Ahmed Rebai

Detection of Chemlali Extra-Virgin Olive Oil Adulteration Mixed with Soybean Oil, Corn Oil, and Sunflower Oil by Using GC and HPLC

Fatty acid composition as an indicator of purity suggests that linolenic acid content could be used as a parameter for the detection of extra/virgin olive oil fraud with 5% of soybean oil. The adulteration could also be detected by the increase of the trans-fatty acid contents with 3% of soybean oil, 2% of corn oil, and 4% of sunflower oil. The use of the ΔECN42 proved to be effective in Chemlali extra-virgin olive oil adulteration even at low levels: 1% of sunflower oil, 3% of soybean oil, and 3% of corn oil. The sterol profile is almost decisive in clarifying the adulteration of olive oils with other cheaper ones: 1% of sunflower oil could be detected by the increase of Δ7-stigmastenol and 4% of corn oil by the increase of campesterol. Linear discriminant analysis could represent a powerful tool for faster and cheaper evaluation of extra-virgin olive oil adulteration.

IGD: a resource for intronless genes in the human genome.

Intronless genes (IGs) fraction varies between 2.7 and 97.7% in eukaryotic genomes. Although many databases on exons and introns exist, there was no curated database for such genes which allowed their study in a concerted manner. Such a database would be useful to identify the functional features and the distribution of these genes across the genome. Here, a new database of IGs in eukaryotes based on GenBank data was described. This database, called IGD (Intronless Gene Database), is a collection of gene sequences that were annotated and curated. The current version of IGD contains 687 human intronless genes with their protein and CDS sequences. Some features of the entries are given in this paper. Data was extracted from GenBank release 183 using a Perl script. Data extraction was followed by a manual curation step. Intronless genes were then analyzed based on their RefSeq annotation and Gene Ontology functional class. IGD represents a useful resource for retrieval and in silico study of intronless genes. IGD is available at http://www.bioinfo-cbs.org/igd with comprehensive help and FAQ pages that illustrate the main uses of this resource.

Association study of CARD8 (p.C10X) and NLRP3 (p.Q705K) variants with rheumatoid arthritis in French and Tunisian populations

The objective of the study was to investigate the association of caspase activating and recruitment domain 8 (CARD8) and nucleotide‐binding oligomerization domain, leucine‐rich repeat and pyrin domain containing 3 (NLRP3) polymorphisms with rheumatoid arthritis (RA) in Tunisian and French populations. CARD8 (c.30T>A, rs2043211) and NLRP3 (c.2113C>A, rs35829419) single nucleotide polymorphisms (SNPs) were genotyped in 100 French RA trio families and 141 Tunisian patients with RA and 191 unrelated healthy controls, using TaqMan® allelic discrimination assay. The genetic analyses for the association and linkage in French families were performed using the comparison of allelic frequencies (AFBAC), the genotype relative risk (GRR) and the transmission disequilibrium test (TDT). Data for case and control samples were analysed by chi‐square‐test, GRR and odds ratio (OR). No significant differences between alleles and genotypes frequencies were detected in French trio and Tunisian patients with RA and controls, either with CARD8 or with NLRP3 SNPs both in French and in Tunisian populations. Moreover, stratifying patients according to the presence of rheumatoid factor (RF), anti‐cyclic peptides antibodies (ACPA), erosion, nodules, other autoimmune disease or HLA‐DRB1*04‐positive subgroups did not show any significant association with CARD8 or NLRP3 (Pu2003≥u20030.05). This study suggests that variations in the innate immunity genes CARD8 (p.C10X) and NLRP3 (p.Q705K) have no effect on RA susceptibility either in the Tunisian or in the French population.

Evaluation of an in silico predicted specific and immunogenic antigen from the OmcB protein for the serodiagnosis of Chlamydia trachomatis infections

BackgroundThe OmcB protein is one of the most immunogenic proteins in C. trachomatis and C. pneumoniae infections. This protein is highly conserved leading to serum cross reactivity between the various chlamydial species. Since previous studies based on recombinant proteins failed to identify a species specific immune response against the OmcB protein, this study evaluated an in silico predicted specific and immunogenic antigen from the OmcB protein for the serodiagnosis of C. trachomatis infections.ResultsUsing the ClustalW and Antigenic programs, we have selected two predicted specific and immunogenic regions in the OmcB protein: the N-terminal (Nt) region containing three epitopes and the C-terminal (Ct) region containing two epitopes with high scores. These regions were cloned into the PinPoint Xa-1 and pGEX-6P-1 expression vectors, incorporating a biotin purification tag and a glutathione-S-transferase tag, respectively. These regions were then expressed in E. coli. Only the pGEX-6P-1 has been found suitable for serological studies as its tag showed less cross reactivity with human sera and was retained for the evaluation of the selected antigens. Only the Ct region of the protein has been found to be well expressed in E. coli and was evaluated for its ability to be recognized by human sera. 384 sera were tested for the presence of IgG antibodies to C. trachomatis by our in house microimmunofluorescence (MIF) and the developed ELISA test. Using the MIF as the reference method, the developed OmcB Ct ELISA has a high specificity (94.3%) but a low sensitivity (23.9). Our results indicate that the use of the sequence alignment tool might be useful for identifying specific regions in an immunodominant antigen. However, the two epitopes, located in the selected Ct region, of the 24 predicted in the full length OmcB protein account for approximately 25% of the serological response detected by MIF, which limits the use of the developed ELISA test when screening C. trachomatis infections.ConclusionThe developed ELISA test might be used as a confirmatory test to assess the specificity of serological results found by MIF.

Monitoring of Quality and Stability Characteristics and Fatty Acid Compositions of Refined Olive and Seed Oils during Repeated Pan- and Deep-Frying Using GC, FT-NIRS, and Chemometrics

Refined olive, corn, soybean, and sunflower oils were used as cooking oils for deep-frying at two different temperatures, 160 and 190 °C, and for pan-frying of potatoes at 180 °C for 10 successive sessions under the usual domestic practice. Several chemical parameters were assayed during frying operations to evaluate the status of the frying oils. Refined olive oil, as frying oil, was found to be more stable than the refined seed oils. In fact, this oil has proven the greatest resistance to oxidative deterioration, and its trans-fatty acid contents and percentages of total polar compounds were found to be lower at 160 °C during deep-frying. Finally, chemometric analysis has demonstrated that the lowest deterioration of the quality of all refined oils occurred in the refined olive oil during deep-frying at 160 °C and the highest deterioration occurred in the refined sunflower oil during pan-frying at 180 °C.

Receptor tyrosine kinases: from biology to pathology

Receptor tyrosine kinases (RTKs) are transmembrane proteins involved in the control of fundamental cellular processes in metazoans. RTKs possess a general structure that includes an extracellular domain, a transmembrane domain and a highly conserved tyrosine kinase domain. RTKs are classified according to their variable extracellular ligand-binding domain. Studies of human RTK members have yielded a wealth of information elucidating their importance. Improper functioning of these enzymes due to mutations, mainly in the kinase domain, is often manifested in various human diseases and is known to be involved in several types of cancer. Here we summarize most of human RTKs, their cognate ligands, as well as related diseases and discuss the eventual use of certain RTKs as new therapeutic targets.

Association of IRF5 gene polymorphisms with rheumatoid arthritis in a Tunisian population

Objective: A strong genetic association of rheumatoid arthritis (RA) with the interferon regulatory factor 5 (IRF5) gene has been described previously in a Swedish population, although this result was not confirmed in a French population. We undertook an association study between IRF5 and the RA phenotype, as well as a study with serological markers of RA, in a Tunisian population. Methods: A single‐nucleotide polymorphism (SNP; rs2004640) was genotyped using a Taqman 5′ allelic discrimination assay on an ABI 7500 real‐time polymerase chain reaction (PCR) instrument in 140 RA patients and 185 controls. Rheumatoid factor (RF) and anti‐citrullinated protein/peptide antibodies (ACPA) were determined by enzyme‐linked immunosorbent assay (ELISA). Association was assessed based on the χ2 test and odds ratios (ORs) with 95% confidence intervals (CIs). Results: The frequency of the TT genotype of the IRF5 SNP rs2004640 differed significantly between patients and controls (p = 0.01). This difference was greater when a subgroup of patients with another ‘autoimmune’ disorder was considered (p = 0.007). A weak but significant association was also found in a subgroup of patients who were positive for ACPA (p = 0.04) or erosion (p = 0.01). Conclusions: Our results indicate that the TT genotype of the IRF5 (rs2004640) dimorphism is associated with RA in a Tunisian population.

High frequency and founder effect of the CYP3A4*20 loss-of-function allele in the Spanish population classifies CYP3A4 as a polymorphic enzyme

Cytochrome P450 3A4 (CYP3A4) is a key drug-metabolizing enzyme. Loss-of-function variants have been reported as rare events, and the first demonstration of a CYP3A4 protein lacking functional activity is caused by CYP3A4*20 allele. Here we characterized the world distribution and origin of CYP3A4*20 mutation. CYP3A4*20 was determined in more than 4000 individuals representing different populations, and haplotype analysis was performed using CYP3A polymorphisms and microsatellite markers. CYP3A4*20 allele was present in 1.2% of the Spanish population (up to 3.8% in specific regions), and all CYP3A4*20 carriers had a common haplotype. This is compatible with a Spanish founder effect and classifies CYP3A4 as a polymorphic enzyme. This constitutes the first description of a CYP3A4 loss-of-function variant with high frequency in a population. CYP3A4*20 results together with the key role of CYP3A4 in drug metabolism support screening for rare CYP3A4 functional alleles among subjects with adverse drug events in certain populations.

Bacillus subtilis bacteriocin Bac 14B with a broad inhibitory spectrum: Purification, amino acid sequence analysis, and physicochemical characterization

Bacillus subtilis strain 14B was used to produce a novel antimicrobial peptide (bacteriocin) called Bac 14B. Pure bacteriocin was obtained after heat and acidic treatments (80°C and pH 4), precipitation by ammonium sulfate, and chromatography on Sephadex G-50 and Mono Q Sepharose columns. Based on MALDI-TOF mass spectrometry analysis, purified Bac 14B is a monomer protein with a molecular mass of 20110.13 Da. N-terminal sequencing allowed for the straightforward identification of its first 12 residues, which were of a pure bacteriocin. It also revealed that this bacteriocin contained a unique sequence, namely M-L-K-A-N-L-Q-N-P-L-N-A, suggesting the identification of a novel compound. Bac 14B was stable for 1 h at temperatures up to 80°C and pH of 4 ∼ 8. It also proved sensitive to various proteases, which demonstrated its protein nature. Bac 14B displayed a bacteriolytical mode of action and a broad range of inhibitory spectra toward Gram-positive and -negative pathogens. Interestingly, based on conventional agronomic seed vigor parameters, the application of Bac 14B (500 activity units/mL) to various crops revealed that this bacteriocin was a potent exogenous enhancer of growth that stimulated the seedling vigor of tomatoes and muskmelons. Compared to those of the control, the germination percentage, shoot weight, shoot height, and root length were all significantly enhanced in Bac 14B-treated plant seeds. Bac 14B also exhibited effective disinfectant properties against a wide range of seedborne diseases and significant effects on the control of damping off diseases, particularly at the pregermination stage. It also proved to be effective against root rot diseases caused by Alternaria solani and other bacterial seedborne pathogens such as wilt diseases. The findings indicate that Bac 14B is the first B. subtilis-produced bacteriocin ever reported to exhibit such promising biological properties.

Population genetics of 17 Y-STR markers in West Libya (Tripoli region).

Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both R(ST) pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations.