Prevalence of self-reported food allergy in Tunisia: General trends and probabilistic modeling.

Background: Food allergy (FA) has become a major public health concern affecting millions of children and adults worldwide. In Tunisia, published data on FA are scarce. Methods: This study, was intended to fill the gap and estimate the frequency of allergy to different foods in the Sfax region, Tunisia, within self-reported FA. One hundred twenty-five (125) children (56% males, 1-17 years old), and 306 adults (17% males, 18-70 years old) were interviewed using a bilingual questionnaire. Results: The number of self-reported food allergens in this sample was 105; allergens were clustered in 8 foods: fruits, seafood, eggs, milk and dairy, cereals, nuts, vegetables, and peanuts. Cutaneous reactions were the most frequent symptoms, in both children and adults. About 40% of children and 30% of adults had a family history of FA. About 81% of adults and 38% of children are allergic to at least 1 non-food allergen. The most prevalent food allergen was the fruit group in both adults and children, followed by seafood. Most food allergies were mutually exclusive and 90% of individuals have a single FA. The relationship between self-declared FA was modeled using a Bayesian network graphical model in order to estimate conditional probabilities of each FA when other FA is present. Conclusions: Our findings suggest that the prevalence of self-reported FA in Tunisia depends on dietary habits and food availability since the most frequent allergens are from foods that are highly consumed by the Tunisian population.

miRNA implication in the pathogenesis and the outcome of Tunisian endemic pemphigus foliaceus.

Pemphigus foliaceus (PF) is a bullous autoimmune skin disease diagnosed through sera and skin analyses. PF severity is associated with maintained anti-Dsg1 sera levels and its prognosis is unpredictable. MicroRNA (miRNA), dynamic regulators of immune function, have been identified as potential biomarkers for some autoimmune diseases. This study aimed to assess the miRNA expression of miR-17-5p, miR-21-5p, miR-146a-5p, miR-155-5p and miR-338-3p using quantitative real-time PCR in peripheral blood mononuclear cells (PBMC) and lesional skin samples from untreated and treated PF patients (both remittent and chronic) over 3 months. Overall, miRNA expression was significantly higher in PBMC than in biopsy samples. Blood miR-21 expression was increased in untreated patients compared to controls and had a diagnostic value with an AUC of 0.78. After 6 weeks, it decreased significantly, similar to anti-Dsg1 antibodies and the PDAI score. In addition, a positive correlation was observed between cutaneous miR-21 expression and the disease activity score. Conversely, cutaneous expressions of miR-17, miR-146a and miR-155 were significantly higher in treated chronic patients compared to remittent ones. The cutaneous level of miR-155 positively correlated with pemphigus activity, making it a potential predictive marker for patients' clinical stratification with an AUC of 0.86.These findings suggest that blood miR-21 and cutaneous miR-155 can be used as supplemental markers for PF diagnosis and activity, respectively in addition to classical parameters.

Study of microbial communities and environmental parameters of seawater collected from three Tunisian fishing harbors in Kerkennah Islands: Statistical analysis of the temporal and spatial dynamics.

Surface seawater, collected from three fishing harbors during different seasons of the years 2015, 2016 and 2017, were assessed for physico-chemical analyses. Results showed that seawater was mainly polluted by hydrocarbons and some heavy metals. Microbial communities' composition and abundance in the studied harbors were performed using molecular approaches. SSCP analysis indicated the presence of Bacteria, Archaea and Eucarya, with dominance of the bacterial domain. Illumina Miseq analysis revealed that the majority of the sequences were affiliated with Bacteria whereas Archaea were detected at low relative abundance. The bacterial community, dominated by Proteobacteria, Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes, Actinobacteria and Chloroflexi phyla, are known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbons degradation and heavy metals resistance. The main objectives of this study are to assess, for the first time, the organic/inorganic pollution in surface seawater of Kerkennah Islands harbors, and to explore the potential of next generation marine microbiome monitoring to achieve the planning coastal managing strategies worldwide.

Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia.

ABSTRACT: Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals.

Charge clusters signatures in prokaryotic proteomes: Temperature-dependence and distribution.

The identification and the screening of Charged Clusters (CCs) residues in proteins is a key analysis to assess any quantitative structure-function correlation in proteins. Here, we present a proteome wide scan for the occurrence of (CCs) in 99292 proteins using a new tool. Finding Clusters Charge in Protein Sequences Program (FCCP). The FCCP has been employed to search CCs in 35 prokaryotic proteomes (7 Psychrophiles, 10 Mesophiles, 9 thermophiles and for 9 hyperthermophiles). A new repository of 855 CC has been created. Results showed that the mapped proteins containing positive and negative charge clusters are mostly transmembrane proteins while the conserved CCs within the same proteome are transposases or involved in DNA binding and integration. Interestingly, the negative charged cluster was associated to bacteria growth's temperature (p=0.002) acting as proteins' core signature. Taken together the various results provide a consistent picture of these screened CCs in terms of its potentials functional roles.

Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome.

BACKGROUND: Studying genetic variation distribution in proteins containing charged regions, called charge clusters (CCs), is of great interest to unravel their functional role. Charge clusters are 20 to 75 residue segments with high net positive charge, high net negative charge, or high total charge relative to the overall charge composition of the protein. We previously developed a bioinformatics tool (FCCP) to detect charge clusters in proteomes and scanned the human proteome for the occurrence of CCs. In this paper we investigate the genetic variations in the human proteins harbouring CCs. RESULTS: We studied the coding regions of 317 positively charged clusters and 1020 negatively charged ones previously detected in human proteins. Results revealed that coding parts of CCs are richer in sequence variants than their corresponding genes, full mRNAs, and exonic + intronic sequences and that these variants are predominately rare (Minor allele frequency < 0.005). Furthermore, variants occurring in the coding parts of positively charged regions of proteins are more often pathogenic than those occurring in negatively charged ones. Classification of variants according to their types showed that substitution is the major type followed by Indels (Insertions-deletions). Concerning substitutions, it was found that within clusters of both charges, the charged amino acids were the greatest loser groups whereas polar residues were the greatest gainers. CONCLUSIONS: Our findings highlight the prominent features of the human charged regions from the DNA up to the protein sequence which might provide potential clues to improve the current understanding of those charged regions and their implication in the emergence of diseases.

Screening for clusters of charge in human virus proteomes.

BACKGROUND: The identification of charge clusters (runs of charged residues) in proteins and their mapping within the protein structure sequence is an important step toward a comprehensive analysis of how these particular motifs mediate, via electrostatic interactions, various molecular processes such as protein sorting, translocation, docking, orientation and binding to DNA and to other proteins. Few algorithms that specifically identify these charge clusters have been designed and described in the literature. In this study, 197 distinctive human viral proteomes were screened for the occurrence of charge clusters (CC) using a new computational approach. RESULTS: Three hundred and seventy three CC have been identified within the 2549 viral protein sequences screened. The number of protein sequences that are CC-free is 2176 (85.3 %) while 150 and 180 proteins contained positive charge (PCC) and negative charge clusters (NCC), respectively. The NCCs (211 detected) were more prevalent than PCC (162). PCC-containing proteins are significantly longer than those having NCCs (p = 2.10-16). The most prevalent virus families having PCC and NCC were Herpesviridae followed by Papillomaviridae. However, the single-strand RNA group has in average three times more NCC than PCC. According to the functional domain classification, a significant difference in distribution was observed between PCC and NCC (p = 2. 10-8) with the occurrence of NCCs being more frequent in C-terminal region while PCC more often fall within functional domains. Only 29 proteins sequences contained both NCC and PCC. Moreover, 101 NCC were conserved in 84 proteins while only 62 PCC were conserved in 60 protein sequences. To understand the mechanism by which the membrane translocation functionalities are embedded in viral proteins, we screened our PCC for sequences corresponding to cell-penetrating peptides (CPPs) using two online databases: CellPPd and CPPpred. We found that all our PCCs, having length varying from 7 to 30 amino-acids were predicted as CPPs. Experimental validation is required to improve our understanding of the role of these PCCs in viral infection process. CONCLUSIONS: Screening distinctive cluster charges in viral proteomes suggested a functional role of these protein regions and might provide potential clues to improve the current understanding of viral diseases in order to tailor better preventive and therapeutic approaches.

Exploring proteome-wide occurrence of clusters of charged residues in eukaryotes.

Clusters of charged residues are one of the key features of protein primary structure since they have been associated to important functions of proteins. Here, we present a proteome wide scan for the occurrence of Charge Clusters in Protein sequences using a new search tool (FCCP) based on a score-based methodology. The FCCP was run to search charge clusters in seven eukaryotic proteomes: Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, and Saccharomyces cerevisiae. We found that negative charge clusters (NCCs) are three to four times more frequent than positive charge clusters (PCCs). The Drosophila proteome is on average the most charged, whereas the human proteome is the least charged. Only 3 to 8% of the studied protein sequences have negative charge clusters, while 1.6 to 3% having PCCs and only 0.07 to 0.6% have both types of clusters. NCCs are localized predominantly in the N-terminal and C-terminal domains, while PCCs tend to be localized within the functional domains of the protein sequences. Furthermore, the gene ontology classification revealed that the protein sequences with negative and PCCs are mainly binding proteins.