Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

Abstract Background Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. citri strain Aw12879 (Xcaw12879, Wellington strain) is restricted to Mexican lime. Results To characterize the mechanism for the differences in host range of XccA and Xcaw, the genome of Xcaw12879 that was completed recently was compared with XccA306 genome. Effectors xopAF and avrGf1 are present in Xcaw12879, but were absent in XccA306. AvrGf1 was shown previously for Xcaw to cause hypersensitive response in Duncan grapefruit. Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Broth (NB) medium and XVM2 medium, which induces hrp gene expression. Two hundred ninety two and 281 genes showed differential expression in XVM2 compared to in NB for XccA306 and Xcaw12879, respectively. Twenty-five type 3 secretion system genes were up-regulated in XVM2 for both XccA and Xcaw. Among the 4,370 common genes of Xcaw12879 compared to XccA306, 603 genes in NB and 450 genes in XVM2 conditions were differentially regulated. Xcaw12879 showed higher protease activity than XccA306 whereas Xcaw12879 showed lower pectate lyase activity in comparison to XccA306. Conclusions Comparative genomic analysis of XccA306 and Xcaw12879 identified strain specific genes. Our study indicated that AvrGf1 contributes to the host range limitation of Xcaw12879 whereas XopAF contributes to virulence. Transcriptome analyses of XccA306 and Xcaw12879 presented insights into the expression of the two closely related strains of X. citri subsp. citri. Virulence genes including genes encoding T3SS components and effectors are induced in XVM2 medium. Numerous genes with differential expression in Xcaw12879 and XccA306 were identified. This study provided the foundation to further characterize the mechanisms for virulence and host range of pathotypes of X. citri subsp. citri.

An experimental and theoretical approach to correct for the scattered radiation in an X-ray computer tomography system for industrial applications

The main problem connected to cone beam computed tomography (CT) systems for industrial applications employing 450 kV X-ray tubes is the high amount of scattered radiation which is added to the primary radiation (signal). This stray radiation leads to a significant degradation of the image quality. A better understanding of the scattering and methods to reduce its effects are therefore necessary to improve the image quality. Several studies have been carried out in the medical field at lower energies, whereas studies in industrial CT, especially for energies up to 450 kV, are lacking. Moreover, the studies reported in literature do not consider the scattered radiation generated by the CT system structure and the walls of the X-ray room (environmental scatter). In order to investigate the scattering on CT projections a GEANT4-based Monte Carlo (MC) model was developed. The model, which has been validated against experimental data, has enabled the calculation of the scattering including the environmental scatter, the optimization of an anti-scatter grid suitable for the CT system, and the optimization of the hardware components of the CT system. The investigation of multiple scattering in the CT projections showed that its contribution is 2.3 times the one of primary radiation for certain objects. The results of the environmental scatter showed that it is the major component of the scattering for aluminum box objects of front size 70 x 70 mm2 and that it strongly depends on the thickness of the object and therefore on the projection. For that reason, its correction is one of the key factors for achieving high quality images. The anti-scatter grid optimized by means of the developed MC model was found to reduce the scatter-toprimary ratio in the reconstructed images by 20 %. The object and environmental scatter calculated by means of the simulation were used to improve the scatter correction algorithm which could be patented by Empa. The results showed that the cupping effect in the corrected image is strongly reduced. The developed CT simulation is a powerful tool to optimize the design of the CT system and to evaluate the contribution of the scattered radiation to the image. Besides, it has offered a basis for a new scatter correction approach by which it has been possible to achieve images with the same spatial resolution as state-of-the-art well collimated fan-beam CT with a gain in the reconstruction time of a factor 10. This result has a high economic impact in non-destructive testing and evaluation, and reverse engineering.

Nutritional strategies to control mycotoxin damages in swine

Mycotoxins are contaminants of agricultural products both in the field and during storage and can enter the food chain through contaminated cereals and foods (milk, meat, and eggs) obtained from animals fed mycotoxin contaminated feeds. Mycotoxins are genotoxic carcinogens that cause health and economic problems. Ochratoxin A and fumonisin B1 have been classified by the International Agency for Research on Cancer in 1993, as “possibly carcinogenic to humans” (class 2B). To control mycotoxins induced damages, different strategies have been developed to reduce the growth of mycotoxigenic fungi as well as to decontaminate and/or detoxify mycotoxin contaminated foods and animal feeds. Critical points, target for these strategies, are: prevention of mycotoxin contamination, detoxification of mycotoxins already present in food and feed, inhibition of mycotoxin absorption in the gastrointestinal tract, reduce mycotoxin induced damages when absorption occurs. Decontamination processes, as indicate by FAO, needs the following requisites to reduce toxic and economic impact of mycotoxins: it must destroy, inactivate, or remove mycotoxins; it must not produce or leave toxic and/or carcinogenic/mutagenic residues in the final products or in food products obtained from animals fed decontaminated feed; it must be capable of destroying fungal spores and mycelium in order to avoiding mycotoxin formation under favorable conditions; it should not adversely affect desirable physical and sensory properties of the feedstuff; it has to be technically and economically feasible. One important approach to the prevention of mycotoxicosis in livestock is the addition in the diets of the non-nutritionally adsorbents that bind mycotoxins preventing the absorption in the gastrointestinal tract. Activated carbons, hydrated sodium calcium aluminosilicate (HSCAS), zeolites, bentonites, and certain clays, are the most studied adsorbent and they possess a high affinity for mycotoxins. In recent years, there has been increasing interest on the hypothesis that the absorption in consumed food can be inhibited by microorganisms in the gastrointestinal tract. Numerous investigators showed that some dairy strains of LAB and bifidobacteria were able to bind aflatoxins effectively. There is a strong need for prevention of the mycotoxin-induced damages once the toxin is ingested. Nutritional approaches, such as supplementation of nutrients, food components, or additives with protective effects against mycotoxin toxicity are assuming increasing interest. Since mycotoxins have been known to produce damages by increasing oxidative stress, the protective properties of antioxidant substances have been extensively investigated. Purpose of the present study was to investigate in vitro and in vivo, strategies to counteract mycotoxin threat particularly in swine husbandry. The Ussing chambers technique was applied in the present study that for the first time to investigate in vitro the permeability of OTA and FB1 through rat intestinal mucosa. Results showed that OTA and FB1 were not absorbed from rat small intestine mucosa. Since in vivo absorption of both mycotoxins normally occurs, it is evident that in these experimental conditions Ussing diffusion chambers were not able to assess the intestinal permeability of OTA and FB1. A large number of LAB strains isolated from feces and different gastrointestinal tract regions of pigs and poultry were screened for their ability to remove OTA, FB1, and DON from bacterial medium. Results of this in vitro study showed low efficacy of isolated LAB strains to reduce OTA, FB1, and DON from bacterial medium. An in vivo trial in rats was performed to evaluate the effects of in-feed supplementation of a LAB strain, Pediococcus pentosaceus FBB61, to counteract the toxic effects induced by exposure to OTA contaminated diets. The study allows to conclude that feed supplementation with P. pentosaceus FBB61 ameliorates the oxidative status in liver, and lowers OTA induced oxidative damage in liver and kidney if diet was contaminated by OTA. This P. pentosaceus FBB61 feature joined to its bactericidal activity against Gram positive bacteria and its ability to modulate gut microflora balance in pigs, encourage additional in vivo experiments in order to better understand the potential role of P. pentosaceus FBB61 as probiotic for farm animals and humans. In the present study, in vivo trial on weaned piglets fed FB1 allow to conclude that feeding of 7.32 ppm of FB1 for 6 weeks did not impair growth performance. Deoxynivalenol contamination of feeds was evaluated in an in vivo trial on weaned piglets. The comparison between growth parameters of piglets fed DON contaminated diet and contaminated diet supplemented with the commercial product did not reach the significance level but piglet growth performances were numerically improved when the commercial product was added to DON contaminated diet. Further studies are needed to improve knowledge on mycotoxins intestinal absorption, mechanism for their detoxification in feeds and foods, and nutritional strategies to reduce mycotoxins induced damages in animals and humans. The multifactorial approach acting on each of the various steps could be a promising strategy to counteract mycotoxins damages.

Phenotype and genotype characterization of Monilinia spp. isolates and preformed antifungal compounds in peach peel fruit at different developmental stages

The brown rot fungi belong to a group of fungal pathogens that causes considerable damage to cultivated fruits trees, particularly stone fruits and apples in the temperate regions of the World and during the postharvest with an important economic impact. In particular in Italy, it is important to monitor the Monilinia population to control economic losses associated to the peach and nectarine market. This motivates the research steps presented in this dissertation on Monilinia Italian isolates. The Monilinia species collected from stone fruits have been identified using molecular analysis based on specific primers. The relevant role of M. fructicola was confirmed and, for the first time, it was found also on apple fruits. To avoid the development of resistant strains and implement valid treatment strategies, the understanding of the fruit natural resistance during different developmental stages and the assessment of the Monilinia sensitivity/resistance to fungicides are required. The relationship between the inhibition spots and the phenolic compounds in peach fruit peel was highlighted in this research. Three methods were used to assess isolate resistance/sensitivity, the amended medium, the Spiral Gradient Endpoint Method (SGD) and the Alamar Blue method. The PCR was used to find possible mutation points in the b-tubulin gene that is responsible for fungicide resistance. Interestingly, no mutation points were observed in resistant M. laxa isolates, suggesting that the resistance could be stimulated by environmental factors. This lead to the study of the effect of the temperature on the resistance and the preliminary results of in vitro tests showed that maximum inhibition was observed at 30°C.

Lo spreco alimentare domestico in Italia: stime, cause ed impatti

Non esiste una definizione standard di spreco alimentare, così come non esistono metodologie uniformi per calcolarlo. Gli studi finora realizzati sullo spreco sono carenti, i dati raccolti spesso insufficienti. Il cibo viene sprecato ad ogni stadio della filiera alimentare, dal campo alla tavola. Nei Paesi Membri dell’Unione Europea, le famiglie – secondo dati elaborati da Eurostat- sono le principali responsabili dello spreco. Secondo la FAO, ogni europeo spreca ogni anno 179 chili di alimenti. Last Minute Market, spin off accademico che si occupa di ridurre e recuperare lo spreco, ha stimato che a livello domestico in Italia si sprecano mediamente il 17% dei prodotti ortofrutticoli acquistati, il 15% di pesce, il 28% di pasta e pane, il 29% di uova, il 30% di carne e il 32% di latticini. Da un punto di vista economico, lo sperpero alimentare significa una perdita di 1.693 euro l’anno per famiglia. Per inquadrare lo spreco alimentare domestico in Italia e gettare luce su dati contrastanti emersi da diversi studi finora realizzati, la tesi – dopo aver presentato stime a livello globale, europeo e italiano – si concentra sull’analisi dei dati emersi da un questionario sullo spreco domestico, compilato da 3.087 italiani tra il mese di novembre e quello di dicembre 2012. L’indagine socio-economica è stata realizzata in collaborazione con la Commissione Europea (DG JCR, Istituto per la Tutela della Salute dei Consumatori) e il Karlsruhe Institut für Technologie. Il questionario è stato posto sulla piattaforma online surveymonkey. La tesi ha avuto come obiettivi l’identificazione di dati quantitativi circa “quanto si spreca” , “cosa si spreca”, l’individuazione delle cause sociali, valoriali, comportamentali e di stile di vita, dello spreco alimentare delle famiglie italiane, l’impatto economico dello spreco sul budget domestico e l’elaborazione di profili di consumatori attraverso la cluster analysis.

Life cycle assessment in construction field: A life cycle cost analysis of reinforcement concrete bridge

The present work is included in the context of the assessment of sustainability in the construction field and is aimed at estimating and analyzing life cycle cost of the existing reinforced concrete bridge “Viadotto delle Capre” during its entire life. This was accomplished by a comprehensive data collection and results evaluation. In detail, the economic analysis of the project is performed. The work has investigated possible design alternatives for maintenance/rehabilitation and end-of-life operations, when structural, functional, economic and also environmental requirements have to be fulfilled. In detail, the economic impact of different design options for the given reinforced concrete bridge have been assessed, whereupon the most economically, structurally and environmentally efficient scenario was chosen. The Integrated Life-Cycle Analysis procedure and Environmental Impact Assessment were also discussed in this work. The scope of this thesis is to illustrate that Life Cycle Cost analysis as part of Life Cycle Assessment approach could be effectively used to drive the design and management strategy of new and existing structures. The final objective of this contribution is to show how an economic analysis can influence decision-making in the definition of the most sustainable design alternatives. The designers can monitor the economic impact of different design strategies in order to identify the most appropriate option.

A multi-regional view on aging societies accounting for the existence of non-tradable goods

This thesis assesses the question, whether accounting for non-tradable goods sectors in a calibrated Auerbach-Kotlikoff multi-regional overlapping-generations-model significantly affects this model’s results when simulating the economic impact of demographic change. Non-tradable goods constitute a major part of up to 80 percent of GDP of modern economies. At the same time, multi-regional overlapping-generations-models presented by literature on demographic change so far ignored their existence and counterfactually assumed perfect tradability between model regions. Moreover, this thesis introduces the assumption of an increasing preference share for non-tradable goods of old generations. This fact-based as-sumption is also not part of models in relevant literature. rnThese obvious simplifications of common models vis-à-vis reality notwithstanding, this thesis concludes that differences in results between a model featuring non-tradable goods and a common model with perfect tradability are very small. In other words, the common simplifi-cation of ignoring non-tradable goods is unlikely to lead to significant distortions in model results. rnIn order to ensure that differences in results between the ‘new’ model, featuring both non-tradable and tradable goods, and the common model solely reflect deviations due to the more realistic structure of the ‘new’ model, both models are calibrated to match exactly the same benchmark data and thus do not show deviations in their respective baseline steady states.rnA variation analysis performed in this thesis suggests that differences between the common model and a model with non-tradable goods can theoretically be large, but only if the bench-mark tradable goods sector is assumed to be unrealistically small.rnFinally, this thesis analyzes potential real exchange rate effects of demographic change, which could occur due to regional price differences of non-tradable goods. However, results show that shifts in real exchange rate based on these price differences are negligible.rn

The Next 10 years in the Management of Peripheral Artery Disease: Perspectives from The 'PAD 2009' Conference

OBJECTIVES: To briefly inform on the conclusions from a conference on the next 10 years in the management of peripheral artery disease (PAD). DESIGN OF THE CONFERENCE: International participation, invited presentations and open discussion were based on the following issues: Why is PAD under-recognised? Health economic impact of PAD; funding of PAD research; changes of treatment options? Aspects on clinical trials and regulatory views; and the role of guidelines. RESULTS AND CONCLUSIONS: A relative lack of knowledge about cardiovascular risk and optimal management of PAD patients exists not only among the public, but also in parts of the health-care system. Specialists are required to act for improved information. More specific PAD research is needed for risk management and to apply the best possible evaluation of evidence for treatment strategies. Better strategies for funding are required based on, for example, public/private initiatives. The proportion of endovascular treatments is steadily increasing, more frequently based on observational studies than on randomised controlled trials. The role of guidelines is therefore important to guide the profession in the assessment of most relevant treatment.

Diagnostic accuracy of magnetic resonance imaging: a prospective evaluation of patients with suspected appendicitis (diamond)

To show the effect of standard magnetic resonance imaging (MRI) in patients with suspected appendicitis on negative laparotomy and perforation rate. Moreover, the economic impact on hospital resources was evaluated.

Atypical transmissible spongiform encephalopathies in ruminants: a challenge for disease surveillance and control

Since 1987, when bovine spongiform encephalopathy (BSE) emerged as a novel disease in cattle, enormous efforts were undertaken to monitor and control the disease in ruminants worldwide. The driving force was its high economic impact, which resulted from trade restrictions and the loss of consumer confidence in beef products, the latter because BSE turned out to be a fatal zoonosis, causing variant Creutzfeldt-Jakob disease in human beings. The ban on meat and bone meal in livestock feed and the removal of specified risk materials from the food chain were the main measures to successfully prevent infection in cattle and to protect human beings from BSE exposure. However, although BSE is now under control, previously unknown, so-called atypical transmissible spongiform encephalopathies (TSEs) in cattle and small ruminants have been identified by enhanced disease surveillance. This report briefly reviews and summarizes the current level of knowledge on the spectrum of TSEs in cattle and small ruminants and addresses the question of the extent to which such atypical TSEs have an effect on disease surveillance and control strategies.

Echinococcus metacestodes as laboratory models for the screening of drugs against cestodes and trematodes

Among the cestodes, Echinococcus granulosus, Echinococcus multilocularis and Taenia solium represent the most dangerous parasites. Their larval stages cause the diseases cystic echinococcosis (CE), alveolar echinococcosis (AE) and cysticercosis, respectively, which exhibit considerable medical and veterinary health concerns with a profound economic impact. Others caused by other cestodes, such as species of the genera Mesocestoides and Hymenolepis, are relatively rare in humans. In this review, we will focus on E. granulosus and E. multilocularis metacestode laboratory models and will review the use of these models in the search for novel drugs that could be employed for chemotherapeutic treatment of echinococcosis. Clearly, improved therapeutic drugs are needed for the treatment of AE and CE, and this can only be achieved through the development of medium-to-high throughput screening approaches. The most recent achievements in the in vitro culture and genetic manipulation of E. multilocularis cells and metacestodes, and the accessability of the E. multilocularis genome and EST sequence information, have rendered the E. multilocularis model uniquely suited for studies on drug-efficacy and drug target identification. This could lead to the development of novel compounds for the use in chemotherapy against echinococcosis, and possibly against diseases caused by other cestodes, and potentially also trematodes.

Lawsonia intracellularis proliferative enteropathy in a filly

Proliferative enteropathy (PE) caused by the obligate intracellular bacterium Lawsonia intracellularis is a disease of high economic impact in swine worldwide. In most other species the disease occurs as a sporadic infection. This paper reports a PE caused by L. intracellularis in a 9-month-old Pura Raza Española filly with a history of profuse diarrhoea. Pathological lesions consisted of a severe proliferative enteritis associated with argyrophilic bacteria in the apical cytoplasm of proliferating crypt epithelium. Characteristic PCR products confirmed the presumptive diagnosis of L. intracellularis infection. To our knowledge this is the first report of PE in a horse in Europe caused by L. intracellularis.

Human and embodied energy analysis applied to water source protection and household water treatment interventions used in Mali, West Africa

As water quality interventions are scaled up to meet the Millennium Development Goal of halving the proportion of the population without access to safe drinking water by 2015 there has been much discussion on the merits of household- and source-level interventions. This study furthers the discussion by examining specific interventions through the use of embodied human and material energy. Embodied energy quantifies the total energy required to produce and use an intervention, including all upstream energy transactions. This model uses material quantities and prices to calculate embodied energy using national economic input/output-based models from China, the United States and Mali. Embodied energy is a measure of aggregate environmental impacts of the interventions. Human energy quantifies the caloric expenditure associated with the installation and operation of an intervention is calculated using the physical activity ratios (PARs) and basal metabolic rates (BMRs). Human energy is a measure of aggregate social impacts of an intervention. A total of four household treatment interventions – biosand filtration, chlorination, ceramic filtration and boiling – and four water source-level interventions – an improved well, a rope pump, a hand pump and a solar pump – are evaluated in the context of Mali, West Africa. Source-level interventions slightly out-perform household-level interventions in terms of having less total embodied energy. Human energy, typically assumed to be a negligible portion of total embodied energy, is shown to be significant to all eight interventions, and contributing over half of total embodied energy in four of the interventions. Traditional gender roles in Mali dictate the types of work performed by men and women. When the human energy is disaggregated by gender, it is seen that women perform over 99% of the work associated with seven of the eight interventions. This has profound implications for gender equality in the context of water quality interventions, and may justify investment in interventions that reduce human energy burdens.

Transcatheter aortic valve replacement in Europe: adoption trends and factors influencing device utilization

OBJECTIVES The authors sought to examine the adoption of transcatheter aortic valve replacement (TAVR) in Western Europe and investigate factors that may influence the heterogeneous use of this therapy. BACKGROUND Since its commercialization in 2007, the number of TAVR procedures has grown exponentially. METHODS The adoption of TAVR was investigated in 11 European countries: Germany, France, Italy, United Kingdom, Spain, the Netherlands, Switzerland, Belgium, Portugal, Denmark, and Ireland. Data were collected from 2 sources: 1) lead physicians submitted nation-specific registry data; and 2) an implantation-based TAVR market tracker. Economic indexes such as healthcare expenditure per capita, sources of healthcare funding, and reimbursement strategies were correlated to TAVR use. Furthermore, we assessed the extent to which TAVR has penetrated its potential patient population. RESULTS Between 2007 and 2011, 34,317 patients underwent TAVR. Considerable variation in TAVR use existed across nations. In 2011, the number of TAVR implants per million individuals ranged from 6.1 in Portugal to 88.7 in Germany (33 ± 25). The annual number of TAVR implants performed per center across nations also varied widely (range 10 to 89). The weighted average TAVR penetration rate was low: 17.9%. Significant correlation was found between TAVR use and healthcare spending per capita (r = 0.80; p = 0.005). TAVR-specific reimbursement systems were associated with higher TAVR use than restricted systems (698 ± 232 vs. 213 ± 112 implants/million individuals ≥ 75 years; p = 0.002). CONCLUSIONS The authors' findings indicate that TAVR is underutilized in high and prohibitive surgical risk patients with severe aortic stenosis. National economic indexes and reimbursement strategies are closely linked with TAVR use and help explain the inequitable adoption of this therapy.

Epidemiology of Brucellosis and Q Fever in Linked Human and Animal Populations in Northern Togo

BACKGROUND: Although brucellosis (Brucella spp.) and Q Fever (Coxiella burnetii) are zoonoses of global importance, very little high quality data are available from West Africa. METHODS/PRINCIPAL FINDINGS: A serosurvey was conducted in Togo's main livestock-raising zone in 2011 in 25 randomly selected villages, including 683 people, 596 cattle, 465 sheep and 221 goats. Additionally, 464 transhumant cattle from Burkina Faso were sampled in 2012. The serological analyses performed were the Rose Bengal Test and ELISA for brucellosis and ELISA and the immunofluorescence assay (IFA) for Q Fever Brucellosis did not appear to pose a major human health problem in the study zone, with only 7 seropositive participants. B. abortus was isolated from 3 bovine hygroma samples, and is likely to be the predominant circulating strain. This may explain the observed seropositivity amongst village cattle (9.2%, 95%CI:4.3-18.6%) and transhumant cattle (7.3%, 95%CI:3.5-14.7%), with an absence of seropositive small ruminants. Exposure of livestock and people to C. burnetii was common, potentially influenced by cultural factors. People of Fulani ethnicity had greater livestock contact and a significantly higher seroprevalence than other ethnic groups (Fulani: 45.5%, 95%CI:37.7-53.6%; non-Fulani: 27.1%, 95%CI:20.6-34.7%). Appropriate diagnostic test cut-off values in endemic settings requires further investigation. Both brucellosis and Q Fever appeared to impact on livestock production. Seropositive cows were more likely to have aborted a foetus during the previous year than seronegative cows, when adjusted for age. This odds was 3.8 times higher (95%CI: 1.2-12.1) for brucellosis and 6.7 times higher (95%CI: 1.3-34.8) for Q Fever. CONCLUSIONS: This is the first epidemiological study of zoonoses in Togo in linked human and animal populations, providing much needed data for West Africa. Exposure to Brucella and C. burnetii is common but further research is needed into the clinical and economic impact.