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Maia, Filipe
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Publications (10 of 55) Show all publications
Reddy, H. K. N., Yoon, C. H., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Xavier Paulraj, L. (2017). Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source. Scientific Data, 4, Article ID 170079.
Open this publication in new window or tab >>Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source
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2017 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed) Published
Abstract [en]

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported similar to 600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-328536 (URN)10.1038/sdata.2017.79 (DOI)000404232100001 ()28654088 (PubMedID)
Projects
eSSENCE
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2017-06-27 Created: 2017-08-25 Last updated: 2017-11-29Bibliographically approved
Kurta, R. P., Donatelli, J. J., Yoon, C. H., Berntsen, P., Bielecki, J., Daurer, B. J., . . . Mancuso, A. P. (2017). Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses. Physical Review Letters, 119(15), 158102:1-7, Article ID 158102.
Open this publication in new window or tab >>Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses
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2017 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 119, no 15, p. 158102:1-7, article id 158102Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-331406 (URN)10.1103/PhysRevLett.119.158102 (DOI)000412840600011 ()
Projects
eSSENCE
Available from: 2017-10-12 Created: 2017-10-13 Last updated: 2018-01-16Bibliographically approved
Sala, S., Daurer, B. J., Hantke, M. F., Ekeberg, T., Loh, N. D., Maia, F. R. N. & Thibault, P. (2017). Ptychographic imaging for the characterization of X-ray free-electron laser beams. In: Rau, C (Ed.), X-RAY MICROSCOPY CONFERENCE 2016 (XRM 2016): . Paper presented at 13th International X-Ray Microscopy Conference (XRM), AUG 15-19, 2016, Diamond Light Source, Oxford, ENGLAND. , Article ID 012032.
Open this publication in new window or tab >>Ptychographic imaging for the characterization of X-ray free-electron laser beams
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2017 (English)In: X-RAY MICROSCOPY CONFERENCE 2016 (XRM 2016) / [ed] Rau, C, 2017, article id 012032Conference paper, Published paper (Refereed)
Abstract [en]

We present some preliminary results from a study aimed at the characterization of the wavefront of X-ray free electron laser (XFEL) beams in the same operation conditions as for single particle imaging (or flash X-ray imaging) experiments. The varying illumination produced by wavefront fluctuations between several pulses leads to a partially coherent average beam which can be decomposed into several coherent modes using ptychographic reconstruction algorithms. Such a decomposition can give insight into pulse-to-pulse variations of the wavefront. We discuss data collected at the Linac Coherent Light Source (LCLS) and FERMI.

Series
Journal of Physics Conference Series, ISSN 1742-6588 ; 849
National Category
Medical Image Processing
Identifiers
urn:nbn:se:uu:diva-346768 (URN)10.1088/1742-6596/849/1/012032 (DOI)000412800900032 ()
Conference
13th International X-Ray Microscopy Conference (XRM), AUG 15-19, 2016, Diamond Light Source, Oxford, ENGLAND
Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2018-03-26Bibliographically approved
Okamoto, K., Miyazaki, N., Song, C., Maia, F., Reddy, H. K. .., Abergel, C., . . . Murata, K. (2017). Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Scientific Reports, 7, Article ID 13291.
Open this publication in new window or tab >>Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 13291Article in journal (Refereed) Published
Abstract [en]

The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 mu m in length and 0.9 mu m in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2017
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-340134 (URN)10.1038/s41598-017-13390-4 (DOI)000413048000102 ()29038566 (PubMedID)
Funder
Swedish Research Council, 62820081109Swedish Research Council, 822-2010-6157Swedish Research Council, 822-2012-5260Swedish Research Council, 828-2012-108Knut and Alice Wallenberg Foundation, KAW-2011.081EU, European Research Council, ERC-291602
Available from: 2018-01-29 Created: 2018-01-29 Last updated: 2018-01-29Bibliographically approved
Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., . . . Maia, F. R. .. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3, Article ID 160061.
Open this publication in new window or tab >>A data set from flash X-ray imaging of carboxysomes
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed) Published
Abstract [en]

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300202 (URN)10.1038/sdata.2016.61 (DOI)000390225400006 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Munke, A., Andreasson, J., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Zook, J. (2016). Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Scientific Data, 3, 160064:1-12, Article ID 160064.
Open this publication in new window or tab >>Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300203 (URN)10.1038/sdata.2016.64 (DOI)000390225700001 ()
Projects
eSSENCE
Available from: 2016-08-01 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., . . . Sliz, P. (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, Article ID 10882.
Open this publication in new window or tab >>Data publication with the structural biology data grid supports live analysis
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2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 10882Article in journal (Refereed) Published
Abstract [en]

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data. sbgrid. org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-283659 (URN)10.1038/ncomms10882 (DOI)000371719200001 ()26947396 (PubMedID)
Funder
NIH (National Institute of Health), P41 GM103403NIH (National Institute of Health), 1S10RR028832NIH (National Institute of Health), 1U54EB020406-01
Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2017-11-30Bibliographically approved
Daurer, B. J., Hantke, M. F., Nettelblad, C. & Maia, F. R. N. (2016). Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time. Journal of applied crystallography, 49, 1042-1047
Open this publication in new window or tab >>Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1042-1047Article in journal (Refereed) Published
National Category
Biophysics Software Engineering
Identifiers
urn:nbn:se:uu:diva-287197 (URN)10.1107/S1600576716005926 (DOI)000377020600036 ()
Projects
eSSENCE
Available from: 2016-04-18 Created: 2016-04-22 Last updated: 2018-01-10Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. N., Hantke, M., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2015). Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nature Communications, 6, Article ID 5704.
Open this publication in new window or tab >>Imaging single cells in a beam of live cyanobacteria with an X-ray laser
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2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 5704Article in journal (Refereed) Published
Abstract [en]

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245040 (URN)10.1038/ncomms6704 (DOI)000350034400002 ()25669616 (PubMedID)
Available from: 2015-02-24 Created: 2015-02-24 Last updated: 2017-12-04Bibliographically approved
Aquila, A., Barty, A., Bostedt, C., Boutet, S., Carini, G., dePonte, D., . . . Williams, G. J. (2015). The linac coherent light source single particle imaging road map. Structural Dynamics, 2(4), Article ID 041701.
Open this publication in new window or tab >>The linac coherent light source single particle imaging road map
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2015 (English)In: Structural Dynamics, Vol. 2, no 4, article id 041701Article in journal (Refereed) Published
Abstract [en]

Intense femtosecond x-ray pulses from free-electron laser sources allow the imag-ing of individual particles in a single shot. Early experiments at the Linac CoherentLight Source (LCLS) have led to rapid progress in the field and, so far, coherentdiffractive images have been recorded from biological specimens, aerosols, andquantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLSheld a workshop to discuss the scientific and technical challenges for reaching theultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap towardreaching atomic resolution, 3D imaging at free-electron laser sources.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-252117 (URN)10.1063/1.4918726 (DOI)000360649200003 ()
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research Knut and Alice Wallenberg FoundationEU, European Research Council
Available from: 2015-05-01 Created: 2015-05-01 Last updated: 2015-10-05Bibliographically approved
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