البيانات الاساسيه

السيره الذاتيه

Curriculum Vitae

Name:  Walid Ismail Mohammed Mohammed Bakeer

Nationality:  Egyptian           

Date of Birth:  21-May-1977     

Married with three children

Home address:  29 Hassan Abdeen Street, Beni-Suef El-Gadida, Beni-Suef, Egypt.

E-mail address:  walid.bakeer@yahoo.com // walid.bakeer@pharm.bsu.edu.eg                        Mobile telephone:  002/ 01020599660

Work address: Microbiology and Immunology department, Faculty of Pharmacy, Beni-Suef University - Ahmed Hegazi Tawil Street, Beni-Suef, Egypt.

General Specialization:- Pharmaceutical Microbiology and Biotechnology

Specific specialization:- Fungal Biotechnology

Educational Qualifications

1. Bachelor in Pharmaceutical Sciences from the Faculty of Pharmacy, Cairo University (Beni-Suef branch) with the general grade “Excellent with honor”. Graduation date on May-1999.

2. Master degree in Microbiology from Faculty of Pharmacy, Cairo University and was awarded in 6^th August-2006.

   The title of the thesis was:- "Study on Post-Antimicrobial effect (PAE) of certain Antimicrobial Agents on certain Bacterial Isolates". Specialty (Clinical and Pharmaceutical Microbiology)

3. Doctor of Philosophy (Ph.D.) in Fungal Biotechnology, University of Bristol, United Kingdom and awarded on 15^th November 2011.

   The title of the thesis was: - "Overexpression of Secondary Metabolism Genes from Magnaporthe grisea and Beauveria bassiana".    Specialty (Fungal Biotechnology)                       

   The certificate from the Egyptian Supreme Council of Universities was issued on    11 –January– 2012 for the equilibration of my British Ph.D. to the Egyptian equivalents gained from Egyptian universities.

Professional Qualifications

2000-2006                   Demonstrator at the department of Microbiology, Faculty of Pharmacy, Cairo University, Beni-Suef campus, Egypt.

 

2006-2012                   Assistant lecturer at the department of Microbiology, Faculty of Pharmacy, Beni Suef University, Egypt. Additionally, a member of the governmental full-time Ph.D. mission (Specialty Biotechnology) in University of Bristol, United Kingdom, from March-2008 till December-2011.

 

2012-Current             Lecturer at the department of Microbiology, Faculty of Pharmacy, Beni-Suef University, Egypt (since 31-01-2012).

Publications

1. Heterologous expression of the ACE1 "PKS-NRPS" from the fungal rice pathogen Magnaporthe grisea. Walid Bakeer, Zhongshu Song, James Marshall, Jerome Collemare, Colin M. Lazarus, Andrew M. Bailey, Thomas J. Simpson Marc-Henri Lebrun, and Russell J. Cox.  The international conference “Directing Biosynthesis” occurred on 15-17^th September 2010, Durham University, United Kingdom, poster presentation.

    

2. The Programming Role of Trans-acting Enoyl Reductases during the Biosynthesis of Highly Reduced Fungal Polyketides. Mary N. Heneghan, Ahmed A. Yakasai, Katherine Williams, Khomaizon A. Kadir, Zahida Wasil, Walid Bakeer, Katja M. Fisch, Andrew M. Bailey, Thomas J. Simpson, Russell J. Cox, and Colin M. Lazarus. Chem. Sci., 2011, 2, 972-979. [Impact Factor 9.14]

    

3. Rational Domain Swaps Decipher Programming in Fungal Highly Reducing Polyketide Synthases and Resurrect an Extinct Metabolite. Katja M. Fisch, Walid Bakeer, Ahmed A. Yakasai, Zhongshu Song, Jennifer Pedrick, Zahida Wasil, Andrew M. Bailey, Colin M. Lazarus, Thomas J. Simpson, and Russell J. Cox. JACS, 2011, 133, 16635–16641. [Impact Factor 10.8]

    

4.  Isolation, Cloning and Sequence Analysis of β-tubulin Gene from Bolinea lutea F23523, a Potential Strobilurin Producing Fungus. Zafar Iqbal, Walid Bakeer. Int. J. Agric. Biol., 2013, 15, 1008‒1012. [Impact Factor 0.94]

    

   Heterologous Expression of the Avirulence gene ACE1 from the fungal rice pathogen Magnaporthe oryzae. Zhongshu Song, Walid Bakeer, James W. Marshall, Ahmed A. Yakasai, Rozida Mohd Khalid, Jerome Collemare, Elizabeth Skellam, Didier Tharreau, Marc-Henri Lebrun, Colin M. Lazarus, Andrew M. Bailey, Thomas J. Simpson and Russell J. Cox. Chem. Sci., 2015, 6, 4837-4845. [Impact Factor 9.14]

    

   Solamargine production by a fungal endophyte of Solanum nigrum. S.S. El-Hawary, R. Mohammed, S.F. AbouZid, W. Bakeer, R. Ebel, A.M. Sayed  and M.E. Rateb. Journal of Applied Microbiology, 2016, 120, 900—911. [Impact Factor 2.8]

 

7-      A study on an aniline degrading Pseudomonas aeruginosa isolate recovered from agricultural wastewater in Egypt. Fatma Molham, Walid Bakeer, Eman El-Gebaly, Magdy Amin. New Egyptian Journal of Microbiology. 2016

 

Selected Conferences attended

1. The Chemistry and Biology of Natural Products IV, 18^th June 2008, University of Bristol, United Kingdom.

2. New Horizons in Natural Product Chemistry, 12^th November 2008, University of Nottingham, United Kingdom.

3. Chemical Biology: A symposium in memory of David R. Kelly, 4^th February 2009, University of Cardiff, United Kingdom.

4. 43^rd European Symposium on Bio-Organic Chemistry (ESPOC) “Vitamins and Cofactors”, 24-26^th April 2009, Gregynog, Powys, Wales, United Kingdom.

5. The Chemistry and Biology of Natural Products V, 17^th June 2009, University of Bristol, United Kingdom.

6. Directing Biosynthesis 2010: Discovery, Evaluation, Function. 15-17^th September 2010, Durham University, United Kingdom.

7. From Natural products to chemical Biology VI, 22^th June 2011, University of Bristol, United Kingdom.

Research Skills

1. Skillful in cloning and over-expression of secondary metabolism genes in bacterial and fungal hosts.

2. Capable of transforming fungi for gene over-expression and genetic engineering to produce new drugs and explore their biosynthesis.

3. Skillful in molecular biology techniques.

4. Skillful in recombination of genes in Yeast.

5. Skillful in gene synthesis and codon optimization for successful expression in prokaryotic and eukaryotic hosts.

6. Skillful in over-expression of genes in E. coli and Yeast for protein isolation and purification as well as optimization for production of soluble proteins.

7. Skillful in fermentation and analysis using LC-MS.

8. Basic knowledge about NMR and High Resolution Mass Spectrometry.

Teaching undergraduate courses and duties

I am teaching the following subjects in faculties of Pharmacy in Beni-Suef University and Nahda University during the previous four years and nine months with competency.

1. Basic microbiology and immunology.

2. Pharmaceutical microbiology.

3. Clinical microbiology.

4. Pharmaceutical biotechnology.

5. Public health and preventive medicine.

6. Cell biology.

7. Pathophysiology.

Teaching postgraduate courses and duties

1. Advanced immunology.

2. Advanced microbiology.

Postgraduate students and research supervision

1. Mohamed Ahmed Sebak. PhD – in progress. Title:- Investigation for the production of biologically active secondary metabolites recovered from some microbial samples.

2. Sayed Ali Galal. Master – in final stages. Title:- Studies on bacterial resistance to merpenem

3. Fatma Molham. Master – in progress. Title:- Study of the genetic basis of biodegradation of some aromatic compounds in the environment.

4. Reham Osama. Master – in progress. Title:- Carbapenem resistance genes in Gram negative pathogenic bacteria and co-incidence with resistance to cephalosporins.

5. Hagar Hemdan. Master – in progress. Title:- Mechanisms of Resistance to Macrolides Antibiotic among Pathogenic Bacteria

6. Ahmed Mohammed Soliman. Master – in progress. Title:- A study on some marine Actinomycetes for production of biologically active compounds

7. Aya Ahmed. Master – in progress. Title:- A study on some marine fungi for production of biologically active compounds.

8. Ola Rady. Master – in progress. Title:- Multi-drug resistance plasmids in pathogenic Enterobacteriaceae and Pseudomonas conferring resistance to aminoglycosides.

9. Aya Abd El-Gawad. Master – "Under registration". Proposed title:- Study on biodegradation of plastics using fungal isolates.

    

 

عنوان رسالة الماجستير

Study on Post-Antimicrobial effect (PAE) of certain Antimicrobial Agents on certain Bacterial Isolates

ملخص رسالة الماجستير

Study on Post-Antimicrobial effect (PAE) of certain Antimicrobial Agents on certain Bacterial Isolates The impact of using a combination therapy on improving the pharmacodynamic parameters (killing activity and postantibiotic effect [PAE]) of certain antimicrobials (aminoglycosides {amikacin and gentamicin}, quinolones {ofloxacin and ciprofloxacin} and β-lactams{meropenem, imipenem, cefuroxime, cefotaxime, cefoperazone, ceftazidime and cefepime) against common opportunistic pathogen“ Enterobacteriaceae” was the focus of this study. Firstly, screening for a number of different members of Enterobacteriaceae sensitive to the previously mentioned antimicrobials was done by identifying and performing disk-diffusion susceptibility testing over a sample of 94 MacConkey isolates, most of them were provided sensitive toward many classes of antimicrobial agents. A nine different enterobacterial isolates namely; E.coli strain 19, Klebsiella pneumonia strain 63, Klebsiella oxytoca strain 68a, Enterobacter cloacae strain 35a, Citrobacter koseri strain 4b, Citrobacter freundii strain 52, Proteus mirabilis strain 5b, Proteus vulgaris strain 50b and Providencia rettgeri 14a were sensitive to antimicrobials of the study and selected the following study steps. Secondly, the minimum inhibitory concentrations {MIC} were determined for the antimicrobials of the study against the 9 selected representative strains via agar dilution method. It was noticed that meropenem has the lowest MIC values while cefuroxime has the highest MIC values against the selected bacteria. After that, the bactericidal activity and the killing rates were investigated for individual antimicrobials and combinations of them against the selected enterobacteria via killing curve methodology. It was found that all antimicrobials used have significant bactericidal activity and it was found also that quinolones; ciprofloxacin and ofloxacin induced the highest killing rate at different multiples of their MICs followed by aminoglycosides; amikacin and gentamicin then carbapenem-β-lactams; imipenem and meropenem and it was noticed that all the previous antimicrobials induced concentration dependent killing activity. Finally, cephalosporine-β-lactams induced the least powerful and only time dependent killing against the various selected bacteria. The killing rates of the combinations of aminoglycosides used (at 2xMIC) with various β-lactams of the study (at 10xMIC) also, the combinations of aminoglycosides (at 2xMIC) with quinolones (at 2xMIC) were investigated via killing curve method against the nine bacterial strains and compared to the killing rate induced by individual agents. The resulted data and figures showed clear synergism between aminoglycosides and β-lactams of the study. While showing indifferent killing activity with aminoglycosides-quinolones combinations from that induced by individual antimicrobial agents against all selected bacteria. The other major concern was the studying of PAE of individual antimicrobials and the combinations, and the study showed that quinolones, aminoglycosides and carbapenem β-lactams induced significant PAEs while cephalosporins-β-lactams induced non-significant or even negative PAEs. We also studied the combinations of aminoglycosides; amikacin and gentamicin (at 2xMIC) with various β-lactams (at 10xMIC) and with quinolones used (at 2xMIC) against the previously selected 9 Enterobacteriaceae. It was observed that combinations of aminoglycosides with β-lactams showed synergistic improvement for PAE-periods, thus, permitting less frequent administration of both agents during the practical situations in therapy. While combinations of aminoglycosides with quinolones did not enhance PAE to reach to synergistic level (not even be additive) and consequently considered indifferent with respect to PAE. So the combinations of aminoglycosides with quinolones have no beneficial impact on dosing frequency of them. Also the impact of the utilization of an antineoplastic agent 5-Flurouracil “ 5-FU” [at 50 μg/ml; corresponding to the maximum achievable plasma concentration] on PAE duration of antimicrobials (at the previous multiple of MIC) against Proteus mirabilis and Providencia rettgeri was studied. The MICs of 5-FU against the 9 Enterobacteriaceae revealed that the MICs of 5-FU against Proteus mirabilis and Providencia rettgeri were below the maximum achievable plasma concentration (50 μg/ml) while, its MICs against the other selected strains much higher than 50 μg/ml. The results showed that the PAEs of 5-FU at 50 μg/ml toward Proteus mirabilis and Providencia rettgeri were high being 2.5 and 2 hours, respectively. It was observed that a synergistic enhancement of PAE of ofloxacin and ciprofloxacin at 2xMIC and of β-lactams; meropenem, cefepime, cefotaxime, ceftazidime and cefoperazone at 10xMIC in presence of 5-FU occurred. While, aminoglycosides; amikacin and gentamicin at 2xMIC induced PAE in presence of 5-FU indifferent from that induced by the antimicrobial alone, against Proteus mirabilis and Providencia rettgeri. Consequently, the patients who take 5-FU as anticancer therapy could lower the dosing frequency of quinolones and β-lactams used for treatment of enterobacterial infection, especially, if bacteria inhibited with 5-FU-MIC below the maximum achievable plasma concentration of 5-FU.

عنوان رسالة الدكتوراه

Overexpression of Secondary Metabolism Genes from Magnaporthe grisea and Beauveria bassiana

ملخص رسالة الدكتوراه

Overexpression of Secondary Metabolism Genes from Magnaporthe grisea and Beauveria bassiana Specialty: Fungal Biotechnology Abstract Magnaporthe grisea is the most devastating fungal pathogen of rice. Certain rice strains are resistant to strains of M. grisea that produce a hybrid polyketide synthase – non-ribosomal peptide synthetase (PKS-NRPS) called avirulence conferring enzyme1 (ACE1) in appressoria. Heterologous expression of the ace1 gene was attempted in Aspergillus oryzae in order to discover the avirulence signal. Initial failure to produce ACE1 was investigated by expressing truncated versions of ace1 fused at their 3’-termini with the egfp reporter gene. This identified mis-splicing of intron-2 as the cause, and removal of this intron led to successful heterologous expression of ACE1 in A. oryzae and discovery of its polyketide product, 12,13-dihydroxymagnaporthepyrone. A similar product, 10,11-dihydroxymagnaporthepyrone was identified in the mycelium of M. grisea clones that had been transformed to overexpress ace1 constitutively. These polyketide-only compounds suggest that the NRPS module of ACE1 might be redundant or require a special amino acid biosynthesised only in appressoria. Beauveria bassiana strains produce tenellin and desmethylbassianin (DMB), hybrid polyketide-tyrosine compounds synthesised by tenellin synthetase (TENS) or its homologue DMB synthetase (DMBS) together with nearly identical post-PKS modifying enzymes. Hexaketide DMB and pentaketide tenellin differ because DMB synthesis involves one extra cycle of chain extension and one less C-methylation. Heterologous co-expression of TENS with the enoyl reductases (ER) from the tenellin or DMB clusters, produced pretenellin A, proving that trans-acting ER do not control programming of highly reducing (HR) fungal PKS. Progressive substitution of TENS functional domains with their DMBS counterparts and heterologous co-expression with either ER resulted in production of compounds with changes that could be mapped to specific domains. Individual domain swaps showed that the C-methyltransferase domain controls its own programming, while the ketoreductase (KR) domain was found to be responsible for the chain-length variation between tenellin and DMB. Heterologous co-expression of TENS with the KR domain swapped from DMBS together with all the other tenellin biosynthetic enzymes produced bassianin, an "extinct metabolite" previously described in B. bassiana but no longer detectable in numerous isolates. This research highlighted that correct intron splicing cannot be relied upon to occur during heterologous expression of every fungal gene in other fungal hosts. Recognition of this problem with respect to the ace1 gene allowed the discovery of the ACE1 polyketide product. This is a significant step towards identifying the ACE1 signal, with potential biotechnological importance in combating M. grisea infection of rice. Finally, heterologous expression of TENS and DMBS domain-swapped chimaeric enzymes led, for the first time, to the discovery of crucial biosynthetic programming determinants in HR PKS-NRPS systems.