UCR

Center for Plant Cell Biology



REU 2015


REU Students and their Summer 2015 Research Programs

Undergraduate students were invited to apply to the Center for Plant Cell Biology (CEPCEB) to pursue individual research projects in the areas of cellular and molecular biology of plants and their pathogens. In 2015, the following eight students were selected for this ongoing 10-week residential summer program.  Please click on the following student links to see photos and read about their Summer 2015 research programs in CEPCEB laboratories.

An REU Poster Session is scheduled in the Genomics lobby at the end of the ten-week program, where students discuss their projects.

REU Student
College/University
CEPCEB Faculty

Emile Cora Barnes

New College of Florida, FL

Van Norman Lab

Riyan Bittar

University of California, Riverside, CA

Jin Lab

Shannon Ferry

University of Rochester, NY

Borkovich Lab

Christopher Hoyt

Harvey Mudd College, CA

Rasmussen Lab

Robert Jimenez

Berkeley City College, CA

Judelson Lab

Marie Schmidt

Vassar College, NY

Walling Lab

Joel A. Velasco

Boise State University, ID

Bailey-Serres Lab

Harry Wedel

Vassar College, NY

Eulgem Lab

 

EMILE CORA BARNES
New College of Florida, FL
Emile Cora Barnes

Isolation and characterization of the root middle cortex (Jaimie Van Norman lab)

The middle cortex is a layer of ground tissue found in many angiosperm roots. It is derived from asymmetric cell division of the root endodermis, and by fluorescence microscopy has been shown to express cortex cell-specific reporter transgenes shortly after formation. Therefore, the middle cortex is generally described as another layer of cortex cells, and has received relatively little attention. The Van Norman lab has identified POLARLY LOCALIZED KINASE 1 (PLK1), a transmembrane protein which shows unique localization patterns in the endodermis, middle cortex, and cortex, suggesting that the middle cortex has unique traits which are able to influence localization of PLK1. This project aims to track the formation of the middle cortex of Arabidopsis thaliana roots through the creation of transgenic lines of plants in which each layer of ground tissue is visualized by fluorescent reporter genes. We will also use fluorescence-activated cell sorting (FACS) to isolate middle cortex cells based on dual expression of PLK1 marker genes and cortex cell marker genes. Isolation of middle cortex by FACS will allow RNA sequencing on a large number of cells, giving extensive, and currently unknown, information necessary to form a detailed transcriptional profile and begin to characterize the middle cortex. This molecular-level resolution of the middle cortex will help to elucidate the identity and function of this tissue, as well as identify genes of interest for further research in intercellular signaling and asymmetric cell division and how these processes work to influence cell fate specification through developmental time.

 

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RIYAN BITTAR
University of California,
Riverside, CA
Ryan Bittar

Development of efficient disease management of citrus HLB disease with Small RNAs regulation (Hailing Jin lab)

Huanglongbing (HLB) is a bacterial pathogen that lives in the phloem of citrus trees and is spread with the assistance of the Asian citrus psyllid. HLB destroys the economic value of citrus trees by rendering the fruits inedible, because of their bitter taste, and causes a serious reduction in fruit yield. Removing infected trees is the major method to stop further spreading of the bacteria and this will rely on early diagnosis of infected trees. HLB is hard to diagnose by symptoms. Small RNAs (sRNA) specifically induced by HLB infection can be used as a more efficient and early diagnosis tool for HLB. Currently miR399 is used to do early diagnosis of infected trees, and lead to the discovery of phosphorus deficiency symptoms seen in HLB infected trees. To identify specific sRNAs response to HLB, and/or other citrus disease pathogens, we constructed sRNA libraries and performed next generation deep sequencing. We characterize a panel of sRNAs that are induced by HLB, from sRNA libraries, to develop a more accurate method for early diagnosis. These specific sRNAs that respond to HLB will give us clues to identify HLB pathogenesis and the master regulator of defense response.

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SHANNON FERRY
University of Rochester, NY
Shannon Ferry

Interaction Studies of GNA-1 with the Arp2/3 Complex Using a Novel Microscopic Method (Katherine Borkovich lab)

Neurospora crassa is a non-pathogenic filamentous fungus, used as a model organism in genetic research. N.crassa is an ideal organism for genetic research because of its simple haploid life cycle. These features allows scientists to manipulate and observe all the genotypic combinations that occur when two strains of fungi are crossed. N. crassa has two alternate lifecycles, an asexual "Macro-condiation" and a sexual cycle, connected by the formation of restrictive, multi-nuclear tube structures, called hyphae. Hyphae grows through polar extension. Hyphae can also produce branches that fuse.

The ability of branches of hyphae to fuse to form a heterokaryon will be used in order to determine the interactions and co-localization of the proteins Arp 2/3 and GNA-1. GNA-1 is a Gα subunit, which plays an important role in the G protein-signaling pathway. G proteins are made up of three subunits, Gα, Gβ, and Gɣ. The Gα subunit can activate important pathways in N.crassa. The protein complex Arp2/3 is responsible for the formation of actin branches. Past research, using yeast two hybrid analysis, has shown an interaction between GNA-1 and Arp2/3. This project seeks to confirm this finding with co-immunoprecipitation and microscopic approaches. GNA-1 and Arp2/3 will be tagged with either GFP (green) or RFP (red) in different strains and the strains will then be fused to form a heterokaryon expressing a GFP and RFP-tagged protein. Co-localization of the proteins can be determined by fluorescent microscopy of the cells during growth and development.

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CHRISTOPHER HOYT
Harvey Mudd College, CA
Christopher Hoyt

Division Plane Modeling in Maize Cells (Carolyn Rasmussen lab)

TANGLED is a microtubule binding protein that is required for proper division plane orientation. Before cellular division, plants assemble a ring around the cell known as the preprophase band. In properly functioning cells, TANGLED guides the developing cell plate during cytokinesis to the location of the preprophase band. Prior studies with plants demonstrate that these new cell wall has the minimum surface area required to divide the cell given that the two new cells will have equal volumes. However, in tangled mutants, the developing cell wall does not return to the location of the preprophase band, and instead will develop irregular divisions that have neither a minimum surface area nor necessarily equal division of the cell's volume. This project uses micrographs of tangled mutant cells to create a three dimensional (3-D) model of the cell. Then, using the rules of division, a computer program will identify the minimum surface area required to divide the cell so that the two new cells have an equal volume. Finally, the ideal cell wall placement determined by the computer program will be compared to the actual division site. If they align, it would imply that the tangled phenotype is not caused by a malfunctioning preprophase band and that TANGLED's function occurs later than preprophase band development in the cellular division cycle. If they do not align, it may suggest that TANGLED directly affects the creation and placement of the preprophase band, indicating that TANGLED leads multiple roles within the cell.  

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ROBERT JIMENEZ
Berkeley City College, CA
Robert Jimenez

Transporter Localization in Phytophthora infestans (Howard Judelson Lab)

Phytophthora infestans is the pathogen responsible for the Irish potato famine in 1845 (late blight disease). The pathogen has been around since the 1800's and is still poorly understood. P. infestans affects potato and tomato foliage, causing hundreds of thousands of dollars of crop loss per year. Like some fungi, Phytophthora also make a structure called haustoria. In fungi these structures are used to take nutrients from their host through transmembrane transporters. While this function has never been proven in oomycetes, we hypothesize that P. infestans also targets transmembrane transporters to its haustoria to obtain amino acids from the host. Our main interest is in two specific amino acid transporter genes that are up-regulated highly at the early stages of infection. We are interested in seeing if these transporters localize to haustoria. To study the localization of these transporters we will be looking at where these up-regulated transporter proteins are within the pathogen. Through cloning we will generate plasmids which tag transporter genes with the fluorescent tag tdTomato. We will transform P. infestans zoospores with our plasmids by using electroporation. These transformants will then be examined by confocal microscopy to see where the transporters are localized within the organism. By studying the localization of these transporters, we will gain new knowledge on P. infestans haustoria. Knowing where the amino acid transporters are localized may provide insight into whether they play a role in nutrient uptake. A better understanding of the transporters may lead to more reliable pathogen prevention methods.   

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MARIE SCHMIDT
Vassar College, NY
Marie Schmidt

The Role of Tomato WHIRLY Proteins in Retrograde Signaling and Plant Defense (Linda Walling lab)

Leucyl aminopeptidase-A (LAP-A) is a stress-induced protein found in the Solanaceae, and is involved in late-wound response signaling. It is located in the plastid, however is able to regulate nuclear gene expression through an unknown mechanism. In Arabidopsis thaliana it has been shown that the transcription factor WHY1 is involved in defense response signaling and is capable of localizing in both the chloroplast and the nucleus, indicating that it is a potential retrograde signal in tomato. In this project all WHY genes in tomato will be identified using BLAST-N. WHY1 proteins from tomato will be tagged with CFP and the WHY1-CFP fusions will be transiently expressed in Nicotiana benthamiana. LAP-A-YFP protein fusions will be used as a positive control. The localization of WHY1 proteins pre and post defense hormone treatments, using jasmonic acid and salicylic acid, will be monitored by visualizing fluorescent protein light emissions. This will determine if tomato WHY1 protein is dual-localizing and induced by stress signals. To determine if WHY1 localization is LAP-A dependent, the WHY1-CFP fusion will then be transiently expressed in tomato lines that are LAP-A silenced, LAP-A overexpressed, and wild type. This procedure will be repeated with tomato WHY2 proteins. These experiments will provide a better understanding of LAP-A defense signaling, and this data may be useful in developing tomato lines with increased insect resistance. 

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JOEL A. VELASCO
Boise State University, ID
Joel A. Velasco

A Toolkit for Study of Cell-type Specific Gene Expression in Rice
(Julia Bailey-Serres lab)

Plant development is exquisitely orchestrated by genetically determined processes that are fine-tuned by environmental cues. This action entails the precise regulation of networks of genes in individual cells over the course of the plant life cycle. To decipher this complex regulation of gene expression we are taking advantage of the TRAP (Translating Ribosome Affinity Purification) technology. This methodology, which was developed in the Bailey-Serres lab for the model plant Arabidopsis thaliana, enables the isolation of ribosomes loaded with mRNA ("the translatome") within specific cells of a leaf, root or other organs. TRAP facilitates the identification of genes that are dynamically turned on and off as the plant responds to stress or other cues. To move the technology to an important crop species, transgenic rice (Oryza sativa) lines have been produced to express a FLAG-epitope-tagged version of ribosomal protein L18 in specific cell types to allow TRAP. My project aims to determine precisely the genomic location of transgenic DNA in each of these lines. This process involves the use of Next-Gen sequencing of transgene-enriched DNA libraries, obtained with a specialized DNA capture technique. The transgene insertion site information and the expression pattern visualized by microscopy for each line will facilitate the selection of the best transgenic lines for future evaluation of gene expression in specific cell types. These genetic resources will be used to 
study how development is perturbed by two major environmental threats to US agriculture: droughts and floods.

 

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HARRY WEDEL
Vassar College, NY
Harry Wedel

Hormetic effects triggered by synthetic elicitor BHTC in
Arabidopsis thaliana (Thomas Eulgem lab)

In a hormetic response, a physical or chemical stimulus that is usually harmful to an organism at high doses produces positive effects at low doses. Through a high-throughput screening, our lab previously identified 114 drug-like compounds that activate plant immune responses. Many of these synthetic elicitors were also found to stimulate hormetic effects in Arabidopsis thaliana (Arabidopsis). The synthetic elicitor BHTC is a particularly strong inducer of hormesis as it triggers robustly enhanced growth of roots at low doses, while suppressing root growth at high doses. Surprisingly, there has not been much work performed regarding the study of hormesis in Arabidopsis, the most effective model system in plants. To further study this effect, wild-type (Col-0) Arabidopsis seedlings will be grown on plates with varying doses of BHTC and the rate of their root growth will be measured. Moreover, this assay will be repeated with known mutants for the purpose of identifying genes required for the hormetic response seen in Arabidopsis. These mutants will include, among others, arx1-3 and slr-1, which are deficient in known auxin-signaling genes. Our lab previously found that the genes responsive to a high dose of BHTC are linked to immunity and differ from those responsive to a low dose of BHTC, which are linked to auxin-related signaling. This suggests a connection between immune responses and auxin signaling in controlling hormesis-associated developmental processes.

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2015 REU Students
2015 REU Students

More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

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Center for Plant Cell Biology
Botany & Plant Sciences Department
2150 Batchelor Hall

Tel: (951) 827-7177
Fax: (951) 827-5155
E-mail: genomics@ucr.edu

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