The Biological Systems Science Division (BSSD) within the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) funds basic research on plants and microbes relevant to several DOE bioenergy and environmental mission areas.BSSD research seeks to understand the fundamental genome-encoded properties of plants and microbes that can be harnessed or redesigned for beneficial purposes.
Current emphases are leading to the discovery, development, and understanding of numerous plant and microbial species with traits suitable for the production of fuels and chemical products from renewable biomass that could be grown synergistically with food or animal feed crops while not competing with other societal needs. Additionally, BSSD further supports research leading to an understanding of the complex and essential interactions among plants, microbial communities, and the environment to find new ways to sustainably produce biomass for a range of bioenergy and bioproduct applications. This research also is relevant for incorporation into larger-scale environmental models such as those developed through the research supported by BER’s Earth and Environmental Systems Sciences programs.
To engage the relevant scientific communities in discussions of these research areas, BER convened the Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment workshop on September 21-23, 2016. Seeking to enable more comprehensive systems biology-based approaches, which typically require measurements of many samples, workshop participants highlighted the need for the development of highly sensitive methods to provide accurate measurements from small sample volumes and that are operable in high-throughput or highly parallel modes.
Publication date: September 2017
Suggested citation for this report: U.S. DOE. 2017. Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment, DOE/SC-0189, U.S. Department of Energy Office of Science. (https://genomicscience.energy.gov/technologies/).
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These fundamental research efforts require new and innovative methods and technologies to elucidate the foundational principles that drive biological systems of interest to DOE’s energy and environmental missions. Characterizing biological systems involves analytical approaches that illuminate cellular components and their form, structure, size, function, spatial location, dynamics, and interactions with the environment. Workshop discussions identified new technologies and combinations of existing capabilities to address the challenges associated with characterizing molecular and cellular systems relevant to bioenergy and environmental research. Participants included technology developers and biology researchers with expertise in cellular ultrastructure and physiology, bioenergy and bioproducts, and environmental microbiology. Attendees developed a series of research and technology development needs across six thematic areas spanning the range of BSSD-supported research. The challenges of studying these systems are many and broad in scope, covering time scales from femtoseconds to weeks and length scales from Angstroms to centimeters. This report addresses this very broad measurement range—from cells and their metabolism and mineralogy (Angstroms to micrometers), to rhizosphere ecosystem processes and community biochemical activity (millimeters to a meter). In this context, the range from micrometers to a meter is referred to as “mesoscale.” Despite the breadth of the challenges, participants identified key needed technologies and improvements in current techniques that could advance BER science. These six major research themes are discussed below.
Fig. 9.2. Spatial and Temporal Resolutions of Imaging Technologies. Summary of imaging and other selected measurement technologies discussed at the workshop. Mature technologies that will benefit from further development include X-ray and neutron crystallography and scattering, scanning probe microscopies, X-ray tomography, synchrotron spectroscopy, and confocal microscopy. Techniques undergoing rapid development and with potential application to the mission of the U.S. Department of Energy’s Office of Biological and Environmental Research (BER) include X-ray free-electron laser ultrafast diffraction, time-resolved X-ray scattering, cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET), infrared imaging methods, super-resolution fluorescence imaging. New technologies not yet fully developed and applied to research supported by BER’s Biological Systems Science Division include dynamic EM, fluctuation scattering, ptychography, and in soil sensors. Key: A, Angstrom; EXAFS, extended X-ray absorption fine structure; fs, femtosecond; ks, kilosecond; μm, micrometer; μs, microsecond; mm, millimeter; ms, millisecond; nm, nanometer; ns, nanosecond; ps, picosecond; s, second; SAXS, small-angle X-ray scattering; SEM, scanning electron microscopy; TEM, transmission electron microscopy; TIRF, total internal reflection fluorescence; USANS, ultrasmall-angle neutron scattering; WAXS, wide-angle X-ray scattering; XANES, X-ray absorption near edge structure.
Several challenges common to all the research themes emerged throughout workshop discussions. Translating information from genomic studies to the molecular and cellular realm for characterization will require increased throughput for existing technologies and the development of new high-throughput approaches. Achieving these goals will necessarily involve more automation and computational algorithms to manage the high data volumes that will be produced. Improved machine-learning approaches and large data-handling capacity will be essential. Integration of disparate data types from multiple and heterogeneous sources remains a challenge, so continued development of integrative and interpretive computational approaches is needed. Similar needs also were discussed at a workshop hosted by DOE’s Office of Advanced Scientific Computing Research (ASCR), the DOE Exascale Requirements Review, held March 28-31, 2016, in Rockville, Md., which generated the meeting report, ASCR Exascale Requirements Review
The tools and methods described in this BER report are critical for advancing the deep understanding of complex, multicomponent systems that are central to bioenergy and the environment. While new technologies are needed for advancing leading-edge biological insights, they are of limited value if they are not readily accessible by the scientists who need them to conduct their research. As new instruments, platforms, and approaches are created, it is important that they be developed in ways that ultimately enable biology researchers to use them, either by adopting them in their own laboratories or by having access to the tools, appropriate expertise, and support at national user facilities. Elements will include robust hardware, physiologically relevant sample preparation and measurement conditions, automation, sophisticated analytical algorithms, and user-friendly interfaces. For facility-based technologies, long-term and productive community access requires recognition of the need for ongoing operational support.
Described in the report are some of the workshop’s identified challenges to studying the biological systems of interest to BSSD, which has a history of developing and supporting highly sophisticated research tools and techniques and ensuring that researchers can access them to advance science in support of the division’s goals. Workshop discussions reflected in this document will help guide the next generation of imaging and analytical instrumentation needed to gain a predictive understanding of biological systems supporting DOE’s energy and environmental missions.