Students, please let me know if you'd like to join the lab and do some research! In particular, we have some possible projects doing:
Bioanalytical chemistry: including proteomics analyses using the LC-MS/MS instrument.
Computational bioinformatics: We have lots of data, and lots of interesting questions. The only prerequisites are an interest in the complexity of biological systems, and enthusiasm for learning a little computer programming. These are extremely valuable skills to learn; it's getting to the point where if you're doing biologically-relevant chemistry, you'll need to do some bioinformatics.
Linking Microbial Communities with Their Function
Physical and Chemical Data
Microbial communities are some of the most diverse and complex ecosystems on the planet, including soils, sediment, natural water, and animal guts. Observing what these communities are doing, and how they are structured, relies on molecular data. We can collect data on a number of different scales, including the environmental conditions and fluxes (via physical and chemical data), phylogenetic structure of communities (via high-throughput sequencing), and the metabolic enzymes being used (via LC-MS/MS proteomics).
Right now we have two primary projects that students are working on in this area: (1.) Optimizing a hexanoic acid-producing bioreactor in collaboration with the Angenent Lab at Cornell University (NSF 1336186), and (2.) investigating the dynamics in benthic microbial communities recovering from a disturbance.
Proteomics is an analytical technique where we use tandem mass spectrometry to profile the proteins present in a biological system. Proteomics provides researchers with the ultimate molecular assessment of what living cells are currently doing, by identifying (and possibly quantifying) which enzymes are present. Particularly with microbes, most things they do are catalyzed by their enzymes!
We recently acquired an LC-MS instrument with proteomics capabilities, thanks to a grant from the National Science Foundation (NSF 1337695). The instrument, pictured below, is a Thermo LTQ-XL linear ion trap mass spectrometer with several ionization sources including ESI, APCI, and NanoSpray. This mass spectrometer is connected to a Thermo UltiMate 3000 UPLC chromatography system with binary pumps that allow for micro flow rates (and nano flow with a splitter). The system also has all the software bells and whistles needed for analyzing data from shotgun proteomics, metabolomics, and quantitative multiple reaction monitoring experiments.
Werner JJ, Rossi F, Conklin P, Chatfield C, Fitzgerald T. "MRI: Acquisition of an LC-MS/MS to Enable Research and Training for Chemistry and Biology Students at SUNY Cortland." NSF 1337695, $270,807, Sept 2013 - Aug 2016.
Angenent LT (PI; Cornell University) and Werner JJ (co-PI, subaward to SUNY Cortland). "SusChEM: Converting Urban Wastes into Longer Chain Chemicals" NSF 1336186, $114,197 subaward to SUNY Cortland ($390,302 total), Sept 2013 - Aug 2016.