The organic laboratory is where we do most of the processing of organic geochemical samples, along with lipid extracts from living organisms. Typical sample processing involves filtration of organic extracts, chemical degradations (such as saponification), column chromatography, evaporation and concentration, and derivatization.
The CEM Mars6 Microwave Reaction System is used to perform many of the organic extractions in the laboratory. Much like a home microwave, it heats up the sample in a teflon vessel along with organic solvents. Unlike a home microwave, it has precise temperature control. After organic extraction, solvents are removed from the sample for further processing.
The Biotage Turbovap II is used to evaporate solvents, concentrating organic extracts. After extraction with the Mars 6, and filtration, evaporation and concentration is typically the next step in the sample processing workflow. We also have a Flexivap workstation for evaporation of smaller samples.
The GCMS is actually two instruments. A gas chromatograph (GC) that contains a column that can separate organic compounds. Second, a quadropole mass spectrometer (MS) that first ionizes each compound eluting from the GC, and then analyzes its mass fragments. Various organic compounds have distinct molecular fingerprints (mass spectra) that can be used, along with their elution time on the GC, to identify them.
The GC-IRMS is an isotope ratio mass spectrometer. Like the GCMS, it has a GC on the front end. This is coupled by an interface to the IRMS. The interface is either a combustion reactor that converts the carbon in organic compounds to CO2 for analysis of carbon isotopes, or a pyrolysis reactor that converts the hydrogen in each compound to H2 for analysis of D/H ratios. The IRMS itself has a filament to ionize the gas, a flight tube down which ions are accelerated, a magnet to separate ions, and five Faraday cups to measure ion currents.
TCEA and EA-IRMS
This IRMS is an isotope ratio mass spectrometer with two inlets. The first inlet is an elemental analyzer (EA) that is capable of converting organic material to N2 and CO2. These gases are then quantified by a thermal conductivity detector (TCD) and then the IRMS is used to measure the stable isotope ratios of the carbon and nitrogen gases relative to standard gases. The second inlet is a high temperature conversion elemental analyzer (TC/EA). This inlet uses high temperature pyrolysis to convert oxygen in solid materials to CO and hydrogen to H2. It is primarily used for the analysis of organic materials, but can also be used to analyze some inorganic materials.
The microbiology laboratory is where we do most of the work related to culturing of microorganisms - streaking cultures on plates, picking colonies, extracting DNA, setting up PCR reactions. It has a biological safety cabinet, a gassing station, a fume hood, centrifuges, thermocycler, gel rig and box, and spectrophotometer.
The gassing station owes its existence to Wil Leavitt. It is custom-built in the laboratory to strip residual oxygen from gases that we use as headspace in sealed microbiological vessels for the growth of anaerobic microbes. Its basic operation consists of running a gas stream over a heated catalyst, then through a 0.45 micron filter into the sample headspace.
The laboratory has several incubators for culturing microorganisms, including a small Thermo Heratherm stationary incubator for petri plates, and two New Brunswick I26 stacking shaking incubators. Our incubators typically hold temperatures of 30 or 37 degrees Celsius.
Our laboratory shares an old but reliable autoclave with several other members of the Department of Earth and Planetary Sciences. We use it to sterilize all of our equipment and material for sterile microbiological work.
An Eppendorf MasterCycler used to perform PCR and other genetic techniques.
The gelbox is a small darkroom with a camera attached. It is used to visualize and record DNA bands after performing electrophoresis. It is fitted with a blue LED lamp.
We use a Nikon Eclipse Ci-L microbiological microscope for observations of bacterial cells. It is equipped with three objective lenses, a phase contrast ring, and a digital camera to record images.
The New Brunswick Bioflo 3000 chemostat is a refurbished unit on loan from Judy Wall. We use it to carefully poise growth rates of aerobic microbial cultures to understand the relationship between growth rate and parameters relating to lipids or isotopes. We also have two house-built chemostats for anaerobic experiments.
All notes and data in our laboratory are recorded electronically. We use a state-of-the art Electronic Laboratory Notebook (ELN) system called Biovia Notebook Cloud to record and curate all data. This has the advantage of making it easy to find data and collaborate, to store protocols, and to quickly search for past experiments. It also makes the data portable, facilitating collaboration outside the laboratory.
The laboratory has a microbalance and a semi-analytical balance, used for weighing samples and lipid extracts.
A benchtop centrifuge for routine centrifugation of cells, lipid extracts, and other materials in the laboratory.
A microcentrifuge used for separations of small samples and DNA spin columns.
The Nanodrop 2000c is a combination cuvette spectrophotometer and micro-spectrophotometer, capable of analyzing samples as small as one microliter. We use it for quantifying DNA and protein, for measuring the optical density of microbial cultures, and for quantifying other samples that absorb in the UV-visible range, such as carotenoids.