Background:

I graduated from the University of Pennsylvania in May 2008 and received a Bachelor of Arts in Biology with a concentration in neuroscience. As an undergraduate, I worked in the lab of Dr. Marc Schmidt on a research project aimed at identifying and characterizing neuronal projections underlying behavioral-state dependence in the song control system of zebra finches. In the fall of 2008, I began my graduate studies in the Botany and Plant Sciences program at UCR.

Introduction:

My IGERT project currently remains undefined as I have yet to complete my rotations as a first-year student. I did my first rotation in the lab of Dr. Xuemei Chen, working primarily on mapping several enhancer mutations identified in a sensitized screen in the ag-10 background. These mutants exhibit enhanced defects in floral determinacy and development. My second and current rotation is with Dr. Zhenbiao Yang; I am developing a screen to efficiently assess the effects of chemicals on pavement cell shape. More specifically, the screen would be used to identify small molecules that interfere with or enhance the actions of ROP GTPases, which are critical for growth and polarity in several plant systems (e.g. pollen tubes, root hair cells, pavement cells). I will begin my third rotation with Dr. Patricia Springer before the end of the year.

Background:

I received my Bachelor of Science (Honors) in Plant Breeding and Genetics from the N.W.F.P Agricultural University, Peshawar, Pakistan in the year 2000. In 2003 I received my M.Phil degree in Biotechnology from the Institute of Biotechnology and Genetic Engineering (IBGE) at the N.W.F.P Agricultural University, during which I did my research work at the National institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad on DNA viruses of the family Geminiviridae that have caused major crop losses in Pakistan. Later I worked at the N.W.F.P Agricultural University for three years as a Lecturer and researcher on exploiting the cation co-tolerance phenomenon in potato plants before joining the University of California, Riverside in 2007 as a Fulbright student for my graduate studies.

Introduction:

Currently I am working in Dr. Thomas Eulgem’s lab examining defense mechanisms in Arabidopsis and tomato that involve WRKY70-like transcription factors and members of the LURP cluster of coordinately expressed defense genes. I am performing experiments that examine possible LURP-dependent mechanisms in tomato by silencing the WRKY70 ortholog in tomato and measuring transcript changes of putative orthologs of Arabidopsis LURP genes (which includes CaBP22). This will partially be done by silencing WRKY70 ortholog in -333_CaBP22::GUS tomato lines and examining the effect of WRKY70 orthologs on defense-related expression of -333_CaBP22:: GUS in tomato. These experiments will address if the “WRKY70/CaBP22 regulatory module” is conserved between different plant species.

I am also working on dissecting the biological and molecular roles of the Arabidopsis gene LURP1 and its paralogs LOR1 (LURP-one related 1) and LOR2. Mutations in LURP1 result in reduced disease resistance to the oomycete Hyaloperonospora parasitica. I am in the process of testing if LOR1 and LOR2 T-DNA mutants that show defense-related phenotypes similar to those of LURP1. In addition I will construct LURP1/LOR1 and LURP1/LOR2 double mutants to address if these genes contribute in an additive or synergistic manner to disease resistance.

In addition to this I will carry out screens of Arabidopsis EMS mutants carrying a -333_CaBP22::GUS reporter gene for lines with altered sensitivity for 3,5-Dichloroanthranilic acid (DCA), a potent synthetic elicitor of disease resistance to virulent strains of the oomycete Hyaloperonospora parasitica . These screens may lead to the identification of the biological target of DCA or defense components operating downstream from DCA perception. The overall goal of my work is to get an insight in to key regulatory networks involved in defense mechanisms and dissection of regulatory networks controlling the defense transcriptome across plant species.

Background:

I completed my studies for a Bachelor of Science degree in Chemistry with a Biochemistry option from California State University, San Bernardino in June 2008.  While attending school, I worked on a joint project with the Department of Chemistry, Department of Physics, and NASA concerning hydrogen fuel cells and their efficacy in a high radiation environment.

Currently, I am interested in inter-disciplinary research and the many opportunities it extends to my Biology and Chemistry background.  I am anxious to expand my experience in those areas as well as improve my communication skills with other non-chemistry students.  As the worlds of Chemistry, Biology, and Computer Science collide, the skills and knowledge afforded by such experience will be invaluable.

Introduction:

My initial research project involves the metabolic studies of Oryza sativa (rice).  This is a joint project with Dr. Julia Bailey-Serres and her post-doctoral fellow Takeshi Fukao.  I am working on analytically determining the effects of submergence on different rice cultivars by examining their metabolic profiles through NMR spectroscopy. Future studies would include further analysis by GC-MS.  This study will provide valuable insight into the metabolic response of these plants and help to provide an explanation for the difference in efficacy among the cultivars.

Background:

I earned my Bachelor's of Science degree in Biochemistry from Biola University in Spring 2007. Subsequently, I began my work at UCR within the Genetics, Genomics and Bioinformatics graduate program. While rotating in my first year, I joined UCR's IGERT program to extend my research aims into the realm of Chemical Genomics.

Introduction:

Currently I am studying G protein signaling in the Borkovich lab. Using the model organism Neurospora crassa, I am examining proteins that regulate the G-protein signaling cascade through analysis of mutants and protein-protein interaction studies. To start, I will be performing high throughput chemical screens to identify compounds that both promote and inhibit key interactions in G protein signaling. Alongside this screen, I will also use randomly generated suppressors of gene deletion mutants to better understand the roles of uncharacterized interactors within the pathway. Lastly, I will be using site-directed mutagenesis combined with bioinformatics applications to predict and confirm exact points of interaction between proteins essential to G protein signaling.

Background:

I graduated from the University of California, Riverside in June 2005, with a bachelor’s degree in computer science.  I transferred to UCR from Mt. San Antonio College, in Walnut, California.

As an undergrad, I was involved in research in other areas of physical sciences. For example, I conducted research at NIST-Boulder under the direction of Dr. Elizabeth Donley, working to develop a double pass acousto-optic modulator to be used to develop the next generation atomic clock. 

Introduction:

I’m currently working with Dr. Reddy Venugopala to study the relationships between cell deformation patterns and cell division patterns. Pattern formation in developmental fields involves precise spatial regulation of gene expression and growth dynamics such as cell division, cell expansion, cell migration and cell death. The information is exchanged between multiple cell layers through cell-cell communication processes to regulate gene expression and growth dynamics. A quantitative and dynamic understanding of the spatial parameters of gene expression dynamics and growth patterns is crucial to model the process of pattern formation. As an example, shoot apical meristem (SAM) stem-cell niche in plants, is a dynamic multilayered structure consisting of about 500 cells and it provides cells for all the above-ground plant structures. The SAM has been divided into distinct functional domains based on differential gene expression patterns and growth patterns. The cells in the outermost L1 layer and the sub-epidermal L2 layer divide in anticlinal orientation (perpendicular to the SAM surface), while the underlying corpus forms a multi-layered structure where cells divide in random orientation.  Within this framework, the SAM is divided into functional zones with distinct gene expression activity.  The central zone (CZ) contains a set of stem-cells and the progeny of stem-cells differentiate within the surrounding peripheral zone (PZ). The CZ also supplies cells to the rib-zone (RZ) located beneath the CZ. Thus, cell fate specification within SAMs is a dynamic process intimately coupled to transient changes in gene activation/repression and changes in growth patterns.

I would like to study cell deformation patterns and how they relate to the cell division patterns. First, by developing computational platforms to identify cells and track their progeny through successive cell divisions from fluorescent 4-D images acquired by using laser scanning confocal microscopy. Second, by introducing experimental manipulations that can alter the cell deformation patterns and analyzing their effects on cell division dynamics. The computationally derived cell growth models will also allow us to understand the causal relationship between cell growth and cell division patterns.

Background:

I received my Bachelor’s degree in Molecular Biology and Biochemistry from the China Agricultural University in July 2007. During my undergraduate study, I was accepted into the Honor’s Program In Life Sciences and received basic training in biology for two years.  During my third year of undergraduate in this honors program, I performed my research in the Molecular Biology and Biochemistry Department. My undergraduate research project was focused on utilizing genetic and molecular approaches to dissect the Abscisic Acid signaling transduction pathway in Arabidopsis.  In the fall of 2007, I started pursuing my doctoral degree in the Department of Botany and Plant Sciences at University of California, Riverside.  Currently, my research project is focused on understanding the molecular events that regulate flower formation in Arabidopsis in Harley Smith’s laboratory.

Introduction:

The aerial organs or the plant are originated from a small pool of cells at the growing tip of the shoot called the shoot apical meristem (SAM).  One of the major developmental phase changes in higher plants is the transition from vegetative to reproductive growth, which is controlled by environmental and intrinsic developmental cues that converge at the SAM.  Two redundant functioning BELL1-like homeobox genes, PENNYWISE (PNY) and its paralogy POUNDFOOLISH (PNF), encode DNA-binding proteins that are essential for the specification of flowers during reproductive development. Biochemistry studies show that PNY/PNF associate with specific members of the KNOX class of homeodomain proteins including SHOOTMERISTEMLESS (STM).  Genetic studies indicate that PNY-STM and PNF-STM regulate early internode patterning events and control floral specification. Expressions of PNY, PNF and STM overlap in the vegetative, inflorescence and floral meristems. My research goal is to understand the how PNY/PNF-STM interactions regulate patterning events in the SAM.

Proteins are modular and often contain multiple domains or sequences that facilitate interactions with other proteins.  Transcription factors are highly modular containing multiple protein-protein interaction sequences as well as domains that associate with specific DNA-binding motifs.  Using chemical genetics, we aim to dissect the function of the protein-protein interactions mediated by PNY/PNF and STM.  Genetic approaches to study the function of transcription factors are useful are limited in that the phenotypes produced are the result of immediate and downstream processes.  My research goal is to utilize chemical genetics to dissect the function of PNY/PNF-STM interactions.  This approach will be combined with live imaging to determine the role PNY/PNF-STM regulate early and late patterning events in the SAM.  This research will be essential for understanding the molecular basis of flower specification.

Background:

I graduated in May 2005 from Indiana University with a Bachelor’s of Science in Informatics and minors in Biology and Chemistry.  During my undergraduate education I experimented on the mes genes of C. elegans determining whether mes-4 functions alone or with other proteins in a macromolecular complex.  Continuing at Indiana University I received a Master’s of Science in Bioinformatics in May of 2007.  During this time my research focused on predicting protein-disease associations through analysis of newly available disease ontology and protein-protein interaction data.  In the fall of 2007 I accepted the IGERT Fellowship at the University of California Riverside and began the doctoral program in Genetics, Genomics, and Bioinformatics with a track in Genomics and Bioinformatics.  During the fall quarter I explored molecular descriptors and chemical space with Dr. Stefano Lonardi.  I am currently rotating in Dr. Michael Pirrung’s laboratory working on molecular descriptors and virtual screening of candidate compounds.

Introduction:

Understanding and identifying ligand enzyme binding is of great importance to the biological community.  This knowledge holds promise of improved drugability as well as providing a fuller understanding of cellular processes.  While High Throughput Screening (HTS) has provided for the identification of many molecular interactions, computational prediction methods classified as Virtual Screening (VS) have been gaining ground in recent years as an alternative or, perhaps more appropriately stated, a complementary approach to compound screening.  VS approaches are designed to computationally bind molecular partners in an attempt to predict biologically true matches.  By applying VS techniques I intend to add to the screening processes in my laboratory.

It was recently estimated that there could be upwards of 10⁶⁰ small carbon-based compounds with molecular masses around the same range as in living organisms.  This is a truly amazing and in many ways entirely ungraspable number.  While this ability is a wonderful thing, it has recently been noticed that the number of biologically active compounds is strikingly correlated with natural product like scaffolds.  In many ways this makes sense.  Natural products, which are compounds created by cellular machinery, have gone through millions of years of trial and error and contain characteristics that allow them to move and more peacefully exist within the cell.  While we initially thought we should hit chemical genomics with every compound we can create, it is starting to look like we should start that process by looking at natural product like molecules.  By analyzing chemical space I am interested in how to better predict binding patterns.

Background:

I obtained my B.S. at UC Davis with a minor in Communications in 2003.  Upon graduation, I worked at Protein Research and Phoenix Pharmaceuticals for one year.  I then participated in a post-bac program at the University of Missouri-Columbia.  I am currently a first year graduate student in the Department of Botany and Plant Sciences.  I research interest in studying plant development and stem cells. 

Introduction:

A functionally important protein in plant developmental regulation has been found to have a homology domain to a protein that contains a pleckstrin homology (PH) domain.  This domain in our protein of interest has been found to bind lipids. The specific goal of my project is to determine which specific lipids bind to this domain and its biological relevance.

I will lipid binding and chemical assays such as NMR and capillary electrophoresis to deduce what specific lipids bind the PH domain.  In addition, I will utilize a battery of genetic as well as molecular biology assays to determine the function of the PH domain. 

Background:

I graduated in June 2003 with a Bachelor degree from California State University, San Bernardino in Chemistry – Biochemistry Option and a minor in Psychology. After graduation, I worked at Robert Mondavi winery and Charles Krug winery in Napa Valley. My work involved various aspects of winemaking such as performing various chemical tests on wine, preparing yeast culture for inoculation, handling tasting set-up, and performing quality control tests during bottling. During this time, I developed interest in understanding simple questions such as how temperature affects maturity of grapes or how nitrogen level changes during maturation of grapevine. I became very interested in studying molecular genetics and decided to pursue graduate study in this field. In fall 2006, I was accepted to the Genetics, Genomics, and Bioinformatics program here at University of California, Riverside. I joined Dr. Zhenbiao Yang’s lab and am currently working on understanding the ROP signaling network in regulating pollen tube growth in Arabidopsis.

Introduction:

ROPs (Rho GTPases from plants), subfamilies of Rho GTPases, are involved in various cellular signaling processes including pollen tube growth. ROP signaling pathway is turned on when ROPs bind GTP (active form) and turned off when ROPs bind GDP (inactive form). Regulatory proteins, RopGAPs (GTPase-activating proteins) help increase GTPase activity of ROPs. Another class of regulatory proteins, RopGEFs (GDP exchange factors) help promote GDP-for-GTP exchange. Out of 11 members of ROPs, three of them ROP 1, 3, and 5 are expressed in pollen and are functionally redundant. Genetic analysis of ROP 1 has shown that overexpressing the constitutively active (CA) mutants of ROP1 leads to swelling of pollen tubes. In contrast, overexpressing the dominant negative of dominant negative (DN) mutants of ROP1 leads to inhibition of pollen tube elongation. The observation of terminal phenotypes of these mutants provided evidence that ROP signaling is involved in pollen tube growth. However, events following ROP activation in regulation pollen tube growth are difficult to determine solely by genetic analysis. Thus, another technique such as chemical genetics would be particularly useful for this study.

Research Project:

Chemical genetics is a relatively recent approach that has been used to study and understand molecular mechanisms and complex interactions in living systems. Identification of chemicals that can specifically modify gene/proteins of interest is key to the success of this chemical genetics approach. In addition, the rapid effect of chemicals allows one to perform a time course study following chemical treatment. Therefore, the initial goal of my work is to identify chemicals that inhibit ROP and RopGAP interaction which lead to accumulation of active form of ROP. For the chemical screen, I use yeast-two-hybrid system which is a tool to study protein-protein interaction. It assumes that when two proteins interact, transcription machinery can be recruited to drive the expression of reporter genes which can be easily quantified. Thus, it provides an excellent system for my screen. Using this system, potential chemicals will be identified as those that cause low expression of reporter gene activities which include histidine and beta-galactosidase. Once chemicals have been identified, other in vitro as well as in vivo assays will be utilized to confirm its effects on ROP and RopGAP interaction. In addition, the specificity of chemicals will also be tested against other type of protein-protein interaction. And the effect of chemicals on pollen growth will also be observed.

"We had an awesome time... Dr. van der Hoorn was very special and open with us about conducting science at the interface between two disciplines ... It was a bonding experience among each of us trainees and the speaker." --Kayla Hamersky (Student)