Mentors and Projects Available

Mentors and Projects Available to Choose From Summer 2019

Jim Bamburg, Department of Biochemistry and Molecular Biology

slide for mitochondrial morphology / activity

Research Profile: Bamburg Research

Project Title: Role of cofilin-1 in Drp1-mediated mitochondrial fission during axon and dendrite maturation and in neuronal culture models of neurodegeneration

Project Description: The project is focused on the role of cofilin-1, a regulator of the actin cytoskeleton, in controlling Drp1-mediated mitochondrial fission in hippocampal neurons. The big questions that we’re trying to answer are: (1) how cofilin-1 alters mitochondrial morphology/activity during axon and dendrite maturation in cultured neurons, and (2) if the formation of cofilin-actin rods, which form in axons and dendrites during neuronal stress, impacts mitochondrial activity or dynamics contributing to synaptic dysfunction or neurodegeneration. Cofilin-actin rods are found in human brain (and in animal models) that suffer from different neurodegenerative diseases and disorders (e.g. Alzheimer’s disease and stroke) and may be responsible for synaptic dysfunction in these conditions.

Learning Outcomes: By the end of the period, we hope that the student will have a better understanding of research through:

  1. Improved general science knowledge (how to develop a hypothesis and design experiments to test it, how to collect data and analyze it, and how to interpret results).
  2. General laboratory skills (accurate preparation of reagents, proper disposal and waste management, etc.).
  3. Project related specific abilities (potentially including the following: sterile techniques, culturing neurons, use of viruses to express or knock-down proteins of interest, live-cell imaging and fluorescence microscopy).

Chaoping Chen, Department of Biochemistry and Molecular Biology

Research Profile: Chen Research

Project Title: Characterization of mutations associated with resistance to HIV-1 protease inhibitorsChen HIV diagram

Project Description: This summer project is part of our ongoing study aiming to understand HIV-1 protease autoprocessing mechanism and to identify novel autoprocessing inhibitors with the action modes distinct from the currently available HIV-1 protease inhibitors. We have established a cell-based phenotypic assay that not only has enabled high-throughput drug discovery but also provided an easy and powerful tool for analyzing mutations found in HIV-1 strains isolated from patients experiencing resistance to HIV-1 protease inhibitor treatment. The REU fellow will examine and determine how these mutations influence the responsiveness to HIV-1 protease inhibitors.

Learning Outcomes: The REU fellow will learn basic protein techniques, such as SDS-PAGE, western blotting and subsequent quantification analysis, and master these techniques to obtain reproducible results to shed new lights into drug resistance mechanism. Through these research activities, the REU fellow will also develop skills of critical thinking, spoken and written communication, and being a productive team player.

Karen Dobos, Dept. of Microbiology, Immunology, and Pathology

Research Profile: Dobos Research

Project Title: Identification of post-translational modifications in Antigen 85B from Mycobacterium tuberculosis.Dobos - research on post-translational modifications on tuberculosis

Project Description: Tuberculosis (TB), caused by Mycobacterium tuberculosis, is the leading cause of death due to an infectious agent worldwide. Classical diagnoses of TB have limitations in terms of sensitivity, time and specificity. Circulating antibodies against Antigen 85B, a secreted protein produced by M. tuberculosis, provide an alternative diagnostic platform, but recombinant versions of Antigen 85B perform poorly in early testing. Post-translational differences likely account for antigenic specificity, and the current project will explore the potential for phosphorylation of native antigen with the final goal of defining the type of post-translational modification and site(s) within the protein.

Learning Outcomes: The selected student will be mentored by senior researchers in the Dobos’ lab who will train the students in laboratory safety and laboratory techniques related to the project. These include: ELISA, gel electrophoresis, trypsin digestion, phosphatase treatment among others.

The student will conduct a series of experiments with the final goal of determining the phosphorylation status of native and recombinant Ag85B and its implication in antibody detection in human sera.

The student will be immersed in a research lab environment, will attend lab meetings and at the end of the summer will give a brief presentation on the status of the project.

Erin Nishimura, Department of Biochemistry and Molecular Biology

Research Description: Nishimura Research

Project Title:  Searching for transcription factors that instruct embryonic body planNishimura research - worm diagram

Project Description: Come help aid us in our search to identify key transcription factors that shape the C. elegans (worm) body plan. The researcher will disrupt critical combinations of genes and identify worms with altered organ identities. We have generated worms with fluorescently labeled organs that will allow for easy identification of developmental mutations. Because there is a high degree of conservation between nematodes and other animal systems, many of the discoveries we will achieve will be relevant to human health and will influence our interpretation of how organ identity is generally achieved.

Learning Outcomes: The research plan will charge the undergraduate researcher to:

  • learn basic lab safety, lab etiquette, and best practices
  • learn worm husbandry
  • conduct screen to identify transcription factor partners
  • help to generate new markers strains in worms
  • present research progress to the lab group to learn scientific communication

 

Christie Peebles, Department of Chemical and Biological Engineering

Research Description: Peebles Research Lab

Project Title: Synthetic Biology – Decoupling translation initiation from gene context in cyanobacteria

Project Description: Cyanobacteria are a promising production host for the sustainable production of a variety of fuels and chemicals.  By leveraging the fields of synthetic biology and metabolic engineering, pathway engineering optimizes biochemical pathways through genetic engineering to increase production of a target molecule within the target host. One of the key bottlenecks in pathway engineering in cyanobacteria is reliable ribosome binding sites (RBS) that can be utilized to modulate protein expression. The Peebles lab works to develop well characterized genetic parts for pathway engineering in cyanobacteria. In this project you will help to design and carry out experiments that aim to insulate an RBS from the context of the gene of interest so that a well-designed RBS library can be used to control gene expression of any gene.

Learning Outcomes: The REU student will gain hands on skills in experimental design, implementation, and troubleshooting.  You will learn a variety of molecular biology techniques including but not limited to PCR and restriction enzyme-based cloning (type II and IIS). You will also learn how to culture E. coli and Synechocystis sp. PCC 6803 and how to detect and quantify protein expression in E. coli and Synechocystis sp. PCC 6803.

Marinus Pilon, Department of Biology

Research Description: Pilon Research

Project Title: Regulation of Iron (Fe) utilization in plant leaves

Project Description: Fe deficiency anemia affects 1/3rd of all humans especially those on a vegetarian diet. When the plant Arabidopsis thaliana is faced with Fe deficiency it down-regulates mRNAs for abundant chloroplast Fe proteins. This regulation may involve reduced mRNA stability or lower promoter activity. To elucidate the mechanism of regulation, we will analyze transgenic plants containing promoter fusion constructs with the Glucuronidase (GUS) marker and measure GUS activity before and after Fe deficiency. Would this regulation affect Fe in crop plants? To address this we will subject agriculturally important species to Fe deficiency and measure accumulation of Fe proteins.

Learning Outcomes: The participant will learn good, safe, laboratory practice and become a co-author on publications. The student will be trained in plant line maintenance and growth, PCR, GUS assays, chlorophyll fluorescence analysis, and western blotting.

Elizabeth Pilon-Smits, Department of Biology

Research Description:  Pilon-Smits Research

Project Title: Characterization of selenate transporters from hyperaccumulator Stanleya pinnata via functional expression in Arabidopsis thaliana and baker’s yeast

Project Description: Selenium (Se) is an essential element, but toxic at high levels. Both Se deficiency and toxicity are widespread Plants growing next to rocksproblems estimated to affect more than a billion people worldwide. Plants may be used to remove excess Se (phytoremediation) while providing enhanced dietary Se (biofortification). Se (selenate) uptake is inhibited by sulfur (S)(sulfate), because both use sulfate transporters. Exceptionally, the plant shown in the picture, Se hyperaccumulator Stanleya pinnata (Brassicaceae) can accumulate Se independently from S, presumably owing to a selenate-specific transporter. This project focuses on a sulfate/selenate transporter that is highly overexpressed in the hyperaccumulator. We hypothesize it has higher selenate specificity. This study’s goal is to functionally characterize this transporter via expression in baker’s yeast and Arabidopsis thaliana.

Learning Outcomes: The gene of interest, as well the counterpart from a related non-accumulator, Stanleya elata, have already been cloned into appropriate yeast and plant expression vectors and transformed. The yeast strains are ready to be characterized. In this REU project, you will learn to measure yeast selenate uptake in the presence or absence of sulfate, and determine selenate specificity. Furthermore, Arabidopsis transgenics for the gene constructs have been obtained, and are being bred to homozygosity. You will help to further characterize the homozygous lines for expression levels (Western blotting) and test them, in comparison with wildtype, for their selenate-specific uptake properties. You will work directly with PhD student Leonardo Lima..

Kenneth Reardon, Department of Chemical and Biological Engineering

Research Description: Reardon Research

Project Title: Enhanced Production of Fuels and Chemicals from Biomass via Electro-Stimulated FermentationElectro-Stimulated Fermentation

Project Description: With the increasing presence of wind and solar energy in the electrical grid, there is the opportunity to use inexpensive, renewable electrons as a resource in chemical production.  Recently, our lab and others have demonstrated that supplying electrons to fermentations of biomass-derived sugars can dramatically change the outcome of the cultivation. However, the mechanisms for this phenomenon are not understood, and strategies to better direct electrons into cellular metabolism have not been developed.  REU students will be involved in analyzing microbial response to e-stimulation and designing and testing new approaches for increasing the production of fuels and chemicals from biomass.

Learning Outcomes: Participants will learn principles of microbial cultivation and bioreactors, measurement methods for fermentation substrates and products, basic concepts of electrochemistry, and analysis of data to determine yields and rates.

Carol Wilusz, Department of Microbiology, Immunology & Pathology

Research Description: Wilusz Research

Project Title: Post-transcriptional control in stem cells and cancerPost-transcriptional control in stem cells

Project Description: We study the post-transcriptional control of gene expression – how mRNAs (and non-coding RNAs) are processed, localized, and degraded – in stem cells and cancer cells.  Project 1 investigates how methylation of mRNAs and its recognition by RNA binding proteins influences pluripotency and differentiation.  We are focused on understanding the function and regulation of the RNA binding protein YTHDF2 which binds methylated mRNAs and targets them for decay.   Project 2 explores a large class of mRNAs encoding zinc finger proteins (ZNFs). These transcripts are unique in that sequences in their coding regions confer short poly(A) tails and nuclear retention.  We believe these mRNAs may moonlight as non-coding RNAs, or may use nuclear retention as a means to restrict expression to specific phases of the cell cycle.  We are working to understand how ZNF mRNAs are processed and localized and what impact it has on their expression.

Learning Outcomes: The student will receive training in cell/molecular biology techniques including one or more of the following approaches: cloning (Gibson assembly), digital PCR to assay gene expression, luciferase reporter assays, western blotting, immunofluorescence, fluorescent in situ hybridization, cell culture etc.  The student will keep an electronic lab notebook and will learn the basics of experimental design and interpretation.   The student will be supervised by the PI and/or a senior graduate student.

Kelly Wrighton, Department of Crop and Soil Sciences

Research Description: Wrighton Research Lab

Project Title: Finding the needles in the microbiome haystack: isolating and characterizing microbes capable of degrading phytochemicals

Project Description: The Wrighton Lab studies microbial metabolisms across ecosystems, using multi-omic data (genomes, metabolomes, transcriptomes, and proteomes) to generate hypotheses about microbiomes that can be subsequently tested in the laboratory. In accordance with this theme, this REU project will uncover how microorganisms interact with plants and their polyphenolic secondary metabolites. Currently, how microorganisms respond to and even degrade these compounds is unknown. This REU researcher will work closely with a graduate student and Dr. Wrighton to cultivate novel microorganisms that can resist and degrade polyphenolics. On a larger scale, knowledge gleaned from this research can have important applications to improve plant biofuel efficiency, animal nutrition in the gut microbiome, and agricultural soil health and productivity.

Learning Outcomes: Research outcomes of the REU for the student will be: (#1) to gain experience in anaerobic microbiology, (#2) to apply molecular techniques to identify isolated microbes, (#3) to use established biochemical assays to assess the capacity for phytochemical degradation, and (#4) to learn to analyze genomic data related to polyphenolic metabolism. The highlight of the REU experience will be the opportunity to design, prepare, and perform an experiment with robust controls in order to monitor isolate growth and assay phytochemical degradation. The REU researcher will be an active member of the Wrighton laboratory, expected to attend weekly laboratory meetings and even present their research to the Wrighton lab team at the end of the summer. The Wrighton lab is highly collaborative, and works across many ecosystems from the human gut to deep subsurface fractured rocks, so the REU researcher will also be exposed to research in other ecosystems.