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:
eBERlight 101: Application of X-ray methods in biological and environmental research workshop
November 19-21, 2024; Argonne National Laboratory, onsite
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 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 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.
Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis
Dementiev A, Lillington SP, Jin S, Kim Y, Jedrzejczak R,Michalska K, Joachimiak A, O'Malley MA.Appl Microbiol Biotechnol. 2023 Oct;107(19):5999-6011. doi: 10.1007/s00253-023-12684-0. PMID: 37548665
A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile
Monica Rosas-Lemus, Supratim Dey, George Minasov, Kemin Tan, Spencer M. Anderson, Joseph Brunzelle, Salvatore Nocadello, Ivan Shabalin, Ekaterina Filippova, Andrei Halavaty, Youngchang Kim, Natalia Maltseva, Jerzy Osipiuk, Wladek Minor, Andrzej Joachimiak, Alexei Savchenko, Wayne F. Anderson, Karla J.F. Satchell, J. Bacteriol. 12 (10), e00507 (2023). DOI: 10.1128/MRA.00507-23
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
Nicole L. Inniss, Travis J. Kochan, George Minasov, Zdzislaw Wawrzak, Changsoo Chang, Kemin Tan, Ludmilla Shuvalova, Olga Kiryukhina, Sergii Pshenychnyi, Ruiying Wu, Ivegeniia Dubrovska, Gyorgy Babnigg, Michael Endres, Wayne F. Anderson, Alan R. Hauser, Andrzej Joachimiak, Karla J.F. Satchell, "A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae," Microbiology 12 (2), e01013 (2023). DOI: 10.1128/mra.01013-22
Doga Yamac Ozgulbas, Don Jensen Jr., Rory Butler, Rafael Vescovi, Ian T. Foster, Michael Irvin, Yasukazu Nakaye, Miaoqi Chu, Eric M. Dufresne, Soenke Seifert, Gyorgy Babnigg, Arvind Ramanathan, Qingteng Zhang, "Robotic pendant drop: containerless liquid for [mu]s-resolved, AI-executable XPCS," Light Sci. Appl. 12, 196 (2023). DOI: 10.1038/s41377-023-01233-z
Vanessa Cupil-Garcia, Joy Q. Li, Stephen J. Norton, Ren A. Odion, Pietro Strobbia, Luca Menozzi, Chenshuo Ma, Jianhong Hu, Rodolfo Zentella, Maxim I. Boyanov, Y. Zou Finfrock, Doga Gursoy, Deirdre Sholto Douglas, Junjie Yao, Tai-Ping Sun, Kenneth M. Kemner, Tuan Vo-Dinh, "Plasmonic nanorod probes’ journey inside plant cells for in vivo SERS sensing and multimodal imaging," Nanoscale <15 (13), 6396-6407 (2023). DOI: 10.1039/D2NR06235F
Pawel M. Wydorski, Jerzy Osipiuk, Benjamin T. Lanham, Christine Tesar, Michael Endres, Elizabeth Engle, Robert Jedrzejczak, Vishruth Mullapudi, Karolina Michalska, Krzysztof Fidelis, David Fushman, Andrzej Joachimiak, Lukasz A. Joachimiak, "Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin," Nat. Commun. <14, 2366 (2023). DOI: 10.1038/s41467-023-38031-5
B. Ellyson, A. Saville, K. Fezzaa, T. Sun, N. Parab, C. Finfrock, C.J. Rietema, D. Smith, J. Copley, C. Johnson, C.G. Becker, J. Klemm-Toole, C. Kirk, N. Kedir, J. Gao, W. Chen, K.D. Clarke, A.J. Clarke, "High strain rate deformation of aged TRIP Ti-10V-2Fe-3Al (wt.%) examined by in-situ synchrotron X-ray diffraction," Acta Mater. <245, 118621 (2023). DOI: 10.1016/j.actamat.2022.118621
Priya Karna, Zou Finfrock, Junjie Li, Yongfeng Hu, Dong-Sheng Yang, "Water-Soluble Copper(I) Hydroxide Catalyst and Its Formation in Ligand-Free Suzuki–Miyaura Cross-Coupling Reactions," J. Phys. Chem. C <127 (12), 5791-5799 (2023). DOI: 10.1021/acs.jpcc.3c00268
Adnan Ozden, Jun Li, Sharath Kandambeth, Xiao-Yan Li, Shijie Liu, Osama Shekhah, Pengfei Ou, Y. Zou Finfrock, Ya-Kun Wang, Tartela Alkayyali, F. Pelayo García de Arquer, Vinayak S. Kale, Prashant M. Bhatt, Alexander H. Ip, Mohamed Eddaoudi, Edward H. Sargent, David Sinton, "Energy- and carbon-efficient CO[subscript 2]/CO electrolysis to multicarbon products via asymmetric ion migration–adsorption," Nat. Energy <8, 179-190 (2023). DOI: 10.1038/s41560-022-01188-2
Peter J Stogios, Sean D Liston, Cameron Semper, Bradley Quade, Karolina Michalska, Elena Evdokimova, Shane Ram, Zbyszek Otwinowski, Dominika Borek, Leah E Cowen, Alexei Savchenko, "Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in Candida albicans," Life Sci. Alliance <5 (8), e202101358 (2022). DOI: 10.26508/lsa.202101358
Nicholas L. Bartelli, Victor J. Passanisi, Karolina Michalska, Kiho Song, Dinh Q. Nhan, Hongjun Zhou, Bonnie J. Cuthbert, Lucy M. Stols, William H. Eschenfeldt, Nicholas G. Wilson, Jesse S. Basra, Ricardo Cortes, Zainab Noorsher, Youssef Gabraiel, Isaac Poonen-Honig, Elizabeth C. Seacord, Celia W. Goulding, David A. Low, Andrzej Joachimiak, Frederick W. Dahlquist, Christopher S. Hayes, "Proteolytic processing induces a conformational switch required for antibacterial toxin delivery," Nat. Commun. <13, 5078 (2022). DOI: 10.1038/s41467-022-32795-y
Ariana D. Forand, Y. Zou Finfrock, Miranda Lavier, Jarvis Stobbs, Li Qin, Sheng Wang, Chithra Karunakaran, Yangdou Wei, Supratim Ghosh, Karen K. Tanino, "With a Little Help from My Cell Wall: Structural Modifications in Pectin May Play a Role to Overcome Both Dehydration Stress and Fungal Pathogens," Plant J. 11 (3), 385 (2022). DOI: 10.3390/plants11030385