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Dr. Alexandre with students

REU Program

Each REU student will conduct an individually tailored research project under the guidance of faculty research mentors with expertise across biophysical, biochemical, genetic, microbial, plant science, neuroscience, mathematic/computational biology, and engineering disciplines.  Potential research projects include the following.

Faculty Mentors and Research Projects


Navigating the Rhizome-plant microbe interactions of beneficial soil bacteria”

REU students will investigate how beneficial soil bacteria of the Azospirillum genus sense their environment and respond by altering their swimming patterns to move toward favorable conditions, using chemotaxis. By using a combination of genetics, state-of-the-art microscopic and cell biological imaging analyses, and mathematic modeling, students will conduct research projects elucidating the molecular mechanisms that couple sensing of cues into behavioral responses that promote bacterial colonization of beneficial niches in the rhizosphere. (Discipline: Microbiology/Genetics)


Ethylene Signal Transduction: From Bacteria to Plants”

Ethylene is a gas that is well known as a plant hormone that controls many aspects of growth, development, and stress responses. More recently, the Binder lab showed that bacteria contain functional ethylene receptors that are being characterized. REU students will conduct projects examining the effects of ethylene on the behavior of bacterial motility and biofilm formation. This information will be correlated with changes in gene transcripts and biochemistry to understand how bacteria sense and respond to ethylene. REU students will learn a variety of methods from biochemistry, molecular biology, genetics, microscopy, and physiology.  (Discipline: Plant Biology and Biochemistry)


Plasmodesmata-mediated cell-cell communication in plants”

Plasmodesmata are plant cellular structures that traverse cell walls to directly connect adjacent protoplasts. Plasmodesmata traffic nutrients and signaling molecules including hormones, small RNAs, and proteins between adjoining cells, but how this trafficking is regulated is not well understood. The Burch-Smith lab has uncovered considerable evidence that chloroplasts regulate plasmodesmata, likely as part of a complex regulatory network for systemic control of nutrient partitioning and development. REU students will use a subset of advanced microscopy, genomics and molecular biology approaches to investigate the chloroplast-plasmodesmata relationship and its significance for plant survival.  (Discipline: Plant Cell Biology and Genomics)


Design principles of Cell morphogenesisCell shape establishment is critical to proper cell function. REU students will investigate how signaling mechanisms are regulated during cell shape establishment in a cell cycle dependent manner.  In particular they will study how a cell determines that it needs to stop polarized growth and start division; and how it senses completion of cell division and resumes polarized growth. Reu students will use the genetic model system fission yeast and use genetic mutants, quantitative live-cell imaging and predictive modeling in projects addressing this question.   (Discipline: Cell Biology and Mathematic Modeling)


Modeling decision-making mechanisms in T cell differentiation” REU students will investigate how the immune system can rapidly deploy a diverse population of T cells, which not only combat infections in a synergistic manner but also protect the body from excessive immune response. The project involves building mathematical models that describe the dynamics of signal transduction and gene expression in T cells, and performing computer simulations that recapitulate the process in which the undifferentiated T cells get specialized. The goal of the research is to improve the understanding of the robust decision-making mechanisms of immune cells at the cellular level, and the beneficial diversification strategy at the tissue (cell population) level. (Discipline: Systems Biology and Computational Mathematic Modeling)


Deciphering the role of perineuronal nets in learning and behavioral tasks in miceREU students will investigate how perineuronal nets act to facilitate or impede plasticity in the whole mouse brain during learning and execution of behaviors. REU students will be introduced to concepts and research methods used to study neural plasticity, trained in state-of-the art epifluorescent microscopy which collects and stitches high-resolution images of entire brain sections, quantify and analyze data.   (Discipline: Cellular Neuroscience and Imaging)


Defining microbe-derived chemicals that shape microbiome assembly” REU students will use a combination of comparative genomics, in vitro biochemical assays, and seedling colonization experiments to examine the plant-microbe and microbe-microbe interactions that direct plant microbiome assembly. In particular, they will study the capacity of Streptomyces isolates to sculpt microbiome composition through their consistent plant colonization and powerful metabolic repertoire. (Discipline: Microbiology and Genomics)


The role of nuclear architecture in cancer cell metastasis”

REU students will investigate factors that influence how well cancer and normal cells migrate through tight spaces using cell culture assays, fluorescence microscopy, and microfluidics. Experiments and image analyses will help determine the mechanisms of cancer drugs that inhibit cell migration and which properties of the nucleus enable or inhibit migration. (Discipline: Experimental and Computational Cellular Systems Biology)


Impact of Soil Microbiome on Plant Disease Resistance” REU students will examine how the plant defense response is modulated by studying the crosstalk among plants, pathogens and soil microbial communities. By integrating genomic, genetic and bioinformatic tools/resources, students will (1) identify host-specific and broad-spectrum beneficial/detrimental microbes and (2) determine the plant host genetic factors that drive these plant-pathogen-microbe interactions. (Discipline: Plant Microbe Interactions and Genomics)


Drowning on Dry Land-Strategies for Adaptation to Flooding and Anaerobic Stress”

Higher plants are obligate aerobes that require a continuous supply of oxygen to support energy demand. Oxygen deprivation stress from flooding, water logging or poor soil aeration leads to an energy crisis and triggers an adaptation program to conserve and recycle precious cellular resources.  As part of this program, plants reshuffle their mRNA resources by selective trafficking of mRNA to stress organelles known as stress granules (SG) and protein bodies (PB) for storage or degradation of unnecessary transcripts to conserve energy. Students will conduct experiments investigating the genetic and molecular basis that underlies how plants perceive low oxygen and trigger adaption to this stress. (Discipline: Biochemistry and Biophysics)


“Forest tree genomic data integration and biocuration”

REU students will work on the Hardwood Genomics Project website, a database of genomic resources built on the Tripal software platform. Students will follow a biocuration pipeline, starting with identifying public data sets, then performing bioinformatic analysis such as annotation of genomes and gene expression analysis, and finally adding data to the website and helping to build user interfaces to the data. This project will provide participants with new skills in bioinformatic analysis and genome data integration as well as familiarity with using high performance computing and website construction. (Discipline: Systems Biology and Bioinformatics)


Understanding and harnessing environmental cues for regulating the bacterial adaptive immunity for effective antibacterial treatment

Bacteria have innate adaptive CRISPR systems to prevent invasion of foreign DNAs (e.g., virus, plasmids). REU students will investigate what environmental signals regulate the expression of the native CRISPR systems of these bacteria and harness the signals to reprogram cells for self-deactivation with useful application as antimicrobial treatment against resistant superbugs harmful to human health. Participating in the project, REU students will gain hands-on experience with system and synthetic biology tools. (Discipline: Synthetic Biology)


Regulation of the Protein Synthesis Apparatus of Plants”

At the core of growth and development in any organism is protein synthesis – the translation of genetic information from mRNA into protein. REU students will conduct research to understand how protein kinase signaling pathways contribute to the regulation of translation by environmental and developmental signals. This work utilizes the genetic resources of Arabidopsis, genome-wide assays of translation, bioinformatics and computational modeling, and a wide range of cell biological reagents. (Discipline: Plant Genomics and Network Modeling