Refinement and standardization of storage procedures for clonal crops. Global Public Goods Phase 2: Part 1. Project landscape and general status of clonal crop in vitro conservation technologies

Among the collective actions of the World Bank-funded Global Public Goods Phase II Project (GPG2), the following collaborative activity: “Refinement and standardization of storage procedures for clonal crops” was given to the CGIAR’s In Vitro Genebanks, represented by the Clonal Crop Task Force (CCTF) composed of genetic resources research staff from the four centres: Bioversity International, CIAT, CIP and IITA. These hold the in trust collections of Musa, cassava, potato, sweetpotato, yam and Andean root and tuber crops (ARTCs). The overarching aims of this activity were to: (1) review the status of vitro conservation in the context of the GPG2 project with an emphasis on the mandated clonal crops; (2) survey the facilities, storage protocols and practices of CGIAR’s clonal crop genebanks; (3) collate and review this information with a view to developing quality and risk management systems to support the production and validation of multi-crop best practice guidelines. Outputs from this activity are designated as a three part ‘trilogy’: Part I, entitled “Project landscape and general status of clonal crop in vitro conservation technologies” introduces the GPG2 project within the CGIAR landscape and overviews the status of in vitro plant conservation in the wider conservation community of practice. This part describes the role of risk and quality management for the effective maintenance of in vitro genebanks in the context of research and the development and validation of best practices

Refinement and standardization of storage procedures for clonal crops. Global Public Goods Phase 2. Part 2: Status of in vitro conservation technologies for: Andean root and tuber crops, cassava, Musa, potato, sweetpotato and yam

Among the collective actions of the World Bank-funded Global Public Goods Phase II Project (GPG2), the following collaborative activity: “Refinement and standardization of storage procedures for clonal crops” was given to the CGIAR’s In Vitro Genebanks, represented by the Clonal Crop Task Force (CCTF) composed of genetic resources research staff from the four centres: Bioversity International, CIAT, CIP and IITA. These hold the in trust collections of Musa, cassava, potato, sweetpotato, yam and Andean root and tuber crops (ARTCs). The overarching aims of this activity were to: (1) review the status of vitro conservation in the context of the GPG2 project with an emphasis on the mandated clonal crops; (2) survey the facilities, storage protocols and practices of CGIAR’s clonal crop genebanks; (3) collate and review this information with a view to developing quality and risk management systems to support the production and validation of multi-crop best practice guidelines. Outputs from this activity are designated as a three part ‘trilogy’: Part II, “Status of in vitro conservation technologies for Andean root and tuber crops, cassava, Musa, potato, sweetpotato and yam” provides a status update on the mandate clonal crops. As tasked by GPG2, it includes lessons learnt, critical point analyses and the priority research needs of CGIAR’s in vitro genebanks

Refinement and standardization of storage procedures for clonal crops. Global Public Goods Phase 2. Part 3: Multi-crop guidelines for developing in vitro conservation best practices for clonal crops

Among the collective actions of the World Bank-funded Global Public Goods Phase II Project (GPG2), the following collaborative activity: “Refinement and standardization of storage procedures for clonal crops” was given to the CGIAR’s In Vitro Genebanks, represented by the Clonal Crop Task Force (CCTF) composed of genetic resources research staff from the four centres: Bioversity International, CIAT, CIP and IITA. These hold the in trust collections of Musa, cassava, potato, sweetpotato, yam and Andean root and tuber crops (ARTCs). The overarching aims of this activity were to: (1) review the status of vitro conservation in the context of the GPG2 project with an emphasis on the mandated clonal crops; (2) survey the facilities, storage protocols and practices of CGIAR’s clonal crop genebanks; (3) collate and review this information with a view to developing quality and risk management systems to support the production and validation of multi-crop best practice guidelines. Outputs from this activity are designated as a three part ‘trilogy’: Part III, “Multi-crop guidelines for developing in vitro conservation best practices for clonal crops” is a compilation of quality and risk management best practices and guidelines from both plant and other bioresources communities. This collective knowledge provided the foundation for developing the GPG2 multi-crop best practice guidelines. They are compiled in two parts. Section I comprises general operational guidelines for quality and risk management in in vitro plant genebanks. Section II provides generic, multi-crop technical guidelines for the medium-term (slow growth) and long-term (cryopreservation) storage of crop germplasm held in In vitro active genebanks (IVAGs) and In vitro base genebanks (IVBGs) respectively

Physical activity through sustainable transport approaches (PASTA): protocol for a multi-centre, longitudinal study

BACKGROUND: Physical inactivity is one of the leading risk factors for non-communicable diseases, yet many are not sufficiently active. The Physical Activity through Sustainable Transport Approaches (PASTA) study aims to better understand active mobility (walking and cycling for transport solely or in combination with public transport) as an innovative approach to integrate physical activity into individuals' everyday lives. The PASTA study will collect data of multiple cities in a longitudinal cohort design to study correlates of active mobility, its effect on overall physical activity, crash risk and exposure to traffic-related air pollution. METHODS/DESIGN: A set of online questionnaires incorporating gold standard approaches from the physical activity and transport fields have been developed, piloted and are now being deployed in a longitudinal study in seven European cities (Antwerp, Barcelona, London, Oerebro, Rome, Vienna, Zurich). In total, 14000 adults are being recruited (2000 in each city). A first questionnaire collects baseline information; follow-up questionnaires sent every 13 days collect prospective data on travel behaviour, levels of physical activity and traffic safety incidents. Self-reported data will be validated with objective data in subsamples using conventional and novel methods. Accelerometers, GPS and tracking apps record routes and activity. Air pollution and physical activity are measured to study their combined effects on health biomarkers. Exposure-adjusted crash risks will be calculated for active modes, and crash location audits are performed to study the role of the built environment. Ethics committees in all seven cities have given independent approval for the study. DISCUSSION: The PASTA study collects a wealth of subjective and objective data on active mobility and physical activity. This will allow the investigation of numerous correlates of active mobility and physical activity using a data set that advances previous efforts in its richness, geographical coverage and comprehensiveness. Results will inform new health impact assessment models and support efforts to promote and facilitate active mobility in cities

Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum.

Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved

Transport mode choice and body mass index: Cross-sectional and longitudinal evidence from a European-wide study.

BACKGROUND: In the fight against rising overweight and obesity levels, and unhealthy urban environments, the renaissance of active mobility (cycling and walking as a transport mode) is encouraging. Transport mode has been shown to be associated to body mass index (BMI), yet there is limited longitudinal evidence demonstrating causality. We aimed to associate transport mode and BMI cross-sectionally, but also prospectively in the first ever European-wide longitudinal study on transport and health. METHODS: Data were from the PASTA project that recruited adults in seven European cities (Antwerp, Barcelona, London, Oerebro, Rome, Vienna, Zurich) to complete a series of questionnaires on travel behavior, physical activity levels, and BMI. To assess the association between transport mode and BMI as well as change in BMI we performed crude and adjusted linear mixed-effects modeling for cross-sectional (n = 7380) and longitudinal (n = 2316) data, respectively. RESULTS: Cross-sectionally, BMI was 0.027 kg/m2 (95%CI 0.015 to 0.040) higher per additional day of car use per month. Inversely, BMI was -0.010 kg/m2 (95%CI -0.020 to -0.0002) lower per additional day of cycling per month. Changes in BMI were smaller in the longitudinal within-person assessment, however still statistically significant. BMI decreased in occasional (less than once per week) and non-cyclists who increased cycling (-0.303 kg/m2, 95%CI -0.530 to -0.077), while frequent (at least once per week) cyclists who stopped cycling increased their BMI (0.417 kg/m2, 95%CI 0.033 to 0.802). CONCLUSIONS: Our analyses showed that people lower their BMI when starting or increasing cycling, demonstrating the health benefits of active mobility

Day-to-day intrapersonal variability in mobility patterns and association with perceived stress: A cross-sectional study using GPS from 122 individuals in three European cities

Many aspects of our life are related to our mobility patterns and individuals can exhibit strong tendencies towards routine in their daily lives. Intrapersonal day-to-day variability in mobility patterns has been associated with mental health outcomes. The study aims were: (a) calculate intrapersonal day-to-day variability in mobility metrics for three cities; (b) explore interpersonal variability in mobility metrics by sex, season and city, and (c) describe intrapersonal variability in mobility and their association with perceived stress. Data came from the Physical Activity through Sustainable Transport Approaches (PASTA) project, 122 eligible adults wore location measurement devices over 7-consecutive days, on three occasions during 2015 (Antwerp: 41, Barcelona: 41, London: 40). Participants completed the Short Form Perceived Stress Scale (PSS-4). Day-to-day variability in mobility was explored via six mobility metrics using distance of GPS point from home (meters:m), distance travelled between consecutive GPS points (m) and energy expenditure (metabolic equivalents:METs) of each GPS point collected (n = 3,372,919). A Kruskal-Wallis H test determined whether the median daily mobility metrics differed by city, sex and season. Variance in correlation quantified day-to-day intrapersonal variability in mobility. Levene's tests or Kruskal-Wallis tests were applied to assess intrapersonal variability in mobility and perceived stress. There were differences in daily distance travelled, maximum distance from home and METS between individuals by sex, season and, for proportion of time at home also, by city. Intrapersonal variability across all mobility metrics were highly correlated; individuals had daily routines and largely stuck to them. We did not observe any association between stress and mobility. Individuals are habitual in their daily mobility patterns. This is useful for estimating environmental exposures and in fuelling simulation studies

Transport most likely to cause air pollution peak exposures in everyday life: Evidence from over 2000 days of personal monitoring

Background Air quality standards are typically based on long term averages – whereas a person may encounter exposure peaks throughout the day. Exposure peaks may contribute meaningfully to health impacts beyond their contribution to long term averages, and therefore should be considered alongside longer-term exposures. We aim to define and explain peak exposure to black carbon air pollution and look at the relationship between short peak exposures and longer term personal exposure. Methods A peak detection algorithm was applied to pooled data from two independent studies. High-resolution personal black carbon monitoring was performed in 175 healthy adult volunteers for a minimum of two 24-h periods per person. At the same time, we retrieved information on the time-activity pattern. Data covered Belgium, Spain, and the United Kingdom. In total, 2053 monitoring days were included. Results Exposure profiles revealed 2.8 ± 1.6 (avg ± SD) peaks per person per day. The average black carbon concentration during a peak was 4206 ng/m³. On 5.5% of the time participants were exposed to peak concentrations, but this contributed to 21.0% of their total exposure. The short time in transport (8%), was responsible for 32.7% of the peaks. 24.1% of the measurements in transport were categorized as peak exposure; while sleeping this was only 0.9%. When considering transport modes, participants were most likely to encounter peaks while cycling (34.0%). Most peaks were encountered at rush hour, from Monday through Friday, and in the cold season. Gender and age had no impact on the presence of peaks. Daily average black carbon exposure showed only a moderate correlation with peak frequency (r = 0.44). This correlation coefficient increased when considering longer term exposure to r > 0.60 from 10 days onward. Conclusions The occurrence of peaks varied substantially over time, across microenvironments and transport modes. Daily average exposure was moderately correlated with peak frequency. Real-time air pollution alerting systems may use the peak detection algorithm to support citizens in self-management of air pollution health effects

Control of star formation by supersonic turbulence

Understanding the formation of stars in galaxies is central to much of modern astrophysics. For several decades it has been thought that stellar birth is primarily controlled by the interplay between gravity and magnetostatic support, modulated by ambipolar diffusion. Recently, however, both observational and numerical work has begun to suggest that support by supersonic turbulence rather than magnetic fields controls star formation. In this review we outline a new theory of star formation relying on the control by turbulence. We demonstrate that although supersonic turbulence can provide global support, it nevertheless produces density enhancements that allow local collapse. Inefficient, isolated star formation is a hallmark of turbulent support, while efficient, clustered star formation occurs in its absence. The consequences of this theory are then explored for both local star formation and galactic scale star formation. (ABSTRACT ABBREVIATED)Comment: Invited review for "Reviews of Modern Physics", 87 pages including 28 figures, in pres