Louise Johnson; Introduction; X-ray lasers
Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure ‘three-dimensional merging’. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.
serial crystallography; free-electron laser; three-dimensional diffraction
To produce a meta-study by completing a systematic review of qualitative research examining determinants of independent active free play in children.
Following systematic electronic and manual searches and application of inclusion/exclusion criteria, 46 studies were retained and subjected to meta-method, meta-theory, and meta-data analyses, followed by a final meta-synthesis.
Identified determinants of independent active free play were child characteristics (age, competence, and gender), parental restrictions (safety concerns and surveillance), neighborhood and physical environment (fewer children to play with, differences in preferences for play spaces between parents and children, accessibility and proximity, and maintenance), societal changes (reduced sense of community, good parenting ideal, changing roles of parents, privatization of playtime and play spaces), and policy issues (need to give children voice). An ecological model depicting these factors, and the relationships therein, was created.
This comprehensive meta-study helps establish a knowledge base for children’s independent active free play research by synthesizing a previously fragmented set of studies. Parents’ perceived safety concerns are the primary barrier to children’s active free play. These safety concerns are moderated by child-level factors (age, competence, gender) and broader social issues. Interventions should focus on community-level solutions that include children’s perspectives. From a methods perspective, the reviewed studies used a range of data collection techniques, but methodological details were often inadequately reported. The theoretical sophistication of research in this area could be improved. To this end, the synthesis reported in this study provides a framework for guiding future research.
Electronic supplementary material
The online version of this article (doi:10.1186/s12966-015-0165-9) contains supplementary material, which is available to authorized users.
Meta-synthesis; Safety; Parents; Theory
The development of X-ray lasers and their applications in crystallography is described. In the birth of this new field, IUCrJ is ideally positioned to present this research to both specialists in crystallography, and to the wider audience in structural biology.
X-ray lasers; XFELs; crystallography
Microgrants are a mechanism for providing funding to community organizations or groups to support health initiatives. Little research to date has examined the use of microgrants in promoting physical activity (PA), and no studies have explored how microgrants may support PA promotion among adolescents. The purpose of this study was to explore the role of microgrants in enhancing PA opportunities for Canadian adolescents.
Employing a case study approach, nine community organizations from across Canada were selected as cases providing sports and physical activities with the support of microgrant funding. Researchers visited each organization and conducted semi-structured interviews with 40 program participants (12–25 years of age, M = 16.3, SD = 2.6) and 17 adult organizers/instructors (23–57 years of age, M = 37.4, SD = 10.0). Interview transcripts were inductively and deductively coded to identify concepts and create a hierarchy of themes.
Analysis produced themes regarding participants’ perceptions of the Funding, Running Programs and Events, the Impact of Program (for the Organization, Teen Participants, and the Community). Opportunities for PA programming would not have been possible without the microgrant funding. Microgrant funding was valuable in promoting PA for adolescents, and they afforded opportunities for adolescents to engage in new and/or nontraditional activities. In addition to promoting PA, the microgrants had benefits for participants and the community organizations including improved organizational capacity.
Microgrants appear to be an effective mechanism for enhancing community capacity to provide PA opportunities for Canadian adolescents by helping to reduce financial barriers and empowering adolescents to take an active role in identifying and hosting new and creative PA events within their communities.
Microgrants; Case study; Adolescent; Physical activity; Sport; Qualitative
Students training in obesity research, prevention, and management face the challenge of developing expertise in their chosen academic field while at the same time recognizing that obesity is a complex issue that requires a multidisciplinary and multisectoral approach. In appreciation of this challenge, the Canadian Obesity Network (CON) has run an interdisciplinary summer training camp for graduate students, new career researchers, and clinicians for the past 8 years. This paper evaluates the effects of attending this training camp on trainees’ early careers. We use social network analysis to examine the professional connections developed among trainee Canadian obesity researchers who attended this camp over its first 5 years of operation (2006–2010). We examine four relationships (knowing, contacting, and meeting each other, and working together) among previous trainees. We assess the presence and diversity of these relationships among trainees across different years and disciplines and find that interdisciplinary contact and working relationships established at the training camp have been maintained over time. In addition, we evaluate the qualitative data on trainees’ career trajectories and their assessments of the impact that the camp had on their careers. Many trainees report that camp attendance had a positive impact on their career development, particularly in terms of establishing contacts and professional relationships. Both the quantitative and the qualitative results demonstrate the importance of interdisciplinary training and relationships for career development in the health sciences.
social network analysis; training; research collaboration; interdisciplinary
An expectation maximization algorithm is implemented to resolve the indexing ambiguity which arises when merging data from many crystals in protein crystallography, especially in cases where partial reflections are recorded in serial femtosecond crystallography (SFX) at XFELs.
Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these ‘stills’. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in the P63 space group (which supports a merohedral twinning indexing ambiguity), the method is validated.
indexing ambiguity; serial femtosecond crystallography (SFX); XFELs; protein crystallography; expectation maximization algorithm
Femtosecond X-ray crystallography allows structural analysis of a difficult-to-crystallize fusion protein that is a potential component of a candidate HIV-1 subunit vaccine.
CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
X-ray crystallography; femtosecond nanocrystallography; HIV-1; gp41; membrane-proximal region; cholera toxin B subunit; crystallization; free-electron lasers
Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously-renewed source of material for serial femtosecond crystallography. Data collected from sub-10 μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.
X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. Here we used an x-ray free-electron laser (XFEL) with individual 50-fs duration x-ray pulses to minimize radiation damage and obtained a high-resolution room temperature structure of a human serotonin receptor using sub-10 µm microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared to the structure solved by traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.
This article examines the time trends in patterns of school travel mode among Canadian children and youth to inform the Active Transportation (AT) indicator of the 2013 Active Healthy Kids Canada Report Card on Physical Activity for Children and Youth. The AT grade was assigned based on a comprehensive synthesis of the 2000 and 2010 Physical Activity Monitor studies from the Canadian Fitness and Lifestyle Research Institute and the 1992, 1998, 2005, and 2010 General Social Survey from Statistics Canada. The results showed that in 2013, AT was graded a D, because less than half of Canadian children and youth used only active modes of transportation to get to and from school. The proportion of Canadian children and youth who used only inactive modes of transportation for school travel increased significantly from 51% to 62% over the last decade. Children and youth from larger communities and those with lower household income levels were significantly more likely to use AT than those living in smaller communities and those in higher income households, respectively. In conclusion, motorized transport for school travel has increased steadily over the last decade across Canada. Regional and socio-demographic disparities should be considered in efforts to increase the number of children using AT.
motor activity/physiology; schools; transportation/methods; child; adolescent; humans
X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1–4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
X-ray diffraction patterns may be obtained from individual submicron protein nanocrystals using a femtosecond pulse from a free-electron X-ray laser. Many “single-shot” patterns are read out every second from a stream of nanocrystals lying in random orientations. The short pulse terminates before significant atomic (or electronic) motion commences, minimizing radiation damage. Simulated patterns for Photosystem I nanocrystals are used to develop a method for recovering structure factors from tens of thousands of snapshot patterns from nanocrystals varying in size, shape and orientation. We determine the number of shots needed for a required accuracy in structure factor measurement and resolution, and investigate the convergence of our Monte-Carlo integration method.
Bragg diffraction achieved from two-dimensional protein crystals using femtosecond X-ray laser snapshots is presented.
X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
two-dimensional protein crystal; femtosecond crystallography; single layer X-ray diffraction; membrane protein
To assess the proportion of children meeting the new Canadian Sedentary Behaviour Guidelines for the Early Years (zero to four years of age) and to describe parental attitudes toward and barriers to reducing screen time.
Participants included 657 children zero to four years of age from the Kingston, Ontario, area. From May to September 2011, parents completed a questionnaire regarding their child’s screen time and their attitudes toward and barriers to reducing their child’s screen time.
RESULTS AND CONCLUSIONS:
Approximately 32% of children younger than two years of age engaged in no screen time and approximately 46% of children two to four years of age engaged in <1 h per day; thereby, meeting the recommendations of the new guidelines. Most parents believed that their child did not engage in excessive screen time. Physicians and other health professionals should inform parents of these new guidelines and provide strategies to help their children meet targets.
Children; Computers; Infant; Parents; Preschool; Television; Video games
Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
The shape transforms of nanocrystals with incomplete unit cells are studied using computer simulations. Structure-factor phases can be retrieved from the molecular transforms after removing the modulating shape transform terms.
X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the ‘diffract-before-destroy’ mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that depends on crystal shape, i.e. the transform of the crystal shape. This shape-transform dividing-out scheme for solving the phase problem has been tested using simulated examples with cubic crystals. It provides a phasing method which does not require atomic resolution data, chemical modification to the sample, or modelling based on the protein databases. It is common to find multiple structural units (e.g. molecules, in symmetry-related positions) within a single unit cell, therefore incomplete unit cells (e.g. one additional molecule) can be observed at surface layers of crystals. In this work, the effects of such incomplete unit cells on the ‘dividing-out’ phasing algorithm are investigated using 2D crystals within the projection approximation. It is found that the incomplete unit cells do not hinder the recovery of the scattering pattern from a single unit cell (after dividing out the shape transforms from data merged from many nanocrystals of different sizes), assuming that certain unit-cell types are preferred. The results also suggest that the dynamic range of the data is a critical issue to be resolved in order to apply the shape transform method practically.
shape transform; nanocrystallography; X-ray free electron lasers; phasing
The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the “diffraction-before-destruction” approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1–4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
New evidence-based physical activity and sedentary behavior guidelines for Canadians were launched in 2011. As a consequence, service organizations that promote physical activity directly to the public needed to change their promotion materials to reflect the new guidelines. Little is known about the rate at which service organizations adopt and integrate new evidence-based guidelines and determinants of guideline adoption. In this natural observational study, we evaluated the rate of online adoption of the new guidelines among key service organizations that promote physical activity and examined participation in a booster webinar as a supplemental dissemination strategy. One hundred fifty nine service organization websites were coded by one of six raters prior to the release of the new guidelines as well as at 3, 6, and 9 months after the release. Online adoption of the guidelines increased during the coding period with 51 % of organizations posting the guidelines or related information on their websites. Organizations’ engagement in a webinar was associated with their adoption of the guidelines. The release of new Canadian Physical Activity and Sedentary Behaviour Guidelines led to increased guideline adoption on service organizations’ websites. However, adoption was not universal. In order for the uptake of the new guidelines to be successful, further efforts need to be taken to ensure that service organizations present physical activity guidelines on their websites. Comprehensive, active dissemination strategies tailored to address organizational barriers are needed to ensure online guideline adoption.
Dissemination; Physical activity guidelines; Diffusion of innovations; Service organizations; Sedentary Behavior Guidelines
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
(170.7160) Ultrafast technology; (170.7440) X-ray imaging; (140.3450) Laser-induced chemistry; (140.7090) Ultrafast lasers; (170.0170) Medical optics and biotechnology
X-ray free electron laser (X-feL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-feL beam using a sponge phase micro-jet.
X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.