Background Colorectal cancer (CRC) is a public health concern and the second most common disease ... more Background Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique. Results Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and am...
Atopic dermatitis (AD) is a relapsing, chronic, and inflammatory skin disorder. Its causes remain... more Atopic dermatitis (AD) is a relapsing, chronic, and inflammatory skin disorder. Its causes remain unclear. Here, we reported the first proteome study of the bacterial community in AD patients. Bacterial community in 7 patients and 1 healthy control using bottom-up proteomics were examined starting with in-solution digestion followed by purification steps with subsequent analysis using LC-MS/MS and ended with data processing and bioinformatic analysis. Overall, great bacterial changes between patient samples and healthy one were noticed with the presence of Staphylococcus aureus, Aeromonas hydrophila, and Shewanella species, and others that were present uniquely in patient samples suggesting their role in AD. Additionally, detection of some important proteins that trigger bacterial pathogenesis and the immune system such as enolase, glyceraldehyde-3-phosphate, Chaperone proteins DnaK and HtpG beside protein pathways needed for bacterial growth and pathogenesis like chaperones and folding catalysts; and Energy metabolism. These new findings of the microbiome and detected proteins could start a new era of proteomics to study the bacterial community as a whole and detect the way it interacts with each other and with the host. SIGNIFICANCE: This paper would represent a reference work for investigations on microbiota that present on AD, from both a microbiological and a functional proteomic point of view. We focused on analysisng bacteria community and proteins produced and its role in the disease, highlighting some functional characteristics of certain proteins and discussing its potential role in AD.
What makes men become informal caregivers: a qualitative study Introdução: O aumento da expectati... more What makes men become informal caregivers: a qualitative study Introdução: O aumento da expectativa de vida tem levado a um aumento do número de pessoas que necessitam de cuidado, sendo a maior parte dele exercido por cuidadores informais e do sexo feminino. Entretanto, diversos estudos têm apontado um aumento no número de cuidadores masculinos. Neste contexto, este estudo pretende elencar motivações que levam homens a serem cuidadores informais. Métodos: Estudo qualitativo com entrevistas semiestruturadas, questionários sociodemográficos e questionários de Zarit em dez cuidadores homens inscritos no programa de atenção domiciliar de duas unidades de saúde de Porto Alegre. Resultados e Discussão: As motivações identificadas na prestação do cuidado foram a obrigação e a reciprocidade. A obrigação foi citada por todos os cuidadores e a falta de rede de apoio pareceu reforçá-la. A reciprocidade foi mencionada em quatro entrevistas e possuía maior correlação com o grau de parentesco "filho". Estudos apontam que a motivação "obrigação" parece se correlacionar com maiores índices de sobrecarga, depressão e ansiedade quando comparado a um cuidado motivado pela reciprocidade. Na escala de Zarit, nenhum cuidador apresentou índice de sobrecarga severa, o que pode ter relação com uma maior procura por suporte social. Conclusão: Nota-se como é amplo e desconhecido o tema da relação da masculinidade com o papel de cuidador. Contudo, observou-se correlação entre o gênero e as motivações como obrigação e reciprocidade na prestação do cuidado, e insinua-se uma maior sobrecarga quando obrigação é o principal fator motivador.
Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science h... more Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.
Egyptian Journal of Aquatic Biology and Fisheries, 2012
This study was initiated to provide the first record of monitoring of 17 βestradiol (E2) residues... more This study was initiated to provide the first record of monitoring of 17 βestradiol (E2) residues in some Egyptian aquatic ecosystems. Samples of water were collected from three water bodies located in the Suez Canal region. Samples were extracted, filtered and examined by HPLC on a C 18 column using Florescence detectors. Results provided evidence of the presence of estradiol in the studied area. Interestingly, marine lakes contained significant levels of 17 β-estradiol (P <0.05). Lower levels were also detected in the rivulet streams supplied by River Nile. Detection of estradiol in the aquatic ecosystems of the Suez Canal region grabs the attention towards the heavy reliance on some esterogenic medicinal products in the area, and the eventual effect on the aquatic systems including biodiversity of a variety of organisms. Therefore, it is recommended to enlarge the detection scanning of estradiol in other Egyptian areas.
Records of Pharmaceutical and Biomedical Sciences, 2019
Atopic dermatitis (AD) is a chronic complex inflammatory skin disorder. AD characterized by multi... more Atopic dermatitis (AD) is a chronic complex inflammatory skin disorder. AD characterized by multiple contributing factors, such as impairment in skin barrier integrity, participation of either innate or adaptive immunity arms, in addition to the pivotal roles of cutaneous microbiome. The analysis of cutaneous microbiota was performed using shotgun metagenomic sequencing on an Illumina HiSeq platform in parallel with 16s rRNA genes using MiSeq sequencing. Two samples for each sequencing technique were collected from one child and one adult subjects with AD. Metagenomic data from 16srRNA was in accordance with those from shotgun sequencing. Taxonomic profile of samples at genus level showed overrepresentation of Streptococcus in child and Staphylococcus in adults. Species level analysis of reads revealed monoclonality of Staphylococcus aureus community in comparison to heterogeneity of Staphylococcus epidermidis. 16S rRNA gene based analysis was unable to provide comprehensive description of bacterial communities, while shotgun metagenomic analyses described the composition of microbiota with high resolution at different taxonomic levels especially subspecies and single nucleotide variants levels. Finally, further studies using shotgun metagenomic approaches will be required for characterization of microbiome in healthy and diseased subjects.
Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology, Jan 20, 2018
The double-stranded RNA dependent protein kinase (PKR) plays a vital role in the immune system. D... more The double-stranded RNA dependent protein kinase (PKR) plays a vital role in the immune system. During HCV infection, PKR has antiviral effect by inhibition of protein synthesis of the HCV. The functional single nucleotide polymorphisms (SNPs) in PKR promoter region might have a relation to HCV disease outcome and response to treatment. The objective of the present work was threefold. First, it proposed an optimized protocol for PCR amplification of PKR promoter. Second, it screened the promoter region of PKR gene in HCV Egyptian patients to detect the possible SNPs' function. Third, to study the association between the detected SNPs and the response to treatment. The functional SNPs in PKR promoter region were detected using DNA sequencing in 40 HCV infected patients; 20 sustained virologic response (SVR) patients and 20 nonresponse (NR) patients after combined interferon/ribavirin therapy. Twenty healthy subjects were included as a control. Two functional SNPs were detected: r...
Aim: In this study, silver Nanoparticles (AgNPs) was synthesized by two processes. Chemical proce... more Aim: In this study, silver Nanoparticles (AgNPs) was synthesized by two processes. Chemical process using natural polymers as citrus pectin (CP), chitosan (Cs) and alginate (Alg) and biological process using aqueous extract of fermented fenugreek by Pleurotus ostreatus (AEFF). Methodology: Gamma radiation was used to improve reduction of silver ions to silver nanoparticles (AgNPs) by a chemical process (citrus pectin, chitosan and alginate) and biological process (aqueous extract of fermented fenugreek by Pleurotus ostreatus). Optimization of conditions using general factorial design was performed. AgNPs were further characterized by UV-Visible, Dynamic
Background: Resistant Pseudomonas aeruginosa is a serious concern for antimicrobial therapy, as t... more Background: Resistant Pseudomonas aeruginosa is a serious concern for antimicrobial therapy, as the common isolates exhibit variable grades of resistance, involving beta-lactamase enzymes, beside native defense mechanisms. Objectives: The present study was designed to determine the occurrence of Metallo-β-Lactamases (MBL) and Amp C harboring P. aeruginosa isolates from Suez Canal university hospital in Ismailia, Egypt. Methods: A total of 147 P. aeruginosa isolates, recovered from 311 patients during a 10-month period, were collected between May 2013 and February 2014; the isolates were collected from urine, wound and sputum. Minimum inhibitory concentration (MIC) determined by agar dilution methods was ≥2 µg/mL for meropenem and imipenem. Identification of P. aeruginosa was confirmed using API 20NE. Metallo-β-Lactamases and Amp C were detected based on different phenotypic methods. Results: Overall, 26.5% of P. aeruginosa isolates (39/147) were carbapenem resistant isolates. Furthermore, 64.1% (25/39) were MBL producers, these isolates were screened by the combined disc and disc diffusion methods to determine the ability of MBL production. Both MBL and Amp C harbored P. aeruginosa isolates were 28% (7/25). Sixty-four percent of P. aeruginosa isolates were multidrug resistant (MDR) (16/25). The sensitivity toward polymyxin, imipenem, norfloxacin, piperacillin-tazobactam and gentamicin was 99%, 91%, 88%, 82% and 78%, respectively. The resistance rate towards cefotaxime, ceftazidime, cefepime, aztreonam and meropenem was 98.6%, 86%, 71.4%, 34% and 30%, respectively. Conclusions: Multidrug resistance was significantly associated with MBL production in P. aeruginosa. Early detection of MBLproducing P. aeruginosa and hospital antibiotic policy prescription helps proper antimicrobial therapy and avoidance of dissemination of these multidrug resistance isolates.
Bibliometric analysis of Egyptian literature on HCV provides the intelligence needed for decision... more Bibliometric analysis of Egyptian literature on HCV provides the intelligence needed for decision makers and gives an insight into research productivity in this area. We propose our database (HCVDBegy) on MS-SQL server by querying PubMed for “HCV and Egypt” with time limit till 31st March 2013. Fifty eight out of the 716 records were excluded and the rest 658 were divided into 22 domains. Analysis used data mining add-ins for Microsoft Excel, including association and regression algorithms. A fluctuation in numbers of papers was noticed from 2004 to 2009 with a steady increase onward. Eighty six percent of publications were the contribution of three or more authors. Top publishing bodies were Cairo and Ain Shams Universities, Faculty of Medicine, National Research Center and National Cancer Institute. Three Egyptian journals came on top, whereas other publishing journals were mainly from the USA. Few controlled clinical trials and meta-analyses were published. HCV epidemiology, review articles and sequence analysis domains were the most cited. Forecasting model showed a breakthrough in numbers of publications on 2013 and 2014 than those forecasted. Dependency network based on association rule model of MeSH topics was also extensively analyzed. Number of publications showed a promising increase which points to the better national awareness of HCV problem. Studying MeSH terms clustering showed some hot topics. We recommend that the PubMed should alarm authors of the challenges of author affiliations. HCVDBegy availability opens the door for more drill down analysis for decision makers.
Vibrio cholerae is a waterborne bacterium inhabiting the aquatic ecosystem. Faecal contamination ... more Vibrio cholerae is a waterborne bacterium inhabiting the aquatic ecosystem. Faecal contamination of water resources, represent modes of dissemination of the bacteria and thus the disease. This study is reporting an association between Vibrio cholerae and chironomids larvae and exuviae, collected from Lake Manzala. The collection sites were chosen to cover the southern sector of the lake that is reportedly characterized by industrial, agricultural and domestic pollution. The only identified species was Chironomus transvaalensis, an East African species. The isolation of Vibrio cholerae was carried out according to the standard microbiological methods, and followed by 16S rRNA sequence analysis. non-O1/ non-O39 Vibrio cholerae was found to be present in all of the examined Chironomus transvaalensis larvae and exuviae. These findings further support the use of chironomids as a monitoring agent of Vibrio cholerae.
Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used f... more Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used for the production of recombinant proteins. BEs should be eliminated in the course of down stream processing of target protein produced by these bacteria. Supermacroporous monolith (continuous bed) columns, so called cryogel columns, with immobilized polyethyleneimine (PEI), polymyxin B (PMB) and lysozyme were employed for BEs capture. Due to the large interconnected pores it was possible to use cryogel columns at flow rates as high as 10 ml/min. The columns packed with Sepharose CL-4B with immobilized PEI, PMB and lysozyme were impossible to use at these high flow rates due to the collapse of the bed. The dynamic capacities of the cryogel columns were nearly independent of the flow rate. In the presence of EDTA, BEs were quantitatively captured from mixtures with a model protein, bovine serum albumin (BSA) at pH 7.2 with practically no protein losses. At pH 3.6 BEs were captured directly from non-clarified E. coli cell lysate resulting in more than 10 4 times BEs clearance.
Abstract In the present investigation an attempt was made to explore the antimicrobial, antioxida... more Abstract In the present investigation an attempt was made to explore the antimicrobial, antioxidant and anticancer activities of ethyl acetate extract of mangrove associated bacterium Bacillus subtilis subsp. subtilis RG. Antimicrobial activity results revealed that, the extract had strongly inhibited growth of gram positive than gram negative bacterial strains and also significantly ( P −1 ; whilst minimum bactericidal/fungicidal concentration (MBC/MFC) was ranged from 90 to 250 and 200 to 300 µg ml −1 , respectively. Antioxidant assay revealed that, this extract had maximum DPPH radical scavenging effect (75.79±5.41%) and reducing power (0.752±0.021 OD) at 1000 µg ml −1 . MTT assay showed potent cytotoxic activity against human breast adenocarcinmoa cells (MCF-7) with the IC 50 value of 46.64±0.79 µg ml −1 . This study tends to indicate that, B. subtilis subsp. subtilis RG isolated from mangrove ecosystem could be potentially explored for the development of new therapeutic agents.
Proceedings of the National Academy of Sciences, 2013
Shipworms are marine wood-boring bivalve mollusks (family Teredinidae) that harbor a community of... more Shipworms are marine wood-boring bivalve mollusks (family Teredinidae) that harbor a community of closely related Gammaproteobacteria as intracellular endosymbionts in their gills. These symbionts have been proposed to assist the shipworm host in cellulose digestion and have been shown to play a role in nitrogen fixation. The genome of one strain of Teredinibacter turnerae , the first shipworm symbiont to be cultivated, was sequenced, revealing potential as a rich source of polyketides and nonribosomal peptides. Bioassay-guided fractionation led to the isolation and identification of two macrodioloide polyketides belonging to the tartrolon class. Both compounds were found to possess antibacterial properties, and the major compound was found to inhibit other shipworm symbiont strains and various pathogenic bacteria. The gene cluster responsible for the synthesis of these compounds was identified and characterized, and the ketosynthase domains were analyzed phylogenetically. Reverse-t...
Red Sea sponges offer potential as sources of novel drugs and bioactive compounds. Sponges harbor... more Red Sea sponges offer potential as sources of novel drugs and bioactive compounds. Sponges harbor diverse and abundant prokaryotic communities. The diversity of Egyptian sponge-associated bacterial communities has not yet been explored. Our study is the first culture-based and culture-independent investigation of the total bacterial assemblages associated with two Red Sea Demosponges, Hyrtios erectus and Amphimedon sp. Denaturing gradient gel electrophoresis fingerprint-based analysis revealed statistically different banding patterns of the bacterial communities of the studied sponges with H. erectus having the greater diversity. 16S rRNA clone libraries of both sponges revealed diverse and complex bacterial assemblages represented by ten phyla for H. erectus and five phyla for Amphimedon sp. The bacterial community associated with H. erectus was dominated by Deltaproteobacteria. Clones affiliated with Gammaproteobacteria were the major component of the clone library of Amphimedon sp. About a third of the 16S rRNA gene sequences in these communities were derived from bacteria that are novel at least at the species level. Although the overall bacterial communities were significantly different, some bacterial groups, including members of Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, and Actinobacteria, were found in both sponge species. The culture-based component of this study targeted Actinobacteria and resulted in the isolation of 35 sponge-associated microbes. The current study lays the groundwork for future studies of the role of these diverse microbes in the ecology, evolution, and development of marine sponges. In addition, our work provides an excellent resource of several candidate bacteria for production of novel pharmaceutically important compounds.
Journal of Pharmaceutical and Biomedical Analysis, 2011
Red Sea sponges offer a potential for production of novel drugs and prototypes. The genus Negomba... more Red Sea sponges offer a potential for production of novel drugs and prototypes. The genus Negombata is a type of sponges abundant in the Red Sea. This sponge produces latrunculins that have well documented antitumor activity in addition to antimicrobial and antiviral effects. The identification of Negombata species is based on morphology and microscopical examination of megascleres of spicules. However, these criteria have proven to be unreliable for identification. Therefore, this study was established to test the accuracy of the spicules based taxonomy against molecular and protein profiles for the two species of Negombata: N. magnifica and N. corticata. About 700bp of cytochrome c oxidase I gene was sequenced from the tissues of the two Negombata species. Additionally total proteins were extracted from Negombata samples collected from different locations during different seasons and separated by denaturing polyacrylamide gel electrophoresis. Characteristic different protein profiles were obtained for both species. The data obtained from cytochrome c oxidase I gene sequencing and protein profiles can reliably differentiate between different species of Negombata in the Red Sea.
A method for high throughput screening of Green Fluorescent Proteins carrying metal binding tags ... more A method for high throughput screening of Green Fluorescent Proteins carrying metal binding tags in bacteria was developed. A random four amino acids tag-peptide library was successfully generated in E. coli. A 96-microtiter plate assembled with metal-iminodiacetic acid small cryogel columns was used for library screening. For the first time we were able to simultaneously screen a metal binding peptide tags library obtained from E. coli against different metal ions. From screening 25 different tags, three clones were able to bind to all metal ions studied (Ni 2+ , Zn 2+ , Co 2+ and Cd 2+). It was clearly demonstrated that the new construct could facilitate the screening of large peptide libraries.
Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used f... more Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used for the production of recombinant proteins. BEs should be eliminated in the course of down stream processing of target protein produced by these bacteria. Supermacroporous monolith (continuous bed) columns, so called cryogel columns, with immobilized polyethyleneimine (PEI), polymyxin B (PMB) and lysozyme were employed for BEs capture. Due to the large interconnected pores it was possible to use cryogel columns at flow rates as high as 10 ml/min. The columns packed with Sepharose CL-4B with immobilized PEI, PMB and lysozyme were impossible to use at these high flow rates due to the collapse of the bed. The dynamic capacities of the cryogel columns were nearly independent of the flow rate. In the presence of EDTA, BEs were quantitatively captured from mixtures with a model protein, bovine serum albumin (BSA) at pH 7.2 with practically no protein losses. At pH 3.6 BEs were captured directly from non-clarified E. coli cell lysate resulting in more than 10 4 times BEs clearance.
Background Colorectal cancer (CRC) is a public health concern and the second most common disease ... more Background Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique. Results Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and am...
Atopic dermatitis (AD) is a relapsing, chronic, and inflammatory skin disorder. Its causes remain... more Atopic dermatitis (AD) is a relapsing, chronic, and inflammatory skin disorder. Its causes remain unclear. Here, we reported the first proteome study of the bacterial community in AD patients. Bacterial community in 7 patients and 1 healthy control using bottom-up proteomics were examined starting with in-solution digestion followed by purification steps with subsequent analysis using LC-MS/MS and ended with data processing and bioinformatic analysis. Overall, great bacterial changes between patient samples and healthy one were noticed with the presence of Staphylococcus aureus, Aeromonas hydrophila, and Shewanella species, and others that were present uniquely in patient samples suggesting their role in AD. Additionally, detection of some important proteins that trigger bacterial pathogenesis and the immune system such as enolase, glyceraldehyde-3-phosphate, Chaperone proteins DnaK and HtpG beside protein pathways needed for bacterial growth and pathogenesis like chaperones and folding catalysts; and Energy metabolism. These new findings of the microbiome and detected proteins could start a new era of proteomics to study the bacterial community as a whole and detect the way it interacts with each other and with the host. SIGNIFICANCE: This paper would represent a reference work for investigations on microbiota that present on AD, from both a microbiological and a functional proteomic point of view. We focused on analysisng bacteria community and proteins produced and its role in the disease, highlighting some functional characteristics of certain proteins and discussing its potential role in AD.
What makes men become informal caregivers: a qualitative study Introdução: O aumento da expectati... more What makes men become informal caregivers: a qualitative study Introdução: O aumento da expectativa de vida tem levado a um aumento do número de pessoas que necessitam de cuidado, sendo a maior parte dele exercido por cuidadores informais e do sexo feminino. Entretanto, diversos estudos têm apontado um aumento no número de cuidadores masculinos. Neste contexto, este estudo pretende elencar motivações que levam homens a serem cuidadores informais. Métodos: Estudo qualitativo com entrevistas semiestruturadas, questionários sociodemográficos e questionários de Zarit em dez cuidadores homens inscritos no programa de atenção domiciliar de duas unidades de saúde de Porto Alegre. Resultados e Discussão: As motivações identificadas na prestação do cuidado foram a obrigação e a reciprocidade. A obrigação foi citada por todos os cuidadores e a falta de rede de apoio pareceu reforçá-la. A reciprocidade foi mencionada em quatro entrevistas e possuía maior correlação com o grau de parentesco "filho". Estudos apontam que a motivação "obrigação" parece se correlacionar com maiores índices de sobrecarga, depressão e ansiedade quando comparado a um cuidado motivado pela reciprocidade. Na escala de Zarit, nenhum cuidador apresentou índice de sobrecarga severa, o que pode ter relação com uma maior procura por suporte social. Conclusão: Nota-se como é amplo e desconhecido o tema da relação da masculinidade com o papel de cuidador. Contudo, observou-se correlação entre o gênero e as motivações como obrigação e reciprocidade na prestação do cuidado, e insinua-se uma maior sobrecarga quando obrigação é o principal fator motivador.
Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science h... more Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.
Egyptian Journal of Aquatic Biology and Fisheries, 2012
This study was initiated to provide the first record of monitoring of 17 βestradiol (E2) residues... more This study was initiated to provide the first record of monitoring of 17 βestradiol (E2) residues in some Egyptian aquatic ecosystems. Samples of water were collected from three water bodies located in the Suez Canal region. Samples were extracted, filtered and examined by HPLC on a C 18 column using Florescence detectors. Results provided evidence of the presence of estradiol in the studied area. Interestingly, marine lakes contained significant levels of 17 β-estradiol (P <0.05). Lower levels were also detected in the rivulet streams supplied by River Nile. Detection of estradiol in the aquatic ecosystems of the Suez Canal region grabs the attention towards the heavy reliance on some esterogenic medicinal products in the area, and the eventual effect on the aquatic systems including biodiversity of a variety of organisms. Therefore, it is recommended to enlarge the detection scanning of estradiol in other Egyptian areas.
Records of Pharmaceutical and Biomedical Sciences, 2019
Atopic dermatitis (AD) is a chronic complex inflammatory skin disorder. AD characterized by multi... more Atopic dermatitis (AD) is a chronic complex inflammatory skin disorder. AD characterized by multiple contributing factors, such as impairment in skin barrier integrity, participation of either innate or adaptive immunity arms, in addition to the pivotal roles of cutaneous microbiome. The analysis of cutaneous microbiota was performed using shotgun metagenomic sequencing on an Illumina HiSeq platform in parallel with 16s rRNA genes using MiSeq sequencing. Two samples for each sequencing technique were collected from one child and one adult subjects with AD. Metagenomic data from 16srRNA was in accordance with those from shotgun sequencing. Taxonomic profile of samples at genus level showed overrepresentation of Streptococcus in child and Staphylococcus in adults. Species level analysis of reads revealed monoclonality of Staphylococcus aureus community in comparison to heterogeneity of Staphylococcus epidermidis. 16S rRNA gene based analysis was unable to provide comprehensive description of bacterial communities, while shotgun metagenomic analyses described the composition of microbiota with high resolution at different taxonomic levels especially subspecies and single nucleotide variants levels. Finally, further studies using shotgun metagenomic approaches will be required for characterization of microbiome in healthy and diseased subjects.
Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology, Jan 20, 2018
The double-stranded RNA dependent protein kinase (PKR) plays a vital role in the immune system. D... more The double-stranded RNA dependent protein kinase (PKR) plays a vital role in the immune system. During HCV infection, PKR has antiviral effect by inhibition of protein synthesis of the HCV. The functional single nucleotide polymorphisms (SNPs) in PKR promoter region might have a relation to HCV disease outcome and response to treatment. The objective of the present work was threefold. First, it proposed an optimized protocol for PCR amplification of PKR promoter. Second, it screened the promoter region of PKR gene in HCV Egyptian patients to detect the possible SNPs' function. Third, to study the association between the detected SNPs and the response to treatment. The functional SNPs in PKR promoter region were detected using DNA sequencing in 40 HCV infected patients; 20 sustained virologic response (SVR) patients and 20 nonresponse (NR) patients after combined interferon/ribavirin therapy. Twenty healthy subjects were included as a control. Two functional SNPs were detected: r...
Aim: In this study, silver Nanoparticles (AgNPs) was synthesized by two processes. Chemical proce... more Aim: In this study, silver Nanoparticles (AgNPs) was synthesized by two processes. Chemical process using natural polymers as citrus pectin (CP), chitosan (Cs) and alginate (Alg) and biological process using aqueous extract of fermented fenugreek by Pleurotus ostreatus (AEFF). Methodology: Gamma radiation was used to improve reduction of silver ions to silver nanoparticles (AgNPs) by a chemical process (citrus pectin, chitosan and alginate) and biological process (aqueous extract of fermented fenugreek by Pleurotus ostreatus). Optimization of conditions using general factorial design was performed. AgNPs were further characterized by UV-Visible, Dynamic
Background: Resistant Pseudomonas aeruginosa is a serious concern for antimicrobial therapy, as t... more Background: Resistant Pseudomonas aeruginosa is a serious concern for antimicrobial therapy, as the common isolates exhibit variable grades of resistance, involving beta-lactamase enzymes, beside native defense mechanisms. Objectives: The present study was designed to determine the occurrence of Metallo-β-Lactamases (MBL) and Amp C harboring P. aeruginosa isolates from Suez Canal university hospital in Ismailia, Egypt. Methods: A total of 147 P. aeruginosa isolates, recovered from 311 patients during a 10-month period, were collected between May 2013 and February 2014; the isolates were collected from urine, wound and sputum. Minimum inhibitory concentration (MIC) determined by agar dilution methods was ≥2 µg/mL for meropenem and imipenem. Identification of P. aeruginosa was confirmed using API 20NE. Metallo-β-Lactamases and Amp C were detected based on different phenotypic methods. Results: Overall, 26.5% of P. aeruginosa isolates (39/147) were carbapenem resistant isolates. Furthermore, 64.1% (25/39) were MBL producers, these isolates were screened by the combined disc and disc diffusion methods to determine the ability of MBL production. Both MBL and Amp C harbored P. aeruginosa isolates were 28% (7/25). Sixty-four percent of P. aeruginosa isolates were multidrug resistant (MDR) (16/25). The sensitivity toward polymyxin, imipenem, norfloxacin, piperacillin-tazobactam and gentamicin was 99%, 91%, 88%, 82% and 78%, respectively. The resistance rate towards cefotaxime, ceftazidime, cefepime, aztreonam and meropenem was 98.6%, 86%, 71.4%, 34% and 30%, respectively. Conclusions: Multidrug resistance was significantly associated with MBL production in P. aeruginosa. Early detection of MBLproducing P. aeruginosa and hospital antibiotic policy prescription helps proper antimicrobial therapy and avoidance of dissemination of these multidrug resistance isolates.
Bibliometric analysis of Egyptian literature on HCV provides the intelligence needed for decision... more Bibliometric analysis of Egyptian literature on HCV provides the intelligence needed for decision makers and gives an insight into research productivity in this area. We propose our database (HCVDBegy) on MS-SQL server by querying PubMed for “HCV and Egypt” with time limit till 31st March 2013. Fifty eight out of the 716 records were excluded and the rest 658 were divided into 22 domains. Analysis used data mining add-ins for Microsoft Excel, including association and regression algorithms. A fluctuation in numbers of papers was noticed from 2004 to 2009 with a steady increase onward. Eighty six percent of publications were the contribution of three or more authors. Top publishing bodies were Cairo and Ain Shams Universities, Faculty of Medicine, National Research Center and National Cancer Institute. Three Egyptian journals came on top, whereas other publishing journals were mainly from the USA. Few controlled clinical trials and meta-analyses were published. HCV epidemiology, review articles and sequence analysis domains were the most cited. Forecasting model showed a breakthrough in numbers of publications on 2013 and 2014 than those forecasted. Dependency network based on association rule model of MeSH topics was also extensively analyzed. Number of publications showed a promising increase which points to the better national awareness of HCV problem. Studying MeSH terms clustering showed some hot topics. We recommend that the PubMed should alarm authors of the challenges of author affiliations. HCVDBegy availability opens the door for more drill down analysis for decision makers.
Vibrio cholerae is a waterborne bacterium inhabiting the aquatic ecosystem. Faecal contamination ... more Vibrio cholerae is a waterborne bacterium inhabiting the aquatic ecosystem. Faecal contamination of water resources, represent modes of dissemination of the bacteria and thus the disease. This study is reporting an association between Vibrio cholerae and chironomids larvae and exuviae, collected from Lake Manzala. The collection sites were chosen to cover the southern sector of the lake that is reportedly characterized by industrial, agricultural and domestic pollution. The only identified species was Chironomus transvaalensis, an East African species. The isolation of Vibrio cholerae was carried out according to the standard microbiological methods, and followed by 16S rRNA sequence analysis. non-O1/ non-O39 Vibrio cholerae was found to be present in all of the examined Chironomus transvaalensis larvae and exuviae. These findings further support the use of chironomids as a monitoring agent of Vibrio cholerae.
Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used f... more Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used for the production of recombinant proteins. BEs should be eliminated in the course of down stream processing of target protein produced by these bacteria. Supermacroporous monolith (continuous bed) columns, so called cryogel columns, with immobilized polyethyleneimine (PEI), polymyxin B (PMB) and lysozyme were employed for BEs capture. Due to the large interconnected pores it was possible to use cryogel columns at flow rates as high as 10 ml/min. The columns packed with Sepharose CL-4B with immobilized PEI, PMB and lysozyme were impossible to use at these high flow rates due to the collapse of the bed. The dynamic capacities of the cryogel columns were nearly independent of the flow rate. In the presence of EDTA, BEs were quantitatively captured from mixtures with a model protein, bovine serum albumin (BSA) at pH 7.2 with practically no protein losses. At pH 3.6 BEs were captured directly from non-clarified E. coli cell lysate resulting in more than 10 4 times BEs clearance.
Abstract In the present investigation an attempt was made to explore the antimicrobial, antioxida... more Abstract In the present investigation an attempt was made to explore the antimicrobial, antioxidant and anticancer activities of ethyl acetate extract of mangrove associated bacterium Bacillus subtilis subsp. subtilis RG. Antimicrobial activity results revealed that, the extract had strongly inhibited growth of gram positive than gram negative bacterial strains and also significantly ( P −1 ; whilst minimum bactericidal/fungicidal concentration (MBC/MFC) was ranged from 90 to 250 and 200 to 300 µg ml −1 , respectively. Antioxidant assay revealed that, this extract had maximum DPPH radical scavenging effect (75.79±5.41%) and reducing power (0.752±0.021 OD) at 1000 µg ml −1 . MTT assay showed potent cytotoxic activity against human breast adenocarcinmoa cells (MCF-7) with the IC 50 value of 46.64±0.79 µg ml −1 . This study tends to indicate that, B. subtilis subsp. subtilis RG isolated from mangrove ecosystem could be potentially explored for the development of new therapeutic agents.
Proceedings of the National Academy of Sciences, 2013
Shipworms are marine wood-boring bivalve mollusks (family Teredinidae) that harbor a community of... more Shipworms are marine wood-boring bivalve mollusks (family Teredinidae) that harbor a community of closely related Gammaproteobacteria as intracellular endosymbionts in their gills. These symbionts have been proposed to assist the shipworm host in cellulose digestion and have been shown to play a role in nitrogen fixation. The genome of one strain of Teredinibacter turnerae , the first shipworm symbiont to be cultivated, was sequenced, revealing potential as a rich source of polyketides and nonribosomal peptides. Bioassay-guided fractionation led to the isolation and identification of two macrodioloide polyketides belonging to the tartrolon class. Both compounds were found to possess antibacterial properties, and the major compound was found to inhibit other shipworm symbiont strains and various pathogenic bacteria. The gene cluster responsible for the synthesis of these compounds was identified and characterized, and the ketosynthase domains were analyzed phylogenetically. Reverse-t...
Red Sea sponges offer potential as sources of novel drugs and bioactive compounds. Sponges harbor... more Red Sea sponges offer potential as sources of novel drugs and bioactive compounds. Sponges harbor diverse and abundant prokaryotic communities. The diversity of Egyptian sponge-associated bacterial communities has not yet been explored. Our study is the first culture-based and culture-independent investigation of the total bacterial assemblages associated with two Red Sea Demosponges, Hyrtios erectus and Amphimedon sp. Denaturing gradient gel electrophoresis fingerprint-based analysis revealed statistically different banding patterns of the bacterial communities of the studied sponges with H. erectus having the greater diversity. 16S rRNA clone libraries of both sponges revealed diverse and complex bacterial assemblages represented by ten phyla for H. erectus and five phyla for Amphimedon sp. The bacterial community associated with H. erectus was dominated by Deltaproteobacteria. Clones affiliated with Gammaproteobacteria were the major component of the clone library of Amphimedon sp. About a third of the 16S rRNA gene sequences in these communities were derived from bacteria that are novel at least at the species level. Although the overall bacterial communities were significantly different, some bacterial groups, including members of Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, and Actinobacteria, were found in both sponge species. The culture-based component of this study targeted Actinobacteria and resulted in the isolation of 35 sponge-associated microbes. The current study lays the groundwork for future studies of the role of these diverse microbes in the ecology, evolution, and development of marine sponges. In addition, our work provides an excellent resource of several candidate bacteria for production of novel pharmaceutically important compounds.
Journal of Pharmaceutical and Biomedical Analysis, 2011
Red Sea sponges offer a potential for production of novel drugs and prototypes. The genus Negomba... more Red Sea sponges offer a potential for production of novel drugs and prototypes. The genus Negombata is a type of sponges abundant in the Red Sea. This sponge produces latrunculins that have well documented antitumor activity in addition to antimicrobial and antiviral effects. The identification of Negombata species is based on morphology and microscopical examination of megascleres of spicules. However, these criteria have proven to be unreliable for identification. Therefore, this study was established to test the accuracy of the spicules based taxonomy against molecular and protein profiles for the two species of Negombata: N. magnifica and N. corticata. About 700bp of cytochrome c oxidase I gene was sequenced from the tissues of the two Negombata species. Additionally total proteins were extracted from Negombata samples collected from different locations during different seasons and separated by denaturing polyacrylamide gel electrophoresis. Characteristic different protein profiles were obtained for both species. The data obtained from cytochrome c oxidase I gene sequencing and protein profiles can reliably differentiate between different species of Negombata in the Red Sea.
A method for high throughput screening of Green Fluorescent Proteins carrying metal binding tags ... more A method for high throughput screening of Green Fluorescent Proteins carrying metal binding tags in bacteria was developed. A random four amino acids tag-peptide library was successfully generated in E. coli. A 96-microtiter plate assembled with metal-iminodiacetic acid small cryogel columns was used for library screening. For the first time we were able to simultaneously screen a metal binding peptide tags library obtained from E. coli against different metal ions. From screening 25 different tags, three clones were able to bind to all metal ions studied (Ni 2+ , Zn 2+ , Co 2+ and Cd 2+). It was clearly demonstrated that the new construct could facilitate the screening of large peptide libraries.
Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used f... more Bacterial endotoxins (BEs) are integrated part of Escherichia coli, a microorganism widely used for the production of recombinant proteins. BEs should be eliminated in the course of down stream processing of target protein produced by these bacteria. Supermacroporous monolith (continuous bed) columns, so called cryogel columns, with immobilized polyethyleneimine (PEI), polymyxin B (PMB) and lysozyme were employed for BEs capture. Due to the large interconnected pores it was possible to use cryogel columns at flow rates as high as 10 ml/min. The columns packed with Sepharose CL-4B with immobilized PEI, PMB and lysozyme were impossible to use at these high flow rates due to the collapse of the bed. The dynamic capacities of the cryogel columns were nearly independent of the flow rate. In the presence of EDTA, BEs were quantitatively captured from mixtures with a model protein, bovine serum albumin (BSA) at pH 7.2 with practically no protein losses. At pH 3.6 BEs were captured directly from non-clarified E. coli cell lysate resulting in more than 10 4 times BEs clearance.
Uploads
Papers by Amro Hanora