eBERlight is a U.S. Department of Energy (DOE)’s Office of Science Biologicaland Environmental Research (BER) resource operating at the AdvancedPhoton Source. The program provides access and user support for severalx-ray-based tools for research in biological, geological, geochemical, andenvironmental sciences, such as:
- Macromolecular Crystallography (MX)
- X-ray Microscopy (X-fluorescence microscopy, XFM, and ptychography)
- X-ray Full-Field Imaging (Computed Tomography, CT)
- X-ray scattering (Small/Wide-Angle X-ray Scattering, SAXS/WAXS)
- X-ray absorption spectroscopy (XAS)
Leveraging additional resources available at Argonne National Laboratoryfor sample preparation and data analysis, eBERlight creates acomprehensive ecosystem to meet the needs of complex environmentaland biological research projects, and to take full advantage of the upgradedlight source.
Results in this report are derived from work performed through the eBERlight program, funded by the U.S. Department of Energy, Office of Biological and Environmental Research at the Advanced Photon Source, a U.S. DOE Office of Science User Facility, supported by the U.S. DOE, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357.
Upcoming event:
The eBERlight 101: Application of X-ray methods in biological and environmental research workshop will be held onsite November 19-21, 2024, at Argonne National Laboratory. Applications are due by August 30, 2024.
The workshop is dedicated to scientific community engaging in bioenvironmental research focusing on the Department of Energy mission and interested in incorporating X-ray methods in their scientific toolkit. The primary focus is on X-ray fluorescence microscopy and X-ray computed tomography – the methods that allow to study physical and chemical properties of bioenvironmental systems, including plants, soils, and microbes. The participants will be introduced to the techniques, data analysis, and relevant beamlines. Attendees can also expect to hear examples of scientific stories that demonstrate the potential applications of these methods in research.
Substantial amount of time will be dedicated to discussing individual participants’ scientific project and potential incorporation of the X-ray methods into their research. The attendees will also learn about the eBERlight program supporting bioenvironmental research community at the Advanced Photon Source user facility.
For efficient engagement, the workshop will be limited to 20 participants. Travel funds will be available for eligible participants. Stay tuned for more details!
eBERlight is working with the Facilities Integrating Collaborations for User Science (FICUS) program to provide researchers with access to world-class resources at Environmental Molecular Sciences Laboratory (EMSL), Joint Genome Institute (JGI), the National Ecological Observatory Network (NEON), the Bio-SANS beamline at the High Flux Isotope Reactor (HFIR) through the Center for Structural Molecular Biology (CSMB), and the Advanced Photon Source (APS). FICUS proposal calls are announced annually. The FY25 call is open for users. Visit the Proposal Calls page for more information.
The 2024 APS/CNM Users Meeting was held on May 6-10, 2024. You can view the poster session booklet here: Poster Session Booklet.pdf (anl.gov).
APS WK#9: Using Synchrotron Light to Probe Earth and Environmental Systems with Dr. Zou Finfrock.
APS WK#11: APS-U-enabled Advanced Tools for Structural Biology: Advancing Enzymatic Catalysis and Drug Discovery through Synchrotron Serial Crystallography with Dr. Karolina Michalska.
Scientists working with eBERlight play a pivotal role in pioneering innovative scientific methodologies. eBERlight recognizes that talent is increasingly diverse. Taking benefit of Argonne’s educational programs, the laboratory foster’s a welcoming and inclusive environment that offers a variety of educational and outreach programs to cultivate the next generation of scientists and engineers. These programs introduce students, early-career scientists, and engineers to mission-driven, high-impact research. There are a variety of research opportunities to work alongside scientific mentors at the laboratory in a paid internship appointment. Students and graduates are encouraged to apply online, or contact eBERlightfor opportunities available.
Graduate students currently pursuing Ph.D. degrees in areas of physics, chemistry, material sciences, biology (non-medical), mathematics, engineering, computer or computational sciences, or specific areas of environmental sciences that are aligned with the mission of the Office of Science are eligible to apply for the supplemental research awards provided by the Office of Science Graduate Student Research (SCGSR) program. Learn how to apply at SCGSR.
Science Highlights
Youngchang Kim, Seung Hwan Lee, Priyanka Gade, Maren Nattermann, Natalia Maltseva, Michael Endres, Jing Chen, Philipp Wichmann, Yang Hu, Daniel G. Marchal, Yasuo Yoshikuni, Tobias J. Erb, Ramon Gonzalez, Karolina Michalska, Andrzej Joachimiak, "Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family," Commun. Chem. 7, 160 (2024). DOI: 10.1038/s42004-024-01242-y
Youngchang Kim, Natalia Maltseva, Christine Tesar, Robert Jedrzejczak, Michael Endres, Heng Ma, Haley L. Dugan, Christopher T. Stamper, Changsoo Chang, Lei Li, Siriruk Changrob, Nai-Ying Zheng, Min Huang, Arvind Ramanathan, Patrick Wilson, Karolina Michalska, Andrzej Joachimiak, "Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies," iScience 27 (2), 108976 (2024). DOI: 10.1016/j.isci.2024.108976
Tsun-Kong Sham, Y. Zou Finfrock, Qunfeng Xiao, Renfei Feng, Sarah Bassnett, "Retrieving images from tarnished daguerreotypes using X-ray fluorescence imaging with an X-ray micro beam with tunable energy," J. Cult. Heritage 67, 53-61 (2024). DOI: 10.1016/j.culher.2024.02.003
Brent R. Verbuyst, Eva Pakostova, Dogan Paktunc, Jeff G. Bain, Y. Zou Finfrock, Emily M. Saurette, Carol J. Ptacek, David W. Blowes, "Microbiological and geochemical characterization of As-bearing tailings and underlying sediments," J. Hazard. Mater. 466, 133554 (2024). DOI: 10.1016/j.jhazmat.2024.133554
Stephanie M. Thibert, Deseree J. Reid, Jesse W. Wilson, Rohith Varikoti, Natalia Maltseva, Katherine J. Schultz, Agustin Kruel, Gyorgy Babnigg, Andrzej Joachimiak, Neeraj Kumar, Mowei Zhou, "Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins," J. Am. Soc. Mass. Spectrom. 35 (5), 912-921 (2024). DOI: 10.1021/jasms.3c00453
Magdalena Broda, Joseph E. Jakes, Luxi Li, Olga A. Antipova, Evan R. Maxey, Qiaoling Jin, "Conservation of model degraded pine wood with selected organosilicons studied by XFM and nanoindentation," Wood Sci. Technol. 58, 649-675 (2024). DOI: 10.1007/s00226-024-01533-6
Prakash Jadhav, Bo Huang, Jerzy Osipiuk, Xiaoming Zhang, Haozhou Tan, Christine Tesar, Michael Endres, Robert Jedrzejczak, Bin Tan, Xufang Deng, Andrzej Joachimiak, Jianfeng Cai, Jun Wang, "Structure-based design of SARS-CoV-2 papain-like protease inhibitors," Eur. J. Med. Chem. 264, 116011 (2024). DOI: 10.1016/j.ejmech.2023.116011
Kemin Tan, Yuk-Ching Tse-Dinh, "Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life," Cell 13 (6), 553 (2024). DOI: 10.3390/cells13060553
Chun Gui, Edward Kalkreuter, Yu-Chen Liu, Gengnan Li, Andrew D. Steele, Dong Yang, Changsoo Chang, Ben Shen, "Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis," Nat. Chem. Biol. 20, 243-250 (2024). DOI: 10.1038/s41589-023-01476-2
Timothy A. Klein, Prakhar Y. Shah, Polyniki Gkragkopoulou, Dirk W. Grebenc, Youngchang Kim, John C. Whitney, "Structure of a tripartite protein complex that targets toxins to the type VII secretion system," Proc. Natl. Acad. Sci. USA 121nbsp;(3), e2312455121 (2024). DOI: 10.1073/pnas.2312455121