Background:

I obtained my Bachelor of Science degree in Biological Sciences with an emphasis in Microbiology in June of 2007 from the University of California, Riverside. I am currently enrolled in UCR’s Genetics, Genomics and Bioinformtatics program and am concentrating in molecular genetics. My main interests are the plant endomembrane system and vesicular trafficking.

Introduction:

Germinating pollen tubes clearly display unidirectional cellular growth. This kind of polarized growth requires calcium gradients, the cytoskeleton, and tip-focused vesicle trafficking, which is organized via Rho-related GTPases. Proteins in somatic cells also travel through a variety of pathways from the ER to the vacuole, and to and from the plasma membrane using endocytic and secretory trafficking pathways (Figure 1). Thus pollen is a good model for other cell types.

Research Plan:

A high-throughput strategy employing the Atto Pathway Confocal microscope will be used to carry out a chemical screen to identify small molecules that inhibit tobacco pollen tube germination. Once compounds have been confirmed to inhibit tobacco pollen growth, these compounds will be evaluated for their ability to induce phenotypes in Arabidopsis seedlings. Specifically, I will examine our laboratory’s large library of endomembrane fusion protein marker lines treated with chemicals that inhibit tobacco pollen tube germination to determine whether these compounds inhibit endomembrane trafficking in other tissues. Following the identification and characterization of these compounds, I will focus on target identification studies of one or several informative chemicals in order to determine their effects on dynamic endomembrane trafficking events such as endocytosis as well as to indentify cognate protein-binding partners using forward and reverse genetics.  Figure 1. The Plant Endomembrane System. The plant endomembrane system contains compartments and trafficking components that are conserved among all eukaryotes and some that are unique to plants. a) Amino-terminal propeptide (NTPP)pathway. b) Carboxy-terminal propeptides (CTPP). c) ER-to-vacuole pathway. d) ER-to-PAC-to-vacuole pathway. e) Secretion pathway. f) CCV endocytosis. g) Receptor-mediated endocytosis. CCP, clathrin-coated pit; CCV, clathrin-coated vesicle; CV, central vacuole; DV, dense vesicle; ER, endoplasmic reticulum; GA, Golgi apparatus; LV, lytic vacuole, N, nucleus; PAC, precursor-accumulating compartment; PB, protein body; PCR, partially-coated reticulum; PSV, protein-storage vacuole; PVC, pre-vacuolar compartment; SV, secretory vesicle. Surpin and Raikhel (2004). Traffic Jams Affect Plant Development and Signal Transduction. Nature Reviews/Molecular Cell Biology 5:100-109.

Background:

I graduated in spring of 2007 from Harvey Mudd College with a Bachelor's degree in biology with a concentration in molecular biology. In the fall of 2007 I began my graduate studies at the University of California, Riverside in the Botany and Plant Sciences program. I am currently starting research in Dr. Linda’s Walling lab where I will focus my studies on plant defense signaling in tomato.

Introduction:

Aminopeptidases are a small subset of the peptidases that are ubiquitous in all living organisms. More than simply housekeeping proteins, aminopeptidases have been shown to have roles in the regulation of plant cell growth, development, homeostasis, and stress response. In particular, leucine aminopeptidases (LAP) are highly conserved proteins that have multiple functions in both eukaryotes and prokaryotes. The solanaceous-specific LAP-A has been shown to be upregulated in floral and fruit development as well as in response to biotic and abiotic stress. The focus of my research will be to understand LAP-A’s role specifically in the JA-dependent plant defense response in Solanum lycopersicum (tomato). I intend to screen chemical libraries for small molecules which either stimulate or inhibit LAP-A’s activity in this pathway. Identified chemicals will hopefully be useful tools to identify LAP-A’s regulation and mechanism of action which will in turn help to gain understanding in the regulation of an important plant signaling pathway.

Background:

Introduction:

Structure similarity searching is one of the major techniques for retrieving chemical and bioactivity information from databases, as well as predicting drug properties of small molecules. The two most commonly used structure search approaches, substructure and structure similarity searches, both have major limitations in identifying local similarities between compounds. New computational methods for identifying these local similarities will have important applications in drug discovery and chemical genomics research, such as advanced QSAR studies, large-scale docking and diversity predictions of entire compound libraries.

The goal of my research project is to build a cheminformatics framework for efficient local similarity searching. This will enable chemical genomics researchers to search for bioactive compounds with higher confidence. In the initial stage, my project will evaluate the usefulness of 'Maximum Common Subgraphs' for local stucture similarity searching. The approach will include the following steps: (1) The computational complexity of the problem will be reduced by using heuristics that are specific to chemical structures and that can result in more effective local similarity measures. (2) Imperfect matching will be allowed by using an error tolerant method. (3) Further performance improvements will be achieved by designing an efficient approximation algorithms.

• Poster titled "Metabolic Profiling Unravels Complex Biological Phenomena in the Model Plant A. thaliana" (presented at the NSF 2008 IGERT Project Meeting held May 18-20, 2008 at the Westin Arlington Gateway)

Background:

I received my Bachelor of Science degree in chemistry from the University of Nebraska at Kearney in 2002. While at Kearney, I carried out collaborative research with the Department of Environmental Quality, United States Geological Survey, and the Environmental Protection Agency on problems such as volatile organic compound contamination in soil, acetanilide herbicide contamination in groundwater, and the accumulation of antibiotics in groundwater. While attending school, I worked for an agricultural testing company called Ward Laboratories, where I analyzed soils, feeds, waters, plants, fertilizers and manures.

After graduating from UNK, I attended Arizona State University, earning a Master of Science degree in 2005. My research at ASU involved the development of surface-plasmon resonance biosensors for the characterization of non-healing cutaneous wounds. The complex nature of the data generated necessitated the use of multivariate statistics such as principal components analysis for signal processing.

I am excited to be an IGERT fellow because it brings scholars from different areas of study into the same arena, which I believe will better overcome the scientific challenges we will face in the 21st century. In addition to valuing integration in science, I feel it is important to be a well-rounded person. Some of my extracurricular interests include teaching science at the community college, enjoying all kinds of dancing, cooking international cuisine at my home, and taking outdoor adventures to the mountains, deserts, forests, and beaches.

Introduction:

The aim of my project is to dissect the metabolic responses of Arabidopsis thaliana to environmental and chemical stress.  One environmental stress we are investigating is low oxygen, which occurs naturally through soil compaction and flooding, but is practically carried out by replacing laboratory air with argon gas in a small chamber or by complete submergence in water.  One method of applying chemical stress is by spraying seedlings with a small molecule known to have herbicidal activity.  This project relies on chemistry, multivariate statistics, computer science, bioinformatics, plant biology and biochemistry to examine and interpret the plant’s complex metabolic profile and how it changes upon these stresses.

Experiments in progress will probe the plant’s response using wildtype (sensitive) and mutant (resistant) plants.  The tissue samples have kindly been prepared by Dr. Cristina Branco-Price, Dr. Takeshi Fukao, and Dr. Angelika Mustroph in the Bailey-Serres lab, although through my lab rotation I have learned how to raise and stress my own plants.  In the work that has been carried out, A. thaliana was grown for seven days, harvested, and freeze dried.  Small molecule metabolites were extracted from dry tissue and subjected to analysis by nuclear magnetic resonance spectroscopy (NMR).  NMR is capable of providing information about which metabolites are present in the plant extract and their relative amounts. 

Using a non-targeted analysis known as metabolic fingerprinting, we gained insight into unexpected metabolic adjustments that occurred in the plants in response to a hypoxic environment.  Metabolite data were compared to transcript profiling data. These experiments generate large datasets with hundreds of highly correlated variables, therefore a battery of statistical tests were employed to extract biologically meaningful patterns from the data.  Metabolic profiling and flux balancing experiments will be used to quantify the direction and magnitude of these adjustments in future experiments.  The data will be used to construct predictive models of primary metabolism, which put the results into context at the molecular, cellular and organismal levels.  This work allows us to build an arsenal of knowledge about the plant metabolome and its dynamic nature within a model system.

Background:

I graduated in 2001 from California State University in Fullerton with my Bachelors in Biology and minors in Chemistry and Biotechnology. Following graduation, I worked in the private sector for Isis Pharmaceuticals manufacturing antisense therapeutics. I left Isis to pursue my graduate studies in the fall of 2004 in the Genomics and Bioinformatics track of the Genetics, Genomics, and Bioinformatics Department here at UCR. Here I began work in the Julia Bailey-Serres lab working on the understanding the response of Arabidopsis to hypoxia and the genes of unknown function in Arabidopsis using publicly available microarray data. Upon acceptance into the IGERT fellowship, I have focused my work on microarrays to apply to chemical genetics. I am also planning a reverse chemical genetics screen for inhibitors of MPK3/6 (MAP kinase 3 and 6) in Arabidopsis.

Introduction:

The field of chemical genetics is an adaptation of the field of drug discovery to the understanding of mechanisms in organisms. The field mirrors classical genetics in that the organism is perturbed using small molecules rather then mutations to dissect processes. With advances in diversity oriented chemical synthesis, the universe of available small molecules have exploded, allowing biologists a large set of tools with which to perturb organisms to study their function. In forward chemical genetics, a library of chemicals are screened against an organism to illicit a desired phenotype. Upon determining a chemical that produced the proper phenotype, the molecular target of that chemical must be determined.

Background:

I graduated Magna Cum Laude in the spring 2003 from California State Polytechnic University, Pomona California with a Bachelors of Science in Biology. I began my graduate work at UCR in the Fall of 2003, where I work in the lab of Dr. Thomas Eulgem.

Background:

Introduction:

Chemical genomics is a systematic approach in biological research and drug discovery. Synthetic organic chemists create combinatorial libraries of compounds to be used in screening. My research uses the plant Arabidopsis thaliana as a model organism for screening compounds from combinatorial libraries. The complete genome of A. thaliana has been sequenced, making it an ideal organism for chemical genomics research. In a screen of 4,800 compounds from the ChemBridge DIVERSetE library performed by previous researchers, fourteen compounds caused excretion of carboxypeptidase Y, a protein normally confined to vacuoles, in yeast. These compounds were then analyzed for their effects on A. thaliana. The two compounds causing the most severe phenotypic effects in A. thaliana were selected for further analysis. The major effects are disruption of vacuole biogenesis and protein sorting as well as root growth inhibition. Characterization of the Sortins and their effects was performed by Lorena Norambuena and Glenn Hicks. These sorting inhibitors are now referred to as Sortin1 and Sortin2. This project uses metabonomics to investigate the metabolic profiles of both Sortin molecules as well as endogenous metabolites in A. thaliana in an attempt to identify the metabolic pathways targeted by Sortin1 and Sortin2. Metabonomics is the study of relative changes of endogenous small molecules in response to a chemical, environmental, or genetic stimulus. Metabonomic analysis of A. thaliana cell and plant extracts is carried out using proton nuclear magnetic resonance spectroscopy (H-NMR) and liquid chromatography coupled with mass spectrometry (LC-MS).

H-NMR and MS data for seedlings grown 7 days in the absence of Sortin1

Metabonomic Analysis

Extracts of seedlings grown in the presence of Sortin1 have been analyzed by 1H-NMR and LC-MS. These methods complement each other very well. While NMR is not as sensitive as MS, it is a good non-destructive method for the identification and quantification of small molecule metabolites. MS is a much more sensitive method, but is destructive to the sample and is mainly used for identification of larger molecular weight metabolites. To capitalize on the complementary nature of NMR and MS, sample extracts are first analyzed by NMR before being transferred to the autosampler for LC-MS analysis. Our preliminary NMR and MS data provide detailed information about the biochemistry of Arabidopsis. To date, many amino acids, sugars, hormones, and other metabolites have been identified. One metabolite of interest is glutamine, showing a dramatic increase in concentration when A. thaliana is grown in the presence of Sortin1. Further analysis is currently underway to characterize the action of Sortin1 and the metabolic pathways that it perturbs. It is known that the Sortins affect vacuolar biogenesis. For this reason, it may be of interest to investigate the effects of the Sortins on lipid biosynthesis. Because of the difficulty in getting both hydrophilic and hydrophobic metabolites into the same solution, extractions to separate lipids, waxes, and chlorophyll from more hydrophilic metabolites will be performed and NMR data acquired for both phases.

	Waters QTOF Micromass Mass Spectrometer Waters Acquity UPLC
	Bruker Avance 600MHz Spectrometer Agilent 1100 HPLC