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.

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.

Single-particle structure determination by correlations of snapshot X-ray diffraction patterns

Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

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.

Femtosecond dark-field imaging with an X-ray free electron laser

The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.

Bedside renal biopsy: ultrasound guidance by the nephrologist

The safety and efficacy of percutaneous biopsy of native kidneys performed entirely by nephrologists at the patient's bedside was evaluated in 101 consecutive patients. The location and depth of the kidney were determined with a portable ultrasound machine, and biopsy was performed with a 15G, automatic, spring-loaded biopsy device without direct ultrasonographic guidance. Renal tissue was obtained in 99 patients, and all samples were adequate for diagnosis, with an average of 33 glomeruli and more than 10 glomeruli in 97%. The number of biopsy attempts was four or fewer in 80% of patients. Three patients developed symptomatic bleeding, all of whom had a risk factor for bleeding, but none required procedures to control the bleeding. Asymptomatic hematuria occurred in two other patients. Overall, the mean decrease in hematocrit was 1.5, with a decrease of 5.0 or greater in six patients. The results are similar to those of previous studies using automatic devices but under direct ultrasound guidance. A subset of 20 patients with abnormal platelet counts, coagulation times, or bleeding times accounted for four of the five patients with complications. We conclude that percutaneous biopsy of native kidneys can be adequately and safely performed in its entirety by nephrologists at the patient's bedside. Furthermore, excellent results can be obtained without direct sonographic guidance. Hemorrhage occurs almost exclusively in those patients with abnormal platelet counts, coagulation times, or bleeding times.

Adenovirus-specific DNA-binding protein inhibits the hydrolysis of DNA by DNase in vitro

The adenovirus-specific DNA-binding protein was isolated from adenovirus type 5-infected KB cells and shown to possess DNase inhibitor activity. The protein decreased the rate of hydrolysis of single-strand DNA proportionately to its concentration in the reaction. Two peaks of activity were obtained upon sedimentation in a glycerol gradient, probably corresponding to the two major adenovirus-specific polypeptides in the preparation (molecular weights, 72,000 and 44,000). The DNase inhibitor activity of the adenovirus DNA-binding protein was distinguishable from that of the cellular DNA-binding protein, which we have described previously (K, Nass and G. D. Frenkel, J. Biol. Chem. 254:3407-3410, 1979), by its pattern of sedimentation and by the effect of temperature on the two activities. For the adenovirus DNA-binding protein, the ratio of DNase inhibitor activity at 43 degrees C to that at 30 degrees C was approximately 14, whereas for the cellular protein this ratio was less than 3. The DNase inhibitor activity with the temperature coefficient of 14 was absent from cells infected with adenovirus type 5 ts125 at 40 degrees C. DNase inhibition is a simple, sensitive, quantitative method for assay of the adenovirus DNA-binding protein.

Adenovirus-induced inhibition of cellular DNase

During the productive infection of KB cells by adenovirus type 5 (Ad5), there is a progressive decrease in the level of cellular DNase activity towards single-stranded DNA, in contrast to DNA polymerase which remains relatively constant throughout the infection. This decrease is prevented by the inhibition of protein synthesis by cycloheximide. The inhibition of DNase activity does not occur after infection by Ad5 ts125, a DNA-negative mutant which fails to induce the adenovirus-specific DNA binding protein. In contrast, infection by Ad5 ts36, a DNA-negative mutant which complements ts125, does result in decreased levels of DNase. A mechanism is discussed in which the DNA binding protein protects viral replicative intermediates from degradation by cellular DNase.