Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration

Background: Helicobacter pylori colonizes the human stomach and is associated with gastritis, peptic ulcer, and gastric cancer. This ubiquitous association between H. pylori and humans is thought to be present since the origin of modern humans. The H. pylori genome encodes for an exceptional number of restriction and modifications (R-M) systems. To evaluate if R-M systems are an adequate tool to determine the geographic distribution of H. pylori strains, we typed 221 strains from Africa, America, Asia, and Europe, and evaluated the expression of different 29 methyltransferases. Results: Independence tests and logistic regression models revealed that ten R-M systems correlate with geographical localization. The distribution pattern of these methyltransferases may have been originated by co-divergence of regional H. pylori after its human host migrated out of Africa. The expression of specific methyltransferases in the H. pylori population may also reflect the genetic and cultural background of its human host. Methyltransferases common to all strains, M. HhaI and M. NaeI, are likely conserved in H. pylori, and may have been present in the bacteria genome since the human diaspora out of Africa. Conclusion: This study indicates that some methyltransferases are useful geomarkers, which allow discrimination of bacterial populations, and that can be added to our tools to investigate human migrations.. - New England Biolabs, Inc. (USA). - We thank Lurdes Monteiro and Sebastian Suerbaum for the H. pylori strains, Patricia Fonseca and Rui Moreira for critical review of the manuscript, and Afonso Cavaco, Antonio Belo and Dinis Pestana for helping on the logistic regression analysis. This work was partially supported by New England Biolabs, Inc. (USA)

Metabolic channeling of phe for lignin biosynthesis in maritime pine

Phenylalanine (Phe) is the main precursor of phenylpropanoids biosynthesis in plants. This vast family of Phe-derived compounds can represent more than 30% of captured photosynthetic carbon, playing essential roles in plants such as cell wall components, defense molecules, pigments and flavors. In addition to its physiological importance, phenylpropanoids and particularly lignin, a component of wood, are targets in plant biotechnology. The arogenate pathway has been proposed as the main pathway for Phe biosynthesis in plants (Maeda et al., 2010). The final step in Phe biosynthesis, catalyzed by the enzyme arogenate dehydratase (ADT), has been considered as a key regulatory point in Phe biosynthesis, due to its key branch position in the pathway, the multiple isoenzymes identified in plants and the existence of a feedback inhibition mechanism by Phe. So far, the regulatory mechanisms underlying ADT genes expression have been poorly characterized, although a strong regulation of the Phe metabolic flux should be expected depending on its alternative use for protein biosynthesis versus phenylpropanoid biosynthesis. This second fate involves a massive carbon flux compared to the first one. Here we report our current research activities in the transcriptional regulation of ADT genes by MYB transcription factors in Pinus pinaster. The conifers channels massive amounts of photosynthetic carbon for phenylpropanoid biosynthesis during wood formation. We have identified the complete ADT gene family in maritime pine (El-Azaz et al., 2016) and a set of ADT isoforms specifically related with the lignification process. The potential control of transcription factors previously reported as key regulators in pine wood formation (Craven-Bartle et al., 2013) will be presented.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Hierarchical statistical techniques are necessary to draw reliable conclusions from analysis of isolated cardiomyocyte studies

Aims It is generally accepted that post-MI heart failure (HF) changes a variety of aspects of sarcoplasmic reticular Ca2+ fluxes but for some aspects there is disagreement over whether there is an increase or decrease. The commonest statistical approach is to treat data collected from each cell as independent, even though they are really clustered with multiple likely similar cells from each heart. In this study, we test whether this statistical assumption of independence can lead the investigator to draw conclusions that would be considered erroneous if the analysis handled clustering with specific statistical techniques (hierarchical tests). Methods and results Ca2+ transients were recorded in cells loaded with Fura-2AM and sparks were recorded in cells loaded with Fluo-4AM. Data were analysed twice, once with the common statistical approach (assumption of independence) and once with hierarchical statistical methodologies designed to allow for any clustering. The statistical tests found that there was significant hierarchical clustering. This caused the common statistical approach to underestimate the standard error and report artificially small P values. For example, this would have led to the erroneous conclusion that time to 50% peak transient amplitude was significantly prolonged in HF. Spark analysis showed clustering, both within each cell and also within each rat, for morphological variables. This means that a three-level hierarchical model is sometimes required for such measures. Standard statistical methodologies, if used instead, erroneously suggest that spark amplitude is significantly greater in HF and spark duration is reduced in HF. Conclusion Ca2+ fluxes in isolated cardiomyocytes show so much clustering that the common statistical approach that assumes independence of each data point will frequently give the false appearance of statistically significant changes. Hierarchical statistical methodologies need a little more effort, but are necessary for reliable conclusions. We present cost-free simple tools for performing these analyses

Video enhancement using adaptive spatio-temporal connective filter and piecewise mapping

This paper presents a novel video enhancement system based on an adaptive spatio-temporal connective (ASTC) noise filter and an adaptive piecewise mapping function (APMF). For ill-exposed videos or those with much noise, we first introduce a novel local image statistic to identify impulse noise pixels, and then incorporate it into the classical bilateral filter to form ASTC, aiming to reduce the mixture of the most two common types of noises - Gaussian and impulse noises in spatial and temporal directions. After noise removal, we enhance the video contrast with APMF based on the statistical information of frame segmentation results. The experiment results demonstrate that, for diverse low-quality videos corrupted by mixed noise, underexposure, overexposure, or any mixture of the above, the proposed system can automatically produce satisfactory results

Nondestructive Evaluation of Fatigue Damage Using Magnetic Measurement Techniques

Fatigue is responsible for most of the mechanically-induced service failures of structural components encountered in industry. Therefore there is a pressing need for the development of nondestructive evaluation (NDE) methods to detect the development of fatigue damage, to monitor its progress and to predict impending failure of components as they come close to the end of their fatigue lives. Magnetic measurements offer promising techniques for these purposes, since the magnetic properties of ferromagnetic materials are sensitive to the microstructural changes caused by fatigue damage [1].</p

Hybrid Meta-heuristics with VNS and Exact Methods: Application to Large Unconditional and Conditional Vertex p-Centre Problems

Large-scale unconditional and conditional vertex p-centre problems are solved using two meta-heuristics. One is based on a three-stage approach whereas the other relies on a guided multi-start principle. Both methods incorporate Variable Neighbourhood Search, exact method, and aggregation techniques. The methods are assessed on the TSP dataset which consist of up to 71,009 demand points with p varying from 5 to 100. To the best of our knowledge, these are the largest instances solved for unconditional and conditional vertex p-centre problems. The two proposed meta-heuristics yield competitive results for both classes of problems

Measurement of the residual stress tensor in a compact tension weld specimen

Neutron diffraction measurements have been performed to determine the full residual stress tensor along the expected crack path in an austenitic stainless steel (Esshete 1250) compact tension weld specimen. A destructive slitting method was then implemented on the same specimen to measure the stress intensity factor profile associated with the residual stress field as a function of crack length. Finally deformations of the cut surfaces were measured to determine a contour map of the residual stresses in the specimen prior to the cut. The distributions of transverse residual stress measured by the three techniques are in close agreement. A peak tensile stress in excess of 600 MPa was found to be associated with an electron beam weld used to attach an extension piece to the test sample, which had been extracted from a pipe manual metal arc butt weld. The neutron diffraction measurements show that exceptionally high residual stress triaxiality is present at crack depths likely to be used for creep crack growth testing and where a peak stress intensity factor of 35 MPa√m was measured (crack depth of 21 mm). The neutron diffraction measurements identified maximum values of shear stress in the order of 50 MPa and showed that the principal stress directions were aligned to within ~20° of the specimen orthogonal axes. Furthermore it was confirmed that measurement of strains by neutron diffraction in just the three specimen orthogonal directions would have been sufficient to provide a reasonably accurate characterisation of the stress state in welded CT specimens

Ethnic Variation in Inflammatory Profile in Tuberculosis

PMCID: PMC3701709This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Riparian ecotones and spatial variation of fish assemblages in Portuguese lowland streams

The first results of a long-term study on the role of riparian ecotones on the population and community dynamics of Iberian stream fish are presented and discussed . Riparian and macrophyte cover, bank slope and depth were among the most important variables affecting fish distribution . In general small fish favoured shallow areas with high macrophyte cover, whereas large fish dominated in deep areas with a high riparian cover . Slight spatial changes in terrestrial prey use were found suggesting a minor role for this resource during autumn . Finally, no significant spatial differences were found for linear growth, although some differences were obtained for the condition facto

The capacity of short-chain fructo-oligosaccharides to stimulate faecal bifidobacteria: a dose-response relationship study in healthy humans

BACKGROUND: Short-chain fructo-oligosaccharides (scFOS) are well-known for their bifidogenicity. In a large study comprising 200 healthy volunteers, we determined the bifidogenic properties of 7 non-digestible carbohydrates administered at a dose of 10 g/d in the diet; we analysed dose-response relationships of the bifidogenic substrates at doses ranging from 2.5 to 10 g/d in comparison with a placebo. The aim of this presentation is to give more details about the dose-response effects of short-chain fructo-oligosaccharides (scFOS). METHODS: Forty healthy volunteers (18 males, 22 females) eating their usual diets were randomly divided into 5 groups of 8 subjects and received scFOS at a dose of 2.5, 5.0, 7.5 and 10 g/d or a placebo for 7 d. Stools were collected before (day (d) 8) and at the end (day (d) 15) of sugar consumption, and tolerance was evaluated using a daily chart. RESULTS (M ± SEM): Bifidobacteria counts increase was higher in scFOS than in placebo group for all doses tested [2.5 g/d (from 9.15 ± 0.59 to 9.39 ± 0.70; P = 0.02); 5 g/d (from 10.21 ± 0.21 to 10.67 ± 0.22; P = 0.03); 7.5 g/d (from 9.28 ± 0.49 to 9.85 ± 0.35;P = 0.01); 10 g/d (from 9.00 ± 0.81 to 10.18 ± 0.60; P = 0.003)]. A significant correlation between the ingested dose of scFOS and faecal bifidobacteria counts was observed at d15 (r(2 )= 0.307, P < 0.001). Total anaerobes increased at the dose of 10 g/d. No significant differences were found for Bacteroides, Lactobacillus, enterobacteria or pH in any group. The frequency of digestive symptoms was not different between scFOS at any of the doses tested and placebo. Bloating was significantly more intense during scFOS ingestion at doses of 2.5 and 5 g/d, but not at doses of 7.5 and 10 g/d. Excess flatus, borborygmi and abdominal pain did not differ from the placebo at any of the doses tested. CONCLUSION: This study showed that scFOS is bifidogenic and well tolerated at doses ranging from 2.5 to 10 g/d, and that there is a dose-response relationship in healthy volunteers