Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder.

One of the brilliant ideas of John Spence when he saw the first diffraction patterns from the Linac Coherent Light Source was that one could solve the crystallographic phase problem by utilising the intensities between Bragg peaks. Because these intensities are due to the Fourier transform of the shape of the crystal, the approach came to be known as "shape-transform phasing." Shape-transform phasing was developed over the next ten years and formed the basis for many other interesting ideas and pursuits. Here we describe the current best implementation of the original idea using a lattice occupancy formalism and show that certain types of crystal defects can also be modelled via this approach, allowing the molecular structure to be recovered from the additional information offered by the inter-Bragg intensities from these crystal defects.

Does preappointment gabapentin affect neurological examination findings? A prospective, randomized and blinded study in healthy cats.

OBJECTIVES: The aim of this study was to evaluate the influence of a preappointment oral dose of gabapentin on the neurological examination of cats. METHODS: A prospective, randomized and blinded clinical trial was conducted in 35 client-owned healthy cats. Cats were scheduled for two appointments and randomly assigned to receive either a placebo or a 100 mg gabapentin capsule prior to the second veterinary visit. A neurological examination was performed during each visit, and the results were compared between groups. Normal/abnormal response rates for each test were based on the number of cats that allowed the test to be performed. RESULTS: Gabapentin was administered to 17 cats. Gait and postural reactions were significantly affected in the gabapentin group. Comparing the gabapentin with the placebo groups, proprioceptive ataxia was identified in 4/17 (23.5%) vs 0/18 cats (P = 0.0288); paw placement deficits were seen in 10/11 (90.9%) vs 1/4 (25%) cats; table tactile placement deficits were identified in 13/17 (76.5%) vs 0/18 cats (P <0.0001); hopping deficits were seen in 5/17 (29.4%) vs 0/16 cats (P = 0.0185); and abnormalities on wheelbarrowing and extensor postural thrust were reported in 5/17 (29.4%) vs 0/18 cats (P = 0.0129). These results had no correlation with age or dose/kg received. No significant difference was noted in the assessment of level and content of consciousness, posture, cranial nerves and spinal nerves. No significant differences were noted in test compliance or examination duration. CONCLUSIONS AND RELEVANCE: Gabapentin significantly altered gait analyses and postural reactions in this group of healthy cats. The administration of gabapentin could lead to false-positive results and, possibly, an incorrect identification of neurological lesions. In contrast, gabapentin did not impair the assessment of cranial nerves and spinal reflexes, which can be assessed in patients receiving the drug.

A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities.

Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The expand-maximize-compress (EMC) algorithm is highly effective at merging single-particle diffraction patterns with missing orientation values, but most implementations exhaustively sample the space of missing parameters and may become computationally prohibitive as the number of degrees of freedom extends beyond orientation angles. This paper describes how the EMC algorithm can be modified to employ Metropolis Monte Carlo sampling rather than grid sampling, which may be favorable for reconstruction problems with more than three missing parameters. Using simulated data, this variant is compared with the standard EMC algorithm.

Evaluation of the effects of gabapentin on the physiologic and echocardiographic variables of healthy cats: a prospective, randomized and blinded study.

OBJECTIVES: The aim of this study was to evaluate, using echocardiography, the effects of oral administration of a single dose of gabapentin on the physiologic variables (heart rate [HR], respiratory rate [RR] and systolic blood pressure [SBP]) and systolic and diastolic cardiac function of healthy cats. METHODS: This was a prospective, randomized and blinded study with 40 healthy cats aged between 6 months and 2 years. The cats' health status was assessed on the first appointment (T1) when they underwent a physical examination, complete blood count, biochemical profile, assessment of physiologic variables and echocardiogram. The echocardiogram was used to measure the left ventricle's (LV) internal diameter during systole and diastole, isovolumic relaxation time, transmitral flow, E-wave deceleration time and HR. The cats were randomly divided into two groups: (1) a treatment group with 20 cats that received a single oral dose of gabapentin (100 mg/cat); and (2) a control group with 20 cats that received a single oral dose of placebo. All variables of the physiologic and echocardiographic variables were re-evaluated 1-3 weeks after T1 (T2), 90 mins after medication or placebo administration. RESULTS: There was no difference in the physiologic variables evaluated in both groups. The proportion of cats in the treatment group that had their ventricular filling waves fused on T1 but did not have them fused on T2 was significantly higher (45%) compared with cats in the control group (15%; P = 0.0384). CONCLUSIONS AND RELEVANCE: There was no difference between the groups in regard to SBP, HR, RR and echocardiographic variables. Gabapentin improved evaluation of diastolic function on echocardiogram because it reduced the fusion of ventricular filling waves during the evaluation of the diastolic function of the LV. Gabapentin did not cause adverse effects on the cardiovascular hemodynamics of young healthy cats.

X-ray diffraction from membrane protein nanocrystals.

Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 µm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.

New light on disordered ensembles: ab initio structure determination of one particle from scattering fluctuations of many copies.

We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.

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

We develop an algorithm capable of imaging a three-dimensional object given a collection of two-dimensional images of that object that are significantly influenced by the curvature of the Ewald sphere. These two-dimensional images cannot be approximated as projections of the object. Such an algorithm is useful in cryo-electron microscopy where larger samples, higher resolution, or lower energy electron beams are desired, all of which contribute to the significance of Ewald curvature.

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

Shape transform phasing of edgy nanocrystals.

Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the molecular densities to be determined from the diffracted intensities directly, without prior information or resolution restrictions. However, the various correlations amongst molecular occupancies/vacancies at the crystal surface result in a subtle yet critical problem in shape transform phasing whereby the sublattices of symmetry-related molecules exhibit a form of partial coherence amongst lattice sites when an average is taken over many crystal patterns. Here an iterative phase retrieval algorithm is developed which is capable of treating this problem; it is demonstrated on simulated data.

Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery.

Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injection molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquid flow conservation. Finally, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.

Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse.

Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.

Simple convergent-nozzle aerosol injector for single-particle diffractive imaging with X-ray free-electron lasers.

A major challenge in high-resolution x-ray free-electron laser-based coherent diffractive imaging is the development of aerosol injectors that can efficiently deliver particles to the peak intensity of the focused X-ray beam. Here, we consider the use of a simple convergent-orifice nozzle for producing tightly focused beams of particles. Through optical imaging we show that 0.5 µm particles can be focused to a full-width at half maximum diameter of 4.2 µm, and we demonstrate the use of such a nozzle for injecting viruses into a micro-focused soft-X-ray FEL beam.

Tomographic femtosecond x-ray diffractive imaging.

A method is proposed for obtaining three simultaneous projections of a target from a single radiation pulse, which also allows the relative orientation of successive targets to be determined. The method has application to femtosecond x-ray diffraction, and does not require solution of the phase problem. We show that the principal axes of a compact charge-density distribution can be obtained from projections of its autocorrelation function, which is directly accessible in diffraction experiments. The results may have more general application to time resolved tomographic pump-probe experiments and time-series imaging.