My name is Dr. Mohamed Samir, lecturer (researcher) of Zoonoses at the Faculty of Veterinary Medicine, Zagazig University. I obtained my PhD in the field of avian influenza viruses and the role of microRNAs as biomarkers for this infection. This is an emerging topic in Veterinary Medicine. Besides teaching at the University, I am carrying out research activities related to the question of how avian influenza viruses emerge and the mechanism behind their host adaptations. As a trainer, I am giving lecturer and training cessions for the Veterinarian about zoonotic diseases and for undergraduates and postgraduates about scientific databases and reference manager programs. 

Academic Degree

Bachelor of Veterinary Medical Science – May 2006 – Faculty of Veterinary Medicine, Zagazig University.
Master of Zoonoses - April 2010 - Faculty of Veterinary Medicine, Zagazig University.
PhD (Viral Zoonoses) – March 2016 – University of Veterinary Medicine (TiHo), Hannover, Germany. 

Academic Positions

Demonstrator, Faculty of Veterinary Medicine, Zagazig University. (2006-2010)
Assistant lecturer, Faculty of Veterinary Medicine, Zagazig University. (2010-2016)
Lecturer, Faculty of Veterinary Medicine, Zagazig University.  (2016 – now)

Academic Training Courses 

- Different methods of preparation of vaccines and antiserum, Dec 2006, Vaccine and Serum Institute, Cairo, Egypt.

- Molecular biology, Feb 2008, Medical Technology Center for Research and Services, Alexandria University, Egypt.

- Basic techniques in cell culture, Nov. 2008, Medical Technology Center for Research and Services, Alexandria University, Egypt.

- Handling of laboratory mice, Jul. 2011, Helmholtz Center for Infection Research, Braunschweig, Germany.
Introduction to statistics, not only for biologists: theoretical and technical part. Jul 2012, Helmholtz Center for Infection Research, Braunschweig, Germany.

- Basics of RNA sequencing, Mar. 2013, Molecular Biotechnology Center, Via Nizza, Torino, Italy.

- Necropsy techniques, Apr. 2013, Pathology Department, Veterinary Medical School, Hannover, Germany.

- Biological colloquium, May 2013, Veterinary Medical School, Hannover, Germany.

 - Bioethics and fundamental of scientific reliability, Apr. 2015, Veterinary Medical School, Hannover, Germany.

- Repetition biometry, Jan. 2016, Veterinary Medical School, Hannover, Germany.

- Animal welfare, Feb. 2016, Veterinary Medical School, Hannover, Germany.

Laboratory Research Skills

- Viral infection (In vivo, in vitro and ex. vivo)
- Virus propagation, titration and characterization  
- Tissue sampling and processing
- Cell culture, primary cells and lung organ culture
- RNA and miRNA extraction and their quality check using Bioanalyzer.
- PCR, qRT-PCR
- Sequence correction and editing
- Phylogenetic analysis (Bioedit and MEGA software)
- Western blotting
- ELISA assay, Plague assay for virus quantification.
- Reverse genetics and cloning

Bioinformatics and genomic analyses experience

- Sequencing and Bioinformatics

* Gene ontology and pathway analysis using Cytoscape.
* Gene functional and annotation study using DAVID annotation tool.

* mRNAs and miRNAs clustering using DIANA tool 
* Phylogenetic analysis using BioEdit and MEGA5.2.
* GeneNorm and Normfinder for selection of reference genes in the qRT-PCR.
* MiRNA analysis online tools (OASIS, miRBase, miRNA viewer, Target scan, DIANA tool).

Research software

Graph Pad Prism -  R - SPSS - EndNote - Adobe Illustrator CS6 - Excel - Photoshop - Chromas 

Teaching Experience

Undergraduates:

Teaching practical courses in microbiology/virology/mycology, 2006-2010 (70 hrs/semester).  
Giving lectures for Veterinary students in Zoonoses (virology and bacteriology): 2016- now.
Preparation of the practical book for the Veterinary students
Participation in preparing/updating the theoretical curriculum
Formulating oral and written exams for undergraduates  

Post-graduates

Supervising PhD, Master and diploma students
Participation in teaching the lectures
 Formulating oral and written exams for post graduates 

Publications

1. Mohamed Samir and Frank Pessler. Small non-coding RNAs associated with viral infectious diseases of veterinary importance: potential clinical applications (2016). Frontiers in Veterinary Science, 3:22. DOI: 10.3389/fvets.2016.00022.

2. Mohamed Samir, Lea Vaas and Frank Pessler. MicroRNAs in the host response to viral infections of veterinary importance (2016). Frontiers in Veterinary Science, 3:86. DOI: 10.3389/fvets.2016.00086.

3. Mohamed Samir, M. Hamed, Fatma A., Nguyen V.,  Hernandez-Vargas E, Frauke Seehusen, Wolfgang Baumgärtner, Hamed, A, Ahmed A. H. Ali and Frank Pessler. An Egyptian HPAI H5N1 isolate from clade 2.2.1.2 is highly pathogenic in an experimentally infected domestic duck breed (Sudani duck) (2017). Transboundary and Emerging Disease, DOI: 10.1111/tbed.12816

4. Mohamed Samir, Ramon O Vidal, Vincenzo Capece, Esteban A. Hernandez Vargas, Stefan Bonn and Frank Pessler. Highly pathogenic influenza A virus (H5N1) induces tissue-specific differential expression of small non-coding RNAs in experimentally infected duck (2016). (In preparation).

5. Mohamed Samir. MicroRNAs as biomarkers in the host response to influenza A virus in humans and animals (2016). PhD thesis. University of Veterinary Medicine (TiHo), Hannover, Germany.

6. Mohamed Samir, M. A. Amin, A. O. Hassan, A. M. Merwad and M. A. I. Awadallah. Prevalence, protein analysis and possible preventive measures against zoonotic anisakid larvae isolated from marine Atherina fish (2015). Helminthologia, 52, 4: 375-383, doi: 10.1515/helmin-2015-0060.

7. Magda, A. A.; Amer, O. H.; Maysa, A. I. A.; Merwad, A. M. A. and Mohamed Samir. Role of Atherina fish in transmitting some trematodes of public health importance. Proceedings of the 3rd Global Fisheries and Aquaculture Research Conference, Foreign Agricultural Relations (FAR), Egypt, 29 November-1 December 2010. 120-133.

8. Mohamed Samir. Role of Atherina species in transmitting some parasitic diseases to man. (2010). Master thesis, Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Egypt.

Projects participation

1. “Pathogenesis of avian influenza in wild birds”. Fund from Zagazig University.

2. “Epidemiology of non-primate hepaci-viruses in Europe”, member, collaboration with Prof. Eike Steinman, Virus transmission group, Helmholtz Center for Infection Research, Braunschweig, Germany. Funding HZI, Germany.

Trainer experiences

1. Trainer for the Veterinary student at the General Organization of Veterinary Services
2. Trainer for the higher graduate students at Zagazig University (Scientific databases and EndNote)

Grants and Awards

1. DAAD “GERLS, German-Egyptian Long-term Scholarship”, a joint program between the DAAD and the Egyptian ministry of Higher Education and Scientific Research. (Grant ID: A/11/92510).

2. “Young Ambassador for the American Society for Microbiology” in Egypt: 2017 - 2018.

Conferences and Workshops

Symposium: Avian influenza virus and public health, Aug 2008, Faculty of Veterinary Medicine, Zagazig University, Egypt. Workshop: Proposal Writing Workshop, Nov 2008, German Academic Exchange Service (DAAD), Conference Centre, Cairo University, Cairo, Egypt. Workshop: Science Year Follow Up Event, Nov 2008, German Academic Exchange Service (DAAD), Conference Centre, Cairo University, Cairo, Egypt. Workshop: Germany alumni fair, Nov 2008, German Academic Exchange Service (DAAD), Conference Centre, Cairo University, Cairo, Egypt. Conference: Sustainability of Environmental Development and Health Promotion, Future vision, Mar 2009, Medical conference, under the theme Faculty of Medicine, Zagazig University, Zagazig, Egypt.  Conference: Veterinary Medicine and challenges, Feb 2010, Faculty of Veterinary Medicine, Zagazig University, Egypt. Conference: 3rd Annual Retreat (Poster presentation), Oct 2012, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany. Conference: 4th Annual Retreat (Oral presentation), Jun 2013, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany.  Symposium: 5th TWINCORE-Symposium (Attendance), Sep 2013, TWINCORE, Center for Clinical and Experimental Animal Research, Hannover, Germany. Conference: 6th Graduate School Day   (Attendance), Nov 2013, University of Veterinary Medicine Hannover (TiHo), Bad Salzdetfurth, Germany. Conference: One Influenza, One World, One Health   (Poster presentation), Sep 2014, St Hilda’s College, Oxford, United Kingdom (UK). Conference: 4th International influenza meeting (Poster presentation), Sep 2014, Flu Research Net and German Research Platform for Zoonoses, Muster University, Germany. Course: Funding Opportunities for Young Scientists (Participation), Sep 2014, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany. Conference: 7th Graduate School Days (oral presentation), Nov 2014, University of Veterinary Medicine Hannover, Hannover, Germany. Conference: 8th Graduate School Days (Oral and poster presentations), Nov 2015, University of Veterinary Medicine Hannover, Hannover, Germany. Course: Scholarly Collaboration (attendance), Jun 2016, German Academic Exchange Service (DAAD), Cairo, Egypt. Course: Constructive Evaluation and Feedback on Students Performance, Sep 2016, German Academic Exchange Service (DAAD), Cairo, Egypt. Course: Team Building for Team Leader, Oct 2016, German Academic Exchange Service (DAAD), Cairo, Egypt. Workshop: Biorisk Management for Avian Influenza, Oct 2016, American Society for Microbiology (ASM), Cairo, Egypt. Workshop: Controlling viral infections to improve food security and the nutrition of Egypt's poorest communities. (Oral and poster presentation). Nov 2016, Cairo University and the University of Surrey, UK. Workshop: Viruses without borders: The global threat of emerging diseases transmitted through vectors and trade. (Oral presentation and poster). Feb 2017, University of Pretoria, South Africa. Workshop: Erasmus Plus program. Oct. 2017, Zagazig University, Egypt. Course: “Funding Resources for Research Projects” Dec. 2017, German Academic Exchange Service (DAAD), Cairo, Egypt.

Professional Membership

American Society for Microbiology (Nr. 1151753706). Young Ambassador for the American Society for Microbiology (ASM) in Egypt.   Science blogger “Alumni portal Germany”. Veterinary Egyptian Syndicate. Egyptian Society for Virology. International Veterinary Vaccinology Network