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1.  Smartphone Apps for Measuring Human Health and Climate Change Co-Benefits: A Comparison and Quality Rating of Available Apps 
JMIR mHealth and uHealth  2016;4(4):e135.
Climate change and the burden of noncommunicable diseases are major global challenges. Opportunities exist to investigate health and climate change co-benefits through a shift from motorized to active transport (walking and cycling) and a shift in dietary patterns away from a globalized diet to reduced consumption of meat and energy dense foods. Given the ubiquitous use and proliferation of smartphone apps, an opportunity exists to use this technology to capture individual travel and dietary behavior and the associated impact on the environment and health.
The objective of the study is to identify, describe the features, and rate the quality of existing smartphone apps which capture personal travel and dietary behavior and simultaneously estimate the carbon cost and potential health consequences of these actions.
The Google Play and Apple App Stores were searched between October 19 and November 6, 2015, and a secondary Google search using the apps filter was conducted between August 8 and September 18, 2016. Eligible apps were required to estimate the carbon cost of personal behaviors with the potential to include features to maximize health outcomes. The quality of included apps was assessed by 2 researchers using the Mobile Application Rating Scale (MARS).
Out of 7213 results, 40 apps were identified and rated. Multiple travel-related apps were identified, however no apps solely focused on the carbon impact or health consequences of dietary behavior. None of the rated apps provided sufficient information on the health consequences of travel and dietary behavior. Some apps included features to maximize participant engagement and encourage behavior change towards reduced greenhouse gas emissions. Most apps were rated as acceptable quality as determined by the MARS; 1 was of poor quality and 10 apps were of good quality. Interrater reliability of the 2 evaluators was excellent (ICC=0.94, 95% CI 0.87-0.97).
Existing apps capturing travel and dietary behavior and the associated health and environmental impact are of mixed quality. Most apps do not include all desirable features or provide sufficient health information. Further research is needed to determine the potential of smartphone apps to evoke behavior change resulting in climate change and health co-benefits.
PMCID: PMC5206483  PMID: 27993762
climate change; noncommunicable diseases; smartphone apps; travel; diet; greenhouse gas emissions; carbon footprint; individual; behavior change
2.  A cross-sectional study of the relationship between parents’ and children’s physical activity 
BMC Public Health  2016;16:1129.
Though parents’ physical activity (PA) is thought to be a predictor of children’s PA, findings have been mixed. The purpose of this study was to examine the relationship between pedometer-measured steps/day of parents’ and their children and potential moderators of this relationship. We also assessed the parent–child PA relationship as measured by questionnaires.
Six-hundred and twelve 7–8 year olds and one of their parents wore Steps Count (SC)-T2 pedometers for four consecutive days. Parents reported their PA from the last seven days and their child’s usual PA. Hierarchical linear regressions were used to assess the parent–child PA relationships, controlling for covariates. Gender (parent, child), gender homogeneity, weight status (parent, child), weight status homogeneity, and socioeconomic status (SES) variables (parent education, household income, area-level SES) were tested as potential moderators of this relationship. Partial r’s were used as an estimate of effect size.
Parents’ steps was significantly related to children’s steps (r partial = .24). For every 1,000 step increase in parents’ steps, the children took 260 additional steps. None of the tested interactions were found to moderate this relationship. Using questionnaires, a relatively smaller parent–child PA relationship was found (r partial = .14).
Physically active parents tend to have physically active children. Interventions designed to get children moving more throughout the day could benefit from including a parent component. Future research should explore the mechanisms by which parents influence their children, and other parent attributes and styles as potential moderators.
PMCID: PMC5086053  PMID: 27793153
Children; Parents; Physical activity; Pedometers; Questionnaires
3.  Native phasing of x-ray free-electron laser data for a G protein–coupled receptor 
Science Advances  2016;2(9):e1600292.
Anomalous signal from sulfur atoms present in most proteins was used for de novo phasing of XFEL data and solving a GPCR structure.
Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.
PMCID: PMC5035125  PMID: 27679816
Crystallography; x-ray free electron laser; serial femtosecond crystallography; SAD; sulfur; GPCR; lipidic cubic phase; native phasing; de novo structure; protein
4.  A mixed methods evaluation of televised health promotion advertisements targeted at older adults 
Evaluation and program planning  2009;32(3):278-288.
The purpose of this research was to evaluate television advertisements targeted at 55–70-year olds that promoted physical activity and fruit and vegetable consumption. Awareness of the campaign, perceived credibility of the source, intentions to visit a promoted website, and intentions to perform the healthy behaviors were evaluated using mixed methods research. Results from a population level survey (n = 1600) showed low unprompted and prompted awareness of the campaign and no differences in intentions or behaviors among those who were aware of the campaign. Unprompted recall resulted in a very wide range of responses including the citation of many commercial advertisers. Qualitative themes that emerged from the focus groups included neutral, positive, and negative comments about the advertisements, source credibility, website considerations specific to seniors, and suggestions about appropriate advertising for older adults. This research showed that the increased attention paid to the advertisements was due in a large part to negative reactions to the character used in the advertisements. Another important finding was the government was not considered to be a credible source of health information. Finally, health promoters should be cautious about websites as the primary source of information, particularly for older adults.
PMCID: PMC5017866  PMID: 19493572 CAMSID: cams718
Television advertisements; Older adults; Survey; Focus groups
5.  Key stakeholder perspectives on the development of walkable neighbourhoods 
Health & place  2009;16(1):43-50.
Evidence supports the link between the built environment and physical activity. This study investigated factors that influence the decisions made by key stakeholders as they relate to neighbourhood development. Seventeen stakeholders including public health and municipal employees (n = 9), city councillors (n = 3), and the private sector (e.g., land developers, food retailers) (n = 5), participated in interviews. Private sector participants considered healthy lifestyle choices (e.g., PA) to be related more to individual choice than did other groups. All groups agreed that consumer behaviour is essential to invoking change but did not agree on who is responsible for invoking change. Common barriers included financial costs, car dependency, and social norms. Facilitators included growing awareness of health and environmental issues and increasing buy-in from governing bodies for innovative neighbourhood development. More work is needed that acknowledges the differences between while integrating the diverse perspectives of those responsible for the planning of neighbourhoods that are conducive for physical activity.
PMCID: PMC5003602  PMID: 19733495 CAMSID: cams714
Neighbourhoods; Built environment; Physical activity; Smart Growth; Stakeholders; Interviews
6.  Physical Activity Information Seeking and Advertising Recall 
Health communication  2011;26(3):246-254.
The purposes of this research were to examine the characteristics of those who look for physical activity-related information, where they find it, and to examine what types of physical activity-related advertisements are recalled (i.e., publicly funded or commercial). These purposes were tested using secondary data analyses from two population health surveys. Results from the first survey (N = 1211) showed that gender, age, education, and activity level differences in who is more likely to search for physical activity-related information. Adding the goal of being active into the model made age and activity level no longer significant but gender and education remained significant factors. The Internet was the most often cited source of physical activity information. The second survey (N = 1600) showed that adults 55 years of age or older and participants with the least amount of education were more than twice as likely to name commercial advertisements than were participants aged 18 – 54 years or those with more education. These results help further our understanding of how publicly funded promotional campaigns fare against commercial advertising and also highlight the need to understand physical activity information seeking behaviour on the Internet and its implications for health promotion.
PMCID: PMC5003607  PMID: 21347937 CAMSID: cams717
7.  An intergenerational study of perceptions of changes in active free play among families from rural areas of Western Canada 
BMC Public Health  2016;16:829.
Children’s engagement in active free play has declined across recent generations. Therefore, the purpose of this study was to examine perceptions of intergenerational changes in active free play among families from rural areas. We addressed two research questions: (1) How has active free play changed across three generations? (2) What suggestions do participants have for reviving active free play?
Data were collected via 49 individual interviews with members of 16 families (15 grandparents, 16 parents, and 18 children) residing in rural areas/small towns in the Province of Alberta (Canada). Interview recordings were transcribed verbatim and subjected to thematic analysis guided by an ecological framework of active free play.
Factors that depicted the changing nature of active free play were coded in the themes of less imagination/more technology, safety concerns, surveillance, other children to play with, purposeful physical activity, play spaces/organized activities, and the good parenting ideal. Suggestions for reviving active free play were coded in the themes of enhance facilities to keep kids entertained, provide more opportunities for supervised play, create more community events, and decrease use of technology.
These results reinforce the need to consider multiple levels of social ecology in the study of active free play, and highlight the importance of community-based initiatives to revive active free play in ways that are consistent with contemporary notions of good parenting.
PMCID: PMC4991208  PMID: 27538781
Play; Children; Youth; Rural; Ecological; Community; Qualitative; Physical activity sport
8.  Macromolecular diffractive imaging using imperfect crystals 
Nature  2016;530(7589):202-206.
The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather 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, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —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 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7.
PMCID: PMC4839592  PMID: 26863980
9.  Creating Neighbourhood Groupings Based on Built Environment Features to Facilitate Health Promotion Activities 
Detailed assessments of the built environment often resist data reduction and summarization. This project sought to develop a method of reducing built environment data to an extent that they can be effectively communicated to researchers and community stakeholders. We aim to help in an understanding of how these data can be used to create neighbourhood groupings based on built environment characteristics and how the process of discussing these neighbourhoods with community stakeholders can result in the development of community-informed health promotion interventions.
We used the Irvine Minnesota Inventory (IMI) to assess 296 segments of a semi-rural community in Alberta. Expert raters “created” neighbourhoods by examining the data. Then, a consensus grouping was developed using cluster analysis, and the number of IMI variables to characterize the neighbourhoods was reduced by multiple discriminant function analysis.
The 296 segments were reduced to a consensus set of 10 neighbourhoods, which could be separated from each other by 9 functions constructed from 24 IMI variables. Biplots of these functions were an effective means of summarizing and presenting the results of the community assessment, and stimulated community action.
It is possible to use principled quantitative methods to reduce large amounts of information about the built environment into meaningful summaries. These summaries, or built environment neighbourhoods, were useful in catalyzing action with community stakeholders and led to the development of health-promoting built environment interventions.
PMCID: PMC4945161  PMID: 23618092 CAMSID: cams5805
Built environment; quantitative methods; health promotion; knowledge exchange; obesity reduction
10.  Built Environment and Active Transport to School (BEATS) Study: protocol for a cross-sectional study 
BMJ Open  2016;6(5):e011196.
Active transport to school (ATS) is a convenient way to increase physical activity and undertake an environmentally sustainable travel practice. The Built Environment and Active Transport to School (BEATS) Study examines ATS in adolescents in Dunedin, New Zealand, using ecological models for active transport that account for individual, social, environmental and policy factors. The study objectives are to: (1) understand the reasons behind adolescents and their parents' choice of transport mode to school; (2) examine the interaction between the transport choices, built environment, physical activity and weight status in adolescents; and (3) identify policies that promote or hinder ATS in adolescents.
Methods and analysis
The study will use a mixed-method approach incorporating both quantitative (surveys, anthropometry, accelerometers, Geographic Information System (GIS) analysis, mapping) and qualitative methods (focus groups, interviews) to gather data from students, parents, teachers and school principals. The core data will include accelerometer-measured physical activity, anthropometry, GIS measures of the built environment and the use of maps indicating route to school (students)/work (parents) and perceived safe/unsafe areas along the route. To provide comprehensive data for understanding how to change the infrastructure to support ATS, the study will also examine complementary variables such as individual, family and social factors, including student and parental perceptions of walking and cycling to school, parental perceptions of different modes of transport to school, perceptions of the neighbourhood environment, route to school (students)/work (parents), perceptions of driving, use of information communication technology, reasons for choosing a particular school and student and parental physical activity habits, screen time and weight status. The study has achieved a 100% school recruitment rate (12 secondary schools).
Ethics and dissemination
The study has been approved by the University of Otago Ethics Committee. The results will be actively disseminated through reports and presentations to stakeholders, symposiums and scientific publications.
PMCID: PMC4885465  PMID: 27221127
Active transport; Physical activity; Adolescents; Built environment; Social ecology
11.  X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex 
Scientific Data  2016;3:160021.
Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
PMCID: PMC4828943  PMID: 27070998
Biological physics; G protein-coupled receptors; Nanocrystallography
12.  Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser 
Nature  2014;513(7517):261-265.
Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth’s oxygenic atmosphere1. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed2 technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the ‘dangler’ Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies3,4. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.
PMCID: PMC4821544  PMID: 25043005
13.  Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser 
Nature  2015;523(7562):561-567.
G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the N- and C- domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.
PMCID: PMC4521999  PMID: 26200343
14.  Coherent convergent-beam time-resolved X-ray diffraction 
The use of coherent X-ray lasers for structural biology allows the use of nanometre diameter X-ray beams with large beam divergence. Their application to the structure analysis of protein nanocrystals and single particles raises new challenges and opportunities. We discuss the form of these coherent convergent-beam (CCB) hard X-ray diffraction patterns and their potential use for time-resolved crystallography, normally achieved by Laue (polychromatic) diffraction, for which the monochromatic laser radiation of a free-electron X-ray laser is unsuitable. We discuss the possibility of obtaining single-shot, angle-integrated rocking curves from CCB patterns, and the dependence of the resulting patterns on the focused beam coordinate when the beam diameter is larger or smaller than a nanocrystal, or smaller than one unit cell. We show how structure factor phase information is provided at overlapping interfering orders and how a common phase origin between different shots may be obtained. Their use in refinement of the phase-sensitive intensity between overlapping orders is suggested.
PMCID: PMC4052862  PMID: 24914153
time-resolved diffraction; coherent convergent beam; phase determination; free-electron X-ray laser; coherent nanodiffraction
15.  7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source 
Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution.
PMCID: PMC4052875  PMID: 24914166
two-dimensional protein crystal; X-ray diffraction; X-ray free-electron laser; crystallographic data analysis; bacteriorhodopsin
16.  X-ray lasers and serial crystallography 
IUCrJ  2015;2(Pt 3):305-306.
A summary is given of the achievements and opportunities which resulted from the first use of an X-ray laser for serial crystallography and related methods in 2009.
PMCID: PMC4420538  PMID: 25995837
X-ray lasers; serial crystallography
17.  Structural basis for bifunctional peptide recognition at human δ-Opioid receptor 
Bi-functional μ- and δ- opioid receptor (OR) ligands are potential therapeutic alternatives to alkaloid opiate analgesics with diminished side effects. We solved the structure of human δ-OR bound to the bi-functional δ-OR antagonist and μ-OR agonist tetrapeptide H-Dmt(1)-Tic(2)-Phe(3)-Phe(4)-NH2 (DIPP-NH2) by serial femtosecond crystallography, revealing a cis-peptide bond between H-Dmt(1) and Tic(2). The observed receptor-peptide interactions are critical to understand the pharmacological profiles of opioid peptides, and to develop improved analgesics.
PMCID: PMC4351130  PMID: 25686086
Bi-functional peptide; opioid receptor; G protein-coupled receptor; protein structure; ligand binding; X-ray free electron laser; serial femtosecond crystallography
18.  Serial femtosecond X-ray diffraction of enveloped virus microcrystals 
Structural Dynamics  2015;2(4):041720.
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.
PMCID: PMC4711640  PMID: 26798819
19.  Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction 
Structural Dynamics  2015;2(4):041719.
The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
PMCID: PMC4711642  PMID: 26798818
20.  Serial femtosecond crystallography of soluble proteins in lipidic cubic phase 
IUCrJ  2015;2(Pt 5):545-551.
A new approach of using lipidic cubic phase as a carrier matrix for delivering soluble protein microcrystals for serial crystallography helps to dramatically reduce protein consumption. The structures of two soluble test proteins have been determined by this method using less than 0.1 mg of each protein.
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.
PMCID: PMC4547822  PMID: 26306196
serial femtosecond crystallography; X-ray free-electron laser; lipidic cubic phase; soluble protein
21.  A novel inert crystal delivery medium for serial femtosecond crystallography 
IUCrJ  2015;2(Pt 4):421-430.
Viscous sample delivery that decreases the net protein consumed in serial femtosecond crystallography is described. The agarose stream has a low background, is compatible with membrane proteins and can be used at a wide range of temperatures.
Serial femtosecond crystallography (SFX) has opened a new era in crystallo­graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.
PMCID: PMC4491314  PMID: 26177184
serial femtosecond crystallography; viscous crystal delivery; protein complexes; membrane proteins; femtosecond studies; nanocrystals; coherent X-ray diffractive imaging; free-electron laser
22.  Data collection strategies for time-resolved X-ray free-electron laser diffraction, and 2-color methods 
Structural Dynamics  2015;2(4):041714.
We compare three schemes for time-resolved X-ray diffraction from protein nanocrystals using an X-ray free-electron laser. We find expressions for the errors in structure factor measurement using the Monte Carlo pump-probe method of data analysis with a liquid jet, the fixed sample pump-probe (goniometer) method (both diffract-and-destroy, and below the safe damage dose), and a proposed two-color method. Here, an optical pump pulse arrives between X-ray pulses of slightly different energies which hit the same nanocrystal, using a weak first X-ray pulse which does not damage the sample. (Radiation damage is outrun in the other cases.) This two-color method, in which separated Bragg spots are impressed on the same detector readout, eliminates stochastic fluctuations in crystal size, shape, and orientation and is found to require two orders of magnitude fewer diffraction patterns than the currently used Monte Carlo liquid jet method, for 1% accuracy. Expressions are given for errors in structure factor measurement for the four approaches, and detailed simulations provided for cathepsin B and IC3 crystals. While the error is independent of the number of shots for the dose-limited goniometer method, it falls off inversely as the square root of the number of shots for the two-color and Monte Carlo methods, with a much smaller pre-factor for the two-color mode, when the first shot is below the damage threshold.
PMCID: PMC4711652  PMID: 26798813
23.  Neighbourhood socioeconomic disadvantage and fruit and vegetable consumption: a seven countries comparison 
Low fruit and vegetable consumption is a risk factor for poor health. Studies have shown consumption varies across neighbourhoods, with lower intakes in disadvantaged neighbourhoods. However, findings are inconsistent, suggesting that socio-spatial inequities in diet could be context-specific, highlighting a need for international comparisons across contexts.
This study examined variations in fruit and vegetable consumption among adults from neighbourhoods of varying socioeconomic status (SES) across seven countries (Australia, Canada, Netherlands, New Zealand, Portugal, Scotland, US).
Data from seven existing studies, identified through literature searches and knowledge of co-authors, which collected measures of both neighbourhood-level SES and fruit and vegetable consumption were used. Logistic regression was used to examine associations between neighbourhood-level SES and binary fruit and vegetable consumption separately, adjusting for neighbourhood clustering and age, gender and education. As much as possible, variables were treated in a consistent manner in the analysis for each study to allow the identification of patterns of association within study and to examine differences in the associations across studies.
Adjusted analyses showed evidence of an association between neighbourhood-level SES and fruit consumption in Canada, New Zealand and Scotland, with increased odds of greater fruit intake in higher SES neighbourhoods. In Australia, Canada, New Zealand and Portugal, those residing in higher SES neighbourhoods had increased odds of greater vegetable intake. The other studies showed no evidence of a difference by neighbourhood-level SES.
Acknowledging discrepancies across studies in terms of sampling, measures, and definitions of neighbourhoods, this opportunistic study, which treated data in a consistent manner, suggests that associations between diet and neighbourhood-level socioeconomic status vary across countries. Neighbourhood socioeconomic disadvantage may differentially impact on access to resources in which produce is available in different countries. Neighbourhood environments have the potential to influence behaviour and further research is required to examine the context in which these associations arise.
PMCID: PMC4456793  PMID: 25997451
Diet; Fruit; Vegetables; Socioeconomic Status; Neighbourhood; International
24.  The birth of a new field† 
PMCID: PMC4052853  PMID: 24914144
Louise Johnson; Introduction; X-ray lasers
25.  Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography 
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.
PMCID: PMC4052869  PMID: 24914160
serial crystallography; free-electron laser; three-dimensional diffraction

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