Afaf I. Shehata

Application of simple sequence repeat (SSR) markers for molecular diversity and heterozygosity analysis in maize inbred lines

There is an important role of understanding the genetic diversity among and within inbred lines at the molecular level for maize improvement in different breeding programs. The present study was devoted to estimate the level of genetic diversity among the inbred lines of maize using the simple sequence repeat analysis (SSR). The application of six different SSR markers successfully provided the information on similarity or diversity as well as the heterozygosity of the allelic loci for all the eight inbred line of maize.

Molecular identification of probiotics lactobacillus strain isolates by amplified ribosomal DNA restriction analysis (ARDRA)

In recent years interest in the probiotic lactobacilli has been stimulated by the use of these bacteria in products that are claimed to confer health benefits on the consumer. The objective of this study is to characterize probiotic Lactobacillus sp isolated from fermented millet drink , fresh milk and raw cow milk. All isolates are focusing on their screened for their probiotic potential activities, including Biochemical characterization and antagonistic activity . A total of seven colonies of lactobacilli isolated from twenty samples of fermented millet drink ,fresh and raw cow milk were obtained based on their colonial/morphological and biochemical characteristics. The Lactobacillus isolates obtained from fermented millet drinks are more effective than isolates from fresh milk and Cow milk as regards their antagonism or inhibition. Microbial identification has been drastically improved both quality and effectiveness wise by molecular methods applications. Molecular characterization of probiotic strains only in phenotypic and physiological characteristics is often with low level of discrimination, probably due to their co-evolution in the same ecological niches. Thus, the nucleotide base techniques provide an accurate basis for phylogenetic analysis and identification. The other specific aim of the study is to analyze a probiotic Lactobacillus sp isolates . The seven selected isolates were identify to species level as L. plantarum, L. lactis , L. acidophilu, and L. helveticus using API 50CH Kits. Amplified Ribosomal DNA Restriction Analysis (ARDRA) using Alu I (AGCT), Mbo I (GATC) and Msp I (CCGG) restriction enzymes and 16S rDNA gene sequencing was identified Lactobacillus isolates under study. ARDRA screening revealed unique patterns among seven isolates, with the same pattern for some the isolates. Gene fragments of 16S rDNA of strains representing specific patterns that needed to be sequence to confirm the identification of these species. These results confirmed that ARDRA is a good tool for identification and discrimination of bacterial species isolated from complex ecosystem and between closely related groups.

Brown macroalgae as bio-indicators for heavy metals pollution of Al-Jubail coastal area of Saudi Arabia

Wastes from both industrial and domestic sources, as well as habitat destruction have a substantial impact on the coastal environments. It causes serious problems in many countries and for several seas and oceans which leads to the extinction of several plant and animal species. Many water resources are no longer suitable for drinking or for agriculture as a result of pollution. The main aim of this study was to investigate the efficiency of four brown macroalage as bioindicators for toxic heavy metals (manganese (Mn), copper (Cu), zinc (Zn), arsenite (As), cadmium (Cd), and lead (Pb)) along Al-jubail industrial city coast at Persian Gulf (Saudi Arabia). Brown macroalage samples were collected from three different sites in three time points, January, March and May, 2010. The four collected brown macroalgae were identified as Sargassum angustifolium, Sargassum boveanum, Sargassum latifolium, and Padina gymnospora. The algal samples were cleaned using sea water and distilled water, dried, and the concentrations of various toxic metals were determined. The average concentrations of Mn, Co, Ni and Cd were within the expected limits of un-contaminated areas. However, the results indicate the high level of Zn ion accumulation in all tested brown algae, showing highest concentration in S. angustifolium > P. gymnospora > S. latifolium > S. boveanum with highest Zn concentration of 991 ± 49.1, 988 ± 47.5, 980 ± 44.2, and 911 ± 39.7 µg g -1 dry weights, respectively. In addition, Cu was detected at high concentration of 92.1 ± 3.7 ig g -1 dry weight in S. boveanum . These results clearly indicate the high pollution levels of Al-jubail industrial city coast with Zn and Cu toxic heavy metals, which is mostly due to uncontrolled disposal of industrial waste into coastal area. Furthermore, the consistency of Zn concentrations in all tested brown algae indicated the efficiency of the tested algae, including P. gymnospora, S. angustifolium, S. latifolium, and S. boveanum, for bioaccumulation and bio-monitoring studies of Zn. Key words : Brown algae, heavy metals, bio-indicators, Sargassum sp., Padina sp.

Genomics, phylogeny and in silico analysis of mitochondrial glutathione S-transferase-kappa from the camel Camelus dromedarius.

The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Peninsula. For most of its life, this species is exposed to both intrinsic and extrinsic genotoxic factors that cause gross DNA alterations in many organisms. GST enzymes constitute an important supergene family involved in protection against the deleterious effects of oxidative stress and xenobiotics. Cloning the camel mitochondrial GST kappa (GSTK) gene and comparing its structural similarities with different species may aid in understanding its evolutionary relics. We cloned the camel GSTK using RT-PCR. This yielded an open reading frame of 678 nucleotides, encoding a protein of 226 amino acid residues. In a comparative analysis, the cloned GSTK was used to screen orthologues from different organisms. Phylogenetic analysis demonstrated that the camel GSTK apparently evolved from an ancestral GSTK gene that predated the appearance of vertebrates, and it grouped with pig, cattle, dog, horse, human and monkey GSTKs. The calculated molecular weight of the translated ORF was 25.52 kDa and the isoelectric point was 8.4. The deduced cGSTK sequence exhibited high identity with many mammals, such as Bactrian camel (99.55%), pig, cattle and human (>74%), and lower identity with other unrelated organisms, such as frog (Xenopus tropicalis, 61%), chicken (Gallus gallus, 57%), salmon (Salmo salar, 49%), sponge (Amphimedon queenslandica, 46%), tick (Amblyomma maculatum, 45%) and roundworm (Caenorhabditis elegans, 33%). A 3D structure was built based on the crystal structure of the human and rat enzymes. The levels of cGSTK expression in five camel tissues were examined via real-time PCR. The highest level of cGSTK transcripts was found in the camel liver, followed by the testis, spleen, kidney and lung.

Mycobiota of Oil-Contaminated Soil Samples and Their Abilities for Dibenzothiophene Desulfurization

ABSTRACT High sulfur content of crude oil leads to poor quality of oil products and many other negative consequences such as corrosion, catalyst poisoning and environmental pollution. Saudi Arabia is seeking to reduce sulfur content in diesel and gasoline to 10 ppm and to lower benzene content in gasoline to 1%. Biotechnological processes such as biodesulfurization can be considered an alternative or complement to conventional oil refining technologies. So, the objective of the present project is to isolate and identify endogenous fungal isolates capable of oil biodesulfurization. From 60 oil-contaminated soil samples collected from Saudi Arabia, 15 species belonged to 9 fungal genera were collected and identified morphologically and with ITS sequencing. Members of Aspergillus, Penicillium and Fusarium were the most prevalent in the investigated samples. Among the collected fungal species, only Stachybotrys bisbyiisolates were able to utilize dibenzothiophene (DBT) as the sole sulfur source. Stachybotrys bisbyi TUSb1 could desulfurize 99% of the DBT (0.3 mM) as the sulfur source by a co-metabolism reaction with other carbon sources through the same pathway as 4S (involves sequential oxidation of the sulfur part and cleaving of the C–S bonds), and produced 2-hydroxy biphenyl (2-HBP) during 7 days of incubation at 30°C and 180 rpm. Stachybotrys bisbyi TUSb1 showed broad specificity for removing sulfur in different sulfur-containing compounds.

Bacterial quality control of domestic and imported brands of bottled water in Saudi Arabia

Water is one of the most abundant and essential commodities of man occupying about 70% of the earth’s surface and 60% of the human body therefore it should be continuously protected against microbial infections. Also, the mineral content in drinking water should be maintained within the acceptable range. Quality control of drinking water emerged with the invention of bottled drinking water. In this study, samples of bottled drinking water from Saudi markets were compared with tap water samples collected from different areas in Riyadh; both samples were tested for the presence of pathogenic bacteria. The bacterial isolates identified by the Biolog system (Hayward, CA, USA) include Bacillus cereus, Staphylococcus sp. and Pseudomonas aeruginosa in bottled drinking water, whereas tap water was mainly contaminated by P. aeruginosa. Bacterial contamination was highly observed in tap water samples and higher mineral content, determined by inductively coupled plasma-mass spectrometry (ICPMS) was also observed in tap water. Bacterial cell count determined as CFU/ml was observed in bottled drinking water. Decreased water bacterial number was achieved with the solar disinfection system (SODIS) for one day with direct exposure to sunlight in polyethylene terephthalate (PET) plastic bottles. Thus water considered to be consumed by humans must maintain good microbial and mineral qualities within the acceptable ranges and must undergo effective treatment in order to reduce bacterial count and infection.

Epidemiological characterization of serotype group B Streptococci neonatal infections associated with interleukin-6 level as a sensitive parameter for the early diagnosis

Group B streptococcal infection (Streptococcus agalactiae) is one of the leading causes of life-threatening disease in the early neonatal period, resulting in sepsis, pneumonia, and meningitis. During invasive infections, an excessive release of pro-inflammatory cytokine, such as interleukin-6 (IL-6), thus IL-6 gene is significant, as a diagnostic marker of systemic infection of the newborns. The present study aimed to describe the epidemiology diagnostic of GBS disease in neonatal by phenotypic and genotypic methods. Nine hundred and ninety-six samples were taken at Maternity and Children Hospital, Jeddah, Saudi Arabia for a period of one year (2011–2012). Results indicated that out of 217 infected samples, twenty (9.23.0%) were positive for group B Streptococci bacteria. This study also shows that female infants are more susceptible than males. The level of IL-6 was higher in mothers above 30 years. Twenty positive Streptococci group B isolates showed bands with the cylE gene primers in the border between 228 bp, 267 bp and 50 bp. Molecular detection by Real time polymerase chain reaction was also done to detect the target (Sip gene) encoding the Sip surface immunogenic protein. Specific primers and TaqMan probe were chosen for this purpose. A Real-time PCR method targeting the sip gene of GBS in neonates after delivery has been evaluated.