Eraqi, W. A., M. T. Elrakaiby, S. A. Megahed, N. H. Yousef, M. S. Elshahed, and A. S. Yassin, "Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis", MICROBIAL ECOLOGY, 2021. AbstractWebsite

Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.

Mohamed, A. A., A. S. Yassin, B. S. Gomaa, H. Darwish, R. S. Mohamed, S. Makled, A. Ramdan, and S. A. - E. * M. M. and Raafat, "Association of Polymorphism in Survivin gene and the risk of Liver Cancer resulting from Hepatitis C Virus among Egyptian patients", CURRENT CANCER DRUG TARGETS, vol. 21, pp. 1 - 1, 2021. AbstractWebsite

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El-Din, H. N. T., A. S. Yassin, Y. M. Ragab, and A. G. M. Hashem, "Phenotype-Genotype Characterization and Antibiotic-Resistance Correlations Among Colonizing and Infectious Methicillin-Resistant Staphylococcus aureus Recovered from Intensive Care Units.", INFECTION AND DRUG RESISTANCE, vol. 2021, issue 14, pp. 1557-1571, 2021.
Metwally, M. A., A. S. Yassin, E. M. Riad, H. M. Hamouda, and M. A. Amin, "Interferon Gamma Release Assay, A Powerful Tool for the Detection of Human and Bovine Tuberculosis in the Greater Cairo Area Compared to Other Diagnostic Tools", SAINS MALAYSIANA, vol. 49, issue 4, pp. 785-792, 2020.
Rabea, S., F. K. Alanazi, A. E. Ashour, M. M. Salem-Bekhit, A. S. Yassin, N. A. Moneib, A. G. M. Hashem, and N. Haq, "Salmonella-innovative targeting carrier: Loading with doxorubicin for cancer treatment", SAUDI PHARMACEUTICAL JOURNAL, vol. 28, issue 10, pp. 1253 - 1262, 2020. AbstractWebsite

Cell- based targeted delivery is recently gain attention as a promising platform for delivery of anticancer drug in selective and efficient manner. As a new biotechnology platform, bacterial ghosts (BGs) have novel biomedical application as targeted drug delivery system (TDDS). In the current work, Salmonellas’ BGs was utilized for the first time as hepatocellular cancer (HCC) in-vitro targeted delivery system. Successful BGs loading and accurate analysis of doxorubicin (DOX) were necessary steps for testing the applicability of DOX loaded BGs in targeting the liver cancer cells. Loading capacity was maximized to reach 27.5 µg/mg (27.5% encapsulation efficiency), by incubation of 10 mg BGs with 1 mg DOX at pH 9 in constant temperature (25 °C) for 10 min. In-vitro release study of DOX loaded BGs showed a sustained release (182 h) obeying Higuchi sustained kinetic release model. The death rate (tested by MTT assay) of HepG2 reached to 64.5% by using of 4 μg/ml, while it was about 51% using the same concentration of the free DOX (P value < 0.0001 One-way ANOVA analysis). The proliferative inhibitory concentration (IC50) of the DOX combined formula was 1.328 µg/ml that was about one third of the IC50 of the free DOX (3.374 μg/ml). Apoptosis analysis (tested by flow-cytometry) showed more accumulation in early apoptosis (8.3%) and late apoptosis/necrosis (91%) by applying 1 μg/ml BGs combined DOX, while 1 μg/ml free DOX showed 33.4% of cells in early apoptosis and 39.3% in late apoptosis/necrosis, (P value˃ 0.05: one-way ANOVA). In conclusion, DOX loaded Salmonellas’ BGs are successfully prepared and tested in vivo with promising potential as hepatocellular cancer (HCC) targeted delivery system.

Sheraba, N. S., M. R. Diab, A. S. Yassin, M. A. Amin, Y. Alhamhoom, and H. H. Zedan, "An Efficient Method for Endotoxin Removal from Snake Antivenoms", CHROMATOGRAPHIA, vol. 83, issue 6, pp. 779 - 787, 2020. AbstractWebsite

Parenterally administered snake antivenom immunoglobulins are the only specific treatment for envenoming by snakebites. Endotoxin removal is a necessary part of good manufacturing practice for antivenom products to avoid life-threatening consequences associated with injecting endotoxin-contaminated product. Optimization of pH is an essential factor in endotoxin purification. This study aimed to compare ultrafiltration, ion-exchange chromatography and affinity resin-based chromatography techniques at different pH values to select the depyrogenation method with the highest endotoxin removal efficiency and optimum protein/product recovery. Affinity resin-based chromatography achieved 91.2% protein recovery at acidic pH without detectable endotoxins, while ion-exchange chromatography achieved 74.42% protein recovery at pH 7.5. In contrast, ultrafiltration achieved the lowest protein recovery compared to other chromatography techniques. In addition, ultrafiltration was ineffective in removing serum albumin (~ 42–57 kDa) and low molecular weight (MW) Fc fragments (~ 24–31 kDa). In conclusion, affinity resin-based chromatography has proven to be the most effective endotoxin removal method, while ultrafiltration may not be appropriate for the removal of bacterial LPS from antivenom sera. Moreover, this study demonstrated the existence of an optimum pH for each chromatographic method for the purpose of producing sterile and endotoxin-free snake antivenoms.

Özdemir, V., Y. K. Arga, R. K. Aziz, M. Bayram, S. N. Conley, C. Dandara, L. Endrenyi, E. Fisher, C. K. Garvey, N. Hekim, et al., "Digging Deeper into Precision/Personalized Medicine: Cracking the Sugar Code, the Third Alphabet of Life, and Sociomateriality of the Cell", OMICS: A Journal of Integrative Biology, vol. 24, no. 2, pp. 62-80, 2020. AbstractWebsite

Precision/personalized medicine is a hot topic in health care. Often presented with the motto “the right drug, for the right patient, at the right dose, and the right time,” precision medicine is a theory for rational therapeutics as well as practice to individualize health interventions (e.g., drugs, food, vaccines, medical devices, and exercise programs) using biomarkers. Yet, an alien visitor to planet Earth reading the contemporary textbooks on diagnostics might think precision medicine requires only two biomolecules omnipresent in the literature: nucleic acids (e.g., DNA) and proteins, known as the first and second alphabet of biology, respectively. However, the precision/personalized medicine community has tended to underappreciate the third alphabet of life, the “sugar code” (i.e., the information stored in glycans, glycoproteins, and glycolipids). This article brings together experts in precision/personalized medicine science, pharmacoglycomics, emerging technology governance, cultural studies, contemporary art, and responsible innovation to critically comment on the sociomateriality of the three alphabets of life together. First, the current transformation of targeted therapies with personalized glycomedicine and glycan biomarkers is examined. Next, we discuss the reasons as to why unraveling of the sugar code might have lagged behind the DNA and protein codes. While social scientists have historically noted the importance of constructivism (e.g., how people interpret technology and build their values, hopes, and expectations into emerging technologies), life scientists relied on the material properties of technologies in explaining why some innovations emerge rapidly and are more popular than others. The concept of sociomateriality integrates these two explanations by highlighting the inherent entanglement of the social and the material contributions to knowledge and what is presented to us as reality from everyday laboratory life. Hence, we present a hypothesis based on a sociomaterial conceptual lens: because materiality and synthesis of glycans are not directly driven by a template, and thus more complex and open ended than sequencing of a finite length genome, social construction of expectations from unraveling of the sugar code versus the DNA code might have evolved differently, as being future-uncertain versus future-proof, respectively, thus potentially explaining the “sugar lag” in precision/personalized medicine diagnostics over the past decades. We conclude by introducing systems scientists, physicians, and biotechnology industry to the concept, practice, and value of responsible innovation, while glycomedicine and other emerging biomarker technologies (e.g., metagenomics and pharmacomicrobiomics) transition to applications in health care, ecology, pharmaceutical/diagnostic industries, agriculture, food, and bioengineering, among others.

Norsigian, C. J., H. Attia, R. Szubin, A. S. Yassin, B. Ø. Palsson, R. K. Aziz, and J. M. Monk, "Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates", Frontiers in cellular and infection microbiology, vol. 9: Frontiers Media S.A., pp. 161 - 161, 2019/05/24. AbstractWebsite

The emergence and spread of metallo-beta-lactamase-producing multidrug-resistant (MDR) Klebsiella pneumoniae is a serious public health threat, which is further complicated by the increased prevalence of colistin resistance. The link between antimicrobial resistance acquired by strains of Klebsiella and their unique metabolic capabilities has not been determined. Here, we reconstruct genome-scale metabolic models for 22 K. pneumoniae strains with various resistance profiles to different antibiotics, including two strains exhibiting colistin resistance isolated from Cairo, Egypt. We use the models to predict growth capabilities on 265 different sole carbon, nitrogen, sulfur, and phosphorus sources for all 22 strains. Alternate nitrogen source utilization of glutamate, arginine, histidine, and ethanolamine among others provided discriminatory power for identifying resistance to amikacin, tetracycline, and gentamicin. Thus, genome-scale model based predictions of growth capabilities on alternative substrates may lead to construction of classification trees that are indicative of antibiotic resistance in Klebsiella isolates.

Attia, H., R. Szubin, A. S. Yassin, J. M. Monk, and R. K. Aziz, "Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt", Microbiology Resource Announcements, vol. 8, no. 7: American Society for Microbiology Journals, 2019. AbstractWebsite

The emergence and spread of metallo-beta-lactamase-producing multidrug-resistant Klebsiella pneumoniae are a serious public health threat. Here, we report the draft genome sequences of four K. pneumoniae strains isolated from Cairo, Egypt, including two panresistant colistin-resistant strains. Genome annotation indicated a number of virulence and resistance genes agreeing with observed phenotypes.

Sheraba, N. S., M. R. Diab, A. S. Yassin, M. A. Amin, and H. H. Zedan, "A Validation study of the Limulus Amebocyte Lysate test as an end-product endotoxin test for Polyvalent Horse Snake Antivenom", PDA Journal of Pharmaceutical Science and Technology, 2019. AbstractWebsite

Snake antivenoms are the only definitive management of snake envenoming's. Endotoxin contamination is a serious threat to the safety of parenteral drugs. A greater understanding of the nature of LAL-Test interferences and the use permissible dilutions has minimized enhancement problems. Common interference mechanisms include suboptimal pH, enzyme or protein modification, and non-specific LAL activation. The study aimed at sorting out the interfering factors before validating the antitoxic sera preparations to avoid false positive results when testing snake venom antiserum samples by (LAL) method. Phase I (Preliminary Screening /Interference Assay) was performed to determine a compatible test dilution, which is then used in Phase II (Inhibition-Enhancement / Validation Study). The results revealed that dilution is the best approach to resolve interferences by a ratio of 1:80 (MVD) plus a specific treatment as heat-activation at 70-80°C for 10 minutes accompanied by rehydration of LAL reagent with Endotoxin Specific Buffer Solution to sort out the enhancement problem.

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