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.

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.

Evolutionary conservation of candidate osmoregulation genes in plant phloem sap-feeding insects.

The high osmotic pressure generated by sugars in plant phloem sap is reduced in phloem-feeding aphids by sugar transformations and facilitated water flux in the gut. The genes mediating these osmoregulatory functions have been identified and validated empirically in the pea aphid Acyrthosiphon pisum: sucrase 1 (SUC1), a sucrase in glycoside hydrolase family 13 (GH13), and aquaporin 1 (AQP1), a member of the Drosophila integral protein (DRIP) family of aquaporins. Here, we describe molecular analysis of GH13 and AQP genes in phloem-feeding representatives of the four phloem-feeding groups: aphids (Myzus persicae), coccids (Planococcus citri), psyllids (Diaphorina citri, Bactericera cockerelli) and whiteflies (Bemisia tabaci MEAM1 and MED). A single candidate GH13-SUC gene and DRIP-AQP gene were identified in the genome/transcriptome of most insects tested by the criteria of sequence motif and gene expression in the gut. Exceptionally, the psyllid Ba. cockerelli transcriptome included a gut-expressed Pyrocoelia rufa integral protein (PRIP)-AQP, but has no DRIP-AQP transcripts, suggesting that PRIP-AQP is recruited for osmoregulatory function in this insect. This study indicates that phylogenetically related SUC and AQP genes may generally mediate osmoregulatory functions in these diverse phloem-feeding insects, and provides candidate genes for empirical validation and development as targets for osmotic disruption of pest species.

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.

Properties of a hybrid zone between highly distinct chromosomal races of the house mouse (Mus musculus domesticus) in Northern Italy, and comparisons with other hybrid zones.

Here we provide the first detailed description of the hybrid zone between the Cremona chromosomal race of house mouse (ICRE; 2n = 22) and the standard all-telocentric race (40ST; 2n = 40), with full karyotypes of 106 individuals from 17 localities along a transect between the 2 races to the west of Lake Garda in Northern Italy. The ICRE race is characterised by 9 pairs of metacentric chromosomes in a homozygous state and we use the metacentric frequency data along the transect to fit tanh metacentric clines. The clines are narrow (5-8 km, standardised width) suggesting low hybrid fitness. However, the lack of occurrence of ICRE × 40ST F(1) hybrids and presence of other hybrid types suggests that the F(1) hybrids initially produced in this hybrid zone were at least partially fertile, despite having 9 meiotic trivalent configurations. We apply the same cline-fitting methodology to 3 previously studied hybrid zones between metacentric races and the 40ST race. Taken together with published clinal data on 4 further metacentric-40ST hybrid zones, we are able to make objective generalisations on the characteristics of such zones in the house mouse. Zones involving 22-chromosome races are narrower, on average, than other metacentric-40ST hybrid zones and do not show a tendency towards the generation of new races as found with zones where the metacentric race has a higher 2n. It appears that metacentric-40ST zones are unlikely to be sites of speciation (even when a 22-chromosome race is involved), although a mosaic structure to the hybrid zone may enhance this possibility. We make a comparison between metacentric-40ST zones and contacts between 2 metacentric races, for a comprehensive perspective of chromosomal hybrid zones in the house mouse.

Natural hybridization between extremely divergent chromosomal races of the common shrew (Sorex araneus, Soricidae, Soricomorpha): hybrid zone in Siberia.

Chromosomal races of the common shrew differ in sets of metacentric chromosomes and on contact may produce hybrids with extraordinarily complex configurations at meiosis I that are associated with reduced fertility. There is an expectation that these may be some of the most extreme tension zones available for study and therefore are of interest as potential sites for reproductive isolation. Here, we analyse one of these zones, between the Novosibirsk race (characterized by metacentrics go, hn, ik, jl, mp and qr) and the Tomsk race (metacentrics gk, hi, jl and mn and acrocentrics o, p, q and r), which form hybrids with a chain-of-nine (CIX) and a chain-of-three (CIII) configuration at meiosis I. At the Novosibirsk-Tomsk hybrid zone, the CIX chromosomes form clines of 8.53 km standardized width on average, whereas the cline for the CIII chromosomes was 52.83 km wide. The difference in these cline widths fits with the difference in meiotic errors expected with the CIX and CIII configuration, and we produce estimates of selection against hybrids with these types of configurations, which we relate to dispersal and age of the hybrid zone. The hybrid zone is located at the isocline at 200 m altitude above sea level; this relationship between the races and altitude is suggested at both coarse and fine scales. This indicates adaptive differences between the races that may in turn have been promoted by the chromosome differences. Thus, the extreme chromosomal divergence between the Novosibirsk and Tomsk may be associated with genic differentiation, but it is still striking that, despite the large chromosomal differences, reproductive isolation between the Novosibirsk and Tomsk races has not occurred.

Natural hybridization between extremely divergent chromosomal races of the common shrew (Sorex araneus, Soricidae, Soricomorpha): hybrid zone in European Russia.

The Moscow and Seliger chromosomal races of the common shrew differ by Robertsonian fusions and possibly whole-arm reciprocal translocations (WARTs) such that their F1 hybrids produce a chain-of-eleven configuration at meiosis I and are expected to suffer substantial infertility. Of numerous hybrid zones that have been described in the common shrew, those between the Moscow and Seliger races involve the greatest chromosomal difference. We collected 211 individuals from this zone to generate a total dataset of 298 individuals from 187 unique global positioning system (GPS) locations within the vicinity of interracial contact. We used a geographic information system (GIS) to map the location of the hybrid zone, which follows a direct route between two lakes, as would be anticipated from tension zone theory. Even within the central area of the hybrid zone, there is a much higher frequency of pure race individuals than hybrid, making this a clear example of a bimodal zone in the sense of Jiggins & Mallet (2000). The zone runs through good habitat for common shrews, but nevertheless it is very narrow (standard cline widths: 3-4 km), as would be anticipated from low hybrid fitness. There is clear potential for an interruption to gene flow and build-up of reproductive isolation. As found in some other hybrid zones, there is a high frequency of novel genetic variants, in this case, new chromosomal rearrangements. Here, we report a de novo Robertsonian fission and a de novo reciprocal translocation, both for the first time in the common shrew. There is an extraordinarily high frequency of de novo mutations recorded in F1 hybrids in the zone and we discuss how chromosomal instability may be associated with such hybrids. The occurrence of a de novo Robertsonian fission is of considerable significance because it provides missing evidence that fissions are the basis of the novel acrocentric forms found and apparently selected for in certain common shrew hybrid zones.

Genetic panmixia and demographic dependence across the North Atlantic in the deep-sea fish, blue hake (Antimora rostrata).

The efficient investment of resources and effort into conservation strategies depends on the accurate identification of management units. At the same time, understanding the processes by which population structure evolves requires an understanding of the conditions under which panmixia may exist. Here, we study a species with an unusual, apparently sex-biased pattern of distribution, and test the hypothesis that distribution processes associated with this pattern (for example, congregating at a single dominant spawning site or periodic mixing during reproduction) could lead to panmixia over a large geographic range. Using 13 microsatellite markers, we compared 393 blue hake (Antimora rostrata) from 11 sample sites across a geographic range of over 3000 km, and found no evidence of population structure. We estimated current effective population size and found it to be large (~15,000) across the sampled area. In addition, we used simulation models to test expectations about demographic correlation among populations and our ability to detect relevant levels of gene flow. All data were consistent with the interpretation of long-range panmixia.

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.

Ecomorphometric variation and sexual dimorphism in the common shrew (Sorex araneus).

We investigated the evolution of the biomechanics of the mandible in island and mainland populations of the common shrew on the west coast of Scotland. We predicted that climatic differences between populations should cause differences in prey composition leading to changes in the mechanical potential (MP) of the mandible. In females, MP was correlated with climate, with greater MP in warmer and drier habitats. In males, MP was significantly greater than in females but there was no relationship between male MP and climate. This led to increased sexual dimorphism in colder and wetter climates. The same pattern was found after a phylogenetic least squares analysis was conducted to account for shared phylogenetic history. We discuss possible reasons for this pattern, including male-male combat and the greater necessity of females to feed as efficiently as possible to meet their extremely high energy requirements during lactation.

Mandible asymmetry and genetic diversity in island populations of the common shrew, Sorex araneus.

Mandibles from 13 island and six mainland populations of common shrews from the west coast of Scotland were subjected to geometric morphometric analysis in order to investigate the relationship between genetic diversity and fluctuating asymmetry. Although population mean shape fluctuating asymmetry (FA) and size FA were significantly inversely correlated with population genetic diversity this result was substantially due to one island. Sanda, the smallest island with by far the lowest genetic diversity, also had the highest FA. When Sanda was removed from the analysis, the relationship was not significant. There was no relationship between genetic diversity and FA at the individual level, whether measured as mean locus heterozygosity or d(2). In general, if genetic variation affects FA at all, the effect is weak and may only be of biological interest in very small populations.

Subcellular localization of cyclic ADP-ribosyl cyclase and cyclic ADP-ribose hydrolase activities in porcine airway smooth muscle.

Recent studies have provided evidence for a role of cyclic ADP-ribose (cADPR) in the regulation of intracellular calcium in smooth muscles of the intestine, blood vessels and airways. We investigated the presence and subcellular localization of ADP-ribosyl cyclase, the enzyme that catalyzes the conversion of beta-NAD(+) to cADPR, and cADPR hydrolase, the enzyme that degrades cADPR to ADPR, in tracheal smooth muscle (TSM). Sucrose density fractionation of TSM crude membranes provided evidence that ADP-ribosyl cyclase and cADPR hydrolase activities were associated with a fraction enriched in 5'-nucleotidase activity, a plasma membrane marker enzyme, but not in a fraction enriched in either sarcoplasmic endoplasmic reticulum calcium ATPase or ryanodine receptor channels, both sarcoplasmic reticulum markers. The ADP-ribosyl cyclase and cADPR hydrolase activities comigrated at a molecular weight of approximately 40 kDa on SDS-PAGE. This comigration was confirmed by gel filtration chromatography. Investigation of kinetics yielded K(m) values of 30.4+/-1.5 and 695. 3+/-171.2 microM and V(max) values of 330.4+/-90 and 102.8+/-17.1 nmol/mg/h for ADP-ribosyl cyclase and cADPR hydrolase, respectively. These results suggest a possible role for cADPR as an endogenous modulator of [Ca(2+)](i) in porcine TSM cells.

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.

A stationary hemispherical SPECT imager for three-dimensional brain imaging.

A completely stationary, hemispherical-coded aperture SPECT imaging system was designed to produce three-dimensional images of the brain. The system consisted of a hemispherical multiple-pinhole coded aperture and 20 small (100 x 100 mm crystal area) digital gamma cameras. Reconstructions and measured performance specifications from two laboratory versions of the imager are presented. The reconstructed field of view of these systems was an ellipsoidal region with semi-diameters of 100 x 100 x 50 mm. The reconstructed spatial resolution for a point source in air at the center of this field was found to be 4.8 mm FWHM and the corresponding system sensitivity was 36 cps/microCi. An analysis using an ideal-observer model indicated that the multiplexed projection data suffered a 21% degradation relative to similar, but nonmultiplexed SPECT data. Therefore, by this measure, the effective sensitivity of the brain imager was 79% of the measured value.

Air activation produced by high-energy medical accelerators.

The activity of 15O and 13N per unit volume of air produced by a 25 and a 45-MeV medical accelerator was determined by direct measurement. The accelerators were operated in such a fashion as to produce maximum activation of the treatment room air. Levels of the order of 1% or less of the maximum permissible concentration in air for 15O and 13N were found immediately after accelerator shutdown. Three different techniques for calibrations of the air detector were investigated.

The dual-ellipse cross vertex path for exact reconstruction of long objects in cone-beam tomography.

We investigate the way data are used in the algorithm proposed by Kudo and Saito for the exact reconstruction of long objects from axially truncated cone-beam projections. Specifically, we show that the algorithm wastes a large part of the data. To overcome the problem, we propose to use a vertex path consisting of two crossing ellipses, for which we devised a new reconstruction algorithm, called the cross algorithm, which does not waste data and is still suitable to exactly handle axial truncation. Results of reconstruction are presented on simulated data and real data from an experimental scanner.

Analytic method based on identification of ellipse parameters for scanner calibration in cone-beam tomography.

This paper is about calibration of cone-beam (CB) scanners for both x-ray computed tomography and single-photon emission computed tomography. Scanner calibration refers here to the estimation of a set of parameters which fully describe the geometry of data acquisition. Such parameters are needed for the tomographic reconstruction step. The discussion is limited to the usual case where the cone vertex and planar detector move along a circular path relative to the object. It is also assumed that the detector does not have spatial distortions. We propose a new method which requires a small set of measurements of a simple calibration object consisting of two spherical objects, that can be considered as 'point' objects. This object traces two ellipses on the detector and from the parametric description of these ellipses, the calibration geometry can be determined analytically using explicit formulae. The method is robust and easy to implement. However, it is not fully general as it is assumed that the detector is parallel to the rotation axis of the scanner. Implementation details are given for an experimental x-ray CB scanner.

Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers.

We give a detailed account of the theoretical analysis and the experimental results of an X-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett.112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i.e., picometers and femtoseconds, using X-ray free-electron lasers.

Is precession electron diffraction kinematical? Part I: "Phase-scrambling" multislice simulations.

Results from multislice simulations are presented which demonstrate that diffracted intensities obtained using precession electron diffraction are less sensitive to the phases of structure factors compared to electron diffraction intensities recorded without precession. Since kinematical diffraction intensities depend only on the moduli of the structure factors, this result supports previous research indicating that the application of precession leads to electron diffraction intensities becoming more kinematical in nature.

Is precession electron diffraction kinematical? Part II A practical method to determine the optimum precession angle.

A series of experiments was undertaken to investigate the kinematical nature of precession electron diffraction data and to gauge the optimum precession angle for a particular system. Kinematically forbidden reflections in silicon were used to show how a large precession angle is needed to minimise multi-beam conditions for specific reflections and so reduce the contribution from dynamical diffraction. Small precession angles were shown to be detrimental to the kinematical nature of some low-order reflections. By varying precession angles, precession electron diffraction data for erbium pyrogermanate were used to investigate the effect of dynamical diffraction on the output from structure solution algorithms. A good correlation was noted between the precession angle at which the rate of change of relative intensities is small and the angle at which the recovered structure factor phases matched the theoretical kinematical structure factor phases.