Current Position: Postdoctoral with P. Hamza Babiker, Biochemistry department college of medicine at Sultan Qaboos University, Oman 

 

 

 

Qualifications:                                                 

 

PhD degree (August 2017):

Biochemistry department

Major: Molecular biology and Biochemistry, college of medicine at Sultan Qaboos University, Oman 

Project title:  

Population structure and genetic diversity of Theileria parasite in Oman

 

Master degree (December 2012):

Master in Medical Microbiology (GPA: 3.49)         

Microbiology & immunology, college of medicine at Sultan Qaboos University, Oman

 

Project title:  

Genetic diversity of Plasmodium falciparum in Yemen and spread of antimalarial drug resistance genotypes

 

Bachelor degree (2010)

Bachelor in Medical Laboratory Science (MLS) (GPA: 3.22), college of science, Sultan Qaboos University, Oman

 

Fields of interest:

Molecular Genetics
Population Genetics
Biochemistry
Bioinformatics

 

Research interest:

 

        I am interested in the field of molecular genetics of infectious diseases, with emphasis on population dynamics of pathogens using advanced genomic approach, with the view of understanding evolution of clinically important traits (virulence, response to therapy and vaccine).

 

 

 

 

Professional experience:

 

Awards:

The best postgraduate thesis award for the academic year, SQU,. 2017/2018
The national research award category II, TRC, Oman, Oct2016,
Travel award to attend “Middle East Biology of Parasite” postgraduate course, University of Bern, Switzerland, August 2016.
Travel award to attend Middle East and South Asia Conference on Epigenetics and Genomics of Infectious Diseases. Jordon (7-9 March 2016).

 

Fellowship

 

International Atomic Energy Agency (IAEA) Training Fellowship, host institute, King Abdullah University of science and Technology (KAUST University), KSA, 15th January to 9th March 2017.
King Abdullah University of science and Technology (KAUST) Training Fellowship, host in Prof. Arnab pain lab in king Abdullah University of science and Technology, KSA, 15th April to 15th June 2016.
European Commission (FP7 INCO 245145, PIROVAC), Training Fellowship, host in Prof Brian Shiels lab, Glasgow university, UK, 26th January to 26th April 2014
International Atomic Energy Agency (IAEA) Training Fellowship, host in Dr. Richard Culleton lab, Nagasaki university, Japan. 1st July to 31st August 2013,

 

 

Innovative achievement during PhD work:

 

I developed a set of microsatellite markers for genetic studies of the small ruminant’s parasite Theileria lestoquardi (Al-Hamidhi et al., 2016).  These markers are now picked up by researchers in other countries to examine the extent of the genetic diversity of Theileria lestoquardi small ruminant theileriosis is common.

 

Major projects research:

 

MSc: Analysis population genetic and drug resistance genes of the human malaria parasite Plasmodium falciparum.

 

Between MSc and PhD:  1) Molecular identification of mycobacterium tuberculosis. 2) Population structure of Plasmodium vivax using whole mitochondrial genome

 

PhD: Analysis of population genetic structure of Theileria parasites in Oman

 

Postdoc: Identification of transmission blocker candidates for T. lestoquardi parasites (October 2017-present)

 

Microbiology and Immunology department with Dr. Crystal koh: “Molecular anaylsis of systemic lupus erythematous (SLE) and rheumatoid arthritis (RA) in SQUH” (October-December 2017).

 

Oman Animal & Plant Genetic Resources Center (OAPGRC): animal and plant database and gene bank (April- present)

 

Medicine department with Dr. Shiyam Kumar: “Circulating cell free DNA as potential cancer biomarker for treatment response in prostate cancer” (May 2018- present).

 

 

Lab work skills:

Genomic DNA extraction using indoor method (chloroform) and commercial kits and concentration measured using Nanodrop and Qubit instrument.
RNA extraction from blood and tissue using commercial kits, and its quantified using Qubit instrument
Polymerase chain reaction (PCR) was used to amplify different target genes
Real-time PCR was used to quantify genomic DNA and cDNA in samples
Sanger sequencing methods was used to detected SNPs on targeted genes
Fragment analysis for genotyping microsatellites that used in analysis of population genetic
DNA cloning using plasmid to get express candidate genes sequence
TruSeq DNA PCR free library was prepared to run for Hiseq illumine to sequence whole genome of parasite from blood

Population genetics indices

Haplotypes construction
Heterozygosity (He)
Wright`s fixation test (FST)
Linkage disequilibrium (LD)
Multiplicity
Mean number of infection (MOI)
Phylogenetic tree
Nucleotide diversity analysis

 

Statistical analysis:

1. R program

2. SPSS program such as:

Test of significance (P-value)
ANOVA
Chi-square test

 

 

  

Peer Reviewed Publications:

 

 

Mohammed H Abdelraheem, Devendra Bansal, Mohammed Idris, Moawia M Mukhtar, Muzamil M Abdel Hamid, Zainb S Imam, Sisay Getachew , Rakesh Sehgal , Hargobinder Kaur, Amal A H Gadalla, Salam Al-Hamidhi, Zainab S Al-Hashami, Ali A Al-Jabri, Ali A Sultan, Hamza A Babiker. Genetic diversity and transmissibility of imported Plasmodium vivax in Qatar and three countries of origin. Scientific report journal (under review)  

 

Awad, H., S. Al-Hamidhi, A.-R. M. El Hussein, Y. M. z. Yousif, K. M. Taha, D. A. Salih, W. Weir and H. A. Babiker (2018). "Theileria lestoquardi in Sudan is highly diverse and genetically distinct from that in Oman." Infection, Genetics and Evolution 62: 46-52.

 

Amira Al-Fahdi, Salama Al-Hamidhi, Mohammed. H. Tageldin, Patrick Bobade, Eugene Johnson, Badar Alqamashoui, Abdel-Rahim Hussain, Huseyin Bilgin Bilgic, Tϋlin Karagenç, Hamza Babiker. Host and breed variation in susceptibility of livestock to natural Theileria sp infection in Oman. Ticks and Tick-borne Diseases, 8(5), 741-748. 

 

Salama Al-Hamidhi, William Weir, Jane Kinnaird, Mohammed Tagledeen, Albano Beja-Pereira , Ivan Morrison, Joanne Thompson, Andy Tait, Brian Shiels ,Hamza Babiker. Theileria lestoquardi displays reduced genetic diversity relative to sympatric Theileria annulata in Oman. Infect Genet Evol. 2016 May 7;43:297-306. doi: 10.1016/j.meegid.2016.05.007

 

Salama Al-Hamidhi, Mohammed. H. Tageldin, William Weir, Amira Al-Fahdi, Eugene Johnson, Patrick Bobade, Badar Alqamashoui, Albano Beja-Pereira, Joanne Thompson, Jane Kinnaird, Brian Shiels, Andy Tait, Hamza Babiker (2015) Genetic diversity and population structure of Theileria annulata in Oman. PLOS ONE, 10(10), e0139581. http://doi.org/ 10.1371/ journal.pone.0139581

 

Bakhiet AM, Abdel-Muhsin AM, Elzaki SE, Al-Hashami Z, Albarwani HS, AlQamashoui BA, Al-Hamidhi S, Idris MA, Elagib AA, Beja-Pereira A, Babiker HA (2015). The effect of a decade of artemisinin-based combination therapy and intense control measures on Plasmodium falciparum population genetic structure in Sudan. Acta Tropica, 148:97-104.

 

Al-Hamidhi S, Mahdy MA, Al-Hashami Z, Al-Farsi H, Al-Mekhlafi AM, Idris MA, Beja-Pereira A, Babiker HA (2013).Genetic diversity of Plasmodium falciparum and distribution of drug resistance haplotypes in Yemen. Malar J., 15.;12(1):24

 

Al-Hamidhi S, Mohammed A.K. Mahdy, Saad M. Bin Dajem , Adel Ali H. Al-Sheikh, Zainab Al-Hashami, Hissa Al-Farsi, Abdulsalam M. Al-mekhlafi,  Mohamed Ahmed Idris, Albano Beja-Pereira  and Hamza A. Babiker. (2013). The prospect of malaria elimination in the Arabian Peninsula: a population genetic approach. Infection, Genetics and Evolution. 2014;27:25-31

 

Salama Al-Hamidhi, Genetic diversity of Plasmodium falciparum in Yemen, and spread of anti-malarial drug resistance genotypes. MSC thesis, College of Medicine and Health Sciences, Sultan Qaboos University, 2012.

 

Salama Al-Hamidhi, Distribution of bacteria in three sources of water in SQU. Bsc thesis, College of Medicine and Health Sciences, Sultan Qaboos University, 2010.

 

 

 

Conference presentation

 

Abir Al-Rumhi, Devendra Bansal, Mohamed H. Abdelraheem, Salama Al-Hamidhi, Amal Gadalla, Ali A. Sultan, Hamza Babiker.Genetic diversity and transmissibility of imported Plasmodium falciparum to the malaria-free state of Qatar. 7th MIM Pan-African Malaria Conference, Senegal,19-23 April 2018
 
Salama Al-Hamidhi, Mohammed. H. Tageldin, Jane Kinnaird, Brian Shiels, Andy Tait, Hamza Babiker, William Weir. Analysis of allelic diversity of two immunodominant antigen genes of T. annulata and T. lestoquardi in Oman. Apicomplexa in Farm animals 4th international meeting, At Madrid (11-14 October 2017)

 

Salama Al-Hamidhi, Mohammed A.K. Mahdy, Zainab Al-Hashami, Hissa Al-Farsi, Abdulsalam M. Al-mekhlafi,  Mohamed Ahmed Idris, Albano Beja-Pareira  and Hamza A. Babiker. Genetic diversity and distribution of drug resistance genotypes among Plasmodium falciparum in Yemen and Saudi Arabia. Middle East and South Asia Conference on Epigenetics and Genomics of Infectious Diseases. Jordon (7-9 march 2016).

 

Salama Al-Hamidhi · Mohammed. H. Tageldin, William Weir, Amira Al-Fahdi Eugene Johnson, Patrick Bobade, Mohamed Idris, Badar Alqamashoui, Albano Beja-Pereira, Jane Kinnaird, Brian Shiels, Andy Tait, Hamza Babiker. Extensive diversity of Theileria annulata parasite among infected cattle in Oman. Regional Conference for Animal Genetics Resource Conservation (23-24 February 2016).

 

Salama Al-Hamidhi1, Mohammed. H. Tageldin1, William Weir2, Amira Al-Fahdi1, Eugene Johnson1, Patrick Bobade1, Mohamed Idris1, Badar Alqamashoui1, Albano Beja-Pereira3 , Jane Kinnaird2, Brian Shiels 2, Andy Tait 2, Hamza Babiker1. Genetic diversity of Theileria annulata in Oman. TRC fourm 2015

 

Amira Al-Fahdi, Salama Al-Hamidhi, Mohammed. H. Tageldin, Patrick Bobade, Eugene Johnson, Badar Alqamashoui, Abdel-Rahim Hussain, Hamza Babiker. Host and breed variation in susceptibility of livestock to natural Theileria sp infection in Oman. Regional Confrence for Animal genetic resources conservation. Muscat, 23-24 Feb 2016.

 

Salama Al-Hamidhi · Mohammed. H. Tageldin · William Weir · Amira Al-Fahdi · Eugene Johnson · Patrick Bobade · Mohamed Idris · Badar Alqamashoui · Albano Beja-Pereira · Jane Kinnaird · Brian Shiels · Andy Tait · Hamza Babiker · population genetic analysis of Theileria annulata in Oman. Conference: Apicomplexa in Farm animals 3rd international meeting, At Edinburgh   (1-3 July 2016)

 

Stephan Larcombe, Jane Kinnaird, Laetitia Lempereur, William Weir, Salama Al-Hamidhi, Hamza Babiker, Brian Shiels. Analysis of sequence diversity of transmission blocking candidate antigene genes reveals a potential association of SPAG1 indels with Theileria parasite speciation and host adaptation. Conference: Apicomplexa in Farm animals 3rd international meeting, At Edinburgh (1-3 July 2016).

 

Salama Al-Hamidhi, Mohammed A.K. Mahdy, Zainab Al-Hashami, Hissa Al-Farsi, Abdulsalam M. Al-mekhlafi,  Mohamed Ahmed Idris, Albano Beja-Pareira  and Hamza A. Babiker. Genetic diversity and distribution of drug resistance genotypes among Plasmodium falciparum in Yemen and Saudi Arabia. Conference abstract. 9th Annual BioMalPar I EVIMalaR Conference: Biology and Pathology of the Malaria Parasite. Germany (13-15 May 2013)

 

Salama Al-Hamidhi, Mohammed A.K. Mahdy, Saad M. Bin Dajem , Adel Ali H. Al-Sheikh, Zainab Al-Hashami, Hissa Al-Farsi, Abdulsalam M. Al-mekhlafi,  Mohamed Ahmed Idris, Albano Beja-Pereira  and Hamza A. Babiker. The prospect of malaria elimination in the Arabian Peninsula: a population genetic approach. 6th MIM Pan-African Malaria Conference,
the International Convention Centre, Durban, South Africa, (6 - 11 October 2013)

 

 

 

Teaching experience:

 

-BIOL2101 spring 2018, college of science

-NURS2032, tutorial (Biochemistry), spring 2017

 

2013- 2017

 Training students in their projects:

5 students medical and 2 international students
4 Master students
1 PhD student

Involve in teaching tutorial (Biochemistry) and involve monitor the exam, and correction and marks enters

 

2010-2012

 

Completed eight courses for master degree in medical microbiology (17/9/2010 - 30/12/2011), which are:

 

Advanced molecular biology
Bioinformatics
Medical microbiology
Medical parasitology
Medical virology
Medical bacteriology
Research methodology
Statistics

 

 

 

Workshop participations:

24th July – 7 August 2016

Middle east, biology of parasite, Bern Université, Switzerland (course)

24th -28 th January 2016

Introductory course in R for statistical analysis (workshop)

(April 2012)

Attendance of two weeks workshop in population genetics introduced by Prof. Alano GonÇalo Beja Pereira, Associate professor, Research Centre in Biodiversity and Genetic Resources, University of Porto, Portugal

- (January 2013)

Attendance of two workshops in skills programs (online questionnaire   design and critical thinking and search design).

 

 

References:

 

Prof. Hamza Babiker

Biochemistry department

College of medicine and health science/ SQU

E-mail: hbabiker@squ.edu.om

Tel:92345094

 

Dr William Weir
University of Glasgow
College of Medical, Veterinary and Life Sciences
Garscube Campus, Bearsden Road, Glasgow, UK
G61 1QH
Tel: 0141 330 5721
Email: willie.weir@glasgow.ac.uk

 

Prof. Arnab Pain

Biological and Environmental Science and Engineering Division

Pathogen Genomics
King Abdullah University of Science and Technology

arnab.pain@kaust.edu.sa 
Phone: +966 (0) 2808-2561