Big Data of Small Things

  • Goals: The Big Data of Small Things team will conduct a systems biology analysis of the model organism, Caenorhabditis elegans. This small nematode has been extensively studied for decades, but not much is known about its metabolic pathways or its life in natural settings. The team will design experiments, make samples, collect metabolomics and other omics data, and analyze the data using sophisticated computational methods. We will also explore ways of studying C. elegans in controlled environments that mimic natural settings.
  • Methods & Technologies: General lab sterile techniques, study design, culturing C. elegans, making CRISPR mutants, sample preparation, fluorescence-based biosorting, nuclear magnetic resonance and mass spectrometry data collection and analysis, statistical analysis and data mining, unknown compound identification, RNAseq, glycomics, establishing natural growth chambers with natural food sources and pathogens.
  • Research/Design Issues: Training and experience in laboratory methods, microinjections, PCR, hands on experience with state-of-the art NMR and MS instrumentation, computer programming, computations involving large clusters, data integration techniques, chemical separation isolation, 2D NMR methods for unknown identification, development of training materials and videos for education, team skills.
  • Meeting Time: 3 pm Fridays in the NMR Overlook Room (Room 2065) at the Complex Carbohydrate Research Center
  • Principal Investigator: Dr. Art Edison, Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, Genetics, Institute of Bioinformatics.

Biodegradation of plastic

  • Goals: Polyethylene terephthalate (PET) is a major component of plastic drinking bottles and other plastic products contributing to a large amount of plastic waste on Earth. The goal of this project is to express, purify, characterize, and crystallize proteins that degrade PET or PET byproducts to better understand the degradation process.
  • Methods & Technologies: General lab sterile techniques, molecular biology (cloning, mutagenesis, gene knockouts), study design, culturing E. coli, purification of proteins from E. coli, characterizing enzymes, genomics/bioinformatics, and crystallography
  • Research/Design Issues: What conditions are necessary for expression of PET degrading proteins in E. coli? What pathways do microorganisms use to degrade plastic and its byproducts? Can PET and other plastics be converted into useful products?
  • Meeting Time: 12:00 on Fridays. Location: B121 Life Sciences.
  • Principal Investigator: Dr. David Blum, Biochemistry & Molecular Biology, Bioexpression and Fermentation Facility

Iron in Bacterial Pathogenesis and Hydrogenases

  • Goals: This project has two primary foci that are derived from the biological importance of the most abundant transition metal on earth: iron. Bacterial pathogens have evolved mechanisms that allow them to utilize heme as an iron source for growth. One goal of this project is to describe the mechanism of heme acquisition, transport, and catabolism in the human hemorrhagic pathogens Vibrio Cholera and Escherichia coli O157:H7. Some members of team will interrogate the physiological role, structure, and bioreactivity of these catabolites with emphasis on exploiting their discoveries for antibiotic development. Other members of the team will pursue the application of biophysical methods to interrogate the mechanism of the enzymes involved in anaerobic heme degradation as well as the mechanism of hydrogenases. These enzymes provide clues to the evolution of electron transport and energy generation/conservation in all living organisms.
  • Methods: Good laboratory practices for molecular biology, biochemistry, and biophysics. Specifically, procedures for molecular cloning/mutagenesis, aerobic and anaerobic bacterial cell growth, enzyme expression, enzyme isolation, assay development as well as characterization of enzyme function by biophysical methods (e.g., electromagnetic spectroscopy, X-ray crystallography, nuclear magnetic resonance, and mass spectroscopy).
  • Research/Design Issues: What is the mechanism of anaerobic heme degradation? What do the atomic structures of the enzymes/proteins involved tell us about the mechanism and the evolution of enzyme function? What are the structures of mechanistic intermediates and catabolites and do these compounds have any therapeutic value?
  • Meeting Time and Location: A222 Davison Life Sciences. Time and day TBD.
  • Principal Investigator: Dr. William Lanzilotta, Biochemistry and Molecular Biology.

Social Psychology of Undergraduate STEM Education

  • Goals: The Social Psychology of Undergraduate STEM Education will conduct analyses of scalable ways of involving undergraduates in STEM research, including the impacts of embedding research into courses and expanding the pool of research mentors to include graduate students and postdoctoral researchers. Although there are national calls for all undergraduate STEM majors to participate in research, little is known about who gets access to these experiences and what makes them effective for students. This VIP team will design and conduct qualitative and quantitative studies to understand how different forms of research experiences influence students’ educational and career trajectories, for example, by affecting their interest in STEM fields or research careers or connecting them with key resources that can help them be successful in college and in STEM.
  • Methods & Technologies: Human subjects research, mixed methods / educational study design, survey design and data collection, interviews and focus group design and conduct, qualitative content analyses of audio and video data, classroom and field observations, descriptive statistics, regression analysis.
  • Research/Design Issues: What are the roles of human, cultural, and social capital in students’ access to research experiences? Are there key features of undergraduate research experiences that promote or hinder student success? How are undergraduate research experiences functioning to influence students’ academic and career trajectories?
  • Meeting Time and Location: B206.2 Davison Life Sciences. Time and day TBD. 
  • Principal Investigator: Dr. Erin Dolan, Biochemistry & Molecular Biology, Math & Science Education.