OUR TRAINEES:
ADAMS, KATRINA L.
Katrina is a first year trainee and is in the Molecular Biology IDP. Her research mentor is Dr. Bennett Novitch. She received a B.S. degree in 2008 from UC San Diego.
Katrina’s Research Project: Deriving motor neurons from embryonic stem cells and induced pluripotent stem cells is an exciting new potential therapy for many devastating neurodegenerative diseases. However, little information is currently known about whether stem cell-derived motor neurons actually mimic natural motor neurons. My project aims to characterize and compare embryonic stem cell and induced pluripotent stem cell-derived motor neurons with human embryo-derived motor neurons. In addition, I aim to evaluate the role of the transcription factor Foxp1 in motor neuron formation. Foxp1 has been shown by my lab to be required for the development of limb innervating motor neurons in vivo. By misexpressing Foxp1 and other motor neuron determinants in embryonic stem cells, I hope to diversify the subtypes of motor neurons that can be generated in vitro.
ANDERSON, JENNIFER L.
Jenny is a third year trainee and is in the Molecular Biology IDP. Her research mentor is Dr. Christopher Denny. She received a B.S. degree in 2006 from UCLA with Honors.
Jenny’s Research Project: Mathematical modeling of signal transduction networks allows for dynamic interactions to be integrated into static pathway maps. Tools such as simulations and sensitivity analysis can identify components of the network that are critical in determining model output. To take advantage of this system, we have created a model of the IGF-I signaling pathway, which has been linked to many types of cancer. After validation of our model in a breast cancer cell line, this model will also be applied to Ewing’s sarcoma. Sensitivity analysis will be performed to identify critical components in the IGF-I pathway in hopes of identifying new therapeutic targets in the treatment of cancer.
CHANG, HOWARD W.
Howard is a second year trainee and is in the Department of Chemistry and Biochemistry. His research mentor is Dr. David Eisenberg. He received a B.S. degree in 2007 from UC San Diego.
Howard’s Research Project: More than 20 human diseases are found to be associated with ordered
protein aggregates. These amyloid-associated diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer's disease, and Parkinson's disease, affect thousands in the United States, causing a variety of organs to malfunction. Recent milestones in structural and computational biology allow us to now attack amyloidoses on an atomic level. To this end, we have adapted the Rosetta Design algorithm to
design tight-packing inhibitors of amyloid formation. We have already demonstrated that this approach is effective in vitro, for the tau protein associated with Alzheimer's disease. I intend to continue developing this tau fibrillation inhibitor for therapeutic purposes. In doing so, I seek to also advance our understanding of Alzheimer's disease; specifically inhibiting fibril formation will help elucidate the role of fibrils in the cytotoxicity of this and other protein aggregation diseases. With success, another objective is to create a general framework for transitioning from a computationally-designed, tight packing peptide to a rational drug for amyloid diseases.
CHOW, DAVID K.
David is a third year trainee and is in the Department of Neurobiology. His research mentor is Dr. Joshua Trachtenberg. He received a B.A. degree in 2005 from Haverford College.
David’s Research Project: Using in vivo 2-photon microscopy, we repeatedly image dendrites and
spines over periods of weeks in mouse cortex. Completed experiments show that adult, neocortical knock out of the gene Pten induces growth of apical dendrites of pyramidal neurons in layer 2/3 of the mouse cortex. Basal dendritic arbors of the same cells, as well as layer 5 apical arbors are unaffected by Pten deletion. Administration of rapamycin, an inhibitor of mTOR, halted, and in some cases reversed aberrant dendrite growth in KO animals. The next phase of our project will investigate the effects of Pten-KO-induced dendritic growth on cortical circuit function. What happens when new synaptic connections are added to an existing, mature cortical network? We will answer this question on using intrinsic signal optical imaging in the visual cortex of Pten-KO mice. Using this technique, we can measure magnitude and organization of cortical response and observe the effects of growing dendrites and newly formed synapses as Pten-KO-induced dendritic growth proceeds in vivo.
DENG, QIMING
“Q” is a third year trainee and is in the Department of Biological Chemistry. His research mentor is Dr. Timothy Lane. He received a B.A. degree in 2006 from DePauw University.
Q’s Research Project: Wnt signaling is a critical regulator of various developmental processes including tissue differentiation, proliferation, and stem cell maintenance. It is not surprising that Wnt overexpression has also been correlated with oncogenesis. We have found Wnt10b overexpression induces mammary tumors in mice and have correlated this with loss of the tumor suppressor p27Kip1, a modulator of G1-S phase transition. The goal of this project is to elucidate the mechanism of Wnt-induced p27 turnover via the ubiquitin-proteasome pathway.
DOMIGAN, COURTNEY K.
Courtney is a second year trainee and is in the Department of Molecular, Cell and Developmental Biology. Her research mentor is Dr. Luisa Iruela-Arispe. She received a B.S. degree in 2007 from UC Santa Cruz.
Courtney’s Research Project: We are interested in the role vascular endothelial growth factor (VEGF) plays as an intracrine growth factor in both vascular development and adult homeostasis. We will address the role of VEGF in development using a chimeric mouse model which will allow us to determine when and where VEGF is required in a cell autonomous manner during development. To address the role of VEGF in adult endothelial homeostasis, the cellular localization of VEGF and subsequent downstream signaling pathways will be elucidated in homeostatic and stress conditions.
DRAGOJLOVIC, MICHELLE L.
Michelle is a first year trainee and is in the Molecular Biology IDP. Her research mentor is Dr. Julian Martinez. She received a B.S. degree in 2007 from UC Irvine.
Michelle’s Research Project: In organs for which a stem cell niche is central in maintaining a
population of stem cells, there must be a fundamental role for the niche in regulating the final dynamics of tissue growth. Our labo is interested in understanding how the growth of a tissue is regulated at the level of a stem cell niche. We utilize the Drosophila hematopoietic organ, the lymph gland, as a genetic model in which to study niche–stem cell interactions and have identified the Target of rapamycin (TOR) pathway as a candidate for studying the role of the niche in this process. My project involves examining the role of the TOR growth signaling pathway in the Drosophila lymph gland and characterizing a specific role for the TOR pathway within the hematopoietic niche, distinct from any function this pathway may have in the progenitor cell or differentiated blood cell populations. I am also examining the integration of signals derived from activated fibroblast growth factor (FGF) receptors into the TOR pathway as a possible mechanism for regulating niche size and in turn lymph gland growth in Drosophila.
DWYER, JENNIFER R.
Jennifer is a second year trainee and is in the Molecular Biology IDP. Her research mentor is Dr. Karen Reue. She received a B.S. degree in 2006 from the University of New Hampshire, Durham.
Jennifer’s Research Project: This research project is focused on characterizing the molecular and physiological functions of Lipin-2 and Lipin-3, members of the lipin protein family. The founding member of this evolutionarily conserved group, Lipin-1, plays a vital role in adipose tissue development and functions as a triglyceride biosynthetic enzyme. While Lipin-2 and Lipin-3 can also perform this enzymatic function, their tissue expression patterns vary greatly from Lipin-1, suggesting similar yet distinct physiological roles for each protein. Interestingly, mutations in human Lipin-2 are responsible for Majeed Syndrome, characterized by anaemia and osteomyelitis, and polymorphisms in human Lipin-2 are correlated with Type 2 Diabetes. Little else is known about the molecular function of Lipin-3. Jennifer is using a combination of knockout mouse models and cellular and molecular approaches to tease apart the unique physiological roles of Lipin-2 and Lipin-3. The role of lipins in lipid metabolism is of general significance due to the number of diseases that are either caused by or complicated by lipid dysregulation.
EDWARDS, MIGUEL V.L.
Miguel is a second year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Stephen Smale. He received a B.A. degree in 2007 from SUNY, Hunter College.
Miguel’s Research Project: In recently published and unpublished work from the Smale lab, strong
evidence has been put forth that pioneer factor interactions in ES cells permit the correct assembly of chromatin at non-regulatory tissue-specific genes in order to allow activation upon differentiation (Xu et. al. 2007). The observation that a small window of unmethylated CpG's was consistently observed within the binding site of FoxA1 at the Albumin enhancer lead to the hypothesis that this window of unmethylation indicates the association of DNA binding proteins with this tissue specific enhancer in ES cells. FoxD3 a related family member of FoxA1 was shown to bind at this site in ES cells. However the mechanism for the aforementioned and how this allows for the correct assembly of chromatin in order to allow activation upon differentiation has yet to be elucidated. This general observation of unmethylated CpG's at the enhancers of tissue specific genes in ES cells has been seen at other genes such as pTCR alpha. I intend to begin to elucidate the mechanism for the establishment of
the unmethylated window and its functional relevance for activation upon differentiation.
ERBILGIN, AYCA
Ayca is a third year trainee and is in the Department of Microbiology, Immunology and Molecular Genetics. Her research mentor is Dr. Jake Lusis. She received a B.S. degree in 2006 from UCLA.
Ayca’s Research Project: Atherosclerosis is characterized by the accumulation of cholesterol, inflammatory cells, smooth muscle cells, and fibrous elements beneath the monolayer of endothelial cells that line the artery wall. I am working on a protocol to isolate and culture aortic endothelial cells from mice so that the inflammatory and atherosclerotic properties of these cells can be studied. My goal is to collect expression data from a panel of inbred and recombinant inbred mice and identify candidate genes that may be studied further.
ERDE, JONATHAN
Jonathan is a first year trainee and is in the Department of Chemistry and Biochemistry. His research mentor is Dr. Joseph Loo. He received a B.S. degree in 2007 from Loyola Marymount University.
Jonathan’s Research Project:Ataxia Telangiectasia, Mutated (ATM) is a nuclear protein kinase at the core of the cellular response to double-stranded DNA breaks induced by ionizing radiation (IR). Loss of functional ATM results in neurodegeneration, cancer predisposition and sensitivity to IR. I am currently employing Stable Isotope Labelling by Amino Acids in Cell Culture (SILAC) in order to study DNA damage repair following IR insult in lymphoblastoid cell lines (LCLs) with functional or aberrant ATM. SILAC-based quantitative proteomics will provide a first look at the effects of IR on protein expression. In the future this quantitative proteomic approach will be utilized to explore the cellular effects of potential radioprotector compounds in LCLs.
FERGUSON, GABRIEL B.
Gabriel is a first year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Julian Martinez. He received a B.S. degree in 2007 from Johns Hopkins University.
Gabriel’s Research Project: I am currently investigating the role of the Hippo pathway in regulating hematopoietic progenitors in Drosophila melanogaster. The Hippo pathway is a highly conserved growth signaling pathway in Drosophila and mammals that functions by negatively regulating the transactivator protein Yorkie (Yki). When Yki is not inhibited it can bind to the TEAD family transcription factor Scalloped (Sd) and enter the nucleus to activate target genes. Our gene expression analysis has confirmed that Yki and other Hippo pathway genes are expressed in the lymph gland, the hematopoietic organ of the Drosophila larva. We have observed significant phenotypes when Yki or Sd are overexpressed in the lymph gland, and we are currently undertaking further genetic manipulations of the Hippo pathway to gain a more specific understanding of its role in regulating hematopoiesis. We are attempting to identify what Yki target genes are necessary for maintaining the hematopoietic progenitors found in the lymph gland while we also gain insight into the global regulatory network that is maintained by Hippo pathway signaling.
FRENCH, C. TODD
Todd is a third year trainee and is in the Department of Microbiology, Immunology and Molecular Genetics. His research mentor is Dr. Jeffrey F Miller. He received a B.S. degree in 2006 from the University of Alabama.
Todd’s Research Project: Type III secretion systems (T3SSs) allow Gram-negative bacteria to inject protein effector molecules into the cytoplasm or plasma membrane of eukaryotic cells. Secreted effectors are capable of modulating a wide range of host cell functions and they play a major role in the virulence strategies of bacteria that encode them. Burkholderia pseudomallei contains three gene clusters that are predicted to encode "injection-type" T3SSs. Relatively little is know about their individual and combinatorial functions during infection. I have identified several novel T3SS effector proteins in B. pseudomallei. My goals are to 1) identify the particular T3SS of B. pseudomallei which exports a given effector, and 2) investigate the roles of B. pseudomallei T3SS effector proteins in pathogenesis using several model systems, including mammalian cells, amoebae, and nematodes. In addition tohighlighting mechanisms of pathogenesis, we expect these studies will identify potential immunogens for the development of vaccines.
GOLDSTEIN, ANDREW S.
Andrew is a third year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Owen Witte. He received a B.A. degree in 2006 from Dartmouth College.
Andrew’s Research Project: Prostate cancer is the second most common cause of cancer-related deaths among males in the United States. Our objective is to understand the contributions of different cell types in the prostate to malignancy (prostate cancer). In order to delineate the epithelial lineage hierarchy of the prostate, we aim to identify stem and progenitor cell types in the murine prostate using cell sorting techniques and functional readouts. To test the contribution of different cell types, we will examine the effect of different oncogenic stimuli on the isolated stem and progenitor cells and their more mature progeny. We hypothesize that certain oncogenic stimuli will transform mature cell types, but that stem and progenitor cells will be the preferred target for transformation. To date, we have identified a subpopulation of prostate basal cells with stem cell characteristics and shown that these cells can give rise to all three cell types of the adult prostate epithelium.
GRIGORIAN, MELINA V.
Melina is a third year trainee and is in the Department of Molecular, Cell and Developmental Biology. Her research mentor is Dr. Volker Hartenstein. She received a B.S. degree in 2004 from CSU Northridge.
Melina’s Research Project: I study hematopoiesis and heart development in Drosophila. I have been studying the role the EGFR pathway may play during this process. Delta is important for deciding the cell fate of the hemangioblast in Drosophila. Based on knock out studies and expression profiles of the proteins important in the EGFR pathway,I think it is likely that EGFR is having an effect on Delta expression levels. pERK, EGFR and Pointed (transcription factor) have all been seen to be expressed in the early cardiogenic mesoderm, colocalizing with Delta expression in that area. Knock out studies looking at an EGFR null mutants have also shown a loss of the lymph gland and a possible increase in cardioblast cells. I have also been studying the timeline of blood cell maturation and the dispersal of the lymph gland (hematopoietic organ) during pupal stages in Drosophila. GFP lines labeling the lymph gland have made this endeavor possible. I have recently started working with a GFP protein trap line that is linked to a gene which functions as a cell-matrix adhesion protein. This line gives me a clear view of chambers within the lymph gland. I have been looking at the expression pattern of this protein from embryonic stages to late pupal stages.
HO, C. KENT
Kent is a third year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Yee Sun. He received a B.S. degree in 2006 from Columbia University.
Kent’s Research Project: Non-coding RNAs has recently come to the forefront of research efforts as they have shown to be flexible and powerful in their ability to regulate protein expression. Since development and differentiation of cells into their final species is a highly coordinated event, the non-coding RNA known as microRNAs have been implicated in such processes because of their ability to inhibit translation of mRNAs without degrading them. Although many miRNAs are already known to exist in the sequenced genomes of mouse and other model organisms, efforts to find the relevant miRNAs have been tedious and time-consuming while having the possibility to miss targets entirely. To this end, I will try to develop a new protocol for discovering the miRNAs that regulate the gene being studied within the context of the system of interest. For this mIR isolation system, an RNA tag will be inserted into the mRNAs of the gene being studied and an RNA binding protein specific to that RNA tag will be used to pull down the mRNA with miRNAs still bound. The relevant miRNAs will be isolated and identified. Once the system has been shown to work with the positive controls, we can use the same system by simply changing the constructs and cloning in the 3'UTRs of the genes of interest. For the positive controls, we'll be using miR9 in NPCs, which has been shown to be bound to gp130 3'UTR and BDNF 3'UTR with miR10-a. If we can pull down those respective mIRs with the 3'UTRs of those genes in the cell system they are usually expressed and interacting, then we know this system should be generally applicable.
IYER, SHANKAR S.
Shankar is a second year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Genhong Cheng. He received a B.A. degree in 2007 from Cornell University.
Shankar’s Research Project: A fundamental aspect of host defense is the ability to recognize and distinguish between myriad infectious agents. With respect to innate immunity, this specificity is dictated largely via the activity of toll like receptors (TLRs). Differential stimulation through distinct TLRs enables host cells to resolve pathogenesis by activating gene networks specifically designed to contain and eliminate the foreign pathogen. While these discrete inflammatory pathways have been studied extensively, little is known about how multiple signaling pathways interact in order to generate an appropriate immune response. Elucidating the mechanisms that govern this crosstalk and their ramifications on the expression of synergistic gene networks is essential to our understanding of immune surveillance. The interaction between competing inflammatory pathways is particularly relevant for the onset of influenza pneumonia. Influenza pneumonia is the leading cause of infection-related deaths and the 8th overall cause of death annually, contributing nearly 60,000 deaths in the United States alone in 2004. While sensitization to secondary bacterial pneumonias after infection by the influenza virus has been well documented, little is known about the mechanisms responsible for this phenomenon. The goal of my work in the Cheng lab is to identify the factors and molecular events that contribute to viral induced immuno-suppression. In this manner, I hope to contribute to our understanding of the crosstalk between anti-viral and anti-microbial response pathways. Ultimately my work could have important consequences for identifying potential therapeutic targets for treating and preventing the onset of influenza pneumonia.
JANSON, CHRISTINE M.
Christine is a third year trainee and is in the Department of Biological Chemistry. Her research mentor is Dr. John Colicelli. She received a B.S. degree in 2006 from Truman State University.
Christine’s Research Project: The RIN family of proteins is involved in linking RAS activation and Rab5 mediated endocytosis. Because RIN3 is enriched in mast cells, we are focusing on defining RIN3’s role in basic mast cell function. In particular, we are studying RIN3's role in receptor endocytosis as it relates to signaling for migration and degranulation. If RIN3 is necessary for mast cell migration and/or degranulation, inhibitors of RIN3 GEF function could be therapeutic for pathologies associated with mast cells.
JOHNSON, MEGHAN E.
Meghan is a first year trainee and is in the Department of Chemistry and Biochemistry. Her research mentor is Dr. Carla Koehler. She received a B.A. degree in 2007 from the University of Pennsylvania.
Meghan’s Research Project: I am currently studying mitochondrial diseases using zebrafish as a model organism. Mitochondrial diseases represent a broad class of afflictions in which mitochondrial function is impaired, and mortality rates are often increased; it is estimated that 1 in 10,000 live births will have a mitochondrial disease. Most mitochondrial diseases affect the muscular and neural systems of the body. Recent studies show that well-known neurodegenerative diseases are potentially associated with proteins localized within the mitochondria. Because the mitochondrial genome is conserved between humans and zebrafish, I am working to generate fish with the same genetic mutations as those present in afflicted people. In doing so, I will be able to study the phenotypes and pathogenesis of these genetically-encoded myopathies.
KURYAN, BENJAMIN G.
Ben is a first year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Michael Carey. He received a B.S. degree in 2007 from UCLA.
Ben’s Research Project: A major question in the field of eukaryotic transcription is how RNA polymerase II transcribes through nucleosomes and shapes the chromatin structure of transcribed regions. I intend to investigate these mechanisms by developing a biochemical elongation assay on a
nucleosomal template. This system will enable the determination what factors are required for elongation, what happens to the histones during elongation, and the significance of histone posttranslational modifications in these processes.
KHARE, SHILPI
Shilpi is a third year trainee and is in the Department of Chemistry and Biochemistry. Her research mentor is Dr. Steven Clarke. She received a B.A. degree in 2005 from UC Berkeley.
Shilpi’s Research Project: My work this past year has been focused on gaining a better understanding of the role protein repair methyltransferases play in resistance to oxidative stress in the organism Caenorhabditis elegans. Reactive oxygen species are produced as by-products of normal metabolism and can directly damage proteins and other cellular components. Cells protect themselves with a variety of antioxidants and detoxification enzymes (Halliwell & Gutteridge, 2007). The expression of these enzymes in response to oxidative stress in Caenorhabditis elegans is primarily initiated by the insulin/insulin-like growth factor (IGF)-1 signaling pathway mediated by the DAF-2 receptor (Honda & Honda, 1999; Gami & Wolkow, 2006; Murakami, 2007). Upon down-regulation of the DAF-2 pathway, the oxidative stress response is activated. In specific, down-regulation of the DAF-2 pathway up-regulates the activity of DAF-16, a transcription factor that promotes the expression of anti-oxidant enzymes (Ogg et al., 1997; Braeckman et al., 2001; Murphy et al., 2003; McElwee et al., 2003). It is of interest to note that C. elegans also down-regulates the DAF-2 pathway in response to starvation as well, and as a result, lifespan is extended (Honda & Honda, 1999). In addition to the DAF-2 pathway, the mitogen-activated protein kinase (MAPK) pathway also responds to environmental stress and regulates development and lifespan by interacting with DAF-16 (Wolf et al., 2007). C. elegans mutants that are hypersensitive to the increased generation of reactive oxygen species exhibit premature aging (Yanase et al., 2002).
LANAGERMAN, JUSTIN B.
Justin is a second year trainee and is in the Molecular Biology IDP. His research mentor is Dr. Stephen Smale. He received a B.S. degree in 2007 from UCLA.
Justin’s Research Project: Unmethylated CpG dinucleotides may mark the enhancers of tissue specific genes even in undifferentiated embryonic stem cells. Using IL12p40 as a model tissue specific gene, we are interested in showing that these enhancer marks are necessary for the function of the gene after differentiation, and in showing how these enhancer marks are functionally created and preserved.
LOPEZ, MIGUEL A.
Miguel is a third year trainee and is in the Department of Microbiology, Immunology, and Molecular Genetics. His research mentor is Dr. Kent Hill. He received a B.S. degree in 2006 from UCLA.
Miguel’s Research Project: Trypanosoma brucei is a protozoan parasite that causes African sleeping sickness. T. brucei exhibits a biphasic lifecycle in which motility is thought to play an important role. Within its insect vector, the parasite must complete a series of specific migrations to mature into a virulent form. Within the mammalian host, the parasite invades the central nervous system; Mortality is associated with the presence of the parasite within the CNS. The means by which these parasites navigate through the respective host environments have yet to be determined. Through the development of a novel assay, we have demonstrated that insect-form T. brucei cellsexhibit highly specific and coordinated social behaviors when plated on agar plates. This phenomenon, termed social motility, is characterized by the assembly of initially dispersed trypanosomes into colonies containing hundreds to thousands of motile parasites. These colonies are then able to actively seek out satellite colonies and initiate a polarized movement in the direction of the satellite colony resulting in the merger of the two colonies. The ability of trypanosomes to coordinate movement in response to external cues might therefore facilitate tropism of the population to specific host tissues. Through a combination of forward genetics screens as well as the targeted knockdown of candidate genes, I hope to identify some of the factors contributing to social motility. More specifically, my project can be summarized by the following three specific aims:
- Test candidate genes for a role in social motility.
- Conduct a chemical genetics screen to identify small molecule inhibitors of social motility
- Employ an RNAi library to isolate social motility mutants in a forward genetic screen.
An understanding of the mechanisms governing social motility will shed light on how trypanosomes migrate within their hosts, and may provide clues to how other microbial pathogens communicate and display specific tropisms.
MACKAY, KENNEN B.
Kennen is a third year trainee and is in the Department of Chemistry and Biochemistry. His research mentor is Dr. Steven Clarke. He received a B.A. degree in 2006 from Colorado College.
Kennen’s Research Project: I am currently investigating the protein Leucine carboxyl methyltransferase (Lcmt1) within a mouse model. LCMT1 specifically methylates a leucine residue at the carboxy terminus of the catalytic subunit of protein phosphatase 2a and controls binding of the regulatory subunit of the phosphatase, thus controlling specificity. PP2A is a major cellular phosphatase and is responsible for virtually all ser/thr dephosphorylations occurring within the cell. We have discovered that full Lcmt1 deletion leads to embryonic lethality, and have since focused on studying heterozygotic animals which show reduced enzyme activity. We are continuing to study mating and behavioral differences in these animals and hop to publish our results soon.
NEAL, SONYA (Associate Member)
Sonya is a second year Associate member of the training grant. She is in the Department of Chemistry and Biochemistry. Her research mentor is Dr. Carla Koehler. She received a B.S. degree in 2007 from UC San Diego.
Sonya’s Research Project: My project investigates the role of redox chemistry in mitochondrial biogenesis. Previous studies, including ours, have shown that the mitochondrial intermembrane space contains a novel oxidative folding pathway. A redox-regulated import pathway consisting of Mia40 was identified to mediate the import of small Tim proteins and cysteine-rich proteins in the intermembrane space. The sulfhydryl oxidase Erv1 also functions in this pathway as a putative oxidant for Mia40. Thus, in my research I hope to reconstitute the disulfide exchange reaction with Mia40, Erv1 and potential substrates, including biochemical characterization of the redox properties of Mia40, Erv1 and substrates. A battery of tests including monobromobimane titration, intrinsic tryptophan fluorescence, and AMS thiol-trapping will be utilized to delineate the role that each cysteine residues play in the thiol/disulfide exchange mechanism.
NGUYEN, HOANGKIM (KAY)
Kay is a first year trainee and is in the Department of Microbiology, Immunology and Molecular Genetics. Her research mentor is Dr. Kent Hill. She received a B.S. degree in 2008 from UC Davis.
Kay’s Research Project: African trypanosomes have been observed to form groups of cells within its insect host vector. In addition, cultivation of these parasites on semisolid agarose within the laboratory has also demonstrated their ability to form parasitic communities. My project aim is to investigate social motility behavior exhibited by African trypanosomes by both a candidate approach and a genetic screen. The lab has recently performed a proteome to isolate several putative flagella surface proteins. We hypothesize that these candidate proteins may be involved in social motility and will be generating RNAi knockdown mutants to investigate the role of these proteins in sensing. We will also be performing an RNAi genetic screen to enrich for social motility mutants through a novel sensing assay developed in our lab. With this study, we hope to discover novel insights into the molecular mechanism of social behavior in the first protozoan parasite to exhibit social motility as well as fundamental aspects of cell-cell communication.
PALOMARES, KARINA (Associate Member)
Karina is a second year Associate member of the training grant. She is in the Department of Microbiology, Immunology and Molecular Genetics. Her research mentor is Dr. Benhur Lee. She received a B.S. degree in 2007 from the U. of Notre Dame.
Karina’s Research Project: Recent studies have demonstrated that the measles virus hemagluttinin
(H) and fusion (F) proteins can efficiently pseudotype HIV-1 based lentiviral vectors, but only when both cytoplasmic tails are suitably truncated. Furthermore, MeV-H/F pseudotyped lentivurses were able to transduce quiescent primary T-cells and B-cells, which are relatively refractory to transduction by VSV-G pseudotypes (Frecha, Blood, 2008). I am currently investigating whether the Nipah virus (NiV) attachment (G) and fusion (F) proteins could be similarly pseudotyped onto lentiviral vectors. NiV-G binds to its receptors (ephrinB2/B3) with picomolar affinity and thus, could be potentially used to target tumorogenic invading microvascular endothelial cells or certain tumor stromal cells themselves that are overexpressing ephrinB2/B3 (Pasquale EB, Cell, 2008). Moreover, ephrinB2 is expressed on hematopoietic, neural, and embryonic stem cells (Ivanova, Science, 2002). Thus, lentivirus pseudotyped with NiV envelope could be used to potentially target stem cells.
PARK, ARNOLD
Arnold is a first year trainee and is in the Department of Microbiology, Immunology and Molecular Genetics. His research mentor is Dr. BenHur Lee. He received a B.A. degree in 2008 from Harvard College.
Arnold’s Research Project: HIV-1 Gag and Nipah virus Matrix are capable of budding on their own in the absence of other viral proteins. Nipah virus is a member of the paramyxoviridae family. While HIV-1 Gag budding has been examined in great detail, little is known about paramyxovirus budding. In our efforts to determine cellular host factors that are involved in Nipah Matrix budding, we made the surprising discovery that co-transfection of 293T cells with HIV-1 Gag and Nipah Matrix led to a dramatic enhancement of Nipah virus Matrix budding. At the minimum, this suggests that HIV-1 gag and Nipah Matrix do not use the identical set of cellular host factors for viral budding. I am currently
investigating the various hypotheses that might explain this surprising phenomenon, and I will seek to identify potentially novel host factors involved in paramyxovirus budding.
PATANANAN, ALEXANDER N.
Alexander is a first year trainee and is in the Department of Chemistry and Biochemistry. His research mentor is Dr. Steven Clarke. He received a B.S. degree in 2008 from UCLA.
Alexander’s Research Project: As organisms age, proteins can spontaneously accumulate covalent damage to become non-functional, or even toxic. The success of organisms may therefore depend on their ability to first identify damaged proteins, and then to either repair or remove these species before they build-up to detrimental levels. L-isoaspartyl O-methyltransferase (PCMT1) is an important enzyme involved in this protein repair. Although approximately 100 days after birth PCMT1 knockout mice plateau in accumulated cellular/tissue isoaspartyl-damaged proteins, subsequent increased levels of damaged urinary peptides and death by massive seizures occur. I will use high-performance liquid chromatography and electron capture dissociation mass spectrometry to detect these abnormal urinary peptides in PCMT1 knockout mice and determine which proteins and tissues are most susceptible to damage. Specific inhibitors and activation markers for autophagic and proteasome pathways in various tissues of these mice will be used to determine if known proteolytic systems and/or novel L-isoaspartyl specific degradation pathways are activated. In addition to investigating isoaspartyl damage in a mouse model, biochemical techniques will be employed to elucidate how Saccharomyces cerevisiae, an organism maintaining low isoaspartyl damage and no PCMT activity,handlesprotein damage.
RAMOS, EMILIO
Emilio is a third year trainee and is in the Department of Chemistry and Biochemistry. His research mentor is Dr. Tomas Ganz. He received a B.S. degree in 2006 from UC San Diego.
Emilio’s Research Project: Hereditary hemochromatosis (HH) is an iron overload disease caused by mutations in the genes enocding HFE, transferrin receptor 2 (TfR2), hemojuvelin (HJV) or hepcidin. Each mutation causes inadequate synthesis of the iron regulatory hormone hepcidin, leading to excessive iron absorption and dysfunction of liver and other organs. Normally, hepcidin is induced by iron loading, but is inappropriately low in HH. We have thus proposed to define the molecular roles played by HFE, TfR2 and HJV in hepcidin regulation by iron in an effort to improve our understanding of the pathogenesis of HH.
RAU, CHRISTOPH D.
Christoph is a second year trainee and is in the Department of Microbiology, Immunology and Molecular Genetics. His research mentor is Dr. Jake Lusis. He received a B.S. degree in 2007 from Harvey Mudd College.
Christoph’s Research Project: Doxorubicin is a chemotherapy drug used to combat a number of cancers, including carcinomas and soft tissue sarcomas. Although it is a very effective drug, it has a side effect of causing cardiotoxicity if a dose above the standard approved dose is administered. Research done in the early 90s pointed to a genetic component to the cardiotoxicity, and a few genes were putatively identified. My project is to use the resources of the Lusis Lab, especially their mouse diversity panel and computational resources to identify additional genes that are involved in this effect.
ROY, KEVIN (Associate Member)
Kevin is a first year Associate member of the training grant. He is in the Department of Chemistry and Biochemistry. His research mentor is Dr. Guillaume Chanfreau. He received a B.S. degree in 2009 from UCLA.
Kevin’s Research Project: Statement: Mitochondrial (Mt) RNA processing is poorly understood relative to nuclear and cytosolic RNA processing. Many mitochondrial transcripts are synthesized as polycistronic precursors which require extensive processing. The processing pathways which produce the mature Mt rRNAs, tRNAs, and mRNAs remain to be fully identified. I am investigating the roles of a putative double-stranded RNA endonuclease (Mt RNAse III) and the mitochondrial 3'-5' exonuclease (Mt degradosome) in yeast mitochondrial RNA metabolism. I have shown that deletion of the Mt RNase III results in accumulation of precursors to the Mt small subunit RNA, suggestive of processing defects. I have also demonstrated that deletion of the Mt degradosome results in complete absence of mature Mt tRNA(Leu), with accumulation of tRNA(Leu) precursors, but with no effect on other Mt tRNAs. This suggests that the Mt degradosome is required for the production of specific Mt tRNAs, in contrast to the current dogma. I will exhaustively examine Mt RNA processing upon inactivation of these Mt RNA processing factors, and will perform in vitro cleavage experiments to verify the activity of these nucleases on their specific substrates. Because many factors in Mt RNA processing are widely conserved, deciphering yeast Mt RNA processing pathways has implications for Mt gene expression in higher eukaryotes.
SITAPARA, RONIKA R.
Ronika is a third year trainee and is in the Molecular Biology IDP. Her research mentor is Dr. Ren Sun. She received a B.A. degree in 2006 from UC Berkeley.
Ronika’s Research Project: When I first joined the lab, I began a research project with a post-doc in the lab. My part was to learn the novel functional genomics profiling system he designed, and to follow up on its results with traditional assays. In gamma-2-herpesviruses, reactivation from latency is mediated by a viral factor, Replication and Transcription activator (RTA). RTA initiates the entire lytic gene expression cascade; thus, its regulation is critical. The mechanism of RTA regulation is poorly understood. We used murine herpesvirus (MHV-68) as a model to study human gammaherpesviruses. The idea is to study functional domains of RTA coding regions and RTA promoter cis-elements at high-resolution in the context of MHV-68 genome. He developed a high-throughput functional profiling system utilizing Mu-transposon mediated 15-nucleotide random insertion mutagenesis and quantitative, high-throughput, fluorescent PCR-profiling by capillary electrophoresis. Of 759 total insertions in the RTA coding region, 307, 128, and 324 were tolerated, attenuating and lethal, respectively, for virus replication. Based on these results, I further investigated 8 mutations in the coding region and 4 mutations in the promoter region. During profiling these mutations were generated randomly, after determining the exact insertion site I individually cloned each RTA coding region or RTA promoter region with a desired mutation. Using traditional assays such as trans-activation assays and complementation assays I was able to validate the functional profiling efficacy in predicting genome locations important for RTA activity. This work will soon be published.
THOMPSON, MICHAEL C.
Michael is a first year trainee and is in the Department of Chemistry and Biochemistry. His research mentor is Dr. Todd Yeates. He received a B.A. degree in 2008 from UC Berkeley.
Michael’s Research Project: The goal of this project is to develop a tool that will be used to
aid in the crystallographic structure determination of RNA molecules that have been resistant to conventional methods of crystallization and phase determination. This reagent will make use of the phenomenon known as 'synthetic symmetry' applied to the small RNA-binding protein U1A, which will be engineered to bind to one or more lanthanide atoms. The 'synthetic symmetry' present in the reagent will be imparted upon the RNA molecules to which it binds, thereby promoting crystallization of those RNA molecules. Additionally, the reagent will allow for simple and efficient phasing by isomorphous replacement and/or anomalous scattering methods due to the presence of lanthanide atoms.
TING, PAMELA Y.F.
Pamela is a first year trainee and is in the Department of Biological Chemistry. Her research mentor is Dr. John Colicelli. She received a B.A. degree in 2008 from UC Berkeley.
Pamela’s Research Project: I am studying the stimulatory interaction of RIN1 with ABL1 and its role in chronic myelogenous leukemia. Previous work in the Colicelli lab has shown that RIN1 overexpression activates BCR-ABL1 kinase activity and transforming potential. RIN1 deletion blocks bone marrow transformation by BCR-ABL. We propose using a TR-FRET based high throughput screen to identify a novel group of BCR-ABL inhibitors that works by blocking RIN1 binding to ABL.
ULGHERAIT, MATTHEW J.
Matt is a first year trainee and is in the Department of Biological Chemistry. His research mentor is Dr. Feng Guo. He received a B.S. degree in 2007 from Drexel University.
Matt’s Research Project: MicroNAs (miRNAs) mediate gene silencing by guiding selective messenger RNA degradation and suppression of protein translation. An ever growing body of evidence demonstrates the importance of miRNAs in regulating diverse cellular processes including development, apoptosis, and tumorigenesis. miRNAs are transcribed from the genome as long primary-miRNAs (pri-miRNAs), which undergo consecutive cleavage steps to yield mature 21-23 nucleotide miRNAs. The first processing step involves cleavage of the pri-miRNAs into ~65 nucleotide intermediate precursors called pre-miRNAs. This cleavage event is mediated by the ribonuclease Drosha and the RNA binding protein DGCR8. The abundance and RNA binding activity of DGCR8 protein critically affects levels of mature miRNAs. While the necessity of DGCR8 protein in regulating global miRNA biogenesis is well defined, the mechanisms that control DGCR8 activity and stability remain largely unexplored. My current work focuses on the elucidating mechanisms which govern pri-miRNA processing via post-translational modifications of DGCR8.
VAN HANDEL, BENJAMIN J.
Ben is a third year trainee and is in the Department of Molecular, Cell and Developmental Biology. His research mentor is Dr. Hanna Mikkola. He received a B.S. degree in 2005 from Northern Michigan University.
Ben’s Research Project: I am interested in the celluar and microenvironmental mechanisms that result in the generation of hematopoietic stem cells in the human embryo. I hope to apply our findings to ultimately be able to generate blood stem cells from pluripotent stem cells for cellular therapies.
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