Enhancing Bioinformatics and Genomics Courses: Building Capacity and Skills via Lab Meeting Activities

Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1-day lab meeting in the framework of two previously organized 3-month courses on “Bioinformatics and Genome Analyses”. The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self-confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses.     

Breast-Feeding Protects Infantile Diarrhea Caused by Intestinal Protozoan Infections

This study investigated the effect of breast-feeding in protection against protozoan infection in infants with persistent diarrhea. Infants were classified into 2 groups; 161 breast-fed infants and the same number of non-breast-fed infants. Microscopic examinations of stool were done for detection of parasites and measuring the intensity of infection. Moreover, serum levels of IgE and TNF-α were measured by ELISA. Cryptosporidium spp., Entamoeba histolytica/Entamoeba dispar, Giardia lamblia, and Blastocystis sp. were demonstrated in infants with persistent diarrhea. The percentage of protozoan infections was significantly lower in breast-fed infants than that in the non-breast-fed infants. The levels of IgE and TNF-α were significantly lower in the breast-fed group than in the non-breast-fed group. There were significant positive associations between the serum levels of IgE and TNF-α and the intensity of parasite infection in the breast-fed group. It is suggested that breast-feeding has an attenuating effect on the rate and intensity of parasite infection.     

An Epidemiological Study of Cutaneous Leishmaniasis in Al-Jabal Al-Gharbi,Libya

Cutaneous leishmaniasis (CL) is an endemic parasitic infection in the Mediterranean region, including Libya and its Al-jabal Al-gharbi province. We aimed at studying the occupational relevance as well as other epidemiological aspects of CL. We investigated 140 CL cases who attended at Gharyan outpatient polyclinic during a period of 6 months in 2009. CL infection was clinically diagnosed and confirmed by demonstration of Leishmania parasites on smears from lesions. Our findings showed that males were more affected than females (P=0.04), and people above 10-years were more affected than younger ones (P=0.0001). A significant percent of CL cases belonged to Al-Kawasem subprovince (P=0.0001). Farm-related activities were the most frequent occupations among CL cases (P=0.04). In addition to farm workers, housewives and students are at risk groups since they are engaged at farm activities. Moreover, those who have occupations that require staying outdoors for a part of night, e.g., policemen, are also at risk. Compared to children, adult CL patients had multiple lesions (P=0.001) that were more prevalent in their upper and lower extremities than the face (P=0.0001). We conclude that CL is a major health problem in Al-jabal Al-gharbi province of Libya. The presence of rodents and sandflies makes it a suitable environment for Leishmania to spread in an endemic epidemiological pattern. Being engaged in farming activities or outdoor occupations increases the risk of infection. Various clinical patterns of CL suggest the presence of more than 1 species of Leishmania at Al-jabal Al-gharbi province. We propose that the 2 species responsible for CL in this area are L. major and L. tropica. Further investigations to identify the leishmanial species responsible for CL at Al-jabal Al-gharbi together with adoption of preventive and control programs are needed.     

Antimicrobial Resistance, Virulence Genes, and Genetic Lineages of Staphylococcus pseudintermedius in Healthy Dogs in Tunisia

Nasal swabs of 100 healthy dogs were obtained in 2011 in Tunisia and tested for Staphylococcus pseudintermedius recovery. Antimicrobial resistance profile and virulence gene content were determined. Multilocus-sequence-typing (MLST) and SmaI-pulsed-field gel electrophoresis (PFGE) were investigated. S. pseudintermedius was recovered in 55 of the 100 tested samples (55 %), and one isolate per sample was further studied. All 55 S. pseudintermedius isolates were susceptible to methicillin (MSSP) but showed resistance to the following antimicrobials (% resistant isolates/resistance gene): penicillin (56.4/blaZ), tetracycline (40/tetM), trimethoprim-sulfamethoxazole (23.7), fusidic acid (9), kanamycin (3.7/aph(3´)-Ia), erythromycin-clindamycin (1.8/erm(B)), streptomycin (1.8/ant(6)-Ia), chloramphenicol (1.8) and ciprofloxacin (1.8). The following toxin genes were identified (% of isolates): lukS/F-I (98.2), expA (5.5), se-int (98.2), sec _canine (1.8), siet (100), sea (5.5), seb (3.6), sec (10.9), sed (54.5), sei (5.5), sej (29.1), sek (3.6), ser (9.1), and hlg _v (38.2). Ten different sequence-types were detected among 11 representative MSSP isolates: ST20, ST44, ST69, ST70, ST78, ST100, ST108, ST160, ST161, and ST162, the last three ones revealing novel alleles or allele combinations. Eleven different PFGE-patterns were identified in these isolates. The nares of healthy dogs could be a reservoir of antimicrobial resistant and virulent MSSP, highlighting the presence of the recently described exfoliating gene expA and several enterotoxin genes.     

Comparative Genomic and Phylogenetic Analyses of Gammaproteobacterial glg Genes Traced the Origin of the Escherichia coli Glycogen glgBXCAP Operon to the Last Common Ancestor of the Sister Orders Enterobacteriales and Pasteurellales

Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria.     

Assessment of genetic diversity of Mediterranean bread wheat using Randomly Amplified Polymorphic DNA (RAPD) markers

The genetic diversity of 14 bread wheat (Triticum aestivum L.) varieties originating from Mediterranean region (Egypt and Greece) was assessed by means of Randomly Amplified Polymorphic DNA (RAPD) markers. Seventeen RAPD markers were used to analyze and compare genetic diversity among the selected wheat varieties. Average of similarity coefficients based on RAPD markers for all of the studied varieties was 0.718. Average and range of genetic similarity coefficients among varieties obtained from both Egypt and Greece independently were 0.765 (from 0.66 to 0.886) and 0.723 (from 0.604 to 0.896), respectively. The cophenetic correlation coefficients of the three RAPD dendrograms (generated for all of the 14 varieties, the seven Egyptian varieties separately and the seven Greek varieties separately) were r = 0.774, 0.80, and 0.74, respectively. Both cluster analysis and Principal Coordinate Analysis (PCOORDA) were able to differentiate between Egyptian and Greek wheat varieties, but PCOORDA was more efficient in its separation. The percentage of variance accounted for the first two principal coordinates was 49.45% of total genetic variance for RAPD. Notable geographical divergence was found between Egyptian and Greek wheat varieties.     

Diazen-1-ium-1,2-diolated nitric oxide donor ester prodrugs of 5-(4-carboxymethylphenyl)-1-(4-methanesulfonylphenyl)-3-trifluoromethyl-1H-pyrazole and its aminosulfonyl analog: Synthesis,biological evaluation and nitric oxide release studies

A new class of hybrid nitric oxide-releasing anti-inflammatory (AI) ester prodrugs (NONO-coxibs) wherein an O²-acetoxymethyl-1-(N-ethyl-N-methylamino)diazen-1-ium-1,2-diolate (13a–b), or O²-acetoxymethyl-1-(2-methylpyrrolidin-1-yl)diazen-1-ium-1,2-diolate (16a–b), NO-donor moiety was covalently coupled to the COOH group of 5-(4-carboxymethylphenyl)-1-(4-methane(amino)sulfonylphenyl)-3-trifluoromethyl-1H-pyrazole (11a–b) was synthesized. The percentage of NO released from these diazen-1-ium-1,2-diolates was significantly higher (59.6–74.6% of the theoretical maximal release of 2 molecules of NO/molecule of the parent hybrid ester prodrug) upon incubation in the presence of rat serum, relative to incubation with phosphate buffer (PBS) at pH 7.4 (5.0–7.2% range). These incubation studies suggest that both NO and the AI compound would be released from the parent NONO-coxib upon in vivo cleavage by non-specific serum esterases. All compounds were weak inhibitors of the COX-1 isozyme (IC₅₀ = 8.1–65.2 μM range) and modest inhibitors of the COX-2 isozyme (IC₅₀ = 0.9–4.6 μM range). The most potent parent aminosulfonyl compound 11b exhibited AI activity that was about sixfold greater than that for aspirin and threefold greater than that for ibuprofen. The ester prodrugs 13b, 16b exhibited similar AI activity to that exhibited by the more potent parent acid 11b when the same oral μmol/kg dose was administered. These studies indicate hybrid ester AI/NO donor prodrugs of this type (NONO-coxibs) constitute a plausible drug design concept targeted toward the development of selective COX-2 inhibitory AI drugs that are devoid of adverse cardiovascular effects.