Femtosecond response of polyatomic molecules to ultra-intense hard X-rays.

X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 1020 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecular system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects-an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure-the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 1020 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

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.

Pulse Energy and Pulse Duration Effects in the Ionization and Fragmentation of Iodomethane by Ultraintense Hard X Rays.

The interaction of intense femtosecond x-ray pulses with molecules sensitively depends on the interplay between multiple photoabsorptions, Auger decay, charge rearrangement, and nuclear motion. Here, we report on a combined experimental and theoretical study of the ionization and fragmentation of iodomethane (CH_{3}I) by ultraintense (∼10^{19} W/cm^{2}) x-ray pulses at 8.3 keV, demonstrating how these dynamics depend on the x-ray pulse energy and duration. We show that the timing of multiple ionization steps leading to a particular reaction product and, thus, the product's final kinetic energy, is determined by the pulse duration rather than the pulse energy or intensity. While the overall degree of ionization is mainly defined by the pulse energy, our measurement reveals that the yield of the fragments with the highest charge states is enhanced for short pulse durations, in contrast to earlier observations for atoms and small molecules in the soft x-ray domain. We attribute this effect to a decreased charge transfer efficiency at larger internuclear separations, which are reached during longer pulses.

Erratum: Delayed Onset of Nonthermal Melting in Single-Crystal Silicon Pumped with Hard X Rays [Phys. Rev. Lett. 120, 265701 (2018)].

This corrects the article DOI: 10.1103/PhysRevLett.120.265701.

Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature.

Water has a number of anomalous physical properties, and some of these become drastically enhanced on supercooling below the freezing point. Particular interest has focused on thermodynamic response functions that can be described using a normal component and an anomalous component that seems to diverge at about 228 kelvin (refs 1-3). This has prompted debate about conflicting theories that aim to explain many of the anomalous thermodynamic properties of water. One popular theory attributes the divergence to a phase transition between two forms of liquid water occurring in the 'no man's land' that lies below the homogeneous ice nucleation temperature (TH) at approximately 232 kelvin and above about 160 kelvin, and where rapid ice crystallization has prevented any measurements of the bulk liquid phase. In fact, the reliable determination of the structure of liquid water typically requires temperatures above about 250 kelvin. Water crystallization has been inhibited by using nanoconfinement, nanodroplets and association with biomolecules to give liquid samples at temperatures below TH, but such measurements rely on nanoscopic volumes of water where the interaction with the confining surfaces makes the relevance to bulk water unclear. Here we demonstrate that femtosecond X-ray laser pulses can be used to probe the structure of liquid water in micrometre-sized droplets that have been evaporatively cooled below TH. We find experimental evidence for the existence of metastable bulk liquid water down to temperatures of 227(-1)(+2) kelvin in the previously largely unexplored no man's land. We observe a continuous and accelerating increase in structural ordering on supercooling to approximately 229 kelvin, where the number of droplets containing ice crystals increases rapidly. But a few droplets remain liquid for about a millisecond even at this temperature. The hope now is that these observations and our detailed structural data will help identify those theories that best describe and explain the behaviour of water.

Delayed Onset of Nonthermal Melting in Single-Crystal Silicon Pumped with Hard X Rays.

In this work, we monitor the onset of nonthermal melting in single-crystal silicon by implementing an x-ray pump-x-ray probe scheme. Using the ultrashort pulses provided by the Linac Coherent Light Source (SLAC) and a custom-built split-and-delay line for hard x rays, we achieve the temporal resolution needed to detect the onset of the transition. Our data show no loss of long-range order up to 150±40 fs from photoabsorption, which we interpret as the time needed for the electronic system to equilibrate at or above the critical nonthermal melting temperature. Once such equilibration is reached, the loss of long-range atomic order proceeds inertially and is completed within 315±40 fs from photoabsorption.

Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source.

Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, thus allowing simultaneous measurements at two separate instruments. In this report, the structure determination of a prototypical protein was performed using serial femtosecond crystallography simultaneously with a femtosecond time-resolved XANES studies of photoexcited spin transition dynamics in an iron spin-crossover system. The results of both experiments using the multiplexed beams are similar to those obtained separately, using a dedicated beam, with no significant differences in quality.

Mechanism and dynamics of fatty acid photodecarboxylase.

Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.

Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns.

We reconstructed the 3D Fourier intensity distribution of monodisperse prolate nanoparticles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast x-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the expansion-maximization-compression framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.

Precrystallization clusters of holoferritin and apoferritin at low temperature.

The formation of small nanosized clusters of the proteins holoferritin and apoferritin at low temperature was studied using small angle x-ray scattering. A strikingly large temperature dependence for the average molecular spacing in the clusters was observed. Calculations of the scattered intensity for various cluster models were performed. Comparison of the data with the simulations revealed the presence of crystalline order in the clusters of size ranging from a few molecules to a few hundred molecules. The crystalline order was found to be preserved with the lattice spacing varying with temperature by up to 20%. The small clusters were observed to grow into large micron-sized crystals when they were annealed and under certain conditions, the small clusters were found to coexist with the large crystals. This suggests that these clusters are closely related to critical nucleation. The data are consistent with an isotropic nucleation pathway, but cannot completely rule out a smaller presence of planar nucleation.

The linac coherent light source single particle imaging road map.

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

Susceptibility to apoptosis of T lymphocytes from elderly humans is associated with increased in vivo expression of functional Fas receptors.

We recently showed that mature T lymphocytes derived from elderly humans were more susceptible to activation-induced cell death than similar cells from young individuals. Because this excessive apoptosis is unrelated to either the age-associated decrease in IL-2 production, a differential Bcl-2 expression or to a modification of the antioxidant pathway, we examined the possibility that the Fas receptor (FasR) is directly implicated in the generation of the unwarranted death signal. We investigated the expression and the function of FasR on T lymphocyte populations from healthy young and elderly individuals. We found that the frequency of FasR+ T cells increases as a function of age. The FasR expressed at the surface of freshly isolated T lymphocytes from elderly donors appear to be fully functional since their ligation by a cytocidal IgM anti-Fas mAb leads to a significant increase in DNA fragmentation in this cell population. Conversely, exposure of T cells derived from aged individuals to an antagonistic anti-FasR mAb partially prevents the age-related increase in apoptotic cell death. The population of FasR+ T lymphocytes is essentially constituted of previously activated CD45RO+ cells and also includes recently activated lymphocytes bearing the CD25 and CD69 activation markers. The accumulation of chronically and recently in vivo activated T-cells with age probably contributes to the amplification of the process of Fas-mediated cell death in T lymphocytes isolated from senescent organisms.

Surface relaxation in protein crystals.

Surface x-ray diffraction measurements were performed on (111) growth faces of crystals of the cellular iron-storage protein, horse spleen ferritin. Crystal truncation rods (CTR) were measured. A fit of the measured profile of the CTR revealed a surface roughness of 48+/-4.5 A and a top layer spacing contraction of 3.9+/-1.5%. In addition to the peak from the CTR, the rocking curves of the crystals displayed unexpected extra peaks. Multiple scattering is demonstrated to account for them. Future applications of the method could allow the exploration of hydration effects on the growth of protein crystals.

[Asthma and diving with a cylinder]. / Asthme et plongée en bouteille.

Undersea diving is an activity that is practised more and more in holiday clubs. There is no precise legislation on the causes of unfitness of the amateur, in contrast to the professional diver, where the medical criteria are strict and controlled. When diving with a cylinder, on descent, the ventilatory load increases with increase of the ambient pressure and dynamic resistance in the airways increases. "As with an insufficient respiration on the surface, a healthy subject when diving has a ventilatory ability that is drastically reduced". Moreover with cylinder ventilation, the diver has available a reserve of gas under pressure from which he inspires with the aid of a breathing apparatus (regulator): he breathes dry gas that is dried before compression in the reservoirs, chilled by the relief valve on leaving the reservoir. This inhalation of cold, dry air associated with a hyperventilation during the descent produces ideal conditions to trigger exercise induced asthma. All subjects who present a bronchial hyperreactivity have the risk when diving with a cylinder of triggering a bronchospasm that is identical with that of a sporting asthmatic. During surfacing: the re-surfacing diver runs the risk of an accident of pulmonary suppression if he does not expire sufficiently during his return to the surface: the mass of intrapulmonary air of the resurfacer dilates and the excess of volume is exhaled by the diver: a volume of air of 5 l at 10 m depth corresponds to a volume of 10 l on the surface. Therefore the airways must remain free: an obstruction of the peripheral airways associated with an urgent re-surfacing produces a very rapid thoracic dilation which is responsible for pulmonary barotrauma (pulmonary barotrauma is frequently lethal with 30% of accidental deaths).

[Poor tolerance of exertion during sports and bronchial hyperreactivity]. / Mauvaise tolérance à l'effort chez le sportif et hyperréactivité bronchique.

135 sportsmen and women, 55 girls, 80 boys, aged from 7 to 30 years, from various sports, who complained of bad tolerance of exertion were examined with an exercise test and isocapnic spontaneous hyperventilation. 61, about 45%, during a hyperventilation test had a fall of V.E.M.S. greater than or equal to 20%, showing bronchial hyperreactivity. After three tests, this fall index was greater than or equal to 50%. 68% of the positive responses were seen in boys and 2/3 of the subjects with a positive response were atopics. No other argument could be maintained from the questioning or clinical history to predict the positive or negative character of the hyperventilation (age, sporting level, symptoms, previous asthma or asthmatic, allergy). H.S.V.I. of the chests of a sporting population that complains of exertion intolerance, therefore allows verification of an H.R.B. assessment of its severity and to follow evolution after treatment.

[The pork-cat syndrome or crossed allergy between pork meat and cat epithelia (2)]. / Le syndrome porc-chat ou l'allergie croisée entre viande de porc et épithélia de chat (2e partie).

Is there a port-cat syndrome in food allergy? Many clinical observations have revealed a frequent association between allergy to cat epithelia in subjects who have allergy to pork meat. This second part, from clinical tests such as skin tests and laboratory tests such as CAP RAST, electrophoresis, Western blot and chromatography, confirms the existence of a crossed reaction between pork meat and cat extract. This crossed reaction is linked with a common epitope. A common protein has been found that has a molecular weight of 67,000 d. for subjects who are sensitive to cat extracts and pork meat.

[The pork-cat syndrome or crossed allergy between pork meat and cat epithelia (1)]. / Le syndrome porc-chat ou l'allergie croisée entre viande de porc et épithélia de chat (1re partie).

This work is a study of the frequency of the association between sensitivity to pork meat and cat epithelia. Comparison with a reference population that was not sensitized to pork meat, shows that this association is highly significant. This suggests therefore the possibility of a crossed allergenicity. If there is a real crossed allergenicity between pork meat and cat epithelia, we suggest that this crossed allergenicity is without doubt much greater and concerns more the meats and epithelia of mammals.

Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector.

Recent advancements at the Linac Coherent Light Source X-ray free-electron laser (XFEL) enabling successful serial femtosecond diffraction experiments using nanometre-sized crystals (NCs) have opened up the possibility of X-ray structure determination of proteins that produce only submicrometre crystals such as many membrane proteins. Careful crystal pre-characterization including compatibility testing of the sample delivery method is essential to ensure efficient use of the limited beamtime available at XFEL sources. This work demonstrates the utility of transmission electron microscopy for detecting and evaluating NCs within the carrier solutions of liquid injectors. The diffraction quality of these crystals may be assessed by examining the crystal lattice and by calculating the fast Fourier transform of the image. Injector reservoir solutions, as well as solutions collected post-injection, were evaluated for three types of protein NCs (i) the membrane protein PTHR1, (ii) the multi-protein complex Pol II-GFP and (iii) the soluble protein lysozyme. Our results indicate that the concentration and diffraction quality of NCs, particularly those with high solvent content and sensitivity to mechanical manipulation may be affected by the delivery process.

Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse.

Physical, biological, and chemical transformations are initiated by changes in the electronic configuration of the species involved. These electronic changes occur on the timescales of attoseconds (10(-18) s) to femtoseconds (10(-15) s) and drive all subsequent electronic reorganization as the system moves to a new equilibrium or quasi-equilibrium state. The ability to detect the dynamics of these electronic changes is crucial for understanding the potential energy surfaces upon which chemical and biological reactions take place. Here, we report on the determination of the electronic structure of matter using a single self-seeded femtosecond x-ray pulse from the Linac Coherent Light Source hard x-ray free electron laser. By measuring the high energy resolution off-resonant spectrum (HEROS), we were able to obtain information about the electronic density of states with a single femtosecond x-ray pulse. We show that the unoccupied electronic states of the scattering atom may be determined on a shot-to-shot basis and that the measured spectral shape is independent of the large intensity fluctuations of the incoming x-ray beam. Moreover, we demonstrate the chemical sensitivity and single-shot capability and limitations of HEROS, which enables the technique to track the electronic structural dynamics in matter on femtosecond time scales, making it an ideal probe technique for time-resolved X-ray experiments.

Femtosecond visualization of lattice dynamics in shock-compressed matter.

The ultrafast evolution of microstructure is key to understanding high-pressure and strain-rate phenomena. However, the visualization of lattice dynamics at scales commensurate with those of atomistic simulations has been challenging. Here, we report femtosecond x-ray diffraction measurements unveiling the response of copper to laser shock-compression at peak normal elastic stresses of ~73 gigapascals (GPa) and strain rates of 10(9) per second. We capture the evolution of the lattice from a one-dimensional (1D) elastic to a 3D plastically relaxed state within a few tens of picoseconds, after reaching shear stresses of 18 GPa. Our in situ high-precision measurement of material strength at spatial (<1 micrometer) and temporal (<50 picoseconds) scales provides a direct comparison with multimillion-atom molecular dynamics simulations.