Proteomics for the Investigation of Surface-Exposed Proteins in Probiotics

Probiotics are commensal microorganisms that are present in the intestinal tract and in many fermented foods and positively affect human health, promoting digestion and uptake of dietary nutrients, strengthening intestinal barrier function, modulating immune response, and enhancing antagonism toward pathogens. The proteosurfaceome, i.e., the complex set of proteins present on the bacterial surface, is directly involved as leading actor in the dynamic communication between bacteria and host. In the last decade, the biological relevance of surface-exposed proteins prompted research activities exploiting the potentiality of proteomics to define the complex network of proteins that are involved in the molecular mechanisms at the basis of the adaptation to gastrointestinal environment and the probiotic effects. These studies also took advantages of the recent technological improvements in proteomics, mass spectrometry and bioinformatics that triggered the development of ad hoc designed innovative strategies to characterize the bacterial proteosurfaceome. This mini-review is aimed at describing the key role of proteomics in depicting the cell wall protein architecture and the involvement of surface-exposed proteins in the intimate and dynamic molecular dialogue between probiotics and intestinal epithelial and immune cells

Green is the colour. Standards, equipment and public spaces as paradigm for the Italian sustainable city

The speed of the urban systems is related with a series of social, economic, and environmental transformations bringing often to a critic state that needs the redefinition of urban elements and relationships, in order to guarantee quality and safety to the inhabitants’ lives. Related to the new spatial conditions of planning is the topic of urban equipment that is an open matter in the urban politics. Their relevance for Italian cities made them a symbol of democratization and quality of the cities, due to the obligatory of minimum quantities of spaces for public services. The 50 years from the issue of DM 1444 allows to express a series of evaluations on the role of the public equipment in the processes of urban transformation and governance. Starting from this analysis, the paper proposes adequate and updated solutions in terms of evolution of the standards categories and their quantitative and qualitative characteristics, deepening the role of the urban facilities as potential sources of innovation. The first part of the paper highlights some elements related to the long period of application of the law, and the results of this application in terms of increase and quality in the urban equipment of the city. The second part explores the motivations behind the need for a comprehensive updating of the subject, referring to concepts such as sustainability, and quality of urban systems. In the third part, starting from new requirements, new needs, new risks affecting urban systems, as well as from critical points of the Italian law structure, the paper proposes new categories of urban planning standards and the related functional requirements they must to satisfy

DECOUPLING OF ENERGY TRANSMISSION BETWEEN SUBSYSTEMS OF A COMPLEX STRUCTURE

Experimental vibroacoustic measurements are very common for the study of emitted noise reduction and vibration energy isolation of structures. The most important case is when structures are subjected to an aerodynamic excitation as Turbulent Boundary Layer (TBL). In this paper, a preliminary study is performed on the energy transmission between subsystems of a structure subjected to TBL. A numerical test is developed on a three-plates-in-row system at high frequencies, through the application of Statistical Energy Analysis (SEA). Parameters such as surface dimensions, thickness and damping loss factor are evaluated in different configurations for a first design of a testbench used for vibroacoustic measurements in a wind tunnel

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

Background: Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics. Results: We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of 'carosello', referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of 'barattiere', a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation. Conclusions: We used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits

Relationship between sperm quality parameters and fatty acid composition of the muscle, liver and testis of European eel

[EN] This study looks at the correlations that fatty acids have with different tissues in the European eel (Anguilla anguilla L.) during hormonally-induced sexual maturation, with different sperm quality parameters. In order to evaluate the different dynamics of the use of fatty acids, a categorization of the results from each sperm quality parameter (volume, concentration, motility and velocity) was performed. Low and moderate correlations were observed between muscle tissue and some sperm quality parameters but no high correlations were found. Eicosapentaenoic add (20:5n3, EPA) in the liver seems to have a role in determining the volume of sperm produced. This can be explained by the fact that EPA is a major requirement in the early phases of sperm production (probably as a component of the spermatozoal membrane). In addition, the levels of alpha-linolenic acid (18:3-n3, ALA) and linoleic acid (18:2-n6, LA) in the liver decreased when sperm motility increased. In all the tissues, a negative correlation was observed between arachidonic acid (20:4n-6, ARA) and the different sperm velocity parameters. The fact that an increase in the consumption of ARA coincides with an increase in the speed of spermatozoa, highlights the important role that this fatty acid plays not only in sperm production, but also in sperm velocity. All this information could prove useful in the development of suitable broodstock diets to improve sperm quality and subsequently, the larval development of this species. (C) 2014 Elsevier Inc All rights reserved.This work was funded by the European Community's Seventh Framework Programme under the Theme 2 "Food, Agriculture and Fisheries, and Biotechnology", grant agreement no. 245257 (PRO-EEL), and COST Office (Food and Agriculture COST Action FA1205: AQUAGAMETE). Victor Gallego, Ilaria Mazzeo and M. Carmen Vilchez had predoctoral grants from the Spanish Ministry of Science and Innovation (MICINN), Generalitat Valenciana, and UPV PAID Programme (2011-S2-02-6521), respectively. David S. Penaranda was supported by a contract co-financed by MICINN and UPV (PTA2011-4948-I). Rosa Baeza was supported by a contract funded by PRO-EEL. Authors want to thank Vicente Javier Moya Salvador for his technical assistance with gas chromatography analyses.Baeza Ariño, R.; Mazzeo, I.; Vilchez Olivencia, MC.; Gallego Albiach, V.; Peñaranda, D.; Pérez Igualada, LM.; Asturiano Nemesio, JF. (2015). Relationship between sperm quality parameters and fatty acid composition of the muscle, liver and testis of European eel. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology. 181:79-86. https://doi.org/10.1016/j.cbpa.2014.11.022S798618

Effect of thermal regime on fatty acid dynamics in male European eels (Anguilla anguilla) during hormonally-induced spermatogenesis

[EN] Little is known about the role of fat and fatty acids in European eel spermatogenesis. The aim of this research was to study the changes in fat content and to carry out a quantitative analysis of the fatty acid composition of the muscle, liver and gonad of European male eels during hormonally induced sexual maturation. Three different thermal regimes were used (two variable: T10 and T15; and one constant: T20) to replicate the changes in temperature that these fish experience during their transoceanic reproductive migration. Spermatogenesis was reached earlier in treatment T20, suggesting that spermatogenesis in the European eel is closely regulated by water temperature. Although eels lose body mass due to the period of fasting that accompanies gonadal growth, no significant changes were found in the fat and fatty acid content of the muscle during the experimental period. With regard to the liver, the levels of palmitic, eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids increased significantly at the start of the spermiation process in all the thermal treatments. In the testis, levels of EPA, arachidonic acid (ARA) and DHA remained constant during the maturation process whereas the levels of the rest of the fatty acids decreased significantly. The stability of the ARA and EPA levels in the testis may have a physiological significance, whereas the stability of the DHA levels may have a structural significance. The results suggest that the progression of spermiation is influenced by water temperature and demonstrate the importance of EPA, ARA and DHA in European eel reproduction. This study demonstrates that complementary research focusing on the lipid composition of commercial diets could improve the sperm quality of this species.Funded by the European Community's 7th Framework Programme under the Theme 2 "Food, Agriculture and Fisheries, and Biotechnology", grant agreement no. 245257 (PRO-EEL). Victor Gallego, Ilaria Mazzeo and M. Carmen Vilchez had predoctoral grants from the Spanish Ministry of Science and Innovation (MICINN), Generalitat Valenciana, and UPV PAID Programme (2011-S2-02-6521), respectively. David S. Penaranda was supported by a contract co-financed by MICINN and UPV (PTA2011-4948-I). Rosa Baeza was supported by contract financed by PRO-EEL. The authors want to thank Vicente Javier Moya Salvador for his technical assistance with gas chromatography analyses.Baeza Ariño, R.; Mazzeo, I.; Vilchez Olivencia, MC.; Gallego Albiach, V.; Peñaranda, D.; Pérez Igualada, LM.; Asturiano Nemesio, JF. (2014). Effect of thermal regime on fatty acid dynamics in male European eels (Anguilla anguilla) during hormonally-induced spermatogenesis. Aquaculture. 430:86-97. https://doi.org/10.1016/j.aquaculture.2014.03.045S869743

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits

A Distinct Genetic Cluster in Cultivated Chickpea as Revealed by Genome-wide Marker Discovery and Genotyping

The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea ( L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy. Remarkably, this cluster was clearly distinct at both genetic and phenotypic levels from germplasm groups reflecting commercial chickpea classification into and seed types. Fixation index estimates for individual polymorphisms pointed out loci and genomic regions that might be of significance for the diversification of agronomic and commercial traits. Overall, our findings provide information on genetic relationships within cultivated chickpea and highlight a gene pool of great interest for the scientific community and chickpea breeding, which is limited by the low genetic diversity available in the primary gene pool

Urine Proteomics Revealed a Significant Correlation Between Urine-Fibronectin Abundance and Estimated-GFR Decline in Patients with Bardet-Biedl Syndrome

Background:/Aims: Renal disease is a common cause of morbidity in patients with Bardet-Biedl syndrome (BBS), however the severity of kidney dysfunction is highly variable. To date, there is little information on the pathogenesis, the risk and predictor factors for poor renal outcome in this setting. The present study aims to analyze the spectrum of urinary proteins in BBS patients, in order to potentially identify 1) disease-specific proteomic profiles that may differentiate the patients from normal subjects; 2) urinary markers of renal dysfunction. Methods: Fourteen individuals (7 males and 7 females) with a clinical diagnosis of BBS have been selected in this study. A pool of 10 aged-matched males and 10 aged-matched females have been used as controls for proteomic analysis. The glomerular filtration rate (eGFR) has been estimated using the CKD-EPI formula. Variability of eGFR has been retrospectively assessed calculating average annual eGFR decline (ΔeGFR) in a mean follow-up period of 4 years (3-7). Results: 42 proteins were significantly over- or under-represented in BBS patients compared with controls; the majority of these proteins are involved in fibrosis, cell adhesion and extracellular matrix organization. Statistic studies revealed a significant correlation between urine fibronectin (u-FN) (r2=0.28; p<0.05), CD44 antigen (r2 =0.35; p<0.03) and lysosomal alfa glucosidase ( r20.27; p<0.05) abundance with the eGFR. In addition, u-FN (r2 =0.2389; p<0.05) was significantly correlated with ΔeGFR. Conclusion: The present study demonstrates that urine proteome of BBS patients differs from that of normal subjects; in addition, kidney dysfunction correlated with urine abundance of known markers of renal fibrosis

From risk to care:the hepatitis C screening and diagnostic cascade in a primary health care clinic in Karachi, Pakistan—a cohort study

Background\ud In the high-prevalence setting of Pakistan, screening, diagnosis and treatment services for chronic hepatitis C (CHC) patients are commonly offered in specialized facilities. We aimed to describe the cascade of care in a Médecins Sans Frontières primary health care clinic offering CHC care in an informal settlement in Karachi, Pakistan.\ud \ud Methods\ud This was a retrospective cohort analysis using routinely collected data. Three different screening algorithms were assessed among patients with one or more CHC risk factors.\ud \ud Results\ud Among the 87 348 patients attending the outpatient clinic, 5003 (6%) presented with one or more risk factors. Rapid diagnostic test (RDT) positivity was 38% overall. Approximately 60% of the CHC patients across all risk categories were in the early stage of the disease, with an aspartate aminotransferase:platelet ratio index score <1. The sequential delays in the cascade differed between the three groups, with the interval between screening and treatment initiation being the shortest in the cohort tested with GeneXpert onsite.\ud \ud Conclusions\ud Delays between screening and treatment can be reduced by putting in place more patient-centric testing algorithms. New strategies, to better identify and treat the hidden at-risk populations, should be developed and implemented