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Understanding of the links between coral reef ecosystems, the goods and services they provide to people, and the wellbeing of human societies.


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Examining the multi-scale dynamics of reefs, from population dynamics to macroevolution


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Coral Reef Studies

From 2005 to 2022, the main node of the ARC Centre of Excellence for Coral Reef Studies was headquartered at James Cook University in Townsville, Queensland (Australia)

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Amin Mohamed Esmail

Amin Mohamed Esmail

PhD graduate

PhD Candidate: Coral Reef Genomics 2012- expected 2016
James Cook University and Australian Institute of Marine Science

Assistant Lecturer: Zoology 2011-2012
Faculty of Science, Benha University, Egypt

Teaching Assistant: Zoology 2006-2011
Faculty of Science, Benha University, Egypt

PhD in Molecular Marine Biology, James Cook University (expected-2016) MSc in Marine Biology, Benha University, Egypt (2011) BSc in Zoology, Benha University, Egypt (2006)

Program 3: Responding to a Changing World, Coral Genomics Group

James Cook University

+61 7 4781 15395

Amin was born in Egypt where he completed his BSc in Zoology (excellent degree with honors) in 2006. He worked as a teaching assistant at Faculty of Science, Benha University, Egypt. As he developed a great interest in coral reef research, he did a Masters project on coral health and disease in the Egyptian Red Sea. This project provided baseline information on coral disease, coral bleaching, and other health issues that affect coral reefs in this region. He is now a PhD student at David Miller’s lab, the ARC center of Excellence for coral reef studies, James Cook University. Amin’s PhD is supervised by Prof David Miller, Prof Bette Willis and Dr David Bourne. His research focuses on studying coral-algal symbioses and the impact of newly discovered coral associated alveolates on coral fitness using molecular and genomics approaches.

Amin’s Curriculum Vitae

Personal profiles:

ResearchGate | Academia | Google scholar | LinkedIn

Research Interests:

Marine Biology, Molecular Biology, Genomics, Metagenomics, Bioinformatics, Coral Reefs, Coral-microbes interactions, Coral Health, Coral-algal symbioses, Chromerids

Project Title:

Transcriptomics of coral-algal symbiosis; towards determining the nature of the relationship between corals and the novel apicomplexan-related alga Chromera using functional genomics

Project Description:

Reef-building corals are considered as meta-organisms where the coral animal lives in mutualistic relationships with photosynthetic dinoflagellates of the genus Symbiodinium and other microorganisms including bacteria, archaea, fungi, and viruses. The coral animal along with its associated microorganisms are collectively referred to as the coral holobiont. Symbiodinium belongs to a group of protists called alveolates and recent study has established that number of other related alveolates are also intimately associated with corals including: the newly discovered chromerids and many apicomplexan-related lineages (ARLs). Chromerida is a newly defined phylum of photoautotrophic alveolates that includes Chromera velia and the recently described species,Vitrella brassicaformis collectively called chromeridsThey were isolated so far from Australian corals, but the association of apicomplexan symbionts with corals was reported in the Caribbean and not yet on the Great Barrier Reef (GBR).  Moreover, the nature of the chromerids and apicomplexans associations with corals is unknown. Currently, there is a great deal of interest in Chromera because it is thought to be the missing link between the photosynthetic dinoflagellates and the non-photosynthetic apicomplexans. Interestingly, all the members of the Apicomplexa group are, so far, identified as parasitic organisms. Because of its close relationship to apicomplexans, Chromera might be a facultative parasite.

The PhD project is divided into the following aims:

1- Understanding the molecular mechanisms underlying establishment of coral-Symbiodinium symbiosis during symbionts uptake by coral larvae. While gene expression studies based on microarrays pointed that the coral transcriptome is largely unresponsive to symbiosis. In this project I will use illumina RNA-Seq “next-gen sequencing technology” to follow the coral transcriptome-wide gene expression over a time-course infection experiment with competent strain of Symbiodinium.

2- Towards determining the nature of the coral-Chromera association. RNA-Seq will be used for the first time in order to profile the changes in the coral transcriptome during Chromera infection of coral larvae. Understanding the coral transcriptional response to Chromera will help determine if Chromera is a coral symbiont or a parasite?

3- Providing a functional genomic resource for a chromerid alga isolated from the Great Barrier Reef (GBR). A de novo assembled transcriptome of Chromera isolated from Montipora digitata on the GBR will be constructed. Comparative transcriptomic approach will be utilised in order to compare whole transcriptomes of Chromera with its symbiotic and parasitic relatives.

4- The availability of a reference data (transcriptome) for Chromera will allow large scale analyses of Chromera responses to different environmental condition. In this project, I will investigate Chromera global responses to mixotrophic culturing and heat stress at the transcriptional level.


Principal supervisor: Prof David Miller

Supervisory committee: Prof Bette Willis, Dr David Bourne, Dr Vivian Cumbo

Publications List:

1- Mohamed, A.R., Cumbo, V., Harii, S., Shinzato, C., Chan, C.X., Ragan, M.A., Bourne, D.G., Willis, B.L., Ball, E.E., Satoh, N. and Miller, D.J. (2016). The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology. doi:10.1111/mec.13659

2- Mohamed, Amin R., Abdel-Hamid A.M. Ali, Hany A. Abdel-Salam (2012) Status of coral reef health in the northern Red Sea, Egypt. In: Yellowless D, Hughes TP (eds) Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia, 9-13 July 2012. 9A Coral bleaching and climate change. James Cook University, Townsville.

3- Amin R Mohamed and Hany A Abdel-Salam (2012) Coral Health and Disease in the Red Sea, Egypt. Lambert Academic Publishing (LAP), Germany, ISBN: 978-3848449620.

4- Hany, A. Abdel-Salam, Abdel-Hamid, A. M Ali,  Amin, R. M. Ismail (2010) Hurghada coral diseases; are they due to the impacts of global warming or mass tourism? Egypt. Acad. J. biolog. Sci., 2 (2): 33- 46.

5- Abdel-Salam, H.A.; Ali, A.A.M. and Mohamed, A. R. (2010) Coral diseases prevalence in El-Ain Al-Sukhna area, Red Sea, Egypt. Proceedings of the 6th International Conference on Biological Sciences, Tanta University,Egypt.

Conference Presentations:

1-Molecular mechanisms underlying establishment of coral-Symbiodinium symbiosis: transcriptomic approach. Accepted abstract and oral presentation at the 13th ICRS.

2- Host transcriptome analysis during onset and establishment of coral-algal symbiosis. Oral   presentation at AIMS@JCU Seminar September 2015.

3- Chromera velia de novo transcriptome construction and analysis. Poster presentation at AIMS@JCU Seminar August 2014.

4- Chromera velia: coral symbiont or parasite? Poster presentation at AIMS@JCU Seminar DayOctober 2013.

5- Status of coral reef health in the northern Red Sea, Egypt. The 12th International Coral Reef Symposium (ICRS) 2012. Oral presentation, Cairns, Queensland. Australia, July 2012.

6- Hurghada coral diseases; are they due to the impacts of global warming or mass tourism? The first International Conference of Biological Sciences, Ain Shams University. Oral presentation, Egypt, September 2010.

7- Coral diseases prevalence in El-Ain Al-Sukhna area, Red Sea, Egypt. The 6th International Conference on Biological Sciences, Tanta University. Poster presentation, Egypt, November 2010.

Awards and Grants:

2016: AIMS@JCU Student Travel Award (AUD 1000) towards science communication

2015: AIMS@JCU Oral Presentation Award (AUD 1200) towards science communication

2014: AIMS@JCU Top-Up scholarship (AUD 5000/ year) for research costs

2014: James Cook University Postgraduate Research Scholarship (JCUPRS)

2014: AIMS@JCU Student Travel Award (AUD 750) towards science communication

2013: AIMS@JCU Poster Presentation Award (AUD 1000) towards science communication



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