FACULTY OF SCIENCE

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Annotation of virulence factors in schistosomes for the development of a SchistoVir database
(Academic Journals, 2013-04) Adebayo, A. S.; Anumudu, C. I.
Scientific efforts in the eradication of neglected tropical diseases, such as those caused by the parasitic helminthes, can be improved if a database of key virulence factors directly implicated in pathogenesis is available. As a first step towards creating SchistoVir, a database of virulence protein factors in schistosomes, in this study, we curated, annotated and aligned sequences of twenty virulence factors identified from the literature, using several bioinformatics tools including UniProtKB, SchistoDB, VirulentPred, InterProScan, ProtScale, MotifScan, TDRtarget, SignalP, MODBASE, PDB and MUSCLE. Among the protein entries, the most frequently occurring amino acid residues were lysine, serine, leucine, glutamine, glycine and cysteine in order of magnitude. Although sequence repeat regions (SRRs) of significant value were identified manually in fifty percent of the proteins (while dipeptide repeats (DiPs) and single amino acid repeats (SAARs) were not), nevertheless, seventy-two percent of the protein entries were classified as virulent by the prediction model, VirulentPred. Most of the entries (eighty percent) did not have target compounds based on the database of available chemical compounds at TDRtargets. Fourteen of the twenty entries (seventy percent) had more than 30 consecutively negative amino acid residues based on the ProtScale’s Kyte and Doolittle hydrophobicity plot. Hence, they would be hydrophobic enough to be transmembrane in location or secretory in nature. Only 7 (tyrosinase, serine protease1, Tspan-1, VAL4, cathepsin b and L and calreticulin) had cleavage sites and signal peptides, while none had a significant signal anchor probability. The annotations and characterization provided by this work and the development of a SchistoVir database will aid in further research of schistosome pathogenesis and control.
Genetic characterization of fin fish species from the Warri River at Ubeji, Niger Delta, Nigeria
(Academic Journals, 2014-07) Asagbra, M. C.; Adebayo, A. S.; Ugwumba, O. A.; Ugwumba, A. A. A.; Anumudu, C. I.
A study to evaluate the genetic similarities and differences among 11 specimens of cichlids and four specimens of mudcatfishes obtained from Warri River was carried out through DNA fingerprinting analysis using random amplified polymorphic DNA (RAPD) amplification with seven decamer primers and dendrograms through unweighted pair-group method with average (UPGMA) cluster analysis. The total number of bands generated by seven RAPD primers, ranged between 2 to 33 for the cichlids and 8 to 28 for catfish family, with band size between 100 to 800 bp. The primers produced 228 bands in total 119 for cichlids and 109 for the catfishes, with 24% polymorphism. Considerable genetic variation was observed within species (especially within Tilapia Zilli, T. guineesis and Clarias gariepinus), between species in same genera (T. zilli and T. guineensis ) and among cichlids and catfishes. The most consistent of the RAPD primers generated 87 bands among the cichlids with 23 bands (26%) polymorphic and 74% conserved. Among the catfishes, the primers produced 69 bands with 16 (23%) polymorphic. The data show that the RAPD technique was useful and sensitive in differentiating various fish genera and species.
Polycyclic aromatic hydrocarbons in water, sediment and fish from the Warri River at Ubeji, Niger Delta, Nigeria
(NISC (Pty) Limited and Taylor & Francis, 2015) Asagbra, M. C.; Adebayo, A. S.; Anumudu, C. I.; Ugwumba, O. A.; Ugwumba, A. A. A.
The Warri River at Ubeji, Nigeria, receives pollutants from an oil refinery. The levels of 16 priority polycyclic aromatic hydrocarbons (PAHs) in water, sediment and the tissue of tilapia from the Warri River were investigated in 2010 using gas chromatography with mass spectrometry. Eleven PAHs were found in the sediment and nine in fish and water, with total mean concentrations of 4 587.7 ng g-1, 1 098.5 ng g-1 and 34 ng ml-1 in sediment, fish tissues and water, respectively. Lower molecular weight PAHs were predominant, with naphthalene accounting for the highest concentration in all samples. Carcinogenic PAHs detected included benzo(a)pyrene, benzo(a)anthracene and chrysene. The predominance of lower molecular weight PAHs in the study area is an indication of recent pollution of petrogenic origin from the Warri Refining and Petrochemical Company’s refinery.