Berkeley Synchrotron Infrared Structural Biology (BSISB) Program

analytical chemistry cover Advances in Technologies for Biology Flyer
On the Cover of Analytical Chemistry SIR Brochure (pdf) Advanced Technologies for Biology (pdf)

SR-FTIR Spectromicroscopy and the Gulf of Mexico Deep-Sea Oil Plume

Assessing the environmental and public health impacts of the Deepwater Horizon oil spill is difficult owing to the extreme depth of the blowout and the large volumes of oil released. One strategy for remediation of the plume is to use the intrinsic bioremediation potential of deep-sea microorganisms to degrade the oil. This strategy depends on a number of environmental factors, including a favorable response of indigenous microorganisms to an increased concentration of hydrocarbons and/or dispersant. To study the effects of the spill, researchers collected deep-water samples from across the Gulf of Mexico and analyzed their physical, chemical, and microbiological properties using a variety of techniques, including synchrotron radiation Fourier-transform infrared (SR-FTIR) spectroscopy at ALS Beamline1.4.3. The studies suggest that the plume did indeed stimulate indigenous deep-sea bacteria that are closely related to known petroleum degraders.

Microbial Response to Oil Spill

Real-Time Chemical Imaging of the Development of Bacterial Biofilms

Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms—dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Berkeley Lab researchers coupled infrared (IR) rays from ALS Beamline 1.4.3 to the first open-channel microfluidic platform to determine the chemistry that shapes biofilm development. This combination of synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy and the microfluidic platform will have a significant impact on several scientific disciplines that require chemical-scale information on biofilm phenotype and function, including Berkeley Lab’s bioenergy efforts and subsurface biogeochemical studies.

Read more »
Microbial Response to Oil Spill

Real-Time Chemical Imaging of Clostridium Cellulolyticum Actions on Miscanthus Giganteus

Utilization of lignocellulolytic bacteria as dedicated energy microorganisms requires new understandings bacteria’s capability that has not been fully considered before. As part of the multi-mode chemical imaging (RMCI) program for microbe-biomass characterizations, we are developing and refining bimodal (fluorescence and synchrotron radiation-based Fourier transform infrared (SR-FTIR spectromicroscopy) chemical imaging. Here we are demonstrating our evolving bimodal imaging technology to non-invasively making molecular measurements of Clostridium cellulolyticum attacking plant biomass in space and time. Our preliminary real-time SR-FTIR results show that in Miscanthus giganteus, C. cellulolyticum can deconstruct pectin, lignin, and cellulose; and that the surface chemistry is quite variable spatially at scales with concentrated features locally.

Read more »
Real-Time Chemical Imaging of Clostridium Cellulolyticum Actions on Miscanthus Giganteus

Multi-Mode Real-Time Chemical Imaging as a System Biology Approach to Decipher Microbial Depolymerization of Lignocellulose

This project aims to develop multi-mode imaging methods to probe at the chemical level plant biomass depolymerization by cellulases, cellulosomes, and other hydrolytic enzymes of living cellulolytic microbes.  The mechanisms of these enzymes require surface chemistry, since the substrates are solids.  It is imperative, therefore, to study not only the enzymes, but also the properties of the substrates as they are degraded.  Furthermore, the production of enzymes is affected by the physiological states of the microorganisms. We are therefore using both single-molecule imaging of enzyme dynamics and Fourier transform infrared spectroscopy of solid substrates with living cellulolytic bacteria to probe plant cell wall depolymerization as a function of space and time.  Using newly developed real-time 3D tracking (RT-3DSPT) microscopes for single-molecule spectroscopy and imaging, we will be able to track cellulase and cellulosome processivity and cooperativity in the degradation of lignocellulose. These new experiments will exploit the genetic tools that we are developing to incorporate fluorescent tags into the enzyme and enzyme complexes to enable tracking.  We will also exploit the high temporal and spatial resolution of synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy to follow changes in the chemical composition of the cell wall substrates as they are depolymerized.  The combined information from SR-FTIR spectroscopy and RT-3DSPT microscopy will provide a unique view of lignocellulose depolymerization in real time.  This research will also aid in the development of efficient suites of hydrolytic enzymes that can be used in the conversion of plant biomass into biofuels, an important goal of the DOE.

Read more »

Multi-Mode Real-Time Chemical Imaging