Ultrafast structural changes within a photosynthetic reaction centre.

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.

Tracking Cavity Formation in Electron Solvation: Insights from X-ray Spectroscopy and Theory.

We present time-resolved X-ray absorption spectra of ionized liquid water and demonstrate that OH radicals, H3O+ ions, and solvated electrons all leave distinct X-ray-spectroscopic signatures. Particularly, this allows us to characterize the electron solvation process through a tool that focuses on the electronic response of oxygen atoms in the immediate vicinity of a solvated electron. Our experimental results, supported by ab initio calculations, confirm the formation of a cavity in which the solvated electron is trapped. We show that the solvation dynamics are governed by the magnitude of the random structural fluctuations present in water. As a consequence, the solvation time is highly sensitive to temperature and to the specific way the electron is injected into water.

Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering.

Dimeric complexes composed of d8 square planar metal centers and rigid bridging ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain in order to assist the development of reliable methods to model metal dimer complexes more broadly. [Ir2 (dimen)4]2+ (dimen = para-diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteract the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the nonequilibrium depletion of the electronic ground state population─often termed the ground state hole─with ultrafast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d8-d8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added, and a hybrid functional, which includes exact exchange, is used.

The Ring-Closing Reaction of Cyclopentadiene Probed with Ultrafast X-ray Scattering.

The dynamics of cyclopentadiene (CP) following optical excitation at 243 nm was investigated by time-resolved pump-probe X-ray scattering using 16.2 keV X-rays at the Linac Coherent Light Source (LCLS). We present the first ultrafast structural evidence that the reaction leads directly to the formation of bicyclo[2.1.0]pentene (BP), a strained molecule with three- and four-membered rings. The bicyclic compound decays via a thermal backreaction to the vibrationally hot CP with a time constant of 21 ± 3 ps. A minor channel leads to ring-opened structures on a subpicosecond time scale.

Ultrafast X-ray scattering offers a structural view of excited-state charge transfer.

Intramolecular charge transfer and the associated changes in molecular structure in N,N'-dimethylpiperazine are tracked using femtosecond gas-phase X-ray scattering. The molecules are optically excited to the 3p state at 200 nm. Following rapid relaxation to the 3s state, distinct charge-localized and charge-delocalized species related by charge transfer are observed. The experiment determines the molecular structure of the two species, with the redistribution of electron density accounted for by a scattering correction factor. The initially dominant charge-localized state has a weakened carbon-carbon bond and reorients one methyl group compared with the ground state. Subsequent charge transfer to the charge-delocalized state elongates the carbon-carbon bond further, creating an extended 1.634 Å bond, and also reorients the second methyl group. At the same time, the bond lengths between the nitrogen and the ring-carbon atoms contract from an average of 1.505 to 1.465 Å. The experiment determines the overall charge transfer time constant for approaching the equilibrium between charge-localized and charge-delocalized species to 3.0 ps.

Hard x-ray - optical four-wave mixing using a split-and-delay line.

New, hard x-ray free electron lasers (FEL) produce intense femtosecond-to-attosecond pulses at angstrom wavelengths, giving access to the fundamental spatial and temporal scales of matter. These revolutionary light sources open the door to applying the suite of nonlinear, optical spectroscopy methods at hard x-ray photon energies. Nonlinear spectroscopy with hard x-rays can allow for measuring the coherence properties of short wavelength excitations with atomic specificity and for understanding how high energy excitations couple to other degrees of freedom in atomic, molecular or condensed-phase systems. As a step in this direction, here we present hard x-ray, optical four-wave mixing (4WM) measurements done at 9.8 keV at the split-and-delay line at the x-ray correlation spectroscopy (XCS) hutch of the Linac Coherent Light Source (LCLS). In this work, we create an x-ray transient grating (TG) from a pair of crossing x-ray beams and diffract optical laser pulses at 400 nm from the TG. The key technical advance here is being able to independently vary the delays of the x-ray pulses. Measurements were made in 3 different solid samples: bismuth germinate (BGO), zinc oxide (ZnO) and yttrium aluminum garnet (YAG). The resulting phase-matched, 4WM signal is measured in two different ways: by varying the x-ray, x-ray pulse delay which can reveal both material and light source coherence properties and also by varying the optical laser delay with respect to the x-ray TG to study how the x-ray excitation couples to the optical properties. Although no coherent 4WM signal was seen in these measurements, the absence of this signal gives important information on experimental requirements for detecting this in future work. Also, our laser-delay scans, although not a new measurement, were applied to different materials than in past work and reveal new examples x-ray induced lattice dynamics in solids. This work represents a key step towards extending nonlinear optics and time-resolved spectroscopy into the hard x-ray regime.

Macromolecular diffractive imaging using imperfect crystals.

The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed--and are of interest as a source of information about the dynamics of proteins--they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.

Structure of photosystem II and substrate binding at room temperature.

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

Prevalence of sacroiliitis among patients referred for hip MR arthrography.

OBJECTIVE: To determine the prevalence of sacroiliitis among patients who have been referred for MR arthrography. MATERIALS AND METHODS: A retrospective search identified 130 consecutive MR arthrograms of the hip performed on a 1.5T Siemens Avanto at our institution from August 2013 to August 2014. Four studies were excluded due to the absence of a coronal short tau inversion recovery sequence of the pelvis, leaving 126 studies for analysis. A musculoskeletal radiology fellow and three attending musculoskeletal radiologists reviewed the images for the presence of bone marrow edema affecting the sacroiliac joints. Only cases of bone marrow edema meeting the Assessment of SpondyloArthritis international Society definition were considered positive. The two-tailed Fisher's exact test was used to compare the prevalence of positive MRI findings among age and gender groups. GraphPad InStat (GraphPad Software) was used for statistical calculations. RESULTS: Patients less than 40 years of age demonstrated a statistically higher prevalence of positive MRI findings of sacroiliitis when compared to patients older than 40 (p = 0.0082). No difference in prevalence was found between genders. Overall prevalence of MRI signal alteration suggestive of sacroiliitis as defined by the Assessment of SpondyloArthritis international Society was 4.8%. Among the six patients with positive findings, two were subsequently diagnosed with spondyloarthritis. CONCLUSION: Hip pain may be a presenting symptom of spondyloarthritis and attention should be paid to the sacroiliac joints during screening examinations, particularly in patients less than 40 years of age.

High-sensitivity x-ray/optical cross-correlator for next generation free-electron lasers.

We design and realize an arrival time diagnostic for ultrashort X-ray pulses achieving unprecedented high sensitivity in the soft X-ray regime via cross-correlation with a ≈1550 nm optical laser. An interferometric detection scheme is combined with a multi-layer sample design to greatly improve the sensitivity of the measurement. We achieve up to 275% of relative signal change when exposed to 1.6 mJ/cm2 of soft X-rays at 530 eV, more than a hundred-fold improvement in sensitivity as compared to previously reported techniques. The resolution of the arrival time measurement is estimated to around 2.8 fs (rms). The demonstrated X-ray arrival time monitor paves the way for sub-10 fs-level timing jitter at high repetition rate X-ray facilities.

Tracking excited-state charge and spin dynamics in iron coordination complexes.

Crucial to many light-driven processes in transition metal complexes is the absorption and dissipation of energy by 3d electrons. But a detailed understanding of such non-equilibrium excited-state dynamics and their interplay with structural changes is challenging: a multitude of excited states and possible transitions result in phenomena too complex to unravel when faced with the indirect sensitivity of optical spectroscopy to spin dynamics and the flux limitations of ultrafast X-ray sources. Such a situation exists for archetypal polypyridyl iron complexes, such as [Fe(2,2'-bipyridine)3](2+), where the excited-state charge and spin dynamics involved in the transition from a low- to a high-spin state (spin crossover) have long been a source of interest and controversy. Here we demonstrate that femtosecond resolution X-ray fluorescence spectroscopy, with its sensitivity to spin state, can elucidate the spin crossover dynamics of [Fe(2,2'-bipyridine)3](2+) on photoinduced metal-to-ligand charge transfer excitation. We are able to track the charge and spin dynamics, and establish the critical role of intermediate spin states in the crossover mechanism. We anticipate that these capabilities will make our method a valuable tool for mapping in unprecedented detail the fundamental electronic excited-state dynamics that underpin many useful light-triggered molecular phenomena involving 3d transition metal complexes.

X-ray diffractive imaging of controlled gas-phase molecules: Toward imaging of dynamics in the molecular frame.

We report experimental results on the diffractive imaging of three-dimensionally aligned 2,5-diiodothiophene molecules. The molecules were aligned by chirped near-infrared laser pulses, and their structure was probed at a photon energy of 9.5 keV (λ ≈ 130 pm) provided by the Linac Coherent Light Source. Diffracted photons were recorded on the Cornell-SLAC pixel array detector, and a two-dimensional diffraction pattern of the equilibrium structure of 2,5-diiodothiophene was recorded. The retrieved distance between the two iodine atoms agrees with the quantum-chemically calculated molecular structure to be within 5%. The experimental approach allows for the imaging of intrinsic molecular dynamics in the molecular frame, albeit this requires more experimental data, which should be readily available at upcoming high-repetition-rate facilities.

100 W high-repetition-rate near-infrared optical parametric chirped pulse amplifier.

New high-repetition-rate x-ray free electron lasers (XFELs) require for their operation highly reliable ultrafast laser systems with high pulse energy, high repetition rate, and high average power. In this Letter, we present high-average-power scaling of near-infrared optical parametric chirped pulse amplification (OPCPA) in potassium titanyl arsenate (KTA) with tunable center wavelengths from 1.5 to 2.0 µm. Using a three-stage amplification scheme and a kW-level InnoSlab Yb:YAG pump amplifier for the final non-collinear KTA stage, we demonstrate an amplified output power of 106.2 W at a center wavelength of 1.75 µm and 100 kHz. Idler absorption introduces a potential upper limit on the average power scaling of center wavelengths <1.70 µm. Future scaling of average power to hundreds of Watts is possible at center wavelengths ≥1.70 µm.

High average power 88 W OPCPA system for high-repetition-rate experiments at the LCLS x-ray free-electron laser.

We present a 100 kHz, sub-20 fs optical parametric chirped-pulse amplifier (OPCPA) system delivering 88.6 W average power at a center wavelength of 800 nm. The seed pulses are derived from the pump laser via white-light continuum generation and are amplified in three non-collinear OPCPA stages. The final two high-power stages are pumped with a 661 W Yb:YAG InnoSlab amplifier. A simple and robust design is used for the OPCPA system to avoid thermal effects and enhance long-term stability, resulting in excellent beam quality and high conversion efficiency. To the best of our knowledge, this is the highest average power OPCPA system reported to date.

Tspan18 is a novel regulator of the Ca2+ channel Orai1 and von Willebrand factor release in endothelial cells.

Ca2+ entry via Orai1 store-operated Ca2+ channels in the plasma membrane is critical to cell function, and Orai1 loss causes severe immunodeficiency and developmental defects. The tetraspanins are a superfamily of transmembrane proteins that interact with specific 'partner proteins' and regulate their trafficking and clustering. The aim of this study was to functionally characterize tetraspanin Tspan18. We show that Tspan18 is expressed by endothelial cells at several-fold higher levels than most other cell types analyzed. Tspan18-knockdown primary human umbilical vein endothelial cells have 55-70% decreased Ca2+ mobilization upon stimulation with the inflammatory mediators thrombin or histamine, similar to Orai1-knockdown. Tspan18 interacts with Orai1, and Orai1 cell surface localization is reduced by 70% in Tspan18-knockdown endothelial cells. Tspan18 overexpression in lymphocyte model cell lines induces 20-fold activation of Ca2+ -responsive nuclear factor of activated T cell (NFAT) signaling, in an Orai1-dependent manner. Tspan18-knockout mice are viable. They lose on average 6-fold more blood in a tail-bleed assay. This is due to Tspan18 deficiency in non-hematopoietic cells, as assessed using chimeric mice. Tspan18-knockout mice have 60% reduced thrombus size in a deep vein thrombosis model, and 50% reduced platelet deposition in the microcirculation following myocardial ischemia-reperfusion injury. Histamine- or thrombin-induced von Willebrand factor release from endothelial cells is reduced by 90% following Tspan18-knockdown, and histamine-induced increase of plasma von Willebrand factor is reduced by 45% in Tspan18-knockout mice. These findings identify Tspan18 as a novel regulator of endothelial cell Orai1/Ca2+ signaling and von Willebrand factor release in response to inflammatory stimuli.

Scattering off molecules far from equilibrium.

Pump-probe gas phase X-ray scattering experiments, enabled by the development of X-ray free electron lasers, have advanced to reveal scattering patterns of molecules far from their equilibrium geometry. While dynamic displacements reflecting the motion of wavepackets can probe deeply into the reaction dynamics, in many systems, the thermal excitation embedded in the molecules upon optical excitation and energy randomization can create systems that encompass structures far from the ground state geometry. For polyatomic molecular systems, large amplitude vibrational motions are associated with anharmonicity and shifts of interatomic distances, making analytical solutions using traditional harmonic approximations inapplicable. More generally, the interatomic distances in a polyatomic molecule are not independent and the traditional equations commonly used to interpret the data may give unphysical results. Here, we introduce a novel method based on molecular dynamic trajectories and illustrate it on two examples of hot, vibrating molecules at thermal equilibrium. When excited at 200 nm, 1,3-cyclohexadiene (CHD) relaxes on a subpicosecond time scale back to the reactant molecule, the dominant pathway, and to various forms of 1,3,5-hexatriene (HT). With internal energies of about 6 eV, the energy thermalizes quickly, leading to structure distributions that deviate significantly from their vibrationless equilibrium. The experimental and theoretical results are in excellent agreement and reveal that a significant contribution to the scattering signal arises from transition state structures near the inversion barrier of CHD. In HT, our analysis clarifies that previous inconsistent structural parameters determined by electron diffraction were artifacts that might have resulted from the use of inapplicable analytical equations.

Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.

Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes.

The Senior Toronto Oncology Panel (STOP) Study: Research Participation for Older Adults With Cancer and Caregivers.

Background: Patient engagement in research may lead to better-designed studies and improved health outcomes. The objectives of this study were to identify the research priorities of older adults with cancer (OAWCs) and their caregivers and examine how to engage these individuals in research teams and what supports are needed. Methods: We conducted 3 public meetings and 7 focus groups to delineate research priorities and the supports needed to facilitate integration of OAWCs and their caregivers on research teams. Results: A total of 33 older adults and 19 caregivers attended a public meeting and 27 older adults and 17 caregivers participated in a focus group. Most of the OAWCs and their caregivers had never participated in research before. Three themes were identified from the focus groups: (1) motivation to be on a team; (2) ability to make meaningful contributions; and (3) logistical considerations to facilitate engagement. Most participants were motivated to be a research team member and be involved in all steps of research if it could benefit them or future patients and caregivers. OAWCs and their caregivers were highly motivated to improve outcomes. Required logistics included flexibility regarding time and location, accessibility to computer technology, transportation support, materials worded in lay language, and attending/having short training sessions, as well as the presence of peer support. Conclusions: OAWCs and their caregivers are very motivated and willing to participate in research and to be research team members. Logistics and the social aspects of being on a team are important.

Transcriptional regulation of importin-α1 by JunD modulates subcellular localization of RNA-binding protein HuR in intestinal epithelial cells.

The RNA-binding protein HuR is crucial for normal intestinal mucosal regeneration by modulating the stability and translation of target mRNAs, but the exact mechanism underlying HuR trafficking between the cytoplasm and nucleus remains largely unknown. Here we report a novel function of transcription factor JunD in the regulation of HuR subcellular localization through the control of importin-α1 expression in intestinal epithelial cells (IECs). Ectopically expressed JunD specifically inhibited importin-α1 at the transcription level, and this repression is mediated via interaction with CREB-binding site that was located at the proximal region of importin-α1 promoter. Reduction in the levels of importin-α1 by JunD increased cytoplasmic levels of HuR, although it failed to alter whole cell HuR levels. Increased levels of endogenous JunD by depleting cellular polyamines also inhibited importin-α1 expression and increased cytoplasmic HuR levels, whereas JunD silencing rescued importin-α1 expression and enhanced HuR nuclear translocation in polyamine-deficient cells. Moreover, importin-α1 silencing protected IECs against apoptosis, which was prevented by HuR silencing. These results indicate that JunD regulates HuR subcellular distribution by downregulating importin-α1, thus contributing to the maintenance of gut epithelium homeostasis.

Long-term recovery from acute cold shock in Caenorhabditis elegans.

BACKGROUND: Animals are exposed to a wide range of environmental stresses that can cause potentially fatal cellular damage. The ability to survive the period of stress as well as to repair any damage incurred is essential for fitness. Exposure to 2 °C for 24 h or longer is rapidly fatal to the nematode Caenorhabditis elegans, but the process of recovery from a shorter, initially non-lethal, cold shock is poorly understood. RESULTS: We report that cold shock of less than 12-hour duration does not initially kill C. elegans, but these worms experience a progression of devastating phenotypes over the next 96 h that correlate with their eventual fate: successful recovery from the cold shock and survival, or failure to recover and death. Cold-shocked worms experience a marked loss of pigmentation, decrease in the size of their intestine and gonads, and disruption to the vulva. Those worms who will successfully recover from the cold shock regain their pigmentation and much of the integrity of their intestine and gonads. Those who will die do so with a distinct phenotype from worms dying during or immediately following cold shock, suggesting independent mechanisms. Worms lacking the G-protein coupled receptor FSHR-1 are resistant to acute death from longer cold shocks, and are more successful in their recovery from shorter sub-lethal cold shocks. CONCLUSIONS: We have defined two distinct phases of death associated with cold shock and described a progression of phenotypes that accompanies the course of recovery from that cold shock. The G-protein coupled receptor FSHR-1 antagonizes these novel processes of damage and recovery.