Theoretical insights into bacterial chemotaxis

Research into understanding bacterial chemotactic systems has become a paradigm for Systems Biology. Experimental and theoretical researchers have worked hand-in-hand for over 40 years to understand the intricate behavior driving bacterial species, in particular how such small creatures, usually not more than 5 µm in length, detect and respond to small changes in their extracellular environment. In this review we highlight the importance that theoretical modeling has played in providing new insight and understanding into bacterial chemotaxis. We begin with an overview of the bacterial chemotaxis sensory response, before reviewing the role of theoretical modeling in understanding elements of the system on the single cell scale and features underpinning multiscale extensions to population models. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1168 For further resources related to this article, please visit the WIREs website.

Distributed classification for pocket data mining

Distributed and collaborative data stream mining in a mobile computing environment is referred to as Pocket Data Mining PDM. Large amounts of available data streams to which smart phones can subscribe to or sense, coupled with the increasing computational power of handheld devices motivates the development of PDM as a decision making system. This emerging area of study has shown to be feasible in an earlier study using technological enablers of mobile software agents and stream mining techniques [1]. A typical PDM process would start by having mobile agents roam the network to discover relevant data streams and resources. Then other (mobile) agents encapsulating stream mining techniques visit the relevant nodes in the network in order to build evolving data mining models. Finally, a third type of mobile agents roam the network consulting the mining agents for a final collaborative decision, when required by one or more users. In this paper, we propose the use of distributed Hoeffding trees and Naive Bayes classifers in the PDM framework over vertically partitioned data streams. Mobile policing, health monitoring and stock market analysis are among the possible applications of PDM. An extensive experimental study is reported showing the effectiveness of the collaborative data mining with the two classifers.

Scheduling satellite-based SAR acquisition for sequential assimilation of water level observations into flood modelling

Satellite-based Synthetic Aperture Radar (SAR) has proved useful for obtaining information on flood extent, which, when intersected with a Digital Elevation Model (DEM) of the floodplain, provides water level observations that can be assimilated into a hydrodynamic model to decrease forecast uncertainty. With an increasing number of operational satellites with SAR capability, information on the relationship between satellite first visit and revisit times and forecast performance is required to optimise the operational scheduling of satellite imagery. By using an Ensemble Transform Kalman Filter (ETKF) and a synthetic analysis with the 2D hydrodynamic model LISFLOOD-FP based on a real flooding case affecting an urban area (summer 2007,Tewkesbury, Southwest UK), we evaluate the sensitivity of the forecast performance to visit parameters. We emulate a generic hydrologic-hydrodynamic modelling cascade by imposing a bias and spatiotemporal correlations to the inflow error ensemble into the hydrodynamic domain. First, in agreement with previous research, estimation and correction for this bias leads to a clear improvement in keeping the forecast on track. Second, imagery obtained early in the flood is shown to have a large influence on forecast statistics. Revisit interval is most influential for early observations. The results are promising for the future of remote sensing-based water level observations for real-time flood forecasting in complex scenarios.

A method for under-sampled ecological network data analysis: plant-pollination as case study

In this paper, we develop a method, termed the Interaction Distribution (ID) method, for analysis of quantitative ecological network data. In many cases, quantitative network data sets are under-sampled, i.e. many interactions are poorly sampled or remain unobserved. Hence, the output of statistical analyses may fail to differentiate between patterns that are statistical artefacts and those which are real characteristics of ecological networks. The ID method can support assessment and inference of under-sampled ecological network data. In the current paper, we illustrate and discuss the ID method based on the properties of plant-animal pollination data sets of flower visitation frequencies. However, the ID method may be applied to other types of ecological networks. The method can supplement existing network analyses based on two definitions of the underlying probabilities for each combination of pollinator and plant species: (1), pi,j: the probability for a visit made by the i’th pollinator species to take place on the j’th plant species; (2), qi,j: the probability for a visit received by the j’th plant species to be made by the i’th pollinator. The method applies the Dirichlet distribution to estimate these two probabilities, based on a given empirical data set. The estimated mean values for pi,j and qi,j reflect the relative differences between recorded numbers of visits for different pollinator and plant species, and the estimated uncertainty of pi,j and qi,j decreases with higher numbers of recorded visits.

Chaos of Wolbachia Sequences Inside the Compact Fig Syconia of Ficus benjamina (Ficus: Moraceae)

Figs and fig wasps form a peculiar closed community in which the Ficus tree provides a compact syconium (inflorescence) habitat for the lives of a complex assemblage of Chalcidoid insects. These diverse fig wasp species have intimate ecological relationships within the closed world of the fig syconia. Previous surveys of Wolbachia, maternally inherited endosymbiotic bacteria that infect vast numbers of arthropod hosts, showed that fig wasps have some of the highest known incidences of Wolbachia amongst all insects. We ask whether the evolutionary patterns of Wolbachia sequences in this closed syconium community are different from those in the outside world. In the present study, we sampled all 17 fig wasp species living on Ficus benjamina, covering 4 families, 6 subfamilies, and 8 genera of wasps. We made a thorough survey of Wolbachia infection patterns and studied evolutionary patterns in wsp (Wolbachia Surface Protein) sequences. We find evidence for high infection incidences, frequent recombination between Wolbachia strains, and considerable horizontal transfer, suggesting rapid evolution of Wolbachia sequences within the syconium community. Though the fig wasps have relatively limited contact with outside world, Wolbachia may be introduced to the syconium community via horizontal transmission by fig wasps species that have winged males and visit the syconia earlier.

Developing international business managers through international study visits to China

Globalization is a key factor in the success of business organizations today, impacting many aspects of management performance. Understanding the global business environment has therefore become a key objective in the teaching of international business on Executive MBA programs. Drawing on the theory of experiential learning, this study examines the relationship between program structure and learning activities of an international study visit (ISV) to China and the learning experience for Executive MBA students. The findings indicate that learning experience may be most effective where the structure of an ISV incorporates certain activities that promote experiential and deep-level learning. Educational implications are discussed.

Widespread supplementary feeding in domestic gardens explains the return of reintroduced Red Kites Milvus milvus to an urban area

Reintroductions are used worldwide to mitigate biodiversity loss. One prominent case is a charismatic raptor of conservation concern, the Red Kite Milvus milvus. This species has been reintroduced across the UK over the last 25 years following its near extinction after centuries of persecution. The species was not expected to recolonize urban areas; its historical association with human settlements is attributed to scavenging on human waste and refuse, a resource now greatly reduced on the streets of modern Western cities. However, the species has become a common day-time visitor to a large conurbation centred on the town of Reading, southern England, approximately 20 km from the first English reintroduction site. Given a near-absence of breeding and roost sites, we investigated foraging opportunities and habitat associations that might explain use by Red Kites of this urban area. Surveys of discarded human foods and road-kill suggested that these could support at most 13−29 kites/day. Face-to-face surveys of a cross-section of residents revealed that 4.5% (equivalent to 4349 households) provided supplementary food for kites. Using estimates of per-household resource provision from another study, we calculated that this level is potentially sufficient to provision 142−320 kites, a substantial proportion of the total estimated to visit the conurbation each day (between 140 and 440). Road transects found positive associations between Red Kites and residential areas. We therefore suggest that the decision made by thousands of individuals to provide supplementary food for Red Kites is the primary factor explaining their day-time abundance in this urban area.

A novel combined biomarker including plasma carotenoids, vitamin C, and ferric reducing antioxidant power is more strongly associated with fruit and vegetable intake than the individual components

BACKGROUND: Monitoring of fruit and vegetable (F&V) intake is fraught with difficulties. Available dietary assessment methods are associated with considerable error, and the use of biomarkers offers an attractive alternative. Few studies to date have examined the use of plasma biomarkers to monitor or predict the F&V intake of volunteers consuming a wide range of intakes from both habitual F&V and manipulated diets. OBJECTIVE: This study tested the hypothesis that an integrated biomarker calculated from a combination of plasma vitamin C, cholesterol-adjusted carotenoid concentration and Ferric Reducing Antioxidant Power (FRAP) had more power to predict F&V intake than each individual biomarker. METHODS: Data from a randomized controlled dietary intervention study [FLAVURS (Flavonoids University of Reading Study); n = 154] in which the test groups observed sequential increases of 2.3, 3.2, and 4.2 portions of F&Vs every 6 wk across an 18-wk period were used in this study. RESULTS: An integrated plasma biomarker was devised that included plasma vitamin C, total cholesterol-adjusted carotenoids, and FRAP values, which better correlated with F&V intake (r = 0.47, P < 0.001) than the individual biomarkers (r = 0.33, P < 0.01; r = 0.37, P < 0.001; and r = 0.14, respectively; P = 0.099). Inclusion of urinary potassium concentration did not significantly improve the correlation. The integrated plasma biomarker predicted F&V intake more accurately than did plasma total cholesterol-adjusted carotenoid concentration, with the difference being significant at visit 2 (P < 0.001) and with a tendency to be significant at visit 1 (P = 0.07). CONCLUSION: Either plasma total cholesterol-adjusted carotenoid concentration or the integrated biomarker could be used to distinguish between high- and moderate-F&V consumers. This trial was registered at www.controlled-trials.com as ISRCTN47748735.

Carotenoids but not flavonoids are associated with improvements in spatial working memory in younger adults in a flavonoid-rich v. -poor fruit and vegetable intervention study

Findings from animal studies suggest that components of fruit and vegetables (F&V) may protect against, and even reverse, age-related decline(1,2) in aspects of cognitive functioning such as spatial working memory (SWM). Human subjects in vivo and in vitro studies indicate that anti-inflammatory, anti-oxidant and cell-signalling properties of flavonoids and carotenoids, non-nutrient components of F&V, may underpin this protective effect(3–5). The Flavonoid University of Reading Study (FLAVURS), designed to explore the dose-response relationship between dietary F&V flavonoids and CVD, enabled the investigation of such an association with SWM. FLAVURS is an 18-week parallel three-arm randomised controlled dietary intervention trial with four time points, measured at 6-weekly intervals from baseline. Low F&V consumers at risk of CVD aged 26–70 years were randomly assigned to high flavonoid (HF), low flavonoid (LF) or control group. F&V intake increased by two daily 80 g portions every 6 weeks, with either HF or LF F&V, in addition to each participant's habitual diet, while controls maintained their habitual diet. At each visit, participants completed a cognitive test battery with SWM as the primary outcome. The HF group showed significantly higher levels of urinary flavonoids than LF or controls at 12 weeks (P<0.001) as expected, but surprisingly only higher levels than LF at 18 weeks (P<0.01). The LF group showed higher levels of plasma carotenoids than the other groups at 18 weeks (P<0.001). No group differences were found for SWM overall, however, age-group sub-analyses (26–50 and 51–70 years of age) showed differences from 0 to 18 weeks for younger adults, with LF improving significantly more than the other two groups on SWM (P<0.05). As nutritional absorption is known to decrease with age, separate stepwise regressions were performed on the two age groups irrespective of dietary group, with urinary flavonoids and plasma carotenoids as predictors. For younger adults, improved SWM performance from 0 to 18 weeks was associated with higher carotenoid levels, β=0.28, t(55)=2.10, P<0.05, accounting for 7.5% of the variance, R2=0.075, F(1,54)=4.41, P=0.040. For older adults, no between-group SWM differences were found. Findings suggest that F&V-based flavonoids and carotenoids may provide benefits for cognitive function, and that carotenoids in particular may improve cognitive performance in SWM. Given that these benefits were restricted to younger adults, future work is needed to test the reliability of this finding, as well as determine the mechanisms by which age-dependent differences in F&V responsiveness occur.

Non-bee insects are important contributors to global crop pollination

Wild and managed bees are well documented as effective pollinators of global crops of economic importance. However, the contributions by pollinators other than bees have been little explored despite their potential to contribute to crop production and stability in the face of environmental change. Non-bee pollinators include flies, beetles, moths, butterflies, wasps, ants, birds, and bats, among others. Here we focus on non-bee insects and synthesize 39 field studies from five continents that directly measured the crop pollination services provided by non-bees, honey bees, and other bees to compare the relative contributions of these taxa. Non-bees performed 25–50% of the total number of flower visits. Although non-bees were less effective pollinators than bees per flower visit, they made more visits; thus these two factors compensated for each other, resulting in pollination services rendered by non-bees that were similar to those provided by bees. In the subset of studies that measured fruit set, fruit set increased with non-bee insect visits independently of bee visitation rates, indicating that non-bee insects provide a unique benefit that is not provided by bees. We also show that non-bee insects are not as reliant as bees on the presence of remnant natural or seminatural habitat in the surrounding landscape. These results strongly suggest that non-bee insect pollinators play a significant role in global crop production and respond differently than bees to landscape structure, probably making their crop pollination services more robust to changes in land use. Non-bee insects provide a valuable service and provide potential insurance against bee population declines.

Genetics and hyperlipidaemia

Hannah is a 30 year old single mother with two young children. She is of Chinese descent and moved to the UK six years ago; she has a good level of English. Recently her mother suffered a heart attack, which prompted Hannah’s first visit to the general practitioner (GP). Meanwhile Hannah performed a predictive genetic test independently through an online company, which showed an increased risk of developing cardiovascular disease (CVD); she has the ɛ4 variant of the APOE gene. The company has recommended a daily supplement and dietary changes. Blood tests showed raised blood lipids and her GP referred Hannah to a dietitian for lifestyle management. Hannah is very concerned and anxious about her health.

Apple pollination: demand depends on variety and supply depends on pollinator identity

Insect pollination underpins apple production but the extent to which different pollinator guilds supply this service, particularly across different apple varieties, is unknown. Such information is essential if appropriate orchard management practices are to be targeted and proportional to the potential benefits pollinator species may provide. Here we use a novel combination of pollinator effectiveness assays (floral visit effectiveness), orchard field surveys (flower visitation rate) and pollinator dependence manipulations (pollinator exclusion experiments) to quantify the supply of pollination services provided by four different pollinator guilds to the production of four commercial varieties of apple. We show that not all pollinators are equally effective at pollinating apples, with hoverflies being less effective than solitary bees and bumblebees, and the relative abundance of different pollinator guilds visiting apple flowers of different varieties varies significantly. Based on this, the taxa specific economic benefits to UK apple production have been established. The contribution of insect pollinators to the economic output in all varieties was estimated to be £92.1M across the UK, with contributions varying widely across taxa: solitary bees (£51.4M), honeybees (£21.4M), bumblebees (£18.6M) and hoverflies (£0.7M). This research highlights the differences in the economic benefits of four insect pollinator guilds to four major apple varieties in the UK. This information is essential to underpin appropriate investment in pollination services management and provides a model that can be used in other entomolophilous crops to improve our understanding of crop pollination ecology.

Matrix Metalloproteinase Expression in Teeth with Apical Periodontitis Is Differentially Modulated by the Modality of Root Canal Treatment

Introduction: The objective of this study was to investigate the expression of matrix metalloproteinases (MM Ps) in apical periodontitis and during the periapical healing phase after root canal treatment. Methods: Apical periodontitis was induced in dog teeth, and root canal treatment was performed in a single visit or by using an additional calcium hydroxide root canal dressing. One hundred eighty days after treatment the presence of inflammation was examined, and tissues were stained to detect bacteria. Bacterial status was correlated to the degree of tissue organization, and to further investigate molecules involved in this process, tissues were stained for MMP-1, MMP-2, MMP-8, and MMP-9. Data were analyzed by using one-way analysis of variance followed by Tukey test or Kruskal-Wallis followed by Dunn test. Results: Teeth with apical periodontitis that had root canal therapy performed in a single visit presented an intense inflammatory cell infiltrate. Periapical tissue was extremely disorganized, and this was correlated with the presence of bacteria. Higher MMP expression was evident, similar to teeth with untreated apical periodontitis. In contrast, teeth with apical periodontitis submitted to root canal treatment with calcium hydroxide presented a lower inflammatory cell infiltrate. This group had moderately organized connective tissue, lower prevalence of bacteria, and lower number of MMP-positive cells, similar to healthy teeth submitted to treatment. Conclusions: Teeth treated with calcium hydroxide root canal dressing exhibited a lower percentage of bacterial contamination, a lower MMP expression, and a more organized extracellular matrix, unlike those treated in a single visit. This suggests that calcium hydroxide might be beneficial in tissue repair processes. (J Endod 2010;36:231-237)

Cone-beam computerized tomographic, radiographic, and histologic evaluation of periapical repair in dogs` post-endodontic treatment

Objective. To evaluate the periapical repair after root canal treatment in the teeth of dogs using CT and conventional radiography and to compare these findings with the gold standard microscopic evaluation. Study design. The animals were divided into three groups according to endodontic treatment performed: Group 1, single-visit endodontic treatment in teeth without apical periodontitis; Group 2, single-visit endodontic treatment in teeth with apical periodontitis; and Group 3, endodontic treatment in teeth with apical periodontitis using calcium hydroxide as a root canal dressing. Group 4 consisted of teeth with apical periodontitis not submitted to root canal treatment and Group 5 consisted of healthy teeth without periapical disease. Radiographic, tomographic, and microscopic evaluations were performed by blind examiners. At 180 days experimental time, CT and radiographic measurements of periapical disease were compared with the gold standard microscopic measurement using intraclass correlation coefficient. Intergroup comparisons considering different methods of periapical lesions measurement or different clinical protocols of root canal treatment were performed by Kruskal Wallis test followed by Dunn. Integrity of lamina dura, presence of radiolucent areas, and presence of root resorption were analyzed by Fisher`s exact test. Results. There was discontinuity of the lamina dura and CPD in all teeth from Groups 2, 3, and 4 evaluated by tomography and radiography 45 days after CPD induction. Radiographically, 180 days after root canal treatment, there was no periapical lesion in teeth from Groups 1 and 3, different from groups 2 and 4 (p < .05). The highest reduction in the CPD size was observed on Group 3 (p < .05). According to the tomographic results, there was decrease of the size of the CPD on Group 3 but not on Groups 2 or 4. However, in all groups the periapical lesions presented larger mesio-distal extension if compared with radiography, both 45 days after CPD induction and 180 days after root canal treatment. At 180 days, CT measurements were closely related to microscopic results (ICC = 0.95) differently from radiographic evaluation (ICC = 0.86). Conclusion. CT Scan evaluation of periapical repair following root canal treatment provided similar information than that obtained by microscopic analysis, whereas radiographic evaluation underestimated the size do periapical lesion. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2009; 108:796-805)

Outcome of Root Canal Treatment in Dogs Determined by Periapical Radiography and Cone-Beam Computed Tomography Scans

The purpose of this study was to compare the favorable outcome of root canal treatment determined by periapical radiographs (PRs) and cone beam computed tomography (CBCT) scans. Ninety-six roots of dogs` teeth were used to form four groups (n = 24). In group 1, root canal treatments were performed in healthy teeth. Root canals in groups 2 through 4 were infected until apical periodontitis (AP) was radiographically confirmed. Roots with AP were treated by one-visit therapy in group 2, by two-visit therapy in group 3, and left untreated in group 4. The radiolucent area in the PRs and the volume of CBCT-scanned periapical lesions were measured before and 6 months after the treatment. In groups 1, 2, and 3, a favorable outcome (lesions absent or reduced) was shown in 57 (79%) roots using PRs but only in 25 (35%) roots using CBCT scans (p = 0.0001). Unfavorable outcomes occurred more frequently after one-visit therapy than two-visit therapy when determined by CBCT scans (p = 0.023). (J Endod 2009; 35:723-726)