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Dr. Alexandre with students

REU Program [Not available for Summer 2023]

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, and engineering disciplines.  Potential research projects include the following:

Faculty Mentors and Research Projects

“Navigating the rhizome-plant microbe interactions of beneficial soil bacteria” (Microbiology/Genetics)  REU students will investigate how beneficial soil bacteria of the Azospirillum or Rhizobium genera sense their environment and respond by altering their swimming patterns to move toward favorable conditions. The students will conduct research projects that will use microbial physiology, microscopy, molecular biology, and plant inoculation experiments. Students will contribute to elucidating the molecular mechanisms that couple sensing of cues into behavioral responses that promote bacterial colonization of plant roots. Students will conduct experiments addressing fitness in plant-microbe associations and interactions between inoculated beneficial bacteria and endogenous microbial soil communities

 “Membrane signaling by receptor kinases in mammalian cells” (Biochemistry/Cell Biology) The research of the Barrera group focuses on the study of membrane receptors. This critical group of membrane proteins is in charge of surveying the extracellular medium of cells and detecting environmental changes which the cell benefits from responding to. As a result of the sensing event, membrane receptor activation occurs in the form of a signaling cascade that starts at the cytoplasm, and later reaches the nucleus, with the result of changes in gene expression. We use biochemical, biophysical and cell biology methods to study the activation and regulation of different membrane receptors, including receptor tyrosine kinases and the T cell receptor. The students will participate in mentored studies to determine the impact of signaling lipids, such as cholesterol and phosphorylated phosphoinositides on the ROR1 tyrosine kinase receptor. These studies will involve Western blot studies of receptor phosphorylation and downstream activity assays.

Ethylene Signal Transduction: From Bacteria to Plants” (Plant Biology/ Microbiology)  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.

“Investigating molecular mechanisms of microbe-host interactions using entomopathogenic nematodes and bacteria” (Microbiology/Genetics)  Students will use bacterial genetics, genomics, microscopy, and molecular and biochemical approaches to investigate the symbiotic interactions of the bacterium Xenorhabdus with its animal hosts. Xenorhabdus is a mutualist of Steinerneman ematodes and a pathogen of a wide range of insects, and experimentation on this system will give students experiences in a broad range of skills in bacteriology, nematology, and entomology. Students will explore research questions that address evolutionary, ecological, and physiological principles underlying the ways in which symbiotic partners sense and respond to each other at the molecular level.

“Neuronal mechanisms of stress resilience” (Behavioral Neuroscience) The research in my laboratory is focused on neural circuits and cellular mechanisms controlling susceptibility and resilience to traumatic stress. We use a multidisciplinary approach and a variety of techniques including inter-cranial microinjections, viral-mediated genetic manipulations, immunofluorescence, in vivo calcium imaging, and rodent behavioral testing. We use a Syrian hamster model because both males and females establish stable dominance relationships and have found that dominant animals develop changes in amygdala neurons that enhance stress resilience. Our current project investigates whether dominant animals exhibit greater calcium activity in select amygdala neurons during traumatic stress compared to subordinate animals. Students engaged in this project will receive training on intra-cranial injection of viral vectors, immunofluorescent approaches to quantify virus expression, quantification of aggressive and submissive behavior, and the use of fiber photometry to quantify calcium activity in awake, freely moving animals.

“Investigating formation of lipid droplets in Saccharomyces cerevisiae” (Cell Biology/Genetics/Imaging) Intracellular membrane-bound organelles are a hallmark of all eukaryotic cells. Understanding how cells generate different organelles that display characteristic morphologies remains one of the central problems in cell biology. Some organelles, like the endoplasmic reticulum (ER) and mitochondria, are self-generating whereas other organelles such as peroxisomes and lipid droplets (LDs) can be generated de novo from specialized subdomains in the ER membrane. Remarkably little is known about the ER subdomains and how they regulate organelle biogenesis. In our lab, we utilize a combination of cell biological, genetics, and biochemical approaches in yeast and mammalian cells to investigate the formation and function of organelles at the ER subdomains in normal and pathological conditions. The REU student would use yeast cells to investigate lipid droplet formation and function using genetic and cell biological approaches including live-cell fluorescence microscopy.

“Deciphering molecular and cellular mechanisms underlying synaptic plasticity in mouse model for neurodevelopmental disorders”.  (Cellular and Behavioral Neuroscience, Imaging, Deep Learning) Rett Syndrome is a neurodevelopmental disorder, like autism spectrum disorder, caused by mutations in MECP2, an X-linked gene. This syndromic disorder is characterized by sustained sensory, cognitive, and motor deficits after an early postnatal period of normal development in girls. Our approaches, which the REU students will be working on, allow us to connect-the-dots between changes in MECP2 protein in the nucleus with organismal behavioral phenotypes over ages. REU students will investigate how GABAergic inhibitory neurons facilitate or impede plasticity in the whole mouse brain during learning and execution of behaviors. REU students will be introduced to concepts, research methods and data analysis used to study neural plasticity and trained in state-of-the art integrative techniques from molecules to behaviors.

“Single-molecule view of dynamics and activation mechanisms of G protein-coupled receptors” (Biochemistry/Biophysics)  Research in the Lamichhane lab focuses on applying and advancing single-molecule fluorescence in studying conformational dynamics and activation mechanism of G protein-coupled receptors and several other DNA and RNA protein interactions. Understanding how the dynamic interactions between biomolecules control their assembly pathway will help us to predict potential defects in such processes caused by different diseases. Detailed information on biomolecular assembly pathways will ultimately guide us towards the design and development of therapeutics targeting each step of assembly. REU students will use single-molecule microscopy and biophysical assays to understand biomolecular dynamics.


“Sensing and Signaling through 3D Genome Structure” (Experimental and Computational Cellular Systems Biology) The DNA inside the nucleus of a eukaryotic cell is usually considered only for its role in information storage. But, to compact the 2-meter-long genome of a mammalian cell into a 10-micron wide nucleus, the genome folds into a complex 3D structure that influences the physical properties of the cell, enables the faithful replication and transmission of genetic information, and allows for the proper regulation of gene expression. Our lab’s goal is to understand the properties and function of this 3D genome structure. We investigate how the 3D genome structure senses and responds to physical deformations of the cell, how the 3D genome structure affects gene regulation – the output of many signaling cascades, and how the physical properties of the 3D genome structure affect the behavior of the whole cell during processes like cell migration. We use a combination of live-cell fluorescence imaging, molecular biology, and high throughput sequencing-based techniques to link visible changes in nuclear structure to rearrangement of interactions between specific genomic loci. Summer UG research students could take on a variety of aspects of these projects, such as quantitative imaging of changes in fluorescently labeled nuclei during different physical stresses or cell migration, and, if there is interest, computational analysis of genomic datasets.

“NanoBioElectronics for the surveillance of human health” (Biochemistry/ Bioengineering) The McFarlane Lab develops sensors for a wide variety of sensing applications that make faster measurements, measure more samples simultaneously, are smaller, and are less costly than traditional sensing systems. These sensing applications can be in the biomedical, agricultural, or environmental fields and range from neutron imaging to glucose sensing to bowel sound detection to temperature measurements. The lab develops electrochemical sensing systems, new electrodes for cell-based sensing, CMOS based neutron detection, lab-on-chip cell-based sensing, multi-modal sensing, energy and power tradeoffs, and hardware and biosensor security. Bacterial cells query extremely complex living environments in a continuous and parallel manner and thereby adapt their processing, sensing, and actuating machinery to promote survival, often on a time scale of seconds to minutes. Biomicroelectronics attempts to tap into this cellular processing power to create hybrid biological-silicon biosensor interfaces capable of sensing and responding to environmental cues. In this research, we are attempting to merge genetically engineered bioluminescent cells with silicon microelectronics to create biosensors for the surveillance of human health.

“Effect of the growth hormone auxin on actin filament organization and organelle movement in Arabidopsis thaliana” (Cell Biology/ Plant Biology)  Cytoplasmic streaming in plant cells is characterized by the rapid movement of organelles along actin filaments. Research from our lab and others has demonstrated that these myosin-driven movements support growth and lead to larger cell sizes. Similarly, the growth hormone auxin also stimulates growth, although it is not known whether the action of auxin involves the actin cytoskeleton and/or organelle movements. The goal of this project is to test whether external application of auxin to plant seedlings alters organelle mobility and/or organization of the actin cytoskeleton. This research will involve quantitative analysis of time-lapse videos of several transgenic plant lines available in the lab that express fluorescent labels for several organelles or actin filaments.


Regulation of flower morphogenesis by cell-cell communications” (Development/Genetics/Plant biology) In nature, a remarkable variety of flower shapes exist. Each flower evolved to ensure efficient pollination and seed dispersal resulting in successful reproduction. For an organ to achieve a specific form, the timing of cell proliferation, the extent of cell elongation, and the establishment of boundaries between organs must be coordinated. One of the key signaling pathways regulating flower shapes and enabling cell-cell communications is the ERECTA family of receptors and their extracellular ligands, EPFLs. REU students will analyze the potential downstream targets of this signaling pathway. They will analyze expression patterns of several genes of interest, create higher order Arabidopsis mutants and analyze their phenotypes.

“Beneficial interactions of marine microbes” (Microbiology/Molecular biology)

The Zinser lab is interested in beneficial interactions between marine microbes and studies how microbes in the ocean form productive communities through their interactions. They utilize culture-based experiments involving physiology, chemistry, and genetic mutation to characterize how bacteria and microbial eukaryotes exchange nutrient resources and cross-protect each other from environmental stresses. Students engaged in this project will co-culture photosynthetic and heterotrophic microbes to investigate how they affect each other’s growth and survival under conditions that simulate the ocean. Students will utilize molecular genetic approaches to discover genes involved in beneficial and/or deleterious interactions that occur between these different microbes, and they  will gain expertise in techniques including microbial cultivation, mutagenesis, DNA sequencing, and flow cytometry.