REU Research Teams

REU students will work to creatively shape the projects to match their interests. REU students will be full participants in all usual lab activities including lab meetings and journal clubs. Mentoring and support will be provided throughout the REU experience as described in the subsequent sections, and will enable students to grow as independent scientists.

Antibiotic Discovery

Professor Kim Lewis and Research Scientist Anthony D’ Onfrio

professor kim lewis and research scientist anthony d'onofrio

Professor Kim Lewis and Research Scientist Anthony D’Onofrio

Research Project Summary: The goal of the project is to discover and characterize new antimicrobial compounds. The project brings together two experts in antimicrobial discovery, Kim Lewis and Anthony D’Onofrio. REU students will screen a library of synthetic compounds, but in addition, attractive antimicrobial-producing microorganisms will be specifically captured from environments where their presence will be determined by their DNA signature, obviating traditional Petri dish isolation. The screen will uncover compounds acting selectively against a given pathogen, providing a new type of specific antibiotics. The compounds will be characterized for activity against a variety of human pathogens.

Student Involvement in Project: Under the direction of Drs. Lewis and D’Onofrio, the REU students will screen a compound library for selective activity against Borrelia burgdorferi, the causative agent of Lyme disease, and screen producing microorganisms against E. coli and S. aureus. Once compounds are identified, their mechanism of action will be studied.

What Students will Learn: Through this interdisciplinary work, the students will gain first-hand experience in experimental design, and in current techniques in microbiology and natural product chemistry.

Broader impacts of this project: There is a great unmet need for new antimicrobials, and this project will examine novel approaches to their discovery – species-selective screening; and focused access to attractive producers. Identifying compounds will validate these approaches, leading to their broad application. Beyond this study, the project will provide students with fundamental skills needed to address a broad range of questions in microbiology, natural product chemistry, and drug discovery.

Using genetic tools to understand oxidative stress

Professor Erin Cram and Assistant Professor Javier Apfeld

Associate Professor Erin Cram and Assistant Professor Javier Apfeld

Professor Erin Cram and Assistant Professor Javier Apfeld

Research Project Summary: The goal of the project is to understand how animals cope with stress. We use the nematode C. elegans, a small transparent roundworm with many advantages for genetics and cell biology for our studies. The Cram lab is focusing on how oxidative stress affects the reproductive system and the Apfeld lab is focusing on neuronal control of oxidant protective responses. We expect to identify genes and processes that are important, not just for worms, but in the biology of all animals.

Student Involvement in Project: Students will help design experiments to reveal the importance of oxidative stresses in animal physiology. Dr. Apfeld will focus on neuronal control of response to oxidative stress and Dr. Cram on the role of redox signaling in the worm’s reproductive system. Students will select candidate genes to study and will design and test their own hypotheses about how these genes might affect the animal’s response to oxidative stress.

What Students will Learn: Students will learn the fundamentals of designing, implementing, and interpreting experiments and communicating their results to others. They will learn how to disrupt gene function in C. elegans using RNA interference and genetic approaches including CRISPR-Cas9, will perform molecular cloning techniques including PCR, DNA electrophoresis, and DNA purification, will help make their own transgenic nematodes, and will visualize fluorescent proteins in living cells using 4D confocal microscopy. Students will learn how to properly use statistics and how to explain what they are doing to a broad range of scientists and non-scientists.

Broader impacts of this project: Our students will learn to use the tools of molecular cell biology and genetics to address scientific questions. Through working in our research team, they will gain in confidence in themselves as capable scientists. Our program is designed to also help them build leadership skills and to learn how to communicate their passion for science to others. This will help them serve as ambassadors for STEM education when they return to their home institutions and move forward in their careers.

Studying wound repair and regeneration in salamanders and mice

Assistant Professor Justin Crane and Associate Professor James Monaghan

Justin Crane and James Monaghan

Assistant Professor Justin Crane and Associate Professor James Monaghan

Research Project Summary: Some animals such as salamander have the amazing ability to repair skin wounds without a scar and even regenerate entire limbs. In contrast, mammals such as mice and humans scar after injury. The Monaghan laboratory studies the cellular basis of wound healing and regeneration in the axolotl salamander, while the Crane laboratory studies skin repair in mice. In this REU project, students will be comparing differences in wound healing and regeneration between these two species using histology and studying gene expression of injured wounds.

Student Involvement in Project: Students will be performing recently developed staining and imaging techniques of mRNA molecules in tissue sections. The approach, called Fluorescence in situ Hybridization, is capable of imaging many mRNA species simultaneously. Students will evaluate gene expression differences between the two species in order to determine the underlying differences that may lead to scarring versus regeneration.

What Students will Learn: Students will learn multiple complex laboratory techniques including histological tissue sectioning, histological staining techniques, fluorescence in situ Hybridization, fluorescence microscopy, and how to quantitatively measure and evaluate gene expression in tissue sections. Overall, the students will become proficient at tissue staining, imaging, and how to use bioinformatic approaches to understand gene expression.

Broader impacts of this project: Discoveries that improve skin repair and regeneration have vast implications for a host of conditions, including burn injuries or wounds, chronic infections and skin cancer. Having students compare Axolotl and mouse mechanisms of cellular repair will provide students with a strong foundation to study cell and molecular biology.

Mitochondrial lineage in developing oocytes

Professor Konstantin Khrapko and Assistant Professor Dori Woods

Professor Konstantin Khrapko and Assistant Professor Dori Woods

Professor Konstantin Khrapko and Assistant Professor Dori Woods

Research Project Summary: The mitochondrial DNA mutator mouse is a unique animal model where different mitochondrial lineages within individual cells are naturally labeled with specific combinations of mutations. These specific mutation combinations allow us to trace mitochondrial lineages within a cell in the same way that the ancestry of individuals within human populations can be determined based on mtDNA mutations. This project unites an expert in ovarian development (Dori Woods) with an expert in mitochondrial genomics and aging (Konstantin Khrapko) to identify the ancestry of individual mitochondria/mtDNA molecules in oocytes. Since mitochondria are maternally inherited, this study is highly pertinent to the mechanisms of mtDNA inheritance and to how we protect ourselves from mtDNA mutational meltdown. This work will be a synthesis of two complementary approaches: reproductive aging with emphasis on mitochondrial function, and intracellular mitochondrial genomics.

Student Involvement in Project: The students will be exposed to several state-of the-art techniques, including individual sorting of mitochondria, full-genome single-molecule PCR, and highly multiplexed next generation sequencing. Most importantly, the students will be confronted with unique and novel data that will need interpretation. The students will participate generating novel hypotheses and the planning of new experiments aimed at testing these hypotheses. Interpreting ancestry/populational dynamics data is particularly suitable for students because it is both intuitive and engaging.

What Students will Learn: The students will acquire basic laboratory techniques, such as PCR and agarose gel electrophoresis, record keeping, and good laboratory notebook practice. Additionally, they will become acquainted with the basics of modern high-tech genomics approaches such like next generation sequencing. Students will have daily interactions with supervisors, graduate students, and postdocs, and will participate in general lab meetings and be required to describe their work in a 15-minute oral presentation at conclusion of their training. Usually successful students get to co-author a paper involving their work.

Broader impacts of this project: Our students will learn important skills during the REU period that will facilitate their scientific discoveries and prove valuable outside of the classroom and laboratory environments. The ability perform hypothesis driven research and analyze data sets hones organizational, analytical, and problem solving skills that promote stronger academics and reflect well in the workforce, even outside of science. Additionally, students will strengthen their abilities to effectively communicate complex ideas, as promoted through participation in lab meetings as well as the oral presentation, and, when warranted, in writing if co-authoring a manuscript.

Bacterial stress response networks governing envelope assembly, the DNA damage response, and biofilm development

Assistant Professor Yunrong (Win) Chai, Assistant Professor Edward Geisinger, Associate Professor Veronica Godoy

head shots of Assistant Professor Yunrong Chai, Assistant Professor Edward Geisinger, Associate Professor Veronica Carter-Godoy

Assistant Professor Yunrong (Win) Chai, Assistant Professor Edward Geisinger, Associate Professor Veronica Godoy

Research Project Summary:The common thread guiding collaborative research between the Chai, Godoy-Carter, and Geisinger groups involves the study of bacterial physiology and genetics especially under the context of antimicrobial stress. In response to many environmental cues, complex gene regulation networks coordinate the production of biofilms, in which bacterial cells act as a super-organism encased in a network of self-produced extracellular matrix molecules. Biofilms are the predominant life form of bacteria and are of utmost medical and environmental significance. Though biofilm assembly is well understood in the model system Bacillus subtilis, it is unclear whether similar or different mechanisms play a role in other bacteria, specifically in opportunistic pathogens (e.g. Acinetobacter baumannii). Moreover, it is not known how biofilms disassemble or how this process is regulated. We have data suggesting that there is a link between bacterial DNA damage response and biofilm assembly and disassembly. The assembly of the multilayered bacterial envelope, which contributes to drug resistance and biofilm production, is also tightly controlled by regulatory networks that coordinate the assembly and remodeling of cellular polymers.  The proposed studies will focus on dissecting the regulation networks controlling envelope biogenesis, biofilm development, and DNA damage responses and their intersections in coordinating population-wide behaviors.

Student Involvement in Project: Students will develop hypotheses, design, and execute experiments, to elucidate the gene interaction networks that control the cell envelope and whether there is a link between biofilm development and the DNA damage response in B. subtilis. Under the direction of Dr. Chai, they will study the genetics and physiology of biofilm assembly and disassembly. Under the direction of Dr. Godoy, they will probe the role of the DNA damage response within cells in a biofilm in A. baumannii, and Dr. Geisinger will address the role of the cell envelope in bacterial survival and virulence.

Students will Learn: All students will gain facility in hypothesis formation and testing, in basic molecular biology techniques and in bacterial genetic analyses. Further, all students will engage in extensive data analysis, gain experience in presenting results in small and large groups, and learn to coordinate efforts in a complex research team.

Broader impacts of this project: Gaining insights into the basic questions of the effects of cell envelope and biofilm development, assembly and disassembly, and the effects of the DNA damage response will provide evidence for a novel and understudied link in bacteria. It will also provide a global view of the sophisticated networks occurring in bacteria to organize their life strategies. Furthermore, understanding the molecular details of biofilm development can provide insights into novel solutions to prevent bacterial biofilms.