Sex-Specific Adherence to the Mediterranean Diet in Obese Individuals.

Adherence to the Mediterranean diet (MedDiet) has long been associated with several health benefits, including a reduced risk of heart disease, diabetes, and obesity. The MedDiet is characterized by a high consumption of foods such as fruits, vegetables, whole grains, fish, and olive oil, along with a moderate intake of red meat and red wine with meals. Some studies report significant differences between men and women in susceptibility to obesity, with women at a higher prevalence of obesity than men. One unexplored aspect, however, concerns the sex difference in MedDiet adherence, which could be influenced by various factors, such as health perceptions, food preferences, and cultural influences. The aim of this study is to assess the effectiveness and impact of MedDiet adherence in men and women, with a focus on its influence on health and well-being, as well as its ability to promote sex equity in healthcare outcomes. Moreover, we aim to measure the overall health improvements in men and women participating in a MedDiet program, including changes in body composition and overall quality of life. This study highlights that the MedDiet is associated with more significant body weight loss in women, although their increase in MedDiet adherence was lower than in men. Trial registration: NCT01890070. Registered 24 June 2013.

Notch3-regulated microRNAs impair CXCR4-dependent maturation of thymocytes allowing maintenance and progression of T-ALL.

Malignant transformation of T-cell progenitors causes T-cell acute lymphoblastic leukemia (T-ALL), an aggressive childhood lymphoproliferative disorder. Activating mutations of Notch, Notch1 and Notch3, have been detected in T-ALL patients. In this study, we aimed to deeply characterize hyperactive Notch3-related pathways involved in T-cell dynamics within the thymus and bone marrow to propose these processes as an important step in facilitating the progression of T-ALL. We previously generated a transgenic T-ALL mouse model (N3-ICtg) demonstrating that aberrant Notch3 signaling affects early thymocyte maturation programs and leads to bone marrow infiltration by CD4+CD8+ (DP) T cells that are notably, Notch3highCXCR4high. Newly, our in vivo results suggest that an anomalous immature thymocyte subpopulation, such as CD4-CD8- (DN) over-expressing CD3ɛ, but with low CXCR4 expression, dominates N3-ICtg thymus-resident DN subset in T-ALL progression. MicroRNAs might be of significance in T-ALL pathobiology, however, whether required for leukemia maintenance is not fully understood. The selection of specific DN subsets demonstrates the inverse correlation between CXCR4 expression and a panel of Notch3-deregulated miRNAs. Interestingly, we found that within DN thymocyte subset hyperactive Notch3 inhibits CXCR4 expression through the cooperative effects of miR-139-5p and miR-150-5p, thus impinging on thymocyte differentiation with accumulation of DNCD3ɛ+CXCR4- cells. These data point out that deregulation of Notch3 in T-ALL, besides its role in sustaining dissemination of abnormal DP T cells, as we previously demonstrated, could play a role in selecting specific DN immature T cells within the thymus, thus impeding T cell development, to facilitate T-ALL progression inside the bone marrow.

Insight into immune profile associated with vitiligo onset and anti-tumoral response in melanoma patients receiving anti-PD-1 immunotherapy.

Introduction: Immunotherapy with checkpoint inhibitors is an efficient treatment for metastatic melanoma. Development of vitiligo upon immunotherapy represents a specific immune-related adverse event (irAE) diagnosed in 15% of patients and associated with a positive clinical response. Therefore, a detailed characterization of immune cells during vitiligo onset in melanoma patients would give insight into the immune mechanisms mediating both the irAE and the anti-tumor response. Methods: To better understand these aspects, we analyzed T cell subsets from peripheral blood of metastatic melanoma patients undergoing treatment with anti-programmed cell death protein (PD)-1 antibodies. To deeply characterize the antitumoral T cell response concomitant to vitiligo onset, we analyzed T cell content in skin biopsies collected from melanoma patients who developed vitiligo. Moreover, to further characterize T cells in vitiligo skin lesion of melanoma patients, we sequenced T cell receptor (TCR) of cells derived from biopsies of vitiligo and primary melanoma of the same patient. Results and discussion: Stratification of patients for developing or not developing vitiligo during anti-PD-1 therapy revealed an association between blood reduction of CD8-mucosal associated invariant T (MAIT), T helper (h) 17, natural killer (NK) CD56bright, and T regulatory (T-reg) cells and vitiligo onset. Consistently with the observed blood reduction of Th17 cells in melanoma patients developing vitiligo during immunotherapy, we found high amount of IL-17A expressing cells in the vitiligo skin biopsy, suggesting a possible migration of Th17 cells from the blood into the autoimmune lesion. Interestingly, except for a few cases, we found different TCR sequences between vitiligo and primary melanoma lesions. In contrast, shared TCR sequences were identified between vitiligo and metastatic tissues of the same patient. These data indicate that T cell response against normal melanocytes, which is involved in vitiligo onset, is not typically mediated by reactivation of specific T cell clones infiltrating primary melanoma but may be elicited by T cell clones targeting metastatic tissues. Altogether, our data indicate that anti-PD-1 therapy induces a de novo immune response, stimulated by the presence of metastatic cells, and composed of different T cell subtypes, which may trigger the development of vitiligo and the response against metastatic tumor.

Sustainability Perception of Italian Consumers: Is it Possible to Replace Meat, and What Is the Best Alternative?

Growing worldwide food demand with its environmental impacts requires a reshaping of food consumption. This study aims to evaluate the degree of Italian consumers' awareness of sustainability and whether protein alternatives to meat could be accepted. A cross-sectional survey was carried out on a group of 815 respondents, representative of the Italian adult population for geography, gender, and age, using multivariate analysis together with cluster analysis. Lack of awareness of the consequences of food choices on the environment was found in 45% of respondents, and 51% reduced their consumption of meat. Typical foods of the Mediterranean diet (84% legumes 82% eggs, and 77% fish) were selected as the preferred sources of protein to replace meat, while insects and insect-based products were less accepted (67%). The importance of meat is the latent factor that explains more than 50% of the common variance observed in the factor analysis. The cluster analysis confirmed the importance of meat for Italian consumers, emphasizing other aspects of the sustainability of food choices. Cluster 1 (25.6%) considered meat very important. Two out of five clusters (clusters 2 and 3, 38%) considered meat replaceable in the diet, and cluster 4 (31.3%) included meat consumers that were willing to be sustainable. Cluster 5 identifies the "unsustainable consumers" (5.7%). In conclusion, besides the perceived importance of meat, there is room for recommendations for its reduction by proposing alternative foods already present in the Mediterranean diet.

Long-term longitudinal study on swine VML model.

BACKGROUND: Volumetric Muscle Loss (VML), resulting from severe trauma or surgical ablation, is a pathological condition preventing myofibers regeneration, since skeletal muscle owns the remarkable ability to restore tissue damage, but only when limited in size. The current surgical therapies employed in the treatment of this pathology, which particularly affects military personnel, do not yet provide satisfactory results. For this reason, more innovative approaches must be sought, specifically skeletal muscle tissue engineering seems to highlight promising results obtained from preclinical studies in VML mouse model. Despite the great results obtained in rodents, translation into human needs a comparable animal model in terms of size, in order to validate the efficacy of the tissue engineering approach reconstructing larger muscle mass (human-like). In this work we aim to demonstrate the validity of a porcine model, that has underwent a surgical ablation of a large muscle area, as a VML damage model. RESULTS: For this purpose, morphological, ultrasound, histological and fluorescence analyses were carried out on the scar tissue formed following the surgical ablation of the peroneus tertius muscle of Sus scrofa domesticus commonly called mini-pig. In particular, the replenishment of the damaged area, the macrophage infiltration and the vascularization at different time-points were evaluated up to the harvesting of the scar upon six months. CONCLUSION: Here we demonstrated that following VML damage, there is an extremely poor regenerative process in the swine muscle tissue, while the formation of fibrotic, scar tissue occurs. The analyses performed up to 180 days after the injury revealed the development of a stable, structured and cellularized tissue, provided with vessels and extracellular matrix acquiring the status of granulation tissue like in human.

Consumers' Attitude towards Sustainability in Italy: Process of Validation of a Duly Designed Questionnaire.

This study aimed to describe the process of validation of a questionnaire assessing Italian consumers' perception of food sustainability. The study has a multiphase design. Phase 1 consisted in translating and structuring the questionnaire. Phase 2 aimed at assessing the validity of the content by experts. Phase 3 consisted of a pilot study (n = 150) carried out to revise the questionnaire based on the reactions of consumers representing the target group of the assessment. The questionnaire showed adequate content validity for 11 out of 14 questions (>0.79) and S-CVI/Ave > 0.80. Cronbach's alpha values ranged from 0.08 to 0.90. The construct with insufficient results (0.08) was changed because it failed to correlate with the rest of the questionnaire. The factor analysis permitted the identification of questions that needed improvement in terms of comprehensibility, elimination of redundancies, and repetitions. The validated questionnaire included 12 questions (71 response options); 3 sections were identified: food sustainability knowledge (4 questions-30 items); sources of proteins alternative to meat (3 questions-20 items); eating behaviors (5 questions-21 items). This study showed the importance of validation before the administration on a large scale of a questionnaire on a topic such as sustainability still lacking large support from consensus documents.

Immune Soluble Factors in the Cerebrospinal Fluid of Progressive Multiple Sclerosis Patients Segregate Into Two Groups.

Primary-progressive (PP) and secondary-progressive (SP) multiple sclerosis (MS) are characterized by neurological deficits caused by a permanent neuronal damage, clinically quantified by the expanded disability status scale (EDSS). Neuronal tissue damage is also mediated by immune infiltrates producing soluble factors, such as cytokines and chemokines, which are released in the cerebrospinal fluid (CSF). The mechanisms regulating the production of a soluble factor are not completely defined. Using multiplex bead-based assays, we simultaneously measured 27 immune soluble factors in the CSF collected from 38 patients, 26 with PP-MS and 12 with SP-MS. Then, we performed a correlation matrix of all soluble factors expressed in the CSF. The CSF from patients with PP-MS and SP-MS had similar levels of cytokines and chemokines; however, the stratification of patients according to active or inactive magnetic resonance imaging (MRI) unveils some differences. Correlative studies between soluble factors in the CSF of patients with PP-MS and SP-MS revealed two clusters of immune mediators with pro-inflammatory functions, namely IFN-γ, MCP-1, MIP-1α, MIP-1ß, IL-8, IP-10, and TNF-α (group 1), and anti-inflammatory functions, namely IL-9, IL-15, VEGF, and IL-1ra (group 2). However, most of the significant correlations between cytokines of group 1 and of group 2 were lost in patients with more severe disability (EDSS ≥ 4) compared to patients with mild to moderate disability (EDSS < 4). These results suggest a common regulation of cytokines and chemokines belonging to the same group and indicate that, in patients with more severe disability, the production of those factors is less coordinated, possibly due to advanced neurodegenerative mechanisms that interfere with the immune response.

Using the MINT Database to Search Protein Interactions.

The Molecular INTeractions Database (MINT) is a public database designed to store information about protein interactions. Protein interactions are extracted from scientific literature and annotated in the database by expert curators. Currently (October 2019), MINT contains information on more than 26,000 proteins and more than 131,600 interactions in over 30 model organisms. This article provides protocols for searching MINT over the Internet, using the new MINT Web Page. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Searching MINT over the internet Alternate Protocol: MINT visualizer Basic Protocol 2: Submitting interaction data.

SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update.

The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regulation) and to the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the up/down-regulation of the target entity. Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled. SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc. We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction. We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant formats, such as PSI-MI CausalTAB and GMT. The data are freely accessible and downloadable at https://signor.uniroma2.it/.

DISNOR: a disease network open resource.

DISNOR is a new resource that aims at exploiting the explosion of data on the identification of disease-associated genes to assemble inferred disease pathways. This may help dissecting the signaling events whose disruption causes the pathological phenotypes and may contribute to build a platform for precision medicine. To this end we combine the gene-disease association (GDA) data annotated in the DisGeNET resource with a new curation effort aimed at populating the SIGNOR database with causal interactions related to disease genes with the highest possible coverage. DISNOR can be freely accessed at http://DISNOR.uniroma2.it/ where >3700 disease-networks, linking ∼2600 disease genes, can be explored. For each disease curated in DisGeNET, DISNOR links disease genes by manually annotated causal relationships and offers an intuitive visualization of the inferred 'patho-pathways' at different complexity levels. User-defined gene lists are also accepted in the query pipeline. In addition, for each list of query genes-either annotated in DisGeNET or user-defined-DISNOR performs a gene set enrichment analysis on KEGG-defined pathways or on the lists of proteins associated with the inferred disease pathways. This function offers additional information on disease-associated cellular pathways and disease similarity.

SIGNOR: a database of causal relationships between biological entities.

Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence. The SIGnaling Network Open Resource, SIGNOR (available on line at http://signor.uniroma2.it), was developed to support such a strategy by providing a scaffold of prior experimental evidence of causal relationships between biological entities. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are complexes, chemicals, phenotypes and stimuli. The information captured in SIGNOR can be represented as a signed directed graph illustrating the activation/inactivation relationships between signalling entities. Each entry is associated to the post-translational modifications that cause the activation/inactivation of the target proteins. More than 4900 modified residues causing a change in protein concentration or activity have been curated and linked to the modifying enzymes (about 351 human kinases and 94 phosphatases). Additional modifications such as ubiquitinations, sumoylations, acetylations and their effect on the modified target proteins are also annotated. This wealth of structured information can support experimental approaches based on multi-parametric analysis of cell systems after physiological or pathological perturbations and to assemble large logic models.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).

MINT, the molecular interaction database: 2012 update.

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.

Enriching the viral-host interactomes with interactions mediated by SH3 domains.

Protein-protein interactions play an essential role in the regulation of most cellular processes. The process of viral infection is no exception and many viral pathogenic strategies involve targeting and perturbing host-protein interactions. The characterization of the host protein subnetworks disturbed by invading viruses is a major goal of viral research and may contribute to reveal fundamental biological mechanisms and to identify new therapeutic strategies. To assist in this approach, we have developed a database, VirusMINT, which stores in a structured format most of the published interactions between viral and host proteome. Although SH3 are the most ubiquitous and abundant class of protein binding modules, VirusMINT contains only a few interactions mediated by this domain class. To overcome this limitation, we have applied the whole interactome scanning experiment approach to identify interactions between 15 human SH3 domains and viral proline-rich peptides of two oncogenic viruses, human papillomavirus type 16 and human adenovirus A type 12. This approach identifies 114 new potential interactions between the human SH3 domains and proline-rich regions of the two viral proteomes.

MINT, the molecular interaction database: 2009 update.

MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.

VirusMINT: a viral protein interaction database.

Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database (http://mint.bio.uniroma2.it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature. VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains. The whole data set can be easily queried through the search pages and the results can be displayed with a graphical viewer. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein-Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40.

SH3-Hunter: discovery of SH3 domain interaction sites in proteins.

SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide-domain pairs. The server can accept a list of peptides and allows users to upload an input file in a proper format. An accurate selection of SH3 domains is available and users can also submit their own SH3 domain sequence. SH3-Hunter evaluates which peptide-domain pair represents a possible interaction pair and produces as output a list of significant interaction sites for each query protein. Each proposed interaction site is associated to a propensity score and sensitivity and precision levels for the prediction. The server prediction capability is based on a neural network model integrating high-throughput pep-spot data with structural information extracted from known SH3-peptide complexes.

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.

BACKGROUND: We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only those matching sites composed of structural regions whose residue order is inverted in the relative protein sequences. RESULTS: A novel case of local analogy was detected between members of the ABC transporter and of the HprK/P families in their ATP binding site. This case cannot be derived by events of circular permutation since the residues of one of the region pairs are located in reverse order in the sequence of the two protein families. One of the analogous binding sites, the one identified in HprK/P, is known to also bind pyrophosphate, which is used as preferred energy source in its kinase and phosphorylase activity. CONCLUSION: The discovery of this striking molecular similarity, also associated to a functional similarity, may help in suggesting new experiments aimed at a deeper understanding of members of the ABC transporter family known to be involved in many serious human diseases.