Categories

• Laboratories

Disciplinary Keywords

• Cavity Ring Down Spectroscopy
• Culturing
• Fluorescence Microscopy
• Gas Chromatography
• Geomicrobiology
• Incubation
• Microbial Studies
• Microbiology
• Optical Microscopy

Instrumentation

Laboratory instrumentation

Instruments

• Anaerobic Chamber

• Autoclaves

• Autoclaves for Sterilization

• Cavity Ring Down Spectrometer

  Nearly every small gas-phase molecule (e.g., CO2, H2O, H2S, NH3) has a unique near-infrared absorption spectrum. At sub-atmospheric pressure, this consists of a series of narrow, well-resolved, sharp lines, each at a characteristic wavelength. Because these lines are well-spaced and their wavelength is well-known, the concentration of any species can be determined by measuring the strength of this absorption, i.e. the height of a specific absorption peak. But, in conventional infrared spectrometers, trace gases provide far too little absorption to measure, typically limiting sensitivity to the parts per million at best. CRDS - Cavity Ring-Down Spectroscopy - avoids this sensitivity limitation by using an effective pathlength of many kilometers. It enables gases to be monitored in seconds or less at the parts per billion level, and some gases at the parts per trillion level.

  In CRDS, the beam from a single-frequency laser diode enters a cavity defined by two or more high reflectivity mirrors. Picarro analyzers use a three-mirror cavity, as in the figure below, to support a continuous traveling light wave. This provides superior signal to noise compared to a two-mirror cavity that supports a standing wave. When the laser is on, the cavity quickly fills with circulating laser light. A fast photodetector senses the small amount of light leaking through one of the mirrors to produce a signal that is directly proportional to the intensity in the cavity.

  When the photodetector signal reaches a threshold level (in a few tens of microseconds), the continuous wave (CW) laser is abruptly turned off. The light already within the cavity continues to bounce between the mirrors (about 100,000 times), but because the mirrors have slightly less than 100% reflectivity (99.999%), the light intensity inside the cavity steadily leaks out and decays to zero in an exponential fashion. This decay, or "ring down", is measured in real-time by the photodetector, and the amount of time it takes for the ring down to happen is determined solely by the reflectivity of the mirrors (for an empty cavity). Consider that for a Picarro cavity of only 25 cm in length, the effective pathlength within the cavity can be over 20 kilometers.

  Now, if a gas species that absorbs the laser light is introduced into the cavity, a second loss mechanism within the cavity (absorption) is now introduced. This accelerates the ring down time compared to a cavity without any additional absorption due to a targeted gas species. Picarro instruments automatically and continuously calculate and compare the ring down time of the cavity with and without absorption due to the target gas species. This produces precise, quantitative measurements that account for any intra-cavity loss that may be changing over time, and it allows the discrimination of loss due to absorption from losses due to the cavity mirrors. Furthermore, the final concentration data is particularly robust because it is derived from the difference between these ring down times and is therefore independent of laser intensity fluctuations or absolute laser power.

  This scheme of comparing the ring down time of the cavity without any absorbing gas, with the ring down time when a target gas is absorbing light is accomplished not by removing the gas from the cavity, but rather by using a laser whose wavelength can be tuned. By tuning the laser to different wavelengths where the gas absorbs light, and then to wavelengths where the gas does not absorb light, the "cavity only" ring down time can be compared to the ring down time when a target gas is contributing to the optical loss within the cavity. In fact, the laser is tuned to several locations across the target gas's spectral absorption line (and ring down measurements are conducted at all these points) and a mathematical fit to the shape of that absorption line is what is actually used to calculate the gas concentration. (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects pision, Goddard Space Flight Center (GSFC) National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords)

• Centrifuge

• Chemostat

  A bioreactor in which constant growth conditions for microorganisms are maintained over prolonged periods of time by supplying the reactor with a continuous input of nutrients and continuous removal of medium. (Source: IUPAC; https://doi.org/10.1515/iupac.64.0052)

• Clean Bench

• Climatic Chamber

• Fluorescence Microscope

  Fluorescence illumination and observation is the most rapidly expanding microscopy technique employed today, both in the medical and biological sciences, a fact which has spurred the development of more sophisticated microscopes and numerous fluorescence accessories. Epi-fluorescence, or incident light fluorescence, has now become the method of choice in many applications and comprises a large part of this tutorial. We have divided the fluorescence section of the primer into several categories to make it easier to organize and download. Please follow the links below to navigate to points of interest. Introductory Concepts - Fluorescence is a member of the ubiquitous luminescence family of processes in which susceptible molecules emit light from electronically excited states created by either a physical (for example, absorption of light), mechanical (friction), or chemical mechanism. Generation of luminescence through excitation of a molecule by ultraviolet or visible light photons is a phenomenon termed photoluminescence, which is formally divided into two categories, fluorescence and phosphorescence, depending upon the electronic configuration of the excited state and the emission pathway. Fluorescence is the property of some atoms and molecules to absorb light at a particular wavelength and to subsequently emit light of longer wavelength after a brief interval, termed the fluorescence lifetime. The process of phosphorescence occurs in a manner similar to fluorescence, but with a much longer excited state lifetime. Anatomy of the Fluorescence Microscope - In contrast to other modes of optical microscopy that are based on macroscopic specimen features, such as phase gradients, light absorption, and birefringence, fluorescence microscopy is capable of imaging the distribution of a single molecular species based solely on the properties of fluorescence emission. Thus, using fluorescence microscopy, the precise location of intracellular components labeled with specific fluorophores can be monitored, as well as their associated diffusion coefficients, transport characteristics, and interactions with other biomolecules. In addition, the dramatic response in fluorescence to localized environmental variables enables the investigation of pH, viscosity, refractive index, ionic concentrations, membrane potential, and solvent polarity in living cells and tissues. Additional information available at: "http://micro.magnet.fsu.edu/primer/techniques/fluorescence/ fluorhome.htm (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects pision, Goddard Space Flight Center (GSFC) National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords)

• Gas Chromatograph

  Gas chromatography - specifically gas-liquid chromatography - involves a sample being vapourised and injected onto the head of the chromatographic column. The sample is transported through the column by the flow of inert, gaseous mobile phase. The column itself contains a liquid stationary phase which is adsorbed onto the surface of an inert solid. (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects pision, Goddard Space Flight Center (GSFC) National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords)

• Glove Box

• Incubator

  An incubator is an apparatus in which environmental conditions, such as temperature and humidity, can be controlled, often used for growing bacterial cultures, hatching eggs artificially, or providing suitable conditions for a chemical or biological reaction. [The American Heritage Dictionary.] (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects pision, Goddard Space Flight Center (GSFC) National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords)

• Optical Microscope

Relationships

• is part of
• GeoBioLab – Helmholtz Laboratory for Integrated Geological and Biological Research