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1. BioXFEL Crystallization Workshop 2021

   Education 2 Mar 2021

   BioXFEL will be sponsoring a remote Crystallization Workshop Friday, April 2nd, 2021.… The workshop will feature both introductory and specialized topics dealing with the crystallization of biological macromolecules and will cover techniques commonly employed in modern structural biology. The workshop will include mix of lectures…

   https://bioxfel.org/content/article/419

2. 2021 Conference Registration Scholarship Deadline

   Events 31 Dec 2020

   Dec 31 2020

   2021 Conference Registration Scholarship … The Annual International BioXFEL conference will be held virtually in 2021.

   https://bioxfel.org/events/details/1252

3. 2021 NSF Annual Site Visit

   Events 8 Jul 2021

   Jul 08 2021

   The Center will be holding its Annual Site Visit July 8-9, 2021.

   https://bioxfel.org/events/details/1256

4. 2021 Panofsky Fellowship Call for Applications

   News 22 Sep 2020

   2021 Panofsky Fellowship at the SLAC National Accelerator Laboratory (SLAC) Call for Applications – Deadline for submission is November 2, 2020 …     Fellowship for early-career research (experiment or theory) in a diverse range of fields related to the SLAC scientific mission:   • Accelerator science & advanced…

   https://bioxfel.org/2021-panofsky-fellowship-call-for-applications

5. External Advisors Meeting 2021

   Events 1 Feb 2021

   Feb 01 2021

   The external advisors to the BioXFEL Center will convene in virtually for an update on Center activities. The Center external advisors are Dirksen Bussiere, James Naismith, Martin Caffrey, Victor Lamzin, Wah Chiu, Carrie Wilmot, Elspeth Garman, Tabbetha Dobbins, Aina Cohen, and Stefano Marchesini. 

   https://bioxfel.org/events/details/1243

6. Phase Retrieval Workshop 2021

   Education 3 Nov 2021

     BioXFEL sponsored a remote Phase Retrieval Workshop Monday, October 18 through Tuesday, October 19 2021.… This two-day online event was delivered to an international audience of over 60 people. On the first day we held a teaching session where we covered the basic math, physics, algorithms, and biological applications of phase…

   https://bioxfel.org/content/article/440

7. 2021 Panofsky Fellowship Deadline

   Events 2 Nov 2020

   Nov 02 2020

   2021 Panofsky Fellowship at the SLAC National Accelerator Laboratory (SLAC) Call for Applications – Deadline for submission is November 2, 2020 … Fellowship for early-career research (experiment or theory) in a diverse range of fields related to the SLAC scientific mission: • Accelerator science & advanced accelerator…

   https://bioxfel.org/events/details/1246

8. Dan Salah Tawfik (1955‐2021)—A giant of protein evolution

   BioXFEL Publications 28 May 2021 Contributor(s): James Fraser

   http://dx.doi.org/10.15252/embr.202153256 journal-article Elias, M.… et al., 2021.… EMBO reports. Available at: http://dx.doi.org/10.15252/embr.202153256.

   https://bioxfel.org/resources/2016

9. Effectiveness of different types of Masks in Aerosol Dispersion in SARS–CoV-2 Infection

   BioXFEL Publications 17 Jun 2021 Contributor(s): Hasan Demirci

   http://dx.doi.org/10.1016/j.ijid.2021.… 029 journal-article Tanisali, G. et al., 2021.… International Journal of Infectious Diseases. Available at: http://dx.doi.org/10.1016/j.ijid.2021.

   https://bioxfel.org/resources/2022

10. John Spence Call for Abstracts

    Past Events 12 Jul 2022

    John Spence had a remarkable scientific impact over an illustrious career spanning nearly 50 years before he passed away in June, 2021.

    https://bioxfel.org/content/article/451

11. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy

    BioXFEL Publications 22 Feb 2021

    http://dx.doi.org/10.1016/j.ultramic.2021.… P.J. et al., 2021.… Ultramicroscopy, p.113234. Available at: http://dx.doi.org/10.1016/j.ultramic.2021.

    https://bioxfel.org/resources/1958

12. Quantitative agreement between dynamical rocking curves in ultrafast electron diffraction for x-ray lasers

    BioXFEL Publications 5 Feb 2021

    http://dx.doi.org/10.1016/j.ultramic.2021.… E. et al., 2021.… Ultramicroscopy, 223, p.113211. Available at: http://dx.doi.org/10.1016/j.ultramic.2021.

    https://bioxfel.org/resources/1990

13. Evidence that specific interactions play a role in the cholesterol sensitivity of G protein-coupled receptors

    BioXFEL Publications 13 Jan 2021 Contributor(s): Wei Liu

    http://dx.doi.org/10.1016/j.bbamem.2021.… et al., 2021.… Biochimica et Biophysica Acta (BBA) - Biomembranes, p.183557. Available at: http://dx.doi.org/10.1016/j.bbamem.2021.

    https://bioxfel.org/resources/1989

14. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight

    BioXFEL Publications 8 Apr 2021

    http://dx.doi.org/10.1080/0889311x.2021.… H. & Helliwell, J.R., 2021.… Crystallography Reviews, pp.1–44. Available at: http://dx.doi.org/10.1080/0889311x.2021.

    https://bioxfel.org/resources/1991

15. High-resolution crystal structures of transient intermediates in the phytochrome photocycle

    BioXFEL Publications 23 Mar 2021 Contributor(s): Melissa Carrillo, suraj pandey, Ishwor Poudyal, Tek Narsingh Malla, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1016/j.str.2021.… 004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carrillo, M. et al., 2021.… Structure. Available at: http://dx.doi.org/10.1016/j.str.2021.

    https://bioxfel.org/resources/1993

16. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules

    BioXFEL Publications 26 Feb 2021 Contributor(s): Vadim Cherezov

    http://dx.doi.org/10.1016/j.jlr.2021.… et al., 2021.… Journal of Lipid Research, 62, p.100059. Available at: http://dx.doi.org/10.1016/j.jlr.2021.

    https://bioxfel.org/resources/1970

17. The Z to E isomerization in Phytochromes revealed by Femtosecond X-ray Pulses from an X-ray Free Electron Laser

    News 25 Mar 2021

    Phytochromes are the molecular eyes of plants and bacteria that regulate cellular response to light, an essential environmental signal. Upon light absorption, the phytochromes change their structures substantially from a conformation that absorbs in the red-light called Pr to another  conformation that absorbs in the far-red light called Pfr,…

    https://bioxfel.org/content/article/421

18. CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

    BioXFEL Publications 22 Sep 2021 Contributor(s): Petra Fromme

    http://dx.doi.org/10.1016/j.matt.2021.… 004 journal-article Shekhar, M., Terashi, G., Gupta, C., Sarkar, D., Debussche, G., Sisco, N. J., Nguyen, J., Mondal, A., Vant, J., Fromme, P., Van Horn, W. D., Tajkhorshid, E., Kihara, D., Dill, K., Perez, A., & Singharoy, A. (2021).… Matter, 4(10), 3195–3216.…

    https://bioxfel.org/resources/2160

19. Search for Assistant Professor in Biophysics at UWM

    Opportunities 15 Sep 2021

    Search for Assistant Professor in Biophysics at the University of Wisconsin Milwaukee The University of Wisconsin-Milwaukee (UWM), a research intensive premier public urban university committed to academic excellence, is located in the commercial and industrial hub of Wisconsin. UW-Milwaukee is one of the two “doctoral cluster” campuses in the…

    https://bioxfel.org/content/article/437

20. Curiosity: a tool for exploring density features in crystallographic and cryoEM maps

    BioXFEL Publications 11 Feb 2022 Contributor(s): Iris Diane Young, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 2781 journal-article Young, I. D., & Fraser, J. S. (2022). Curiosity: a tool for exploring density features in crystallographic and cryoEM maps. Biophysical Journal, 121(3), 528a. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2120

21. Connecting glutamine synthetase biophysics to the cellular environment

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 1035 journal-article Greene, E. R., Thompson, E., Lee, D. J., Arada, A., Chen, D., & Fraser, J. (2022). Connecting glutamine synthetase biophysics to the cellular environment. Biophysical Journal, 121(3), 348a. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2121

22. BioXFEL Conference 2022

    Uncategorised 20 Oct 2021

    The National Science Foundation BioXFEL Science and Technology Center is pleased to announce that it will be hosting its ninth annual international conference virtually February 8-10, 2021.

    https://bioxfel.org/2022-conference

23. Using deep mutational scanning to identify the determinants of antibiotic resistance

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 665 journal-article Macdonald, C. B., Kelley, A., Pellegrino, J., Coyote-Maestas, W., & Fraser, J. (2022). Using deep mutational scanning to identify the determinants of antibiotic resistance. Biophysical Journal, 121(3), 422a. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2122

24. Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 2487 journal-article Kelley, A. M., Macdonald, C. B., & Fraser, J. (2022). Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD. Biophysical Journal, 121(3), 48a. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2119

25. Integration of software tools for integrative modeling of biomolecular systems

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 2555 journal-article Hancock, M., Peulen, T.-O., Webb, B., Fraser, J. S., Adams, P. D., & Sali, A. (2022). Integration of software tools for integrative modeling of biomolecular systems. Biophysical Journal, 121(3), 31a. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2125

26. Deconvoluting receptor trafficking, regulation, and function using massively parallel assays

    BioXFEL Publications 11 Feb 2022 Contributor(s): James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.… 2700 journal-article Nedrud, D., He, Y., Schmidt, D., Fraser, J., & Coyote-Maestas, W. (2022). Deconvoluting receptor trafficking, regulation, and function using massively parallel assays. Biophysical Journal, 121(3), 2a. https://doi.org/10.1016/j.bpj.2021.

    https://bioxfel.org/resources/2118

27. Vitamin C Binds to SARS Coronavirus-2 Main Protease Essential for Viral Replication

    BioXFEL Publications 4 May 2021 Contributor(s): Tek Narsingh Malla, suraj pandey, Ishwor Poudyal, George Phillips, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1101/2021.… 02.442358 AbstractThere is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, PL-pro, and the 3C-like protease known…

    https://bioxfel.org/resources/2041

28. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

    BioXFEL Publications 16 Aug 2021 Contributor(s): Gihan Kaushylal Ketawala, Sabine Botha, Brandon Hayes, Mark S. Hunter, Christopher Kupitz, Edward Snell, Hasan Demirci

    http://dx.doi.org/10.1016/j.str.2021.… 007 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Durdagi, S. et al., 2021.… Structure. Available at: http://dx.doi.org/10.1016/j.str.2021.

    https://bioxfel.org/resources/2071

29. Time-resolved functional expansion of visual rhodopsin detected by x-ray scattering

    BioXFEL Publications 11 Feb 2022 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2021.… 1313 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Alvarez, R. C., Perera, S. M. D. C., Kosheleva, I. V., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2022). Time-resolved functional expansion of visual rhodopsin detected by x-ray…

    https://bioxfel.org/resources/2117

30. Characterization of a Spatially resolved multi-element laser ablation ion source

    BioXFEL Publications 26 Nov 2021

    http://dx.doi.org/10.1016/j.ijms.2021.… , Chambers, C., Chen, D., Feng, Z., Fraser, J., Ito, Y., Lan, Y., Mendez, S., Medina Peregrina, M., Rasiwala, H., Richez, L., Roy, N., Simpson, R., Dilling, J., Fairbank, W., Kwiatkowski, A. A., & Brunner, T. (2022). Characterization of a Spatially resolved multi-element laser ablation ion…

    https://bioxfel.org/resources/2203

31. Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain

    BioXFEL Publications 14 Jan 2021 Contributor(s): David Case

    http://dx.doi.org/10.1101/2021.… 08.425965 AbstractSince the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human angiotensin converting enzyme 2 (ACE2)…

    https://bioxfel.org/resources/1964

32. Few-fs resolution of a photoactive protein traversing a conical intersection

    News 4 Nov 2021

    The structural dynamics of a molecule are determined by the underlying potential energy landscape. Conical intersections are funnels connecting otherwise separate potential energy surfaces. Posited almost a century ago, conical intersections remain the subject of intense scientific interest. In biology, they have a pivotal role in vision,…

    https://bioxfel.org/content/article/441

33. NSF STC Directors Meeting

    Events 31 Aug 2021

    Aug 31 2021

      NSF STC Directors Meeting 2021 …   Exploratory Research:  The Foundation for Groundbreaking Discoveries   August 31 – September 1, 2021 …   Hosted by:  Biology with X-ray Free Electron Lasers (BioXFEL) via Zoom   Note all times are listed in Eastern Daylight Time   BioXFEL is pleased to host the 2021…

    https://bioxfel.org/events/details/1261

34. BioXFEL Research Support Call for Proposals

    News 8 Apr 2021

    The NSF BioXFEL Science and Technology Center has funding intended to support research at US institutions. This support is for the application of X-ray free electron lasers to structural biology in collaboration with the BioXFEL STC. The aim is to foster collaboration with the BioXFEL Center and respond to current research needs and new…

    https://bioxfel.org/90k-2021

35. The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies

    BioXFEL Publications 22 Oct 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1016/j.ymthe.2021.… 014 journal-article Durdagi, S., Avsar, T., Orhan, M. D., Serhatli, M., Balcioglu, B. K., Ozturk, H. U., Kayabolen, A., Cetin, Y., Aydinlik, S., Bagci-Onder, T., Tekin, S., Demirci, H., Guzel, M., Akdemir, A., Calis, S., Oktay, L., Tolu, I., Butun, Y. E., Erdemoglu, E., … Yumak, Y.…

    https://bioxfel.org/resources/2108

36. Mediator structure and conformation change

    BioXFEL Publications 10 Feb 2021 Contributor(s): Rayees Mattoo, David Bushnell, Roger Kornberg

    http://dx.doi.org/10.1016/j.molcel.2021.

    https://bioxfel.org/resources/1980

37. Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein

    BioXFEL Publications 22 Feb 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1101/2021.… 21.432153 ABSTRACTHIV-1 continues to be a global health concern since AIDS was first recognized by the World Health Organization (WHO). It is estimated that there were 38 million people infected with HIV-1 and 1.5 million deaths in 2019 alone. A better understanding of the details of the HIV…

    https://bioxfel.org/resources/1971

38. Lab Management Workshop Series

    Education 30 Sep 2020

    BioXFEL is sponsoring a workshop series that will cover a core set of interpersonal and collaborative skills that scientists need to do their current jobs as well as skills they will need when they move on to other positions in academia or the private sector. The first workshop (“Difficult conversations in the research workplace: Fundamentals…

    https://bioxfel.org/content/article/407

39. LCLS PCS Proposal Deadline

    Events 1 Oct 2021

    Oct 01 2021

    LCLS Beamtime Proposal schedule and submission process can be found below.  Follow this link for further information. LCLS Beamtime Proposal Schedule  Mode of AccessRun CycleProposal Call StatusDeadlineCycle BeginsCycle Ends Scientific Campaign LCLS 20 Accepting Proposals via the User Portal 19 July 2021 … Jan 2022 Jun…

    https://bioxfel.org/events/details/1260

40. LCLS Beamtime Proposal Deadline

    Events 19 Jul 2021

    Jul 19 2021

    LCLS Beamtime Proposal schedule and submission process can be found below.  Follow this link for further information. LCLS Beamtime Proposal Schedule  Mode of AccessRun CycleProposal Call StatusDeadlineCycle BeginsCycle Ends Scientific Campaign LCLS 20 Accepting Proposals via the User Portal 19 July 2021 … Jan 2022 Jun…

    https://bioxfel.org/events/details/1259

41. BioXFEL scientists make a molecular movie of a biological process to convert sunlight to chemical energy

    News 25 Mar 2021

    Many organisms use sunlight to fuel cellular functions. But exactly how does this conversion of solar energy into chemical energy unfold? In a recent experiment, an international team of scientists, including several research groups from the BioXFEL Science and Technology Center, used  time-resolved serial femtosecond crystallography (TR-SFX)…

    https://bioxfel.org/content/article/420

42. Brookhaven Postoctoral Position

    Opportunities 17 Nov 2021

    Brookhaven National Laboratory (www.bnl.gov) delivers discovery science and transformative technology to power and secure the nation's future. Brookhaven Lab is a multidisciplinary laboratory with seven Nobel Prize-winning discoveries, 37 R&D 100 Awards, and more than 70 years of pioneering research. The Lab is primarily supported by the U.S.…

    https://bioxfel.org/content/article/442

43. Classical molecular dynamics

    BioXFEL Publications 11 Mar 2021 Contributor(s): David Case

    http://dx.doi.org/10.1063/5.0045455 journal-article Brooks, C.L. et al., 2021.

    https://bioxfel.org/resources/1963

44. PEGylated Serp-1 Markedly Reduces Pristane-Induced Experimental Diffuse Alveolar Hemorrhage, Altering uPAR Distribution, and Macrophage Invasion

    BioXFEL Publications 18 Feb 2021 Contributor(s): Ryan Boyd, Petra Fromme

    http://dx.doi.org/10.3389/fcvm.2021.… The prevalence of DAH is reported to range from 1 to 5%, but while DAH is considered a rare complication there is a reported 50–80% mortality. There is at present no proven effective treatment for DAH and the therapeutics that have been tested have significant side effects. There is a clear…

    https://bioxfel.org/resources/1978

45. Visualization of biomolecular structures by WAXS and MD

    BioXFEL Publications 21 Oct 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1107/s0108767321098755 journal-article He, W., Chen, Y.-L., Kirmizialtin, S., & Pollack, L. (2021).

    https://bioxfel.org/resources/2103

46. The ideal crystal for structural biology

    BioXFEL Publications 21 Oct 2021 Contributor(s): Edward Snell, Diana Monteiro, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s0108767321098901 journal-article Snell, E., Monteiro, D., & Bowman, S. (2021).

    https://bioxfel.org/resources/2132

47. Structural biology in the time of COVID-19: perspectives on methods and milestones

    BioXFEL Publications 22 Apr 2021 Contributor(s): Miranda Lynch, Edward Snell, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s2052252521003948 The global COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has wreaked unprecedented havoc on global society, in terms of a huge loss of life and burden of morbidity, economic upheaval and social disruption. Yet the sheer magnitude and uniqueness of this event has…

    https://bioxfel.org/resources/1996

48. Macromolecular movies, storybooks written by nature

    BioXFEL Publications 3 Nov 2021 Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1007/s12551-021-00846-1 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Schmidt, M., 2021.

    https://bioxfel.org/resources/2078

49. Few-fs resolution of a photoactive protein traversing a conical intersection

    BioXFEL Publications 3 Nov 2021

    http://dx.doi.org/10.1038/s41586-021-04050-9 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Hosseinizadeh, A. et al., 2021.

    https://bioxfel.org/resources/2077

50. A science education model for large collaborative centers

    BioXFEL Publications 5 Mar 2021 Contributor(s): Sarah Woodruff

    http://dx.doi.org/10.1063/4.0000081 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Bauer, W.J. & Woodruff, S.B., 2021.

    https://bioxfel.org/resources/1987

51. Selecting XFEL single-particle snapshots by geometric machine learning

    BioXFEL Publications 18 Feb 2021 Contributor(s): Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Russell Fung, Abbas Ourmazd, Peter Schwander

    http://dx.doi.org/10.1063/4.0000060 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Cruz-Chú, E.R. et al., 2021.

    https://bioxfel.org/resources/1955

52. Sodium Binding in Cysteinyl Leukotriene G Protein-Coupled Receptors

    BioXFEL Publications 12 Feb 2021 Contributor(s): Vadim Cherezov

    http://dx.doi.org/10.1016/j.bpj.2020.11.987 journal-article Shaulskaia, V. et al., 2021.

    https://bioxfel.org/resources/1969

53. BioXFEL Crystallization Workshop

    Events 2 Apr 2021

    Apr 02 2021

    BioXFEL will be sponsoring a remote Crystallization Workshop Friday, April 2nd, 2021.

    https://bioxfel.org/events/details/1255

54. SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata

    BioXFEL Publications 1 Apr 2021

    http://dx.doi.org/10.1002/bip.23427 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Marchany‐Rivera, D. et al., 2021.

    https://bioxfel.org/resources/1984

55. Call for Proposals - Experiments at European XFEL

    Uncategorised 10 Nov 2020

    The European X-Ray Free-Electron Laser Facility (European XFEL, https://www.xfel.eu) encourages the scientific community worldwide to submit proposals for User Experiments via the User Portal to the European XFEL (UPEX) until Wednesday, 16 December 2020 16:00 (local Hamburg/Schenefeld time - CET) Beamtime will be allocated to successful…

    https://bioxfel.org/content/article/410

56. ORACLE reveals a bright future to fight bacteria

    BioXFEL Publications 15 Apr 2021 Contributor(s): James Fraser

    http://dx.doi.org/10.7554/elife.68277 A new way to alter the genome of bacteriophages helps produce large libraries of variants, allowing these bacteria-killing viruses to be designed to target species harmful to human health. journal-article Coyote-Maestas, W., & Fraser, J. S. (2021).

    https://bioxfel.org/resources/2123

57. Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces

    BioXFEL Publications 10 Dec 2020

    http://dx.doi.org/10.1016/j.foodhyd.2020.106522 journal-article Edmonds, R.S. et al., 2021.

    https://bioxfel.org/resources/1981

58. Amyloid‐β analysis from brain cells using microfluidics and mass spectrometry

    BioXFEL Publications 15 Mar 2022 Contributor(s): Alexandra Ros

    http://dx.doi.org/10.1002/alz.054274 journal-article Villarreal, J. C., Egatz‐Gomez, A., Liu, J., Ros, R., Noutsios, G. T., Sandrin, T. R., Coleman, P. D., & Ros, A. (2021).

    https://bioxfel.org/resources/2134

59. What it takes for a successful mix-and-inject serial crystallography experiment: from a sample preparation and sample delivery perspective

    BioXFEL Publications 21 Oct 2021 Contributor(s): Kara Zielinski, Lois Pollack

    http://dx.doi.org/10.1107/s0108767321099219 journal-article Zielinski, K., & Pollack, L. (2021).

    https://bioxfel.org/resources/2104

60. Molecular Dynamics Simulations Unravel the Mysteries of Hemoglobin Diseases

    BioXFEL Publications 12 Feb 2021 Contributor(s): David Case

    http://dx.doi.org/10.1016/j.bpj.2020.11.1905 journal-article Samuel, P.P. & Case, D.A., 2021.

    https://bioxfel.org/resources/1962

61. Reply to: Limitations of the iterative electron density reconstruction algorithm from solution scattering data

    BioXFEL Publications 1 Mar 2021

    http://dx.doi.org/10.1038/s41592-021-01083-w journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Grant, T.D., 2021.

    https://bioxfel.org/resources/1973

62. Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications

    BioXFEL Publications 26 Oct 2021

    http://dx.doi.org/10.1021/acs.langmuir.1c02004 journal-article Finney, T. J., Parikh, S. J., Berman, A., Sasaki, D. Y., & Kuhl, T. L. (2021).

    https://bioxfel.org/resources/2106

63. Breaking the Boundary between Solution X-Ray Scattering and Molecular Dynamics Simulations of Structured Nucleic Acids

    BioXFEL Publications 12 Feb 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2020.11.1995 journal-article Chen, Y.-L. et al., 2021.

    https://bioxfel.org/resources/1956

64. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering

    BioXFEL Publications 12 Feb 2021 Contributor(s): Konstantinos Karpos, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2020.11.1003 journal-article Menon, C.S.K. et al., 2021.

    https://bioxfel.org/resources/1957

65. A glycan gate controls opening of the SARS-CoV-2 spike protein

    BioXFEL Publications 19 Aug 2021 Contributor(s): Ghoncheh Mashayekhi, Abbas Ourmazd

    http://dx.doi.org/10.1038/s41557-021-00758-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sztain, T. et al., 2021.

    https://bioxfel.org/resources/2072

66. Surface coatings for microfluidic biomedical devices

    BioXFEL Publications 16 Aug 2021

    http://dx.doi.org/10.1016/b978-0-12-819971-8.00003-2 book-chapter Sonker, M., Abdallah, B.G. & Ros, A., 2021.

    https://bioxfel.org/resources/2073

67. A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

    BioXFEL Publications 20 Dec 2021 Contributor(s): James Fraser

    http://dx.doi.org/10.1038/s41589-021-00919-y journal-article Jayaraman, V., Lee, D. J., Elad, N., Vimer, S., Sharon, M., Fraser, J. S., & Tawfik, D. S. (2021).

    https://bioxfel.org/resources/2110

68. Pushing the boundaries in crystallization screening: making automated user-accessible crystallization work

    BioXFEL Publications 21 Oct 2021 Contributor(s): Sarah EJ Bowman, Miranda Lynch, Edward Snell

    http://dx.doi.org/10.1107/s0108767321098470 journal-article Bowman, S., Lynch, M., Lauricella, A., & Snell, E. (2021).

    https://bioxfel.org/resources/2131

69. Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV ‐2 spike protein receptor‐binding domain

    BioXFEL Publications 10 Aug 2021 Contributor(s): David Case

    http://dx.doi.org/10.1002/prot.26208 journal-article Williams, J.K. et al., 2021.

    https://bioxfel.org/resources/2075

70. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry

    BioXFEL Publications 5 Apr 2021 Contributor(s): Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.0c04112 journal-article Yang, M. et al., 2021.

    https://bioxfel.org/resources/2034

71. Decoding hidden structural information in solution wide-angle X-ray scattering (WAXS): from ensemble modeling to machine learning

    BioXFEL Publications 21 Oct 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1107/s0108767321098731 journal-article Chen, Y.-L., & Pollack, L. (2021).

    https://bioxfel.org/resources/2102

72. Extended properties of magnetic spins of zinc ferrite nanoparticles in the THz frequency range

    BioXFEL Publications 24 Nov 2020 Contributor(s): Petra Fromme

    http://dx.doi.org/10.1016/j.jmmm.2020.167574 journal-article Abdellatif-Youssef, M. et al., 2021.

    https://bioxfel.org/resources/1976

73. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses

    BioXFEL Publications 12 Feb 2021 Contributor(s): David Bushnell, Roger Kornberg, Henry Chapman

    http://dx.doi.org/10.1016/j.bpj.2020.11.1697 journal-article Xavier, P.L. et al., 2021.

    https://bioxfel.org/resources/1965

74. Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

    BioXFEL Publications 12 Feb 2021 Contributor(s): Nadia Zatsepin, Derek Mendez, Petra Fromme, Richard Kirian

    http://dx.doi.org/10.1016/j.bpj.2020.11.1006 journal-article Grant, T.D. et al., 2021.

    https://bioxfel.org/resources/1975

75. UWM Opening: Research Associate

    Opportunities 6 Aug 2021

    Research Associate Position College of Letters and Science Department of Physics  August 2021 

    https://bioxfel.org/content/article/432

76. Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray scattering experiments

    BioXFEL Publications 21 Oct 2021 Contributor(s): Michael Thompson, James Fraser

    http://dx.doi.org/10.1107/s0108767321097841 journal-article Thompson, M., Wolff, A., Barad, B., Vasquez, W. N., Brown, N., Cho, H. S., Schotte, F., Stadnytskyi, V., Anfinrud, P., & Fraser, J. (2021).

    https://bioxfel.org/resources/2105

77. EuXFEL Proposal Deadline

    Events 3 Dec 2021

    Dec 03 2021

    8th Call for Regular Proposals for User Experiments, call for Protein Crystal Screening Proposals and Expressions of Interest in Long-Term Proposals The 8th call for regular proposals at European X-Ray Free-Electron Laser Facility (European XFEL) is open until Friday 03 December 2021 16:00 (local Hamburg/Schenefeld time – Central European Time…

    https://bioxfel.org/events/details/1265

78. Macromolecular phasing using diffraction from multiple crystal forms

    BioXFEL Publications 8 Dec 2020 Contributor(s): Henry Chapman

    http://dx.doi.org/10.1107/s2053273320013650 A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated…

    https://bioxfel.org/resources/1967

79. BioXFEL Postdoctoral Research Award

    Events 1 Mar 2021

    Mar 01 2021

    BioXFEL Postdoctoral Research Award The BioXFEL STC has reserved discretionary funds intended to support a unique project for a postdoctoral scholar of the BioXFEL Center. This funding is competitive and will be awarded based on the merit of the work to be accomplished and its cohesiveness with the goals of the Center. Our first fellowship was…

    https://bioxfel.org/events/details/1196

80. The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

    BioXFEL Publications 23 Apr 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1126/sciadv.abf6106 Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental…

    https://bioxfel.org/resources/2013

81. Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

    BioXFEL Publications 24 Nov 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1038/s41598-021-02180-8 AbstractThe ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential…

    https://bioxfel.org/resources/2107

82. Polo: an open-source graphical user interface for crystallization screening

    BioXFEL Publications 19 Feb 2021 Contributor(s): Ethan T Holleman, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s1600576721000108 Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to…

    https://bioxfel.org/resources/1986

83. State of the structure address on MET receptor activation by HGF

    BioXFEL Publications 17 Apr 2021 Contributor(s): James Fraser

    http://dx.doi.org/10.1042/bst20200394 The MET receptor tyrosine kinase (RTK) and its cognate ligand hepatocyte growth factor (HGF) comprise a signaling axis essential for development, wound healing and tissue homeostasis. Aberrant HGF/MET signaling is a driver of many cancers and contributes to drug resistance to several approved therapeutics…

    https://bioxfel.org/resources/2136

84. BioXFEL Postdoctoral Research Award

    Education 6 Sep 2016

    Purpose:  The BioXFEL STC has reserved discretionary funds intended to support a unique project for a postdoctoral scholar of the BioXFEL Center. This funding is competitive and will be awarded based on the merit of the work to be accomplished and its cohesiveness with the goals of the Center. Our first fellowship was awarded to Michael Thompson.…

    https://bioxfel.org/content/article/173

85. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

    BioXFEL Publications 26 Jan 2021 Contributor(s): Henry Chapman

    http://dx.doi.org/10.1107/s2059798320016071 The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety…

    https://bioxfel.org/resources/1968

86. The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature

    BioXFEL Publications 29 Jul 2021 Contributor(s): suraj pandey, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1107/s2059798321005830 (6–4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6–4) photolyase [Dm(6–4)photolyase] at room and cryogenic temperatures are reported. The…

    https://bioxfel.org/resources/2069

87. BioXFEL $90k Applications Due

    Events 26 Apr 2021

    Apr 26 2021

    Announcement of BioXFEL discretionary research support  The NSF BioXFEL Science and Technology Center has funding intended to support research at US institutions. This support is for the application of X-ray free electron lasers to structural biology in collaboration with the BioXFEL STC. The aim is to foster collaboration with the BioXFEL Center…

    https://bioxfel.org/events/details/1258

88. Reach Out Science Communication Competition

    Events 6 Apr 2021

    Apr 06 2021

      Don’t miss the 2021 (virtual) Reach Out Science Slams!

    https://bioxfel.org/events/details/1257

89. Solution structure(s) of trinucleosomes from contrast variation SAXS

    BioXFEL Publications 12 Apr 2021 Contributor(s): Lois Pollack

    http://dx.doi.org/10.1093/nar/gkab290 Abstract Nucleosomes in all eukaryotic cells are organized into higher order structures that facilitate genome compaction. Visualizing these organized structures is an important step in understanding how genomic DNA is efficiently stored yet remains accessible to information-processing machinery.…

    https://bioxfel.org/resources/2014

90. Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

    BioXFEL Publications 22 Mar 2021 Contributor(s): Chufeng Li, suraj pandey, Mark S. Hunter, Uwe Weierstall, Nadia Zatsepin, John Spence, Marius Schmidt, haiguang liu

    http://dx.doi.org/10.1073/pnas.2020486118 Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac…

    https://bioxfel.org/resources/1988

91. The XBI BioLab for life science experiments at the European XFEL

    BioXFEL Publications 2 Dec 2020 Contributor(s): Petra Fromme, Jozef Uličný

    http://dx.doi.org/10.1107/s1600576720013989 The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology…

    https://bioxfel.org/resources/1977

92. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening

    BioXFEL Publications 14 Jun 2021 Contributor(s): Shuo Sui, Sarah Perry

    http://dx.doi.org/10.1107/s1600576721004155 A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and…

    https://bioxfel.org/resources/2021

93. Synchronous RNA conformational changes trigger ordered phase transitions in crystals

    BioXFEL Publications 19 Mar 2021 Contributor(s): Chelsie E Conrad, Max Oliver Wiedorn, Chufeng Li, Mark S. Hunter, Nadia Zatsepin, suraj pandey, Marius Schmidt, John Spence, Henry Chapman

    http://dx.doi.org/10.1038/s41467-021-21838-5 AbstractTime-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed…

    https://bioxfel.org/resources/1966

94. X-ray-Based Techniques to Study the Nano–Bio Interface

    BioXFEL Publications 2 Mar 2021 Contributor(s): Henry Chapman, Marius Schmidt

    http://dx.doi.org/10.1021/acsnano.0c09563 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sanchez-Cano, C. et al., 2021.

    https://bioxfel.org/resources/1995

95. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

    BioXFEL Publications 4 Aug 2021 Contributor(s): Hasan Demirci

    http://dx.doi.org/10.1038/s41598-021-95236-8 AbstractOligomerization of Pr55Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55Gag. However, the exact binding site of IP6 on MA remains…

    https://bioxfel.org/resources/2074

96. Spence Symposium at ASU

    Events 11 Oct 2022

    Oct 11 2022

    John Spence had a remarkable scientific impact over an illustrious career spanning nearly 50 years before passing away in June, 2021.

    https://bioxfel.org/events/details/1271

97. Graduate Studies at UB

    Opportunities 26 Oct 2021

    Research. Enzyme function is potentially linked to the entire protein conformational space sampled by enzyme and enzyme-intermediate complexes during catalysis. Importantly, this holds for lowly populated conformational sub-spaces of higher free energy, which can differ distinctly from the lowest free energy conformational sub-space typically…

    https://bioxfel.org/content/article/439

98. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

    BioXFEL Publications 8 Sep 2021 Contributor(s): suraj pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Ishwor Poudyal, Jay-How Yang, Kara Zielinski, Matthias Frank, Rebecca Jeanne Jernigan, Mitchell Miller, Garrett Charles Nelson, Abbas Ourmazd, John Spence, Peter Schwander, Henry Chapman, Petra Fromme, George Phillips, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1107/s2052252521008125 Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL).…

    https://bioxfel.org/resources/2070

99. Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

    BioXFEL Publications 20 Dec 2021 Contributor(s): Sabine Botha, Gihan Kaushylal Ketawala, Brandon Hayes, Christopher Kupitz, Hasan Demirci

    http://dx.doi.org/10.3390/cryst11121579 Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing;…

    https://bioxfel.org/resources/2109

100. Fundamentals of Negotiating Workshop

     Events 31 Jan 2021

     Jan 31 2021

     Workshop 1: Sunday, January 31, 2021

     https://bioxfel.org/events/details/1247