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.

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, , 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.

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.

Eraqi, W. A., M. T. Elrakaiby, S. A. Megahed, N. H. Yousef, M. S. Elshahed, and A. S. Yassin, "The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt)", OMICS: A Journal of Integrative Biology, vol. 22, no. 8, pp. 553-564, 2018. AbstractWebsite

Abstract World freshwater supplies are in need of microbiome diversity analyses as a first step to future ecological studies, and to monitor water safety and quality. The Nile is a major north-flowing river in Africa that displays both spatial and temporal variations in its water quality. Here, we present the first microbiome analysis of the Nile River water in two seasons: (1) summer representing the wet season, and (2) winter representing the dry season, as sampled around Cairo, the capital of Egypt. Surface river water samples were collected from selected locations along the path of river, and the microbial composition was analyzed by next-generation sequencing of the 16S rRNA gene. We found a striking stability in the Nile microbiome community structure along the examined geographical urban sites and between the wet and dry seasons as evidenced by the high proportion of shared operational taxonomic unit values among all samples. The community was dominated by the Cyanobacteria (mainly Synechococcus), Actinobacteria candidate family (ACK-M1), and Proteobacteria (mainly family Comamonadaceae). Among these dominant taxa, Synechococcus exhibited seasonal driven variation in relative abundance. Other taxa were predominantly rare across all seasons and locations, including genera members of which have been implicated as pathogens such as Acinetobacter, Aeromonas, and Legionella. In addition, comparisons with data on freshwater microbiome in other world regions suggest that surface water communities in large rivers exhibit limited variation. Our results offer the first insights on microbial composition in one of the most notable rivers near a large metropolis.

Rabea, S., M. M. Salem-Bekhit, F. K. Alanazi, A. S. Yassin, N. A. Moneib, and A. G. M. Hashem, "A novel protocol for bacterial ghosts’ preparation using tween 80", Saudi Pharmaceutical Journal, vol. 26, no. 2, pp. 232 - 237, 2018. AbstractWebsite
Hashem, Y. A., H. M. Amin, T. M. Essam, A. S. Yassin, and R. K. Aziz, Biofilm formation in enterococci: genotype-phenotype correlations and inhibition by vancomycin, , vol. 7, issue 1, pp. 5733, 2017. AbstractWebsite

Enterococci are nosocomial pathogens that can form biofilms, which contribute to their virulence and antibiotic resistance. Although many genes involved in biofilm formation have been defined, their distribution among enterococci has not been comprehensively studied on a genome scale, and their diagnostic ability to predict biofilm phenotypes is not fully established. Here, we assessed the biofilm-forming ability of 90 enterococcal clinical isolates. Major patterns of virulence gene distribution in enterococcal genomes were identified, and the differentiating virulence genes were screened by polymerase chain reaction (PCR) in 31 of the clinical isolates. We found that detection of gelE in Enterococcus faecalis is not sufficient to predict gelatinase activity unless fsrAB, or fsrB alone, is PCR-positive (P = 0.0026 and 0.0012, respectively). We also found that agg is significantly enriched in isolates with medium and strong biofilm formation ability (P = 0.0026). Additionally, vancomycin, applied at sub minimal inhibitory concentrations, inhibited biofilm in four out of five strong biofilm-forming isolates. In conclusion, we suggest using agg and fsrB genes, together with the previously established gelE, for better prediction of biofilm strength and gelatinase activity, respectively. Future studies should explore the mechanism of biofilm inhibition by vancomycin and its possible use for antivirulence therapy.

ElKenawy, N. M., A. S. Yassin, H. N. Elhifnawy, and M. A. Amin, "Optimization of prodigiosin production by Serratia marcescens using crude glycerol and enhancing production using gamma radiation", Biotechnology Reports, vol. 14, pp. 47 - 53, 2017. AbstractWebsite
Bahy, R. H., H. M. Hamouda, A. S. Shahat, A. S. Yassin, and M. A. Amin, "Development and evaluation of a novel vaccine against prevalent invasive multi-drug resistant strains of Streptococcus pneumoniae.", PeerJ, vol. 4, pp. e2737, 2016. Abstract

Streptococcus pneumoniae is a pathogen that causes serious invasive infections, such as septicemia, meningitis and pneumonia in addition to mild upper respiratory tract infections. Protection from pneumococcal diseases is thought to be mediated mainly by serotype-specific antibodies to capsular antigens. Pneumococcal conjugate vaccine consists of sugars (polysaccharides) from the capsule of the bacterium S. pneumoniae that are conjugated to a carrier protein. Three pneumococcal conjugated vaccines, each directed against a group of serotypes, are registered in Egypt; however, local vaccine production is required to cover the most prevalent serotypes. In this work, capsular polysaccharide from the most current and prevalent serotypes in Egypt were extracted, purified and conjugated to bovine serum albumin (BSA). The polysaccharide protein conjugate was purified through ultrafiltration technique and molecular size distribution was compared to an available vaccine. The immunogenicity of the prepared vaccine was examined via two methods: First, by measuring the levels of the elicited antibodies in the sera of the vaccinated mice; second, by challenging the vaccinated groups of mice with approximately 10(7) CFU of each specific serotype and determining the degree of protection the developled vaccine offers. Our results show that the developed conjugated capsular polysaccharide vaccine is highly immunogenic and protective in mice. This finding illustrates the importance of tracking the most recent and predominant peneumococcal serotypes to generate effective vaccines, instead of using expensive imported vaccines with large number of serotypes which might not be even present in the community.