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2020
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.

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.

2019
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.

2018
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
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2017
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
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2016
Elhosseiny, N. M., O. M. El-Tayeb, A. S. Yassin, S. Lory, and A. S. Attia, "The secretome of Acinetobacter baumannii ATCC 17978 type II secretion system reveals a novel plasmid encoded phospholipase that could be implicated in lung colonization.", International journal of medical microbiology : IJMM, vol. 306, issue 8, pp. 633-641, 2016 Dec. Abstract

Acinetobacter baumannii infections are compounded with a striking lack of treatment options. In many Gram-negative bacteria, secreted proteins play an important early role in avoiding host defences. Typically, these proteins are targeted to the external environment or into host cells using dedicated transport systems. Despite the fact that medically relevant species of Acinetobacter possess a type II secretion system (T2SS), only recently, its significance as an important pathway for delivering virulence factors has gained attention. Using in silico analysis to characterize the genetic determinants of the T2SS, which are found clustered in other organisms, in Acinetobacter species, they appear to have a unique genetic organization and are distributed throughout the genome. When compared to other T2SS orthologs, individual components of the T2SS apparatus showed the highest similarity to those of Pseudomonas aeruginosa. A mutant of Acinetobacter baumannii strain ATCC 17978 lacking the secretin component of the T2SS (ΔgspD), together with a trans-complemented mutant, were tested in a series of in vitro and in vivo assays to determine the role of T2SS in pathogenicity. The ΔgspD mutant displayed decreased lipolytic activity, associated with attenuated colonization ability in a murine pneumonia model. These phenotypes are linked to LipAN, a novel plasmid-encoded phospholipase, identified through mass spectroscopy as a T2SS substrate. Recombinant LipAN showed specific phospholipase activity in vitro. Proteomics on the T2-dependent secretome of ATCC 17978 strain revealed its potential dedication to the secretion of a number of lipolytic enzymes, among others which could contribute to its virulence. This study highlights the role of T2SS as an active contributor to the virulence of A. baumannii potentially through secretion of a newly identified phospholipase.

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.

Bahy, R. H., H. M. Hamouda, A. S. Shahat, A. S. Yassin, and M. A. Amin, "Emergence of Neoteric Serotypes Among Multidrug Resistant Strains of Streptococcus pneumoniae Prevalent in Egypt", Jundishapur J Microbiol, vol. 9, no. 4, pp. e30708, 2016. AbstractWebsite
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Hassan, M., T. Essam, A. S. Yassin, and A. Salama, "Optimization of rhamnolipid production by biodegrading bacterial isolates using Plackett–Burman design", International Journal of Biological Macromolecules, vol. 82, pp. 573 - 579, 2016. AbstractWebsite

Abstract Biosurfactants are biological surfactants produced by microorganisms. Pseudomonas species are well known for the production of the rhamnolipid biosurfactant. In this work, the production of rhamnolipid biosurfactant by Pseudomonas spp. was investigated and further optimized. Two Plackett–Burman designs to study the effect of carbon source, nitrogen source, C/N ratio, iron concentration, magnesium concentration, phenol toxicity, pH, temperature, agitation and sampling time were tested. The first design revealed an optimization that increased biosurfactant productivity by almost two to fivefolds for the tested isolates. However, using the second design showed no remarkable increase in biosurfactant productivity. An additional validation run was adopted using the predicted optimal medium with predicted optimal conditions. The validation run showed remarkable increase in the productivity of the tested isolates. The use of microorganisms with biodegradation ability coupled with optimization of the parameters affecting productivity provides an efficient strategy for biosurfactant production.

Eraqi, W. A., A. S. Yassin, A. E. Ali, and M. A. Amin, "Utilization of Crude Glycerol as a Substrate for the Production of Rhamnolipid by Pseudomonas aeruginosa", Biotechnology Research International, vol. 2016, pp. 9, 2016. Abstract
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2015
Farag, M. A., D. A. Al-Mahdy, R. S. E. Dine, S. A. Fahmy, A. Yassin, A. Porzel, and W. Brandt, "StructureActivity Relationships of Antimicrobial Gallic Acid Derivatives from Pomegranate and Acacia Fruit Extracts against Potato Bacterial Wilt Pathogen.", Chemistry & biodiversity, vol. 12, issue 6, pp. 955-62, 2015 Jun. Abstract

Bacterial wilts of potato, tomato, pepper, and or eggplant caused by Ralstonia solanacearum are among the most serious plant diseases worldwide. In this study, the issue of developing bactericidal agents from natural sources against R. solanacearum derived from plant extracts was addressed. Extracts prepared from 25 plant species with antiseptic relevance in Egyptian folk medicine were screened for their antimicrobial properties against the potato pathogen R. solancearum by using the disc-zone inhibition assay and microtitre plate dilution method. Plants exhibiting notable antimicrobial activities against the tested pathogen include extracts from Acacia arabica and Punica granatum. Bioactivity-guided fractionation of A. arabica and P. granatum resulted in the isolation of bioactive compounds 3,5-dihydroxy-4-methoxybenzoic acid and gallic acid, in addition to epicatechin. All isolates displayed significant antimicrobial activities against R. solanacearum (MIC values 0.5-9 mg/ml), with 3,5-dihydroxy-4-methoxybenzoic acid being the most effective one with a MIC value of 0.47 mg/ml. We further performed a structure-activity relationship (SAR) study for the inhibition of R. solanacearum growth by ten natural, structurally related benzoic acids.

Sheraba, N. S., M. R. Diab, A. S. Yassin, M. A. Amin, and H. H. Zedan, "Quality Control Testing for Tracking Endotoxin-Producing Gram-Negative Bacteria during the Preparation of Polyvalent Snake Antivenom Immunoglobulin.", PDA journal of pharmaceutical science and technology / PDA, vol. 69, issue 4, pp. 499-510, 2015 Jul-Aug. Abstract

UNLABELLED: Snake bites represent a serious public health problem, particularly in rural areas worldwide. Antitoxic sera preparations are antibodies from immunized animals and are considered to be the only treatment option. The purification of antivenom antibodies should aim at obtaining products of consistent quality, safety, efficacy, and adherence to good manufacturing practice principles. Endotoxins are an integral component of the outer cell surface of Gram-negative bacteria. They are common contaminates of the raw materials and processing equipment used in the manufacturing of antivenoms. In this work, and as a part of quality control testing, we establish and examine an environmental monitoring program for identification of potential sources of endotoxin-producing Gram-negative bacteria throughout the whole steps of antivenom preparation. In addition, we follow all the steps of preparation starting from crude plasma till finished product using a validated sterility and endotoxin testing.Samples from air, surface, and personnel were collected and examined through various stages of manufacturing for the potential presence of Gram-negative bacteria. A validated sterility and endotoxin test was carried out in parallel at the different production steps. The results showed that air contributed to the majority of bacterial isolates detected (48.43%), followed by surfaces (37.5%) and then personnel (14%). The most common bacterial isolates detected were Achromobacter xylosoxidans, Ochrobactrum anthropi, and Pseudomonas aeruginosa, which together with Burkholderia cepacia were both also detected in cleaning water and certain equipment parts. A heavy bacterial growth with no fungal contamination was observed in all stages of antivenom manufacturing excluding the formulation stage. All samples were positive for endotoxin including the finished product.Implementation and continued evaluation of quality assurance and quality improvement programs in aseptic preparation is essential in ensuring the safety and quality of these products.

LAY ABSTRACT: Antitoxic sera preparations are the only treatment option for snake bites worldwide. They are prepared by immunizing animals, usually horses, with snake venom and collecting horse plasma, which is then subjected to several purification steps in order to finally prepare the purified immunoglobulins. Components of the bacterial cell wall known as endotoxins can constitute a potential hazardous contamination known as pyrogen in antisera, which can lead to fever and many other adverse reactions to the person subjected to it.In this work, we monitored the environment associated with the different steps of production and purification of snake antivenom prepared from immunized horses. We examined the air quality, surface, and personnel for possible sources of contamination, particularly the presence of Gram-negative bacteria, which is the major source of endotoxin presence. We also monitored all stages of preparation by sterility and endotoxin testing. Our results showed that air contributed to the majority of bacterial isolates. Sterility testing revealed the presence of bacterial contamination in all the intermediate steps, as only the final preparation after filtration was sterile. Endotoxin was present in all tested samples and the final product. Good manufacturing practice procedures are essential in any facility involved in antisera production.

Elhosseiny, N. M., M. A. Amin, A. S. Yassin, and A. S. Attia, "Acinetobacter baumannii universal stress protein A plays a pivotal role in stress response and is essential for pneumonia and sepsis pathogenesis.", International journal of medical microbiology : IJMM, vol. 305, issue 1, pp. 114-23, 2015 Jan. Abstract

Acinetobacter baumannii is one of the most significant threats to global public health. This threat is compounded by the fact that A. baumannii is rapidly becoming resistant to all relevant antimicrobials. Identifying key microbial factors through which A. baumannii resists hostile host environment is paramount to the development of novel antimicrobials targeting infections caused by this emerging pathogen. An attractive target could be a molecule that plays a role in the pathogenesis and stress response of A. baumannii. Accordingly, the universal stress protein A (UspA) was chosen to be fully investigated in this study. A platform of A. baumannii constructs, expressing various levels of the uspA gene ranging from zero to thirteen folds of wild-type level, and a recombinant E. coli strain, were employed to investigate the role of UspA in vitro stress and in vivo pathogenesis. The UspA protein plays a significant role in protecting A. baumannii from H2O2, low pH, and the respiratory toxin 2,4-DNP. A. baumannii UspA protein plays an essential role in two of the deadliest types of infection caused by A. baumannii; pneumonia and sepsis. This distinguishes A. baumannii UspA from its closely related homolog, the Staphylococcus aureus Usp2, as well as from the less similar Burkholderia glumae Usps. Heterologous and overexpression experiments suggest that UspA mediates its role via an indirect mechanism. Our study highlights the role of UspA as an important contributor to the A. baumannii stress and virulence machineries, and polishes it as a plausible target for new therapeutics.

Hashem, Y. A., A. S. Yassin, and M. A. Amin, "Molecular characterization of Enterococcus spp. clinical isolates from Cairo, Egypt.", Indian journal of medical microbiology, vol. 33 Suppl, pp. S80-6, 2015 Feb. Abstract

PURPOSE: Enterococci are responsible for serious diseases such as bacteraemia, endocarditis and urinary tract infections. The ability of enterococci to cause such diseases is due to acquisition of certain virulence factors such as haemolysin, gelatinase and enterococcus surface protein. This study has been conducted to investigate the occurrence of virulence factors and resistance to various antibiotics with emphasis on vancomycin in the Enterococcus spp.

MATERIALS AND METHODS: Clinical specimens were collected and isolates were identified by proper microscopic, culture and biochemical tests. Susceptibility and degree of resistance of the isolates to various antibiotics were determined. Virulence factors were examined by phenotypic tests followed by molecular methods. Bioinformatics analysis was used to detect regions in the genomes that might have originated from horizontal gene transfer.

RESULT: The presence or absence of virulence genes did not affect the pattern of antimicrobial resistance in Enterococcus isolates; consequently, no relationship was found between virulence factors and resistance to different antibiotics used. Bioinformatics analysis showed that the virulence genes were mainly transferred by transposons.

CONCLUSION: Among the enterococci, environmental factors may interfere in the expression of virulence factors. Horizontal gene transfer plays an important role in the spread of resistance and virulence genes.

Raouf, H. E., A. S. Yassin, S. A. Megahed, M. S. Ashour, and T. M. Mansour, "Seroprevalence of occult hepatitis B among Egyptian paediatric hepatitis C cancer patients.", Journal of viral hepatitis, vol. 22, issue 2, pp. 101-9, 2015 Feb. Abstract

Occult hepatitis B infection is characterized by the presence of hepatitis B virus (HBV) DNA in the serum in the absence of hepatitis B surface antigen (HBsAg). Prevalence of hepatitis C virus (HCV) infections in Egypt is among the highest in the world. In this study, we aim at analysing the rates of occult HBV infections among HCV paediatric cancer patients in Egypt. The prevalence of occult HBV was assessed in two groups of paediatric cancer patients (HCV positive and HCV negative), in addition to a third group of paediatric noncancer patients, which was used as a general control. All groups were negative for HBsAg and positive for HCV antibody. HBV DNA was detected by nested PCR and real-time PCR. HCV was detected by real-time PCR. Sequencing was carried out in order to determine HBV genotypes to all HBV patients as well as to detect any mutation that might be responsible for the occult phenotype. Occult hepatitis B infection was observed in neither the non-HCV paediatric cancer patients nor the paediatric noncancer patients but was found in 31% of the HCV-positive paediatric cancer patients. All the detected HBV patients belonged to HBV genotype D, and mutations were found in the surface genome of HBV leading to occult HBV. Occult HBV infection seems to be relatively frequent in HCV-positive paediatric cancer patients, indicating that HBsAg negativity is not sufficient to completely exclude HBV infection. These findings emphasize the importance of considering occult HBV infection in HCV-positive paediatric cancer patients especially in endemic areas as Egypt.

El-Batal, A. I., N. M. ElKenawy, A. S. Yassin, and M. A. Amin, "Laccase production by Pleurotus ostreatus and its application in synthesis of gold nanoparticles", Biotechnology Reports, vol. 5, pp. 31 - 39, 2015. AbstractWebsite
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2014
Lu, Z., D. Barnard, T. R. Shaikh, X. Meng, C. A. Mannella, A. Yassin, R. Agrawal, T. Wagenknecht, and T. - M. Lu, "Gas-Assisted Annular Microsprayer for Sample Preparation for Time-Resolved Cryo-Electron Microscopy.", Journal of micromechanics and microengineering : structures, devices, and systems, vol. 24, issue 11, pp. 115001, 2014 Nov 1. Abstract

Time-resolved cryo electron microscopy (TRCEM) has emerged as a powerful technique for transient structural characterization of isolated biomacromolecular complexes in their native state within the time scale of seconds to milliseconds. For TRCEM sample preparation, microfluidic device [9] has been demonstrated to be a promising approach to facilitate TRCEM biological sample preparation. It is capable of achieving rapidly aqueous sample mixing, controlled reaction incubation, and sample deposition on electron microscopy (EM) grids for rapid freezing. One of the critical challenges is to transfer samples to cryo-EM grids from the microfluidic device. By using microspraying method, the generated droplet size needs to be controlled to facilitate the thin ice film formation on the grid surface for efficient data collection, while not too thin to be dried out before freezing, i.e., optimized mean droplet size needs to be achieved. In this work, we developed a novel monolithic three dimensional (3D) annular gas-assisted microfluidic sprayer using 3D MEMS (MicroElectroMechanical System) fabrication techniques. The microsprayer demonstrated dense and consistent microsprays with average droplet size between 6-9 μm, which fulfilled the above droplet size requirement for TRCEM sample preparation. With droplet density of around 12-18 per grid window (window size is 58×58 μm), and the data collectible thin ice region of >50% total wetted area, we collected ~800-1000 high quality CCD micrographs in a 6-8 hour period of continuous effort. This level of output is comparable to what were routinely achieved using cryo-grids prepared by conventional blotting and manual data collection. In this case, weeks of data collection process with the previous device [9] has shortened to a day or two. And hundreds of microliter of valuable sample consumption can be reduced to only a small fraction.

Shaikh, T. R., A. S. Yassin, Z. Lu, D. Barnard, X. Meng, T. - M. Lu, T. Wagenknecht, and R. K. Agrawal, "Initial bridges between two ribosomal subunits are formed within 9.4 milliseconds, as studied by time-resolved cryo-EM.", Proceedings of the National Academy of Sciences of the United States of America, vol. 111, issue 27, pp. 9822-7, 2014 Jul 8. Abstract

Association of the two ribosomal subunits during the process of translation initiation is a crucial step of protein synthesis. The two subunits (30S and 50S) of the bacterial 70S ribosome are held together by 12 dynamic bridges involving RNA-RNA, RNA-protein, and protein-protein interactions. The process of bridge formation, such as whether all these bridges are formed simultaneously or in a sequential order, is poorly understood. To understand such processes, we have developed and implemented a class of microfluidic devices that mix two components to completion within 0.4 ms and spray the mixture in the form of microdroplets onto an electron microscopy grid, yielding a minimum reaction time of 9.4 ms before cryofixation. Using these devices, we have obtained cryo-EM data corresponding to reaction times of 9.4 and 43 ms and have determined 3D structures of ribosomal subunit association intermediates. Molecular analyses of the cryo-EM maps reveal that eight intersubunit bridges (bridges B1a, B1b, B2a, B2b, B3, B7a, B7b, and B8) form within 9.4 ms, whereas the remaining four bridges (bridges B2c, B4, B5, and B6) take longer than 43 ms to form, suggesting that bridges are formed in a stepwise fashion. Our approach can be used to characterize sequences of various dynamic functional events on complex macromolecular assemblies such as ribosomes.

Metwally, M. A., A. S. Yassin, T. M. Essam, H. M. Hamouda, and M. A. Amin, "Detection, characterization, and molecular typing of human Mycoplasma spp. from major hospitals in Cairo, Egypt.", TheScientificWorldJournal, vol. 2014, pp. 549858, 2014. Abstract

Mycoplasmas are fastidious slow growing organisms lacking a cell wall and mostly isolated from the mucosal surfaces of the respiratory and genitourinary tracts. There is a dearth of information regarding clinical Mycoplasma spp. isolates among Egyptian patients. A total of 170 samples were collected from patients and apparently healthy personnel in local public hospitals in Cairo, Egypt. Isolation of Mycoplasma spp. was carried out using appropriate culture media and further identification was carried out by biochemical tests followed by serotyping using specific antisera. Confirmation was done by PCR for detection of different Mycoplasma spp. using genus-specific primers targeting 16S ribosomal RNA gene. Characterization of the antibiotic resistance and sensitivity pattern against different antimicrobials was carried out using disc diffusion test. The results indicated the presence of six Mycoplasma spp. in 22.94% of the samples. Mycoplasmas were detected more frequently in throat swabs than sputum. Mycoplasma pneumoniae was highly sensitive to macrolides and quinolones but less sensitive to aminoglycosides and tetracyclines. Molecular techniques were found to be of more rapid, highly sensitive, able to detect nonviable organisms, and cost effective. These results shed light on difficulties of Mycoplasma detection and the superiority of molecular techniques over culture.

Ramadan, M. A., S. A. Megahed, K. M. Eltaweel, and A. S. Yassin, "Potential in vitro anti-Helicobacter activity of bacteriocin and bacteriocin-like compounds produced by lactobacilli", Journal of Microbiology, Biotechnology and Food Sciences, vol. 4, issue 2, pp. 160-163, 2014.
Sheraba, N. S., A. S. Yassin, A. Fahmy, and M. A. Amin, "Quantitative suspension tests for the evaluation of bactericidal, fungicidal and sporicidal effects of biocides used in vaccine production facility", African Journal of Microbiology Research, vol. 8, issue 5, pp. 417-424, 2014.
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