Helicobacter pylori and gastroduodenal pathology: New threats of the old friend

The human gastric pathogen Helicobacter pylori causes chronic gastritis, peptic ulcer disease, gastric carcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma. It infects over 50% of the worlds' population, however, only a small subset of infected people experience H. pylori-associated illnesses. Associations with disease-specific factors remain enigmatic years after the genome sequences were deciphered. Infection with strains of Helicobacter pylori that carry the cytotoxin-associated antigen A (cagA) gene is associated with gastric carcinoma. Recent studies revealed mechanisms through which the cagA protein triggers oncopathogenic activities. Other candidate genes such as some members of the so-called plasticity region cluster are also implicated to be associated with carcinoma of stomach. Study of the evolution of polymorphisms and sequence variation in H. pylori populations on a global basis has provided a window into the history of human population migration and co-evolution of this pathogen with its host. Possible symbiotic relationships were debated since the discovery of this pathogen. The debate has been further intensified as some studies have posed the possibility that H. pylori infection may be beneficial in some humans. This assumption is based on increased incidence of gastro-oesophageal reflux disease (GERD), Barrett's oesophagus and adenocarcinoma of the oesophagus following H. pylori eradication in some countries. The contribution of comparative genomics to our understanding of the genome organisation and diversity of H. pylori and its pathophysiological importance to human healthcare is exemplified in this review

Zinc transporter 8 and MAP3865c homologous epitopes are recognized at T1D onset in Sardinian children

Our group has recently demonstrated that Mycobacterium avium subspecies paratuberculosis (MAP) infection significantly associates with T1D in Sardinian adult patients. Due to the potential role played by MAP in T1D pathogenesis, it is relevant to better characterize the prevalence of anti-MAP antibodies (Abs) in the Sardinian population, studying newly diagnosed T1D children. Therefore, we investigated the seroreactivity against epitopes derived from the ZnT8 autoantigen involved in children at T1D onset and their homologous sequences of the MAP3865c protein. Moreover, sera from all individuals were tested for the presence of Abs against: the corresponding ZnT8 C-terminal region, the MAP specific protein MptD, the T1D autoantigen GAD65 and the T1D unrelated Acetylcholine Receptor. The novel MAP3865c281–287 epitope emerges here as the major C-terminal epitope recognized. Intriguingly ZnT8186–194 immunodominant peptide was cross-reactive with the homologous sequences MAP3865c133–141, strengthening the hypothesis that MAP could be an environmental trigger of T1D through a molecular mimicry mechanism. All eight epitopes were recognized by circulating Abs in T1D children in comparison to healthy controls, suggesting that these Abs could be biomarkers of T1D. It would be relevant to investigate larger cohorts of children, followed over time, to elucidate whether Ab titers against these MAP/Znt8 epitopes wane after diagnosis

Gene expression profiling of Mycobacterium avium subsp. paratuberculosis in simulated multi-stress conditions and within THP-1 cells reveals a new kind of interactive intramacrophage behaviour

Recent studies have identified in Mycobacterium avium subsp. paratuberculosis (MAP), already known as a pathogen in ruminants, a potential zoonotic agent of some autoimmune diseases in humans. Therefore, considering the possible risk for public health, it is necessary a thorough understanding of MAP's gene expression during infection of human host as well as the identification of its immunogenic and/or virulence factors for the development of appropriate diagnostic and therapeutic tools.In order to characterize MAP's transcriptome during macrophage infection, we analyzed for the first time the whole gene expression of a human derived strain of MAP in simulated intraphagosomal conditions and after intracellular infection of the human macrophage cell line THP-1 by using the DNA-microarray technology. Results showed that MAP shifts its transcriptome to an adaptive metabolism for an anoxic environment and nutrient starvation. It up-regulates several response factors to oxidative stress or intracellular conditions and allows, in terms of transcription, a passive surface peptidoglycan spoliation within the macrophage along with an intensification of the anabolic activity for lipidic membrane structures.These results indicate a possible interactive system between MAP and its host cell based on the internal mimicry unlike other intracellular pathogens, bringing new hypothesis in the virulence and pathogenicity of MAP and its importance in human health

Stochastic gradient approach for energy and supply optimisation in water systems management

Under conditions of water scarcity, energy saving in operation of water pumping plants and the minimisation of water deficit for users and activities are frequently contrasting requirements, which should be considered when optimising large-scale multi-reservoirs and multi-users water supply systems. Undoubtedly, a high uncertainty level in predicted water resources due to hydrologic input variability and water demand behaviour characterizes this problem. The aim of this paper is to provide an efficient decision support system considering emergency water pumping plants activation schedules. The obtained results should allow the water system’s authority to adopt a robust decision policy, minimising the risk of harmful future decisions concerning the water resource management. The model has been here developed to manage this problem, in order to reduce the damages due to shortage of water and the energy-cost requirements of pumping plants. Particularly, in optimisation, we look for optimal rules considering both historical and generated synthetic scenarios of hydrologic inputs to reservoirs. Hence, using synthetic series, we can analyse climate change impacts and optimise the activation rules considering future hydrologic occurrences. A simulation model has been coupled with an optimization module using the stochastic gradient method to get robust pumping activation thresholds. This method allows to solve complex problems, solving efficiently large size real cases due to high number of data and variables. Thresholds values are identified in terms of critical storage levels in supply-reservoirs. Application of the modelling approach has been developed on a real case study in a water-shortage prone area in south-Sardinia (Italy), characterized by Mediterranean climate and high annual variability in hydrological input to reservoirs. By applying the combined simulation procedure, a robust decision strategy in pumping activation was obtained. Developing the stochastic gradient model, a main programming supports has been built by MATLAB efficiently interfaced with CPLEX for optimisation and Excel for inputs and results representation

Genetic affinities within a large global collection of pathogenic <i>Leptospira</i>: implications for strain identification and molecular epidemiology

Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP) for Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method was compared to an in-house multilocus sequence typing (MLST) method based on polymorphisms in three housekeeping genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighbor-joining trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland India and Sri Lanka, implying that such strains share genetic relationships and that leptospiral strains might be frequently circulating between the islands and the mainland

Mycobacterium avium subsp. paratuberculosis as a trigger of type-1 diabetes: destination Sardinia, or beyond?

Type 1 diabetes mellitus (T1DM) is a multifactorial autoimmune disease in which the insulin producing β cell population is destroyed by the infiltrated T lymphocytes. Even though the exact cause of T1DM is yet to be ascertained, varying degree of genetic susceptibility and environmental factors have been linked to the disease progress and outcome. Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate zoonotic pathogen that causes chronic infection of intestines in ruminants, the Johne's disease. MAP that can even survive pasteurization and chlorination has also been implicated to cause similar type of enteritis in humans called Crohn's disease. With the increasing recognition of the link between MAP and Crohn's disease, it has been postulated that MAP is an occult antigen which besides Crohn's could as well be thought to trigger T1DM. Epitope homologies between mycobacterial proteins (Hsp 65) and pancreatic glutamic acid decarboxylase (GAD 65) and infant nutrition studies implicate MAP as one of the triggers for T1DM. PCR and ELISA analyses in diabetic patients from Sardinia suggest that MAP acts as a possible trigger for T1DM. Systematic mechanistic insights are needed to prove this link. Unfortunately, no easy animal model(s) or in-vitro systems are available to decipher the complex immunological network that is triggered in MAP infection leading to T1DM

The close relationship between the Golgi trafficking machinery and protein glycosylation

La glicosilazione è la più comune modifica post-traduzionale delle proteine; media la loro corretta piegatura e stabilità, nonché il loro trasporto attraverso il trasporto secretorio. I cambiamenti nei glicani legati all'N e all'O sono stati associati a molteplici condizioni patologiche tra cui disturbi congeniti della glicosilazione, malattie infiammatorie e cancro. La glicosilazione della glicoproteina al Golgi coinvolge l'azione coordinata di centinaia di glicosiltransferasi e glicosidasi, che vengono mantenute nella posizione corretta attraverso il traffico di vescicole retrograde tra le cisterne di Golgi. In questa recensione, descriviamo il macchinario molecolare coinvolto nel traffico di vescicole e nel tethering presso l'apparato di Golgi e gli effetti delle mutazioni nel contesto della biosintesi dei glicani e delle malattie umane.Glycosylation is the most common post-translational modification of proteins; it mediates their correct folding and stability, as well as their transport through the secretory transport. Changes in N- and O-linked glycans have been associated with multiple pathological conditions including congenital disorders of glycosylation, inflammatory diseases and cancer. Glycoprotein glycosylation at the Golgi involves the coordinated action of hundreds of glycosyltransferases and glycosidases, which are maintained at the correct location through retrograde vesicle trafficking between Golgi cisternae. In this review, we describe the molecular machinery involved in vesicle trafficking and tethering at the Golgi apparatus and the effects of mutations in the context of glycan biosynthesis and human diseases

Stochastic gradient methods for energy saving and a correct management in complex water supply systems

The management optimization of complex multi-source and multi-demand water resource systems under a high uncertainty level has been a subject of interest in the research literature (Labadie, 2004; Cunha &amp; Sousa, 2010; Yuan et al., 2016). In this context, energy saving in operation of water pumping plants and reduction of water deficit for users and activities are frequently conflicting issues. Dealing with these problems, the definition of optimal activation rules for emergency activation of pumping stations are a relevant topic recently treated in Lerma et al. (2015) and Napolitano et al. (2016). In this study we want to define a trade-off between costs and risks considering the minimization of water shortage damages and the pumping operative costs, under different hydrological scenarios occurrences possibilities. Consequently, optimization results should provide the water system Authorities with a robust information about the optimal activation rules considering a large set of generated scenarios of hydrologic inputs to reservoirs. Using synthetic series it is possible to take into account the climate change impacts and balance the rules while also considering future behavior under the risk of the occurrence of shortages and the cost of early warning procedures to avoid water scarcity, mainly related to activation of emergency water transfers. Thereafter, this problem has been faced considering an efficient optimization tool based on the Stochastic Gradient method (SQG), see Ermoliev &amp; Wets (1988) and Gaivoronski (2005). Testing the effectiveness of this proposal, an application of the modelling approach has been developed in a water shortage prone area in South-Sardinia (Italy)