Structure of a bacterial type IV secretion core complex at subnanometre resolution

Type IV secretion (T4S) systems are able to transport DNAs and/or proteins through the membranes of bacteria. They form large multiprotein complexes consisting of 12 proteins termed VirB1-11 and VirD4. VirB7, 9 and 10 assemble into a 1.07 MegaDalton membrane-spanning core complex (CC), around which all other components assemble. This complex is made of two parts, the O-layer inserted in the outer membrane and the I-layer inserted in the inner membrane. While the structure of the O-layer has been solved by X-ray crystallography, there is no detailed structural information on the I-layer. Using high-resolution cryo-electron microscopy and molecular modelling combined with biochemical approaches, we determined the I-layer structure and located its various components in the electron density. Our results provide new structural insights on the CC, from which the essential features of T4S system mechanisms can be derived

On `maximal' poles of zeta functions, roots of b-functions and monodromy Jordan blocks

The main objects of study in this paper are the poles of several local zeta functions: the Igusa, topological and motivic zeta function associated to a polynomial or (germ of) holomorphic function in n variables. We are interested in poles of maximal possible order n. In all known cases (curves, non-degenerate polynomials) there is at most one pole of maximal order n which is then given by the log canonical threshold of the function at the corresponding singular point. For an isolated singular point we prove that if the log canonical threshold yields a pole of order n of the corresponding (local) zeta function, then it induces a root of the Bernstein-Sato polynomial of the given function of multiplicity n (proving one of the cases of the strongest form of a conjecture of Igusa-Denef-Loeser). For an arbitrary singular point we show under the same assumption that the monodromy eigenvalue induced by the pole has a Jordan block of size n on the (perverse) complex of nearby cycles.Comment: 8 pages, to be published in Journal of Topolog

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

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

Nanobodies that block gating of the P2X7 ion channel ameliorate inflammation

International audienceIon channels are desirable therapeutic targets, yet ion channel-directed drugs with high selectivity and few side effects are still needed. Unlike small-molecule inhibitors, antibodies are highly selective for target antigens but mostly fail to antagonize ion channel functions. Nanobodies-small, single-domain antibody fragments-may overcome these problems. P2X7 is a ligand-gated ion channel that, upon sensing adenosine 5′-triphosphate released by damaged cells, initiates a proinflammatory signaling cascade, including release of cytokines, such as interleukin-1b (IL-1b). To further explore its function, we generated and characterized nanobodies against mouse P2X7 that effectively blocked (13A7) or potentiated (14D5) gating of the channel. Systemic injection of nanobody 13A7 in mice blocked P2X7 on T cells and macrophages in vivo and ameliorated experimental glomerulonephritis and allergic contact dermatitis. We also generated nanobody Dano1, which specifically inhibited human P2X7. In endotoxin-treated human blood, Dano1 was 1000 times more potent in preventing IL-1b release than small-molecule P2X7 antagonists currently in clinical development. Our results show that nanobody technology can generate potent, specific therapeu-tics against ion channels, confirm P2X7 as a therapeutic target for inflammatory disorders, and characterize a potent new drug candidate that targets P2X7

Wearable sensors for personal monitoring and estimation of inhaled traffic-related air pollution: evaluation of methods

Physical activity and ventilation rates have an effect on an individual’s dose and may be important to consider in exposure–response relationships; however, these factors are often ignored in environmental epidemiology studies. The aim of this study was to evaluate methods of estimating the inhaled dose of air pollution and understand variability in the absence of a true gold standard metric. Five types of methods were identified: (1) methods using (physical) activity types, (2) methods based on energy expenditure, METs (metabolic equivalents of task), and oxygen consumption, (3) methods based on heart rate or (4) breathing rate, and (5) methods that combine heart and breathing rate. Methods were compared using a real-life data set of 122 adults who wore devices to track movement, black carbon air pollution, and physiological health markers for 3 weeks in three European cities. Different methods for estimating minute ventilation performed well in relative terms with high correlations among different methods, but in absolute terms, ignoring increased ventilation during day-to-day activities could lead to an underestimation of the daily dose by a factor of 0.08–1.78. There is no single best method, and a multitude of methods are currently being used to approximate the dose. The choice of a suitable method for determining the dose in future studies will depend on both the size and the objectives of the study

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

Physical activity and sedentary behaviour in daily life: A comparative analysis of the Global Physical Activity Questionnaire (GPAQ) and the SenseWear armband

Reduction of sedentary time and an increase in physical activity offer potential to improve public health. However, quantifying physical activity behaviour under real world conditions is a major challenge and no standard of good practice is available. Our aim was to compare the results of physical activity and sedentary behaviour obtained with a self-reported instrument (Global Physical Activity Questionnaire (GPAQ)) and a wearable sensor (SenseWear) in a repeated measures study design. Healthy adults (41 in Antwerp, 41 in Barcelona and 40 in London) wore the SenseWear armband for seven consecutive days and completed the GPAQ on the final day. This was repeated three times. We used the Wilcoxon signed rank sum test, Spearman correlation coefficients, mixed effects regression models and Bland-Altman plots to study agreement between both methods. Mixed models were used to assess the effect of personal characteristics on the absolute and relative difference between estimates obtained with the GPAQ and SenseWear. Moderate to vigorous energy expenditure and duration derived from the GPAQ were significantly lower (p0.59). Results for sedentary behaviour did not differ, yet were poorly correlated (r<0.25). The differences between all variables were reproducible across repeated measurements. In addition, we observed a relationship between these differences and BMI, body fat and physical activity domain. Due to the lack of a standardized protocol, results from different studies measuring physical activity and sedentary behaviour are difficult to compare. Therefore, we suggested an easy-to-implement approach for future studies adding the GPAQ to the wearable of choice as a basis for comparisons

Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis

BACKGROUND: Acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at pH2 and obtains energy by the oxidation of sulfur and iron. It is used in the biomining industry for the recovery of metals and is one of the causative agents of acid mine drainage. Effective tools for the study of its genetics and physiology are not in widespread use and, despite considerable effort, an understanding of its unusual physiology remains at a rudimentary level. Nearly complete genome sequences of A. ferrooxidans are available from two public sources and we have exploited this information to reconstruct aspects of its sulfur metabolism. RESULTS: Two candidate mechanisms for sulfate uptake from the environment were detected but both belong to large paralogous families of membrane transporters and their identification remains tentative. Prospective genes, pathways and regulatory mechanisms were identified that are likely to be involved in the assimilation of sulfate into cysteine and in the formation of Fe-S centers. Genes and regulatory networks were also uncovered that may link sulfur assimilation with nitrogen fixation, hydrogen utilization and sulfur reduction. Potential pathways were identified for sulfation of extracellular metabolites that may possibly be involved in cellular attachment to pyrite, sulfur and other solid substrates. CONCLUSIONS: A bioinformatic analysis of the genome sequence of A. ferrooxidans has revealed candidate genes, metabolic process and control mechanisms potentially involved in aspects of sulfur metabolism. Metabolic modeling provides an important preliminary step in understanding the unusual physiology of this extremophile especially given the severe difficulties involved in its genetic manipulation and biochemical analysis