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The thyroid-stimulating hormone receptor (TSHR) has been indicated as a putative domestication gene in chicken. Comparison of WGS identified a variant in residue 558 of the transmembrane domain (TM) of TSHR, where the domestic chicken (GGD) presents an arginine, whereas the red jungle fowl (RJF) shares a conserved glycine with other vertebrates. This variant has been demonstrated to be associated with phenotypes that are important for domestication and related to thyroid regulation, such as less fearful behavior, reduced aggressive behavior and reduced dependence on seasonal reproduction in GGD as compared with RJF. By means of molecular dynamics simulations, we highlighted the structural and dynamic differences of variant Gly558Arg in the TSHR TM domain. Alterations in TM helix flexibility, structure and protein overall motion are described. The so-called 'arginine snorkeling' of residue 568 in GGD is observed and we hypothesize it as the originating force that produces the observed whole-protein perturbation in the helix bundle dynamics, capable of altering the TSHR signal transduction. The results are discussed in the context of their implications for a better understanding of biological mechanisms in chicken under control of the thyroid, such as body metabolism, as well as for their usefulness in biomedical research., (© 2019 Stichting International Foundation for Animal Genetics.)

Peptide marker identification is one of the most important steps in the development of a mass spectrometry (MS) based method for allergen detection, since the robustness and sensitivity of the overall analytical method will strictly depend on the reliability of the proteotypic peptides tracing for each allergen. The European legislation in place issues the mandatory labelling of fourteen allergenic ingredients whenever used in different food formulations. Among these, six allergenic ingredients, namely milk, egg, peanut, soybean, hazelnut and almond, can be prioritized in light of their higher occurrence in food recalls for undeclared presence with serious risk decision. In this work, we described the results of a comprehensive evaluation of the current literature on MS-based allergen detection aiming at collecting all available information about proteins and peptide markers validated in independent studies for the six allergenic ingredients of interest. The main features of the targeted proteins were commented reviewing all details available about known isoforms and sequence homology particularly in plant-derived allergens. Several critical aspects affecting peptide markers reliability were discussed and according to this evaluation a final short-list of candidate markers was compiled likely to be standardized and implemented in MS methods for allergen analysis., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and fast method to measure gene expression. Reproducibility of the analyses is the main limitation of RT-qPCR experiments. Galaxy is an open, web-based, genomic workbench for a reproducible, transparent, and accessible science. Our aim was developing a new Galaxy tool for the analysis of RT-qPCR expression data. Our tool was developed using Galaxy workbench version 19.01 and functions implemented in several R packages. We developed PIPE-T, a new Galaxy tool implementing a workflow, which offers several options for parsing, filtering, normalizing, imputing, and analyzing RT-qPCR data. PIPE-T requires two input files and returns seven output files. We tested the ability of PIPE-T to analyze RT-qPCR data on two example datasets available in the gene expression omnibus repository. In both cases, our tool successfully completed execution returning expected results. PIPE-T can be easily installed from the Galaxy main tool shed or from Docker. Source code, step-by-step instructions, and example files are available on GitHub to assist new users to install, execute, and test PIPE-T. PIPE-T is a new tool suitable for the reproducible, transparent, and accessible analysis of RT-qPCR expression data.

Introduction: This population-based study aims to evaluate the association between maternal pregestational diabetes and risk of acute lymphoblastic leukemia (ALL) in the offspring., Methods: All 241,958 children born in three Northern Italy provinces 1998-2010 were followed from birth until first cancer diagnosis (National Childhood Cancer Register), age 15 years, or 31 December 2017. We computed hazard ratio (HR) and 95% CI of ALL in relation to the presence of maternal diabetes through Cox proportional regression models., Results: We observed 145 cases of ALL, with a higher incidence in children born to women with pregestational diabetes compared to the others (12.4 vs 4.6). Adjusted hazard ratio of ALL was 2.6 (CI, 0.6-10.5) for maternal diabetes., Discussion: We estimated higher risks of ALL in the offspring of women with pregestational diabetes. These results are consistent with previous findings and compatible with a role of prenatal glycaemic environment in childhood cancer aetiology., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

FAD synthase, the last enzyme of the pathway converting riboflavin to FAD, exists in humans in different isoforms, with isoforms 1, 2 and 6 being characterized at the functional and molecular levels. Isoform 2, the cytosolic and most abundant FADS, consists of two domains: a PAPS reductase C-terminus domain (here named FADSy) responsible for FAD synthesis, and an N-terminus molybdopterin-binding resembling domain (MPTb - here named FADHy), whose FAD hydrolytic activity is hidden unless both Co 2+ and chemical mercurial reagents are added to the enzyme. To investigate the hFADS2 hydrolytic function under conditions closer to the physiological context, the hydrolytic activity was further characterized. Co 2+ induced FAD hydrolysis was strongly stimulated in the presence of K + , reaching a Vmax higher than that of FAD synthesis. The pH dependence together with the inhibition of the hydrolysis by NaF and KI allow excluding that the reaction occurs via a NUDIX type catalysis. The K 0.5 for K + or Co 2+ was 7.2 or 0.035 mM, respectively. Other monovalent or divalent cations can partially substitute K + or Co 2+ . Reduced glutathione stimulated whereas NADH inhibited the hydrolytic activity. The latter aspects correlate with an interconnection of the homeostasis of NAD and FAD., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Adverse psychosocial experiences have been shown to modulate individual responses to immune challenges and affect mitochondrial functions. The aim of this study was to investigate inflammation and immune responses as well as mitochondrial bioenergetics in an experimental model of Paediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus (PANDAS). Starting in adolescence (postnatal day 28), male SJL/J mice were exposed to five injections (interspaced by two weeks) with Group-A beta-haemolytic streptococcus (GAS) homogenate. Mice were exposed to chronic psychosocial stress, in the form of protracted visual exposure to an aggressive conspecific, for four weeks. Our results indicate that psychosocial stress exacerbated individual response to GAS administrations whereby mice exposed to both treatments exhibited altered cytokine and immune-related enzyme expression in the hippocampus and hypothalamus. Additionally, they showed impaired mitochondrial respiratory chain complexes IV and V, and reduced adenosine triphosphate (ATP) production by mitochondria and ATP content. These brain abnormalities, observed in GAS-Stress mice, were associated with blunted titers of plasma corticosterone. Present data support the hypothesis that challenging environmental conditions, in terms of chronic psychosocial stress, may exacerbate the long-term consequences of exposure to GAS processes through the promotion of central immunomodulatory and oxidative stress., Competing Interests: The authors declare no conflict of interest.

Risk-based approaches to managing allergens in foods are being developed by the food industry and regulatory authorities to support food-allergic consumers to avoid ingestion of their problem food, especially in relation to the traces of unintended allergens. The application of such approaches requires access to good quality data from clinical studies to support identification of levels of allergens in foods that are generally safe for most food-allergic consumers as well as analytical tools that are able to quantify allergenic food protein. The ThRAll project aims to support the application of risk-based approaches to food-allergen management in two ways. First, a harmonized quantitative MS-based prototype reference method will be developed for the detection of multiple food allergens in standardized incurred food matrices. This will be undertaken for cow's milk, hen's egg, peanut, soybean, hazelnut, and almond incurred into two highly processed food matrices, chocolate and broth powder. This activity is complemented by a second objective to support the development and curation of data on oral food challenges, which are used to define thresholds and minimum eliciting doses. This will be achieved through the development of common protocols for collection and curation of data that will be applied to allergenic foods for which there are currently data gaps.

The increasing demand for healthy baked goods boosted studies on sourdough microbiota with beneficial metabolic traits, to be used as potential functional starters. Here, yeast populations of traditional sourdoughs collected from four Tuscan bakeries were investigated. Among 200 isolated strains, 78 were randomly selected and molecularly characterized. Saccharomyces cerevisiae was dominant, representing the only species detected in three out of the four sourdoughs. The fourth one harbored also Kazachstania humilis. Inter-delta regions analysis revealed a high intraspecific polymorphism discriminating 16 biotypes of S. cerevisiae isolates, which clustered based on their origin. Representative isolates from each biotype group were individually used to ferment soft and durum wheat flour, aiming at evaluating their pro-technological, nutritional and functional features. During fermentation under standardized conditions, all strains were able to grow of ca. 2 log cycles, but only S. cerevisiae L10Y, D18Y and D20Y had a significantly shorter latency phase in both flours. Overall, the highest volumes were reached after 16 h of fermentation in both soft and durum fermented dough. S. cerevisiae D2Y produced the highest dough volume increase. K. humilis G23Y was the only strain able to increase the total free amino acids concentration of the doughs. Overall, values of phytase activity were significantly higher in durum compared to the corresponding soft fermented dough. K. humilis G23Y and S. cerevisiae D20Y, D24Y showed a threefold higher phytase activity than spontaneously fermented control, and the highest concentration of total phenols. Almost all the strains led to increases of antioxidant activity, without significant differences among them. Investigations on the resistance of the strains to simulated gastric and intestinal conditions, that is considered a pre-requisite for the selection of probiotics, revealed the ability to survive in vitro by many of the strains considered. This study proposed the best performing yeast strains selected among autochthonous sourdough yeasts based on their pro-technological, nutritional and functional traits to be used as starters for making sourdough baked goods or functional cereal-based beverages. Although some yeast strains combined several technological and nutritional traits, the association of more selected strains seemed to be a requisite to get optimal sourdough characteristics., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For this, it is necessary to characterize human phenotypes at the molecular and functional levels, by exploiting gene annotations and known relations among genes, diseases and phenotypes. This characterization makes it possible to implement tools for retrieving functions shared among phenotypes, co-occurring in the same patient and facilitating the formulation of hypotheses about the molecular causes of the disease., Results: We introduce PhenPath, a new resource consisting of two parts: PhenPathDB and PhenPathTOOL. The former is a database collecting the human genes associated with the phenotypes described in Human Phenotype Ontology (HPO) and OMIM Clinical Synopses. Phenotypes are then associated with biological functions and pathways by means of NET-GE, a network-based method for functional enrichment of sets of genes. The present version considers only phenotypes related to diseases. PhenPathDB collects information for 18 OMIM Clinical synopses and 7137 HPO phenotypes, related to 4292 diseases and 3446 genes. Enrichment of Gene Ontology annotations endows some 87.7, 86.9 and 73.6% of HPO phenotypes with Biological Process, Molecular Function and Cellular Component terms, respectively. Furthermore, 58.8 and 77.8% of HPO phenotypes are also enriched for KEGG and Reactome pathways, respectively. Based on PhenPathDB, PhenPathTOOL analyzes user-defined sets of phenotypes retrieving diseases, genes and functional terms which they share. This information can provide clues for interpreting the co-occurrence of phenotypes in a patient., Conclusions: The resource allows finding molecular features useful to investigate diseases characterized by multiple phenotypes, and by this, it can help researchers and physicians in identifying molecular mechanisms and biological functions underlying the concomitant manifestation of phenotypes. The resource is freely available at http://phenpath.biocomp.unibo.it .

A high-precision exact-matching quadruple isotope dilution method (ID 4 MS) was employed for the quantitation of nitrate in an air-dried spinach powder Certified Reference Material (CRM). The analyte was extracted in hot water following addition of 15 NO[Formula: see text] internal standard. The blend was then treated with sulfamic acid to remove nitrite and with triethyloxonium tetrafluoroborate to promote aqueous conversion of nitrate into volatile EtONO 2 . The derivative was analyzed by headspace GC-MS with 3-min elution time. The method performance was validated with a series of tests which demonstrated adequate selectivity and ruggedness. This method supported the development of novel SPIN-1 CRM giving a modest contribution to its uncertainty (u char = 0.85%). With respect to previous attempts, the SPIN-1 was proven stable, homogeneous (u hom = 0.44%), and suitable for spinach monitoring under EU regulations. On dried basis, the nitrate content of SPIN-1 was found to be 22.53 ± 0.43 mg/g (U c = 1.9%, k = 2). The material was also used in an inter-laboratory study where four laboratories employed a total of ten measurement methods. Graphical Abstract SPIN-1 Certified Reference Material for nitrate in spinach powder.

Over the last years, great efforts have been devoted to develop effective gluten detoxification strategies with a consequent detrimental alteration of the technological properties as well. Obtaining low-gluten products without affecting the rheological properties of wheat could still be considered a new challenge to face. In this investigation, we presented a comprehensive characterization of durum wheat genotypes aimed at identifying low gluten ones, which combine the potential lower toxicity/immunogenicity with conserved yield and rheological properties to encompass the perspective usability for bread or pasta making. A preliminary profiling of gluten proteins was accomplished by immunoassay-based quantification and liquid chromatography coupled to UV detection, focusing on the gliadin fraction as main responsible for immunoreactivity in celiac disease patients. In addition, data on grain protein content, grain yield per spike, dry gluten and gluten index were collected in order to provide complementary information about productivity-related traits and quali-quantitative characteristics related to wheat nutritional value and its technological properties. The whole pool of data was statistically evaluated driving to the selection of a preferred list of candidate low-toxicity genotypes that were subjected to in-vitro simulated gastroduodenal digestion and untargeted HR-MS/MS peptide identification. Finally, an in-silico risk assessment of potential toxicity for celiac disease patients was performed according to the most recent guidance provided by EFSA.

Background: Extracting fundamental information from data, thus underlining hidden structures or removing noisy information, is one of the most important aims in different scientific fields especially in biological and medical sciences. In this article, we propose an innovative complex network application able to identify salient links for detecting the effect of Alzheimer's disease on brain connectivity. We first build a network model of brain connectivity from structural Magnetic Resonance Imaging (MRI) data, then we study salient networks retrieved from the original ones., Results: Investigating informative power of the salient skeleton features in combination with those of the original networks we obtain an accuracy of [Formula: see text] for the distinction of Alzheimer disease (AD) patients from normal controls (NC). This performance significantly overcomes accuracy of the original network features. Moreover salient networks are able to correctly discriminate normal controls (NC) from AD patients and NC from subjects with mild cognitive impairment that will convert to AD (cMCI). These evaluations, performed on an independent dataset, give an accuracy of [Formula: see text] and [Formula: see text] respectively for NC-AD and NC-cMCI classifications. Therefore, most of the informative content of the original networks is kept after the 92 [Formula: see text] and 82 [Formula: see text] reduction respectively in the number of nodes and links. In addition, the present approach, applied to a publicly available MRI dataset from the Alzheimer Disease Neuroimaging Initiative (ADNI), brings out also some interesting aspects related to the topologies and hubs of the networks., Conclusions: The experimental results demonstrate how salient networks can highlight important brain network characteristics and structural pathological changes, while reducing considerably data complexity and computational requirements.

PRRS is one of the main viral diseases in pig production, causing huge economic losses to the swine industry worldwide. The virus shows an intrinsic genomic instability and is able to change continuously, with the emergence of new strains, with different pathogenicity patterns. Commercially available vaccines only partially prevent or counteract the disease and the correlated losses. Moreover, the emergence of highly virulent and pathogenetic isolates represents a particular concern for PRRS control and diagnosis. The purpose of this study was to evaluate the efficacy of a modified-live virus (MLV) PRRSV-1 commercial vaccine in reducing the severity of the disease and minimizing losses upon challenge with a highly pathogenic PRRSV-1.1 Italian isolate (PRRSV-1_PR40/2014). Four different groups were compared: C (unvaccinated-uninfected), VAC-C (vaccinated-uninfected), PR40 (unvaccinated-infected) and VAC-PR40 (vaccinated-infected). The tested vaccine provided partial, but statistically significant clinical, virological and pathological protection after challenge under experimental conditions. In particular, vaccinated animals showed reduced viremia in terms of duration and magnitude, reduced respiratory signs and pathological lesions. Vaccination was able to trigger adaptive immunity able to respond efficiently also against the HP PR40 isolate. Vaccinated animals showed higher average daily weight gain, even during the viremic period, compared to non-vaccinated challenged pigs., (Copyright © 2018 Elsevier B.V. All rights reserved.)

This study was aimed to investigate the activity of the Asteraceae species Taraxacum officinale against the root-knot nematode Meloidogyne incognita. Leaf and root extracts of T. officinale were tested in vitro at a range of 62.5-1000 and 250-1000 μg mL -1 concentrations on nematode juveniles and eggs, respectively, whereas treatments with 10-40 g kg -1 soil rates of dry leaf and root T. officinale biomass were applied to soil infested by M. incognita in greenhouse experiments on potted tomato. Peak 36 and 50% juvenile mortality and 14.8 and 23.8% egg hatchability reduction were recorded at the maximum concentration of leaf and root extracts, respectively. Soil treatments with T. officinale leaf and root material strongly suppressed nematode multiplication and gall formation on tomato roots and significantly increased plant growth. Chicoric acid and 3-O- and 3,5-di-O-caffeoylquinic acid were found to be the main components of leaf and root extract, respectively, and proved, as the total hydroalcoholic extracts from T. officinale leaf and root material, for an antioxidant activity. Data from this study indicate the suitability of plant materials from T. officinale for a potential formulation of nematicidal products to include in sustainable nematode management strategies.

The original publication of this paper contains a mistake. Data on Table 1 under TR and TL column have been interchanged: that is compounds 1-12 and their amounts refer to TL; compounds 1-8 and related amounts refer to TR (see Fig. 1).

Selenium, a trace element to which humans are exposed mainly through diet, has been involved in the etiology of human cancer. We investigated the long-term effects of selenium exposure on cancer incidence using data from a natural experiment in Northern Italy. During the 1970s-1980s, in a part of the Italian municipality of Reggio Emilia, residents were inadvertently exposed to unusually high levels of inorganic hexavalent selenium (selenate) through drinking water. We followed the exposed residents for 28years, generating data on incidence (when available) and mortality rates for selected cancer sites; the remaining municipal residents comprised the unexposed (reference) group. We observed no substantial difference in overall cancer incidence comparing exposed and unexposed cohorts. We detected, however, a higher incidence of cancer at some sites, and for a few of them, namely cancers of the buccal cavity and pharynx, melanoma, urinary tract and lymphoid tissue, the excess incidence was particularly evident in the first period of follow-up but decreased over time. Overall, these results suggest that consumption of water with levels of selenium in its inorganic hexavalent form close to the European standard, 10μg/L, may have unfavourable effects on cancer incidence., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Background: The triple-dip recession taking place in Italy in 2008-2014 impacted negatively on health, mainly by increasing the rate of unemployment. This increased the prevalence of mental health disorders, while reducing the number of available places on vocational rehabilitation programs (VRPs) delivered by the psychiatric services., Objectives: To explore the different points of views of stakeholders (namely, users and professionals) involved in VRPs developed inside an Italian Community Mental Health Center (CMHC)., Methods: A sample of users, psychiatrists, educators and nurses of an Italian CMHC involved in VRPs took part in a focus group. Content analysis was performed with MAXQDA 12, by developing a hierarchical code system a posteriori (i.e., derived from the data). The respondent validation phase was carried out by means of a multiple-choice questionnaire, administered to all participants., Results: A total of 86 emerging issues were coded, divided into two macro-areas: Positive and Negative Reinforcements (48 contributions, 56%, and 38 contributions, 44%, respectively), further subdivided into three areas: professional (service) factors, personal (i.e, user-related) factors, and work environment features (including relationships in the workplace). Some contributions raised issues concerning occupational health protection (e.g. need of information about the rights and duties of the users-workers, as well as the risks they are exposed to in the workplace)., Conclusions: The analysis suggested to address specific issues concerning work and VRPs by means of psycho-education group interventions currently carried out at CMHCs, and pointed to the need to foster collaboration between mental health professionals and the occupational health physician of the company where the VRP is started and where the user might be employed.

Background: Hippocampal atrophy is a supportive feature for the diagnosis of probable Alzheimer's disease (AD). However, even for an expert neuroradiologist, tracing the hippocampus and measuring its volume is a time consuming and extremely challenging task. Accordingly, the development of reliable fully-automated segmentation algorithms is of paramount importance., Materials and Methods: The present study evaluates (i) the precision and the robustness of the novel Hippocampal Unified Multi-Atlas Network (HUMAN) segmentation algorithm and (ii) its clinical reliability for AD diagnosis. For these purposes, we used a mixed cohort of 456 subjects and their T1 weighted magnetic resonance imaging (MRI) brain scans. The cohort included 145 controls (CTRL), 217 mild cognitive impairment (MCI) subjects and 94 AD patients from Alzheimer's Disease Neuroimaging Initiative (ADNI). For each subject the baseline, repeat, 12 and 24 month follow-up scans were available., Results: HUMAN provides hippocampal volumes with a 3% precision; volume measurements effectively reveal AD, with an area under the curve (AUC) AUC 1  = 0.08 ± 0.02. Segmented volumes can also reveal the subtler effects present in MCI subjects, AUC 2  = 0.76 ± 0.05. The algorithm is stable and reproducible over time, even for 24 month follow-up scans., Conclusions: The experimental results demonstrate HUMAN is a precise segmentation algorithm, besides hippocampal volumes, provided by HUMAN, can effectively support the diagnosis of Alzheimer's disease and become a useful tool for other neuroimaging applications.

FAD synthase (FADS, EC 2.7.7.2) is the last essential enzyme involved in the pathway of biosynthesis of Flavin cofactors starting from Riboflavin (Rf). Alternative splicing of the human FLAD1 gene generates different isoforms of the enzyme FAD synthase. Besides the well characterized isoform 1 and 2, other FADS isoforms with different catalytic domains have been detected, which are splice variants. We report the characterization of one of these novel isoforms, a 320 amino acid protein, consisting of the sole C-terminal 3'-phosphoadenosine 5'-phosphosulfate (PAPS) reductase domain (named FADS6). This isoform has been previously detected in Riboflavin-Responsive (RR-MADD) and Non-responsive Multiple Acyl-CoA Dehydrogenase Deficiency (MADD) patients with frameshift mutations of FLAD1 gene. To functionally characterize the hFADS6, it has been over-expressed in Escherichia coli and purified with a yield of 25 mg·L -1 of cell culture. The protein has a monomeric form, it binds FAD and is able to catalyze FAD synthesis (k cat about 2.8 min -1 ), as well as FAD pyrophosphorolysis in a strictly Mg 2+ -dependent manner. The synthesis of FAD is inhibited by HgCl₂. The enzyme lacks the ability to hydrolyze FAD. It behaves similarly to PAPS. Combining threading and ab-initio strategy a 3D structural model for such isoform has been built. The relevance to human physio-pathology of this FADS isoform is discussed., Competing Interests: The authors declare no conflict of interest.

Bacterial antibiotic resistance is a natural phenomenon, seriously affecting the treatment of infections. The biggest danger is that current antibiotics are not able to eradicate the resistant strains. In recent years, alternative antibacterial substances are being sought, which can help in these cases. Fatty acids and monoglycerides are known among the natural substances for their antimicrobial properties and, important detail, bacteria do not develop resistance to them. In this work, we studied the antimicrobial effects of a monoglyceride blend against some multi-resistant Enterococci and Escherichia coli strains. Based on literature data, a blend of fatty acids and their monoglycerides was created and its antimicrobial activity was evaluated against 37 strains of E. coli and 17 Enterococci presenting resistance to at least two antibiotics. A different behavior was observed in the two groups of bacteria, proving that alternative substances can be considerate for the potential treatment of multidrug-resistant strains.

Fusarium fujikuroi causes bakanae ("foolish seedling") disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for production of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chemical product analyses. GA production was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight additional F. fujikuroi isolates from distant geographic regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the number and expression of secondary metabolite gene clusters. Whilst most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amounts of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three additional polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Analysis of additional field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.

Highly pathogenic (HP) isolates of the PRRS virus started emerging in North America and Asia in the late 1990s. More recently, they have emerged in Europe. These isolates are characterized by high viral loads, severe general clinical signs and high mortality, in sows, weaners and growers. Their genome shows a discontinuous aminoacids deletion in the non-structural protein 2 (NSP2). The present study was aimed at characterizing the clinical, pathological and immunological features of a highly pathogenetic, Italian PRRSV-1 subtype 1 isolate (PRRSV1_PR40/2014), following experimental infection in conventional 4-weeks-old pigs. The PRRSV1_PR40/2014 infected group showed severe clinical signs (high fever and dispnoea). Pathological lesions, including severe lymphocytopenia in bronchial lymph-nodes and thymus were also recorded. Higher serum PRRSV genome copies and lower virus neutralizing antibody titer were observed in the PR40 group, when compared to the group infected with a conventional PRRSV strain. The genetic analysis of the strain, and the phenotypic features observed in the field and reproduced in the experimental study, confirmed the high pathogenicity of the Italian PRRSV-1 subtype 1 PR40 isolate., (Copyright © 2017 Elsevier B.V. All rights reserved.)

This systematic literature review collects and summarizes research on consumer acceptance and preferences for nutrition-modified and functional dairy products, to reconcile, and expand upon, the findings of previous studies. We find that female consumers show high acceptance for some functional dairy products, such as yogurt enriched with calcium, fiber and probiotics. Acceptance for functional dairy products increases among consumers with higher diet/health related knowledge, as well as with aging. General interest in health, food-neophobia and perceived self-efficacy seem also to contribute shaping the acceptance for functional dairy products. Furthermore, products with "natural" matches between carriers and ingredients have the highest level of acceptance among consumers. Last, we find that brand familiarity drives consumers with low interest in health to increase their acceptance and preference for health-enhanced dairy products, such as probiotic yogurts, or those with a general function claim., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Diffusion tensor imaging (DTI) is a promising imaging technique that provides insight into white matter microstructure integrity and it has greatly helped identifying white matter regions affected by Alzheimer's disease (AD) in its early stages. DTI can therefore be a valuable source of information when designing machine-learning strategies to discriminate between healthy control (HC) subjects, AD patients and subjects with mild cognitive impairment (MCI). Nonetheless, several studies have reported so far conflicting results, especially because of the adoption of biased feature selection strategies. In this paper we firstly analyzed DTI scans of 150 subjects from the Alzheimer's disease neuroimaging initiative (ADNI) database. We measured a significant effect of the feature selection bias on the classification performance (p-value  <  0.01), leading to overoptimistic results (10% up to 30% relative increase in AUC). We observed that this effect is manifest regardless of the choice of diffusion index, specifically fractional anisotropy and mean diffusivity. Secondly, we performed a test on an independent mixed cohort consisting of 119 ADNI scans; thus, we evaluated the informative content provided by DTI measurements for AD classification. Classification performances and biological insight, concerning brain regions related to the disease, provided by cross-validation analysis were both confirmed on the independent test.

SnO 2 nanocrystals were prepared by precipitation in dodecylamine at 100 °C, then they were reacted with vanadium chloromethoxide in oleic acid at 250 °C. The resulting materials were heat-treated at various temperatures up to 650 °C for thermal stabilization, chemical purification and for studying the overall structural transformations. From the crossed use of various characterization techniques, it emerged that the as-prepared materials were constituted by cassiterite SnO 2 nanocrystals with a surface modified by isolated V(IV) oxide species. After heat-treatment at 400 °C, the SnO 2 nanocrystals were wrapped by layers composed of vanadium oxide (IV-V mixed oxidation state) and carbon residuals. After heating at 500 °C, only SnO 2 cassiterite nanocrystals were obtained, with a mean size of 2.8 nm and wrapped by only V 2 O 5 -like species. The samples heat-treated at 500 °C were tested as RhB photodegradation catalysts. At 10 -7  M concentration, all RhB was degraded within 1 h of reaction, at a much faster rate than all pure SnO 2 materials reported until now.

Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term "microbial dark matter" was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water.

Coherent Diffractive Imaging is a lensless technique that allows imaging of matter at a spatial resolution not limited by lens aberrations. This technique exploits the measured diffraction pattern of a coherent beam scattered by periodic and non-periodic objects to retrieve spatial information. The diffracted intensity, for weak-scattering objects, is proportional to the modulus of the Fourier Transform of the object scattering function. Any phase information, needed to retrieve its scattering function, has to be retrieved by means of suitable algorithms. Here we present a new approach, based on a memetic algorithm, i.e. a hybrid genetic algorithm, to face the phase problem, which exploits the synergy of deterministic and stochastic optimization methods. The new approach has been tested on simulated data and applied to the phasing of transmission electron microscopy coherent electron diffraction data of a SrTiO 3 sample. We have been able to quantitatively retrieve the projected atomic potential, and also image the oxygen columns, which are not directly visible in the relevant high-resolution transmission electron microscopy images. Our approach proves to be a new powerful tool for the study of matter at atomic resolution and opens new perspectives in those applications in which effective phase retrieval is necessary., Competing Interests: The authors declare no competing financial interests.

Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16) Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32) hybrids, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture., (Copyright © 2016 Rosellini et al.)

A few studies have suggested an association between maternal exposure to ambient air pollution from vehicular traffic and risk of congenital anomalies in the offspring, but epidemiologic evidence is neither strong nor entirely consistent. In a population-based case-control study in a Northern Italy community encompassing 228 cases of birth defects and 228 referent newborns, we investigated if maternal exposure to PM10 and benzene from vehicular traffic during early pregnancy, as estimated through a dispersion model, was associated with excess teratogenic risk. In conditional logistic regression analysis, and with adjustment for the other pollutant, we found that higher exposure to PM10 but not benzene was associated with increased risk of birth defects overall. Anomaly categories showing the strongest dose-response relation with PM10 exposure were musculoskeletal and chromosomal abnormalities but not cardiovascular defects, with Down syndrome being among the specific abnormalities showing the strongest association, though risk estimates particularly for the less frequent defects were statistically very unstable. Further adjustment in the regression model for potential confounders did not considerably alter the results. All the associations were stronger for average levels of PM10 than for their maximal level. Findings of this study give some support for an excess teratogenic risk following maternal exposure during pregnancy to PM10, but not benzene. Such association appears to be limited to some birth defect categories., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Aspergillus flavus is an efficient producer of mycotoxins, particularly aflatoxin B₁, probably the most hepatocarcinogenic naturally-occurring compound. Although the inducing agents of toxin synthesis are not unanimously identified, there is evidence that oxidative stress is one of the main actors in play. In our study, we use menadione, a quinone extensively implemented in studies on ROS response in animal cells, for causing stress to A. flavus. For uncovering the molecular determinants that drive A. flavus in challenging oxidative stress conditions, we have evaluated a wide spectrum of several different parameters, ranging from metabolic (ROS and oxylipin profile) to transcriptional analysis (RNA-seq). There emerges a scenario in which A. flavus activates several metabolic processes under oxidative stress conditions for limiting the ROS-associated detrimental effects, as well as for triggering adaptive and escape strategies.

Odin is a protein belonging to the ANKS family, and has two tandem Sam domains. The first, Odin-Sam1, binds to the Sam domain of the EphA2 receptor (EphA2-Sam); this interaction could be crucial for the regulation of receptor endocytosis and might have an impact on cancer. Odin-Sam1 associates with EphA2-Sam by adopting a "mid-loop/end-helix" model. In this study three peptide sequences, encompassing the mid-loop interacting portion of Odin-Sam1 and its C-terminal α5 helix, were designed. Their conformational properties were analyzed by CD and NMR. In addition, their abilities to interact with EphA2-Sam were investigated by SPR studies. The peptides adopt a predominantly disordered state in aqueous buffer, but a higher helical content is evident in the presence of the cosolvent trifluoroethanol. Dissociation constants towards EphA2-Sam were in the high micromolar range. The structural findings suggest further routes for the design of potential anti-cancer therapeutics as inhibitors of EphA2-Sam heterotypic interactions., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity., (© 2014 John Wiley & Sons Ltd.)

Neurodegenerative diseases are frequently associated with structural changes in the brain. Magnetic resonance imaging (MRI) scans can show these variations and therefore can be used as a supportive feature for a number of neurodegenerative diseases. The hippocampus has been known to be a biomarker for Alzheimer disease and other neurological and psychiatric diseases. However, it requires accurate, robust, and reproducible delineation of hippocampal structures. Fully automatic methods are usually the voxel based approach; for each voxel a number of local features were calculated. In this paper, we compared four different techniques for feature selection from a set of 315 features extracted for each voxel: (i) filter method based on the Kolmogorov-Smirnov test; two wrapper methods, respectively, (ii) sequential forward selection and (iii) sequential backward elimination; and (iv) embedded method based on the Random Forest Classifier on a set of 10 T1-weighted brain MRIs and tested on an independent set of 25 subjects. The resulting segmentations were compared with manual reference labelling. By using only 23 feature for each voxel (sequential backward elimination) we obtained comparable state-of-the-art performances with respect to the standard tool FreeSurfer.

The present systematic review was performed to assess consumer purchasing behaviour towards fish and seafood products in the wide context of developed countries. Web of Science, Scopus, ScienceDirect and Google Scholar engines were used to search the existing literature and a total of 49 studies were identified for inclusion. These studies investigated consumer purchasing behaviour towards a variety of fish and seafood products, in different countries and by means of different methodological approaches. In particular, the review identifies and discusses the main drivers and barriers of fish consumption as well as consumers' preferences about the most relevant attributes of fish and seafood products providing useful insights for both practitioners and policy makers. Finally, main gaps of the existing literature and possible trajectories for future research are also discussed., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Chiral 5-arylbenzothiadiazine derivatives have recently attracted particular attention because they exhibit an interesting pharmacological activity as AMPA receptor (AMPAr) positive modulators. However, investigations on their configurational stability suggest a rapid enantiomerization in physiological conditions. In order to enhance configurational stability, preserving AMPAr activity, we have designed the novel compound (R,S)-7-chloro-9-(furan-3-yl)-2,3,3a,4-tetrahydro-1H-benzo[e]pyrrolo[2,1-c][1,2,4]thiadiazine 5,5-dioxide bearing a pyrrolo moiety coupled with the 5-(furan-3-yl) substituent on benzothiadiazine core. A stereoselective synthesis was projected to obtain single enantiomer of the latter compound. Absolute configuration was assigned by X-ray crystal structure. Patch clamp experiments evaluating the activity of single enantiomers as AMPAr positive allosteric modulator showed that R stereoisomer is the active component. Molecular modeling studies were performed to explain biological results. An on-column stopped-flow bidimensional recycling HPLC procedure was applied to obtain on a large scale the active enantiomer with enantiomeric enrichment starting from the racemic mixture of the compound., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Purpose. To assess near visual acuity in a presbyopic age group following hyperopic photorefractive keratectomy (PRK). Setting. Private practice in Siena, Italy. Methods. In this retrospective single-surgeon comparative study, PRK with mitomycin C was performed to correct hyperopia using Bausch & Lomb 217z laser for 120 eyes of 60 patients in the presbyopic age group (mean spherical equivalent SE +2.38 D ± 0.71 D and mean age 52 ± 5.09). 120 eyes of 60 age-matched controls (mean age 54 ± 5.09) had their unaided near vision measured. Results. At 12 months mean SE was -0.10 D ± 0.27 D in the PRK group. Mean best corrected visual acuity (BSCVA) was 0.005 ± 0.022  log MAR; 2 eyes lost ≥0.1 log MAR. Mean uncorrected visual acuity was 0.04 ± 0.077  log MAR. Mean distance corrected near visual acuity (DCNVA) in the PRK group was J3.73 ± 1.06. This was statistically better (P < 0.05) than the mean unaided near visual acuity in the control group J4.07 ± 1.08. Conclusion. PRK was found to be safe, predictable, and an effective way of correcting hyperopia in this age group. It was also found to give better than expected near vision.

Fusapyrone (FP), an antifungal natural compound, was tested against the three main ochratoxigenic species of the Aspergillus section Nigri. The MICs at 24 h were 6.0, 11.6, and 9.9 mug/ml for Aspergillus carbonarius, Aspergillus tubingensis, and Aspergillus niger, respectively. Strong inhibition of growth and morphological changes were still observed at half the MIC after 7 days. The application of a 100 mug/ml FP solution in a laboratory assay on artificially inoculated grapes resulted in a significant reduction (up to 6 orders of magnitude) of A. carbonarius CFU counts. Dramatic reductions of the ochratoxin A (OTA) content, compared to the content of the positive control (average amount of OTA, 112.5 ng/g of grape; three experiments), were obtained with the application of either 100 or 50 mug/ml of FP (0.6 or 5.1 ng/g of grape, respectively).