Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses

Several research lines are currently ongoing to address the multitude of facets of the pandemic COVID-19. In line with the One-Health concept, extending the target of the studies to the animals which humans are continuously interacting with may favor a better understanding of the SARS-CoV-2 biology and pathogenetic mechanisms; thus, helping to adopt the most suitable containment measures. The last two decades have already faced severe manifestations of the coronavirus infection in both humans and animals, thus, circulating epitopes from previous outbreaks might confer partial protection from SARS-CoV-2 infections. In the present study, we provide an in-silico survey of the major nucleocapsid protein epitopes and compare them with the homologues of taxonomically-related coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Protein sequence alignment provides evidence of high sequence homology for some of the investigated proteins. Moreover, structural epitope mapping by homology modelling revealed a potential immunogenic value also for specific sequences scoring a lower identity with SARS-CoV-2 nucleocapsid proteins. These evidence provide a molecular structural rationale for a potential role in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies

Gut–brain axis and neurodegeneration : State-of-the-art of meta-omics sciences for microbiota characterization

Recent advances in the field of meta-omics sciences and related bioinformatics tools have allowed a comprehensive investigation of human-associated microbiota and its contribution to achieving and maintaining the homeostatic balance. Bioactive compounds from the microbial community harboring the human gut are involved in a finely tuned network of interconnections with the host, orchestrating a wide variety of physiological processes. These includes the bidirectional crosstalk between the central nervous system, the enteric nervous system, and the gastrointestinal tract (i.e., gut\u2013brain axis). The increasing accumulation of evidence suggest a pivotal role of the composition and activity of the gut microbiota in neurodegeneration. In the present review we aim to provide an overview of the state-of-the-art of meta-omics sciences including metagenomics for the study of microbial genomes and taxa strains, metatranscriptomics for gene expression, metaproteomics and metabolomics to identify and/or quantify microbial proteins and metabolites, respectively. The potential and limitations of each discipline were highlighted, as well as the advantages of an integrated approach (multi-omics) to predict microbial functions and molecular mechanisms related to human diseases. Particular emphasis is given to the latest results obtained with these approaches in an attempt to elucidate the link between the gut microbiota and the most common neurodegenerative diseases, such as multiple sclerosis (MS), Alzheimer\u2019s disease (AD), Parkinson\u2019s disease (PD), and amyotrophic lateral sclerosis (ALS)

Antimicrobial Effects of Conditioned Medium From Amniotic Progenitor Cells in vitro and in vivo : toward Tissue Regenerative Therapies for Bovine Mastitis

There is increasing evidence to suggest that, in addition to their regenerative effect, mesenchymal stromal cells (MSCs), and their secretome have an anti-inflammatory and antimicrobial role in the innate immune response in conditions such as sepsis. However, there is no published information on the effect of MSCs in bovine mastitis. Mastitis often results in extensive tissue damage due to multi-microorganism co-infection. This study investigated the ability of amniotic-derived conditioned medium (CM), in vitro and in vivo, to counteract microbial action and restore healthy tissue capable of milk production. Following determination of a dose\u2013response curve, 10,000 colony-forming units (CFU) of Staphylococcus aureus (S. aureus) were inoculated into bovine mammary epithelial cell culture with and without 10% CM (supplemented either at the time of bacteria inoculation or after 4 h). Acridine orange staining was used to assess cell viability/apoptosis. Additionally, an in vivo study was performed using 48 dairy cows with acute and chronic mastitis, treated with CM (treated group) or antibiotics (control group). In vitro results showed that CM can attenuate bacterial growth, as evaluated by the number of CFU. After 24 h of culture with S. aureus, 89.67% of mammary epithelial cells treated with CM were still alive, whereas all cells cultured without CM were dead. Rates of epithelial cell survival (60.67%) were similar when CM was added 4 h after bacteria inoculation. There was no difference in somatic cell count between cases of acute mastitis in the CM-treated or control group in the in vivo study. However, relapses in chronic mastitis were less common in the group receiving CM. Our results show that CM is able to mitigate bacterial growth in vitro and may be particularly useful in the treatment of chronic mastitis, aiding restoration of milk production in cows that would otherwise be removed from the production cycle

Immunoinformatic analysis of the SARS-CoV-2 envelope protein as a strategy to assess cross-protection against COVID-19

Envelope protein of coronaviruses is a structural protein existing in both monomeric and homo-pentameric form. It has been related to a multitude of roles including virus infection, replication, dissemination and immune response stimulation. In the present study, we employed an immunoinformatic approach to investigate the major immunogenic domains of the SARS-CoV-2 envelope protein and map them among the homologue proteins of coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Also, when not available, we predicted the envelope protein structural folding and mapped SARS-CoV-2 epitopes. Envelope sequences alignment provides evidence of high sequence homology for some of the investigated virus specimens; while the structural mapping of epitopes resulted in the interesting maintenance of the structural folding and epitope sequence localization also in the envelope proteins scoring a lower alignment score. In line with the One-Health approach, our evidences provide a molecular structural rationale for a potential role of taxonomically related coronaviruses in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies

Current preventive policies and practices against Vaccine-Preventable Diseases and tuberculosis targeted for workers from hospitals of the Sardinia Region, Italy

Introduction. Health care Workers are exposed to infectious diseases more than the general population. Many of these infections are preventable by vaccination. The objective in this study is to investigate whether, how, and which vaccination underwent Sardinia Health Care Workers (HCWs) and the variability of policies in different Hospital Health Managements of the whole region. Methods. In March 2013, we enrolled the Hospital Health Management of all the 32 Sardinia hospitals. We investigate on immunity against vaccine-preventable diseases and education campaigns about recommended vaccinations for HCWs. Flu, hepatitis B, measles-mumps-rubella, varicella and tuberculosis were the objects of our research. Results. In most of the hospitals, influenza vaccination coverage among HCWs is less than 6%. Hepatitis B antibody assay was performed in all the respondent hospitals but only 14 had available data as collected electronically. Most of the hospitals did not perform serological tests for the evaluation of antibodies against Varicella, Measles, Mumps and Rubella in their HCWs. In 30 hospitals Mantoux test was replaced or integrated by "in vitro" test for health surveillance protocols. Conclusions. This method produced a large amount of data in small time and at a low cost. Sending back data to respective Hospital Health Management (HHM) we took a step towards greater awareness of the issue of biological risks of HCWs and of vaccine coverage

Proteomics evaluation of molecular mechanisms involved in pathogenesis of Salmonella spp.

Salmonella species are an important group of enteric pathogens which could be penetrate the intestinal epithelial barrier and are capable of causing disease (i.e. they are pathogenic). Many foods, particularly foods of animal origin and other foods which may be subject to faecal contamination have been identified as vehicles for the transmission of this pathogen to humans. Those of particular importance include meat, poultry, eggs, milk, fruit and vegetables. Spread of this pathogen may occur in the food processing environment through cross contamination from raw food or infected food handlers. The molecular bases for Salmonella adherence to and invasion of epithelial cells are distinct and complex and a large number of Salmonella genes are required for entry into cultured epithelial cells. Salmonella enterica serotypes are closely related genetically but they are significantly different in pathogenic potentials. Deep inside the relative responsible mechanisms may be a key to more general understanding of the invasiveness of intestinal bacterial infections. This study represents a classic proteomic approach combining 2D gel electrophoresis and mass spectrometry for the comparative analysis of the proteomes of different species of Salmonella isolated from food with the principle aim to find biomarkers to understand pathogenesis mechanism

Serum protein profiling of early and advanced stage Crohn's disease

AbstractCrohn's disease (CD) represents a highly debilitating disease of difficult diagnosis and increasing incidence. Serum protein profiling of early stage Crohn's disease (ES) CD was investigated in order to improve the comprehension of the very early pathologic mechanisms and to support the difficult diagnostic procedures currently available. Inflammatory proteins and complement 3 chain C (C3c) were over-represented during ES CD, clusterin, retinol binding protein, α1-microglobulin and transthyretin were under-represented. A C3c isoform was found to be present only during ES CD. By now, lack of specific antibodies to detect isoforms made it impossible to perform alternative validation

Indagine proteomica del seme bovino per la valutazione della fertilit\ue0

Ipofertility is one of the most common problems and main cause of economic losses in dairy production. Bull infertility represent a significant component on unsuccessful pregnancy. In this study, proteomic analysis was applied to compare the sperm protein expression profile from high and low fertility bulls. It has been found that expression of several proteins (9 different 2-D spots) is related to high and low fertility bulls (p<0.05). These proteins are involved in sperm-egg interaction and cell cycle regulation. Proteomic analysis of sperm can be a valuable tool to identify protein changes related to fertility

Peptidomics in veterinary science : focus on bovine paratuberculosis

Bacterial infections represent a serious burden both for animal production and human health (zoonosis). Faster and more reliable diagnosis are mandatory in order to avoid economic losses and antibiotics misuse. The development of new potential diagnostic strategies for the immunodetection of pathogens is closely linked to the discovery of small polypeptides with immunogenic or immunoreactive activity. The candidate peptides used for this purpose must have several properties principally represented by their specificity and their location in the bacterial cell. Both proteomics, peptidomics and bioinformatics represent powerful complementary tools to discover specific immunoreactive peptides useful for diagnosis or vaccine. Peptidomics of Mycobacterium avium subsp. paratuberculosis (MAP) represents a good example of the potential of this discovery-phase. This review reports a comprehensive update of the current scientific knowledge about proteins and peptides of MAP with already documented humoral response. These findings, together with bioinformatics tools available, could be extremely useful to design a better strategy for subclinical bovine paratuberculosis diagnosis. The knowledge provided also represents a reliable example on the workflow to be followed in the direction of the diagnosis of other diseases through a peptidomic approach

Comparative proteomics to evaluate multi drug resistance in Escherichia coli

Drug resistance in food-borne bacterial pathogens is an almost inevitable consequence of the use of antimicrobial drugs, used either therapeutically or to avoid infections in food-producing animals. In the past decades, the spread and inappropriate use of antibiotics have caused a considerable increase of antibiotics to which bacteria have developed resistance and, moreover, bacteria are becoming resistant to more than one antibiotic simultaneously. Understanding mechanisms at the molecular level is extremely important to control multi-resistant strains and to develop new therapeutic strategies. In the present study, comparative proteomics was applied to characterize membrane and cytosolic proteome in order to investigate the regulation of protein expression in multi-resistance E. coli isolated from young never vaccinated water buffalo. Results highlighted differentially expressed proteins under multi drug resistance conditions giving new insights about mechanisms involved in resistance, as quorum sensing mechanisms, and suggesting possible novel bacterial targets to develop alternative antibiotic drugs. \ua9 2012 The Royal Society of Chemistry