glutamate toxicity tests we will first characterize
NMDA receptor expression in cells collected 2, 5,7,10, 14, 21 days in vitro. Once the
developmental time course is determined we will injure a second set of tissue and determine
how injury effects NMDAR development.The preliminary stage of these experiments is
to verify that we can reproduce observed in-vivo pathologies and pathophysiologies in in-
vitro. The ability to utilize in-vitro techniques will allow for high-throughput pre-clinical
screening of therapies in an attempt to formulate improved methods for treatment of TBI.

Personal Statement

  The CBST Summer Internship was the most intellectually enriching experience of my life. The CBST staff carefully planned a first week program which facilitated our transition from the academic setting into the research environment. The first week intensive, the weekly seminars, and the CBST retreat provided unique intellectual and social experiences during which many bonds were created.
     During this summer I worked at the Center for Neuroscience, more specifically in Dr. Bruce Lyeth’s Laboratory where the focus of research is on Traumatic Brain Injury. There I was exposed to new terminology, new laboratory techniques, and a different way of thinking-it was analogous to learning a new language. This learning process was greatly facilitated by the interest, availability and willingness to help of my mentors: Dr. Bruce Lyeth, Dr. Gene Gurkoff, and Justin Beller. It was/is an honor to be involved in such cutting edge research and to be mentored by such a great group of individuals. I am also very thankful for the opportunity to prolong this research experience throughout the academic year. 
     This internship provided something I could have never gotten by attending infinite amount of lectures: real life experience. It is one thing to be given an answer, but having the possibility to find your own answer is something that everyone interested in science should have exposure to, thus I encourage anyone interested in a career in science to apply for this internship. I would like to thank Dr. Ana Corbacho and the CBST staff for this opportunity. 

Leah Meza 

UNDERGRADUATE INSTITUTION 
   Solano Community College
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Kit Lam, M.D., Ph.D., Professor of Internal Medicine,
   		      Division of Hematology/Oncology, School of Medicine, 
                    UC Davis Cancer Center, Sacramento, CA
   Secondary Mentor: Harry Tseng, Wenwu Xiao, and Nianhuan Yao.
   Laboratory: Center for Neuroscience, UC Davis, Davis, CA and   
                Oak Park Research, UC Davis Medical Center, Sacramento, CA

Scientific Abstract

IDENTIFICATION OF BINDING AFFINITY OF PEPTIDES AGAINST BREAST CANCER CELLS

Leah Meza, Harry Tseng, Wenwu Xiao, Nianhuan Yao, Kit S. Lam

In the United States, one out of eight women will develop breast cancer in their lifetime. There is a need for the development of safe and effective diagnostic and therapeutic agents for breast cancer. Using “one-bead-one-compound” (OBOC) combinatorial library method, the Lam laboratory has previously identified several targeting cyclic peptides against breast cancer cell lines (MDA-MB-231). LXY1, a cyclic peptide with high binding specificity to 3 integrin was discovered. Using flow cytometry analysis, the binding affinity (Kd) of LXY1 to 3 integrin on MDA-MB-231 breast cancer cells was determined to be approximately 0.4 µM. Based on the established structure-activity relationship (SAR) study, two highly focused cyclic peptide libraries were further designed, synthesized, and screened against MDA-MB-231 breast cancer cells under stringent conditions. LXY3, a cyclic peptide with a high binding affinity (IC50=57 nM) was developed. We have designed and synthesized about 50 analogues of LXY3 in solution phase. The use of flow cytometry to determine binding affinity is slow.  We therefore have developed a competitive adherence inhibition assay to measure the relative binding affinity (IC50) of these peptides to intact MDA-MB-231 cells. In this assay, serial dilution of soluble peptides were added to 96-well plates to inhibit the binding of MDA-MB-231 breast cancer cells to immobilized LXY1 ligand. Using this method, the affinity of LXY4 to MDA-MB-231 was found to be ten times stronger than that of LXY3 (LXY3 IC50=7.1µM, LXY4 IC50=0.7µM). In this study, we have demonstrated that the competitive adherence inhibition assay is much more efficient than the flow cytometry assay; and with this method, we were able to select LXY4 as our candidate compound for further studies. The in vivo targeting characteristic of LXY4 peptide will be evaluated in a breast cancer xenograft mouse model with optical imaging. This will provide important information for its further development into a novel therapeutic agent for breast cancer.

Coming back for a second year as a CBST intern has been one of the best decisions I have made. Returning to such a positive environment gave me excitement to spend my summer in the lab again. My mentor trusted me to handle my project independently since I had all the essential techniques down from last summer. Being a part of this research really made me feel like I was an important part of the project. Even though I was a second year intern, I was still constantly gaining new knowledge and experience in the lab. This year we developed a technique that was much more efficient than what I was using last summer. The CBST program has also given me opportunities to be a part of other future projects as well, and to be involved in the lab for the school year. Getting to know a whole new group of CBST interns has been one of the best parts. Everyone was very friendly and just as eager as the group from the previous year. The CBST staff made every seminar, retreat, and activity really enjoyable and will be in my memories forever. This made the whole experience one that I wish did not have to end. 

Emily J. Mills

UNDERGRADUATE INSTITUTION 
   University of California, Davis
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Atul N. Parikh Ph.D., Associate Professor, 
        	      Department of Applied Science 
   Secondary Mentor: Dan H. Bricarello   
   Laboratory: Department of Applied Science, 3007 Engineering III
	          University of California, Davis

Scientific Abstract

I have grown a lot as a result of my CBST summer internship.  My fellow interns were all amazing, intelligent and interesting people who I really enjoyed spending time with.   The program was  well organized and Ana Corbacho made all the activities fun as well as educational.  I really enjoyed the first week intensive, it allowed all of the interns to get to know each other and form friendships that made the rest of the program so much more enriching.  My experience with my lab has also been wonderful, both my primary and secondary mentors are always willing to help with any questions, and the rest of the lab is also extremely friendly and supportive.   I feel like I've made a significant contribution to the project I'm working on and I feel much more confident in my ability to think scientifically.  CBST annual retreat was also an amazing opportunity to be exposed to all the most recent developments in the field of biophotonics as well as to speak with graduate students and doctors to get a better understanding my own academic future.  This program has reinforced my decision to work towards a doctorate degree and eventually a career in medical research.

Brenda Montanez

UUNDERGRADUATE INSTITUTION 
   Napa Valley College 
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor:  Sebastian Wachsmann-Hogiu, PhD 
                    CBST Facilities Director
   Secondary Mentors: Cynthia V. Pagba
   Laboratory:  Oak Park Research, UC Davis Medical Center, Sacramento, CA

Surface Enhanced Raman Spectroscopy (SERS) is a process that uses metallic nanoparticles
(50-100nm) for the amplification of the very weak Raman scattering signal.This allows
the measurement of Raman vibrations of molecules at very low concentrations, down to
the single molecule level. However, the application of SERS in the development of sensors,
in general, is being hindered by certain problems (for instance, signal fluctuations) that
are inherent with the SERS process. In this study we want to look into this phenomenon
by monitoring the changes in the SERS spectra of the molecule p-Aminothiophenol
(PATP) bound to silver nanoparticles every ms for a period of 100 ms with respect to
temperature and intensity of the excitation light. Preliminary results show drastic changes
in Raman intensities as well as significant shifts of the vibrational bands as the power was
increased. Understanding the origins and nature of such fluctuations in the spectra may
help us understand the SERS process and therefore allow us to improve the development of
SERS-based biosensors. Such biosensors can be used in the detection of certain biologically
important molecules such as cancer biomarkers, biological threat agents, and biomolecules
that are associated with infectious diseases.

Personal Statement

Thien Huong Nguyen

UNDERGRADUATE INSTITUTION 
   San Jose State University
   Major: Chemistry, concentration on biochemistry

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Chong-xian Pan, M.D., Ph.D., 
                     Division of Hematology/Oncology, 
                     School of Medicine, 
                     UC Davis Medical Center, Sacramento, CA
   Secondary Mentor: HongYong, DVM
   Laboratory: Oak Park Research, UC Davis Medical Center, Sacramento, CA

The summer internship with the Center for Biophotonics Science and Technology (CBST) gave me unforgettable memories. This is a great opportunity for me to understand how wonderful a research program can be. I learned numerous laboratory techniques and use those to perform independent experiments. Through the weekly meetings, I learned many skills from laboratory, biophotonic concepts to communication, interview, and presentation. The 3-day annual retreat meeting at Lake Tahoe resort is also a great chance for me to know what I can be in the future. If you want a combination of research and fun, I will say go for CBST summer internship. It's wonderful chance to connect classroom to reality.

Ngabo Nzigira 

UNDERGRADUATE INSTITUTION 
   Consumnes River College
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Julia Evans, Ph.D. 
   Secondary Mentor: Stacey S. Choi, Rovert j. Zawadzki, John S. Werner.
   Laboratory: Vision Science and Advanced Retinal Imaging Laboratory, 
                 Department of Ophthalmology, UC Davis Medical Center  

Scientific Abstract

USING IN VIVO ULTRA-HIGH RESOLUTION RETINAL IMAGINGTO ASSESS EYE DISEASE

Ngabo S. Nzigira, Stacey S. Choi, Julia W. Evans, Rovert j. Zawadzki, John S. Werner

Personal Statement

   This past summer I was given the tremendous opportunity by the Center for Biophotonics (CBST), to be an undergraduate summer intern. Personally I was given a great opportunity to reflect on where I want my life to go and what path I want to travel. I was very interested in a career in ocular health care prior to the summer research, and upon conveying this to the research coordinator she was able to place me in a lab that focused on vision science and retinal imaging. The opportunities provided to me while in this lab were invaluable I was able to learn about the visual system more in depth than I ever had, and be given an amazing opportunity to image patient’s retinas myself. In addition I was given an opportunity to shadow ophthalmologists in both the clinic and in the surgical environment.
    I however believe that the most important lessons I learned this summer didn’t come from the cool things I did or heard researchers present, but from the wisdom of people who have gone down the paths I have before me. I remember some of my fondest memories just sitting over lunch and talking to my principal and secondary mentors about life and growing up, and getting quality advice from a place that I know is of experience. 
Ana was really good about gathering a panel of industry professionals together to share their life experiences and the details of their journey towards the end of our internship. She didn’t know before hand but there was a common link between all the individuals including herself, and that was an uncompromising attitude to find happiness in the work they did. I realized something before that I never considered; I’ve been focused so much on getting to the finish line as far as getting to a career, that I never consider the possibility of getting there and finding out its not right for me. These professionals have all dealt with that feeling and have had the guts to turn around and start all over at something else, which had no more promise of happiness than the last career, but they did it. I don’t fear not knowing and I welcome change, and I now have a model of courage to apply to my life when things don’t go my way.  
    The summer research program brought together a lot of great individuals with varying backgrounds and even more varying career goals. I really commend CBST for their intern selections this year, when I saw the research presentations, I not only saw fascinating science and good work but I saw the faces of individuals who will grow and make the world a better place. I only hope to join them, thank you CBST and Ana Corbacho.
    

Benjamin R. Perea

UNDERGRADUATE INSTITUTION 
   Consumnes River College
   Major: Chemistry

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Delmar S. Larsen, Ph.D., Assistant Professor
   Secondary Mentor: Melissa P. Hill.
   Laboratory: Department of Chemistry, UC Davis

Pyridoxal 5’-Phosphate (PLP), the biologically active form of vitamin B6, is a crucial 
coenzyme to numerous metabolical functions within the human body. Studied here is 
the photodynamics of PLP in solution alone and in combinations with other amino acid 
substrates. Irradiation of PLP with 440 nm (blue) light leads to a photoproduct being 
generated; we show that the kinetics behind this formation can be manipulated through 
the elimination of oxygen within the sample, the addition of heavy atoms, and various 
amino acids which form chemical bonds with PLP known as “Schiff bases.”The extent 
of these manipulations was quantitatively measured with the assistance of a UV/Vis 
spectrophotometer and high intensity LEDs. Previous studies have shown that PLP 
has a distinct visible light spectrum with an absorption peak at 388 nm, and that the 
photoproduct, Pyridoxamine 5’-phosphate is created as a result of irradiation of PLP with 
440 nm light.This results in a new peak at 305 nm increasing in magnitude as exposure 
time increases. Consequently, the peak at 388nm undergoes a rapid decline in magnitude 
over time.The addition of the heavy atom iodine within the sample slows this decrease at 
388nm by as much as 40%, thus slowing the increase at 305 nm – the result being that less photoproduct was formed. As multiple neurotransmitters including serotonin, epinephrine, norepinephrine, and gamma-aminobutyric acid require PLP in their synthesis this information will be used to develop new therapies for PLP-dependent enzyme disorders.

Tamara Restrepo

UNDERGRADUATE INSTITUTION 
   El Camino College
   Major: Biochemistry

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Delmar S. Larsen, Ph.D., Assistant Professor 
   Secondary Mentors: Melissa Hill
   Laboratory: Department of Chemistry, UC Davis

This study was undertaken to understand the most fundamental interactions between light
and non-light activated enzymes. Our research specifically explores the photochemistry
of Vitamin B6 in its active form: pyridoxal 5’-phosphate (PLP), which serves as a cofactor
in a variety of chemistries in biological systems such as transaminations, decarboxylations,
deaminations, and others. The unique chromophore structure of PLP and its ability to form
Schiff base linkages enables it to be used as a potential indicator of events occurring at the
catalytic site of a PLP-dependent enzyme.
PLP-dependent enzymes catalyze reactions on a millisecond time scale and, as a result,
little is known about their ultrafast (femtosecond, picosecond, and nanosecond) dynamics
that dictate the progression of the enzymatic catalysis. PLP and its Schiff base generate
photoproducts on an ultrafast time scale; however, the nature of these products is
unknown. Using optical spectroscopy and High Performance Liquid Chromatography,
the photoproducts of PLP and PLP in a model Schiff base to valine in solution were
determined.Triplet quenchers (i.e., heavy atoms) were then used to determine whether
the photoproduct was generated via a triplet state or through the essential “quinonoid”
intermediate. Results showed that both PLP and PLP in its Schiff base were affected by
triplet state chemistry. Our findings open new doors to monitoring enzymatic activity on
the ultrafast time scales with greater understanding of their essential dynamics, and allows
for other applications aiming to enhance enzymatic reaction rates with the application of
light.

Personal Statement

The Center for Biophotonics Science and Technology (CBST) summer 2008 internship was an extraordinary experience.  The other interns and staff members were highly supportive and willing to share their motivation with the group.  Moreover, the laboratory environment was welcoming, and the research team members were willing to answer questions and guide us throughout the project. At first, I hesitated to leave Los Angeles to move up north for the eight week duration of the program, not knowing that the learning experience and the many skills I gained would tremendously compensate for my effort.  During the two months, we had group meetings at least once a week that aimed to prepare us for interviews and scientific presentations, among other skills that I highly enjoyed.  The annual retreat at Lake Tahoe provided us with an opportunity to listen to the graduate oral presentations, as well as to admire the beautiful views of the lake.  I highly recommend other students who want to experience interdisciplinary research to undertake this opportunity which will leave a sense of what it is to be a real scientist on an everyday basis.  I am very thankful to CBST and each and everyone who made possible my participation in the summer internship. I have become a better educated individual, which in the long run is what matters the most, and will continue to grow from the skills I have acquired from this experience.

George David Suarez

UNDERGRADUATE INSTITUTION 
   University of California, Davis
   Major: Applied Physics

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Ting Guo, Ph.D., Professor of Chemistry
   Secondary Mentor: Rhiannon Porter
   Laboratory: Nanofast Lab, UC Davis, Davis, CA  

THIN FILMTARGET DEVICE FOR ULTRAFAST LASER-DRIVEN x-RAY PRODUCTIONTO IMPROVE PERFORMANCE IN x-RAY ABSORPTION SPECTROSCOPY 

George David Suarez, Ting Guo

UNDERGRADUATE INSTITUTION 
   University of California, Davis
   Major: Biochemistry

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Stacey Harmer, Ph.D., Assistant Professor 
   Secondary Mentors: Matthew Jones, Samantha Harris
  
   Laboratory: 

UNDERGRADUATE INSTITUTION 
   Skyline College 
   Major: Biology

CBST 2008 SUMMER INTERNSHIP
   Primary Mentor: Henning Stahlberg, Ph.D., Associate Professor
   Secondary Mentors: Lenin Dominguez-Ramirez, Molly McDevitt
   Laboratory: Molecular and Cellular Biology, 
                College of Biological Sciences, UC Davis