Measuring atomic-resolution images of materials with x-ray photons during chemical reactions or physical transformations resides at the technological forefront of x-ray science. New x-ray-based ...experimental capabilities have been closely linked with advances in x-ray sources, a trend that will continue with the impending arrival of x-ray-free electron lasers driven by electron accelerators. We discuss recent advances in ultrafast x-ray science and coherent imaging made possible by linear-accelerator-based light sources. These studies highlight the promise of ultrafast x-ray lasers, as well as the technical challenges and potential range of applications that will accompany these transformative x-ray light sources.
Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, ...single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.
Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the ...administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.
Thick diffractive optical elements offer a promising way to achieve focusing or imaging at a resolution approaching 1 nm for x-ray wavelengths shorter than about 0.1 nm. Efficient focusing requires ...that these are fabricated with structures that vary in period and orientation so that rays obey Bragg's law over the entire lens aperture and give rise to constructive interference at the focus. Here the analysis method of ray-tracing of thick diffractive optical elements is applied to such lenses to optimise their designs and to investigate their operating and manufacturing tolerances. Expressions are provided of the fourth-order series expansions of the wavefront aberrations and transmissions of both axi-symmetric lenses and pairs of crossed lenses that each focuses in only one dimension like a cylindrical lens. We find that aplanatic zone-plate designs, whereby aberrations are corrected over a large field of view, can be achieved by axi-symmetric lenses but not the crossed lenses. We investigate the performance of 1 nm-resolution lenses with focal lengths of about 1 mm and show their fields of view are mainly limited by the acceptance angle of Bragg diffraction, and that aberrations can limit the performance of lenses with longer focal lengths. We apply the ray-tracing formalism for a tolerancing analysis of imperfect lenses and examine some strategies for the correction of their aberrations.
The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the ...particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.
Pink-beam serial crystallography Meents, A; Wiedorn, M O; Srajer, V ...
Nature communications,
11/2017, Letnik:
8, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial ...synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, "pink", beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.
Abstract
We report the discovery of a 10 comoving megaparsec (cMpc)-scale structure traced by massive submillimeter galaxies (SMGs) at
z
∼ 4.6. These galaxies are selected from an emission line ...search of ALMA Band 7 observations targeting 184 luminous submillimeter sources (
S
850
μ
m
≥ 6.2 mJy) across 1.6 degrees
2
in the COSMOS field. We identify four C
ii
emitting SMGs and two probable C
ii
emitting SMG candidates at
z
= 4.60–4.64 with velocity-integrated signal-to-noise ratio of S/N > 8. Four of the six emitters are near-infrared blank SMGs. After excluding one SMG whose emission line is falling at the edge of the spectral window, all galaxies show clear velocity gradients along the major axes that are consistent with rotating gas disks. The estimated rotation velocities of the disks are 330–550 km s
−1
and the inferred host dark-matter halo masses are ∼2–8 × 10
12
M
⊙
. From their estimated halo masses and C
ii
luminosity function, we suggest that these galaxies have a high (50%–100%) duty cycle and high (∼0.1) baryon conversion efficiency (SFR relative to baryon accretion rate), and that they contribute ≃2% to the total star formation rate density at
z
= 4.6. These SMGs are concentrated within just 0.3% of the full survey volume, suggesting they are strongly clustered. The extent of this structure and the individual halo masses suggest that these SMGs will likely evolve into members of a ∼10
15
M
⊙
cluster at
z
= 0. This survey reveals a synchronized dusty starburst in massive halos at
z
> 4, which could be driven by mergers or fed by smooth gas accretion.
Achromatic focusing systems for hard X-rays are examined which consist of a refractive lens paired with a diffractive lens. Compared with previous analyses, we take into account the behaviour of ...thick refractive lenses, such as compound refractive lenses and waveguide gradient index refractive lenses, in which both the focal length and the position of the principal planes vary with wavelength. Achromatic systems formed by the combination of such a thick refractive lens with a multilayer Laue lens are found that can operate at a focusing resolution of about 3 nm, over a relative bandwidth of about 1%. With the appropriate distance between the refractive and diffractive lenses, apochromatic systems can also be found, which operate over relative bandwidth greater than 10%. These systems can be used to focus short pulses without distorting them in time by more than several attoseconds. Such systems are suitable for high-flux scanning microscopy and for creating high intensities from attosecond X-ray pulses.
ABSTRACT
We present integral field spectroscopy observations, covering the O iii λλ4959, 5007 emission‐line doublet of eight high‐redshift (z = 1.4–3.4) ultraluminous infrared galaxies (ULIRGs) that ...host active galactic nucleus (AGN) activity, including known submillimetre luminous galaxies. The targets have moderate radio luminosities that are typical of high‐redshift ULIRGs (L1.4 GHz = 1024–1025 W Hz−1) and therefore are not radio‐loud AGNs. We decouple kinematic components due to the galaxy dynamics and mergers from those due to outflows. We find evidence in the four most luminous systems (LO III ≳1043 erg s−1) for the signatures of large‐scale energetic outflows: extremely broad O iii emission (full width at half‐maximum ≈ 700–1400 km s−1) across ≈4–15 kpc, with high velocity offsets from the systemic redshifts (up to ≈850 km s−1). The four less luminous systems have lower quality data displaying weaker evidence for spatially extended outflows. We estimate that these outflows are potentially depositing energy into their host galaxies at considerable rates (Ė≈1043–1045 erg s−1); however, due to the lack of constraints on the density of the outflowing material and the structure of the outflow, these estimates should be taken as illustrative only. Based on the measured maximum velocities (vmax ≈ 400–1400 km s−1) the outflows observed are likely to unbind some fraction of the gas from their host galaxies, but are unlikely to completely remove gas from the galaxy haloes. By using a combination of energetic arguments and a comparison to ULIRGs without clear evidence for AGN activity, we show that the AGN activity could be the dominant power source for driving all of the observed outflows, although star formation may also play a significant role in some of the sources.
Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a ...riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
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![FIR-luminous [C ii] Emitter...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0004-637X_1538-4357/small "FIR-luminous [C ii] Emitters in the ALMA-SCUBA-2 COSMOS Survey (AS2COSMOS): The Nature of Submillimeter Galaxies in a 10 Comoving Megaparsec-scale Structure at z ∼ 4.6")
