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Rania Siam

Brief Biography

Rania Siam is a tenured professor of microbiology at the School of Science and Engineering, The American University in Cairo. Siam served as the chair of the biology department from 2012-2018. Prior to this she was the founding director of the Biotechnology Graduate Program from the time it was founded in 2007 until 2012. Siam's research interests lies in understanding the environmental communities residing in harsh environments in the Red Sea. Siam is the group leader of the Red Sea Marine Microbiology Group. The group is particularly interested in the "polyextremophiles" that constitute the microbial assemblage of deep and hot brines pools in the Red Sea. Twenty-five brine pools have been described to date in the Red Sea, however, knowledge of the microbial communities that inhabit these pools, and how these organisms are affected by and contribute to the geochemical properties of their extreme environments, remains sparse. Siam’s research team explores the unique microbial communities in these environments to understand the microbial evolution of such microbes that allow them to survive under harsh environments. Additionally, they exploit such unique microbial communities to discover enzyme with unique properties that can be used in biotechnology.

Professor Siam holds a PhD in microbiology and immunology in 2001 from the faculty of medicine, McGill University in Montreal, Canada. She earned an MBBCh from Ain Shams University, Faculty of Medicine. Siam held several post-doctoral positions including McGill Oncology Group, Royal Victoria Hospital in Montreal, Quebec, Canada. She also held positions at the Salk Institute for Biological Studies, Molecular and Cellular Biology Laboratories, La Jolla, CA, USA and The Scripps Research Institute, Department of Molecular and Experimental Medicine, La Jolla, CA, USA. Recently she was a visiting scholar at the Scripps Institution of Oceanography.

Research Interest
  • Environmental genomics
  • Metagenomics
  • Microbial ecology
  • Geochemistry
  • BIOL 130/1410 Current Health Issues
  • BIOL 211/2230 Molecular and Cell Biology
  • BIOL 430/4330 Tumor Biology
  • BIOT 502/5202 Molecular and Cell Biology
  • BIOT 590/ 5940 Graduate Seminar I

Peer-Reviewed Publications

  • Ziko, L, Adel M, Malash,M, Siam, R. (2019) Insights into Red Sea brine pool specialized metabolism gene clusters encoding potential metabolites for biotechnological applications and extremophile survival. Marine Drugs. Accepted.
  • Kegere, J, Ouf, A, Siam, R and Wael, M. (2019) Fabrication of Polyvinyl Alcohol / Chitosan / Bidens Pilosa Composite Electrospun Nanofibers with Enhanced Antibacterial Activities. American Chemical Society  Omega. Accepted.
  • Ziko, L, Saqr, AA, Ouf, A, Gimpel, M, Aziz, RK, Neubauer, P, Siam, R. (2019) Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool. Microbial cell factories. 18:56 https://doi.org/10.1186/s12934-019-1103-3
  • Hussein, NA, Cho, S-H. Laloux, G, Siam, R, Collet , J-F. (2018) Distinct domains of Escherichia coli IgaA connect envelope stress sensing and down-regulation of the Rcs phosphorelay across subcellular compartments. PLOS Genetics. Published: May 31, 2018.
  • Elbehery AH, Aziz RK, Siam R. ( (2017) Insertion sequences enrichment in extreme Red sea brine pool vent. Extremophiles. Mar;21(2):271-282. doi: 10.1007/s00792-016-0900-4. 
  • Elbehery AH, Leak DJ, Siam R. (2017) Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool. Microb Biotechnol. 2017 Jan;10(1):189-202. doi: 10.1111/1751-7915.12468. Epub 2016 Dec 22.
  • Adel M, Elbehery AHA, Aziz SK, Aziz RK, Grossart H-P, Siam R. (2016) Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments. Scientific Reports. 6:32704. doi: 10.1038/srep32704.

  • Elbaz NM, Ziko L, Siam R, Mamdouh W. (2016) Core-Shell Silver/Polymeric Nanoparticles-Based Combinatorial Therapy against Breast Cancer In-vitro. Scientific Reports. 6: 30729. doi:  10.1038/srep30729.

  • Mustafa, GA, Abd-Elgawad, A, Ouf, A, Siam, R. (2016) The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants. Environmental Pollution. Volume 214, Pages 892–902

  • The MetaSUB International Consortium. (2016) The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome.  3;4(1):24. doi: 10.1186/s40168-016-0168-z.

  • Elbehery AHA, Aziz RK, Siam R. (2016) Antibiotic resistome: improving detection and quantification accuracy for comparative metagenomics. OMICS: A Journal of Integrative Biology. 20(4): 229-238. doi:10.1089/omi.2015.0191.

  • ​Sonbol SA, Ferreira AJS, Siam R. Red Sea Atlantis II brine pool nitrilase with unique thermostability profile and heavy metal tolerance. BMC Biotechnology. 2016;16:14. doi:10.1186/s12896-016-0244-2.

  • Antunes A, Alam I, Simões MF, Daniels C, Ferreira AJ, Siam R, El-Dorry H, Bajic VB. First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea. Genomics, Proteomics & Bioinformatics. 2015;13(5):304-309. doi:10.1016/j.gpb.2015.06.004.

  • Kopf A, Bicak M, Kottmann R, et al., 2015. The Ocean Sampling Day Consortium.
    Gigascience. 2015 Jun 19;4:27. doi: 10.1186/s13742-015-0066-5. eCollection 2015.
    Saadeldin MK, Shawer H, Mostafa A, Kassem NM, Amleh A, Siam R. (2015) New genetic variants of LATS1 detected in urinary bladder and colon cancer. Front Genet. 2015 Jan 13;5:425. doi: 10.3389/fgene.2014.00425. eCollection 2014.
    Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy M, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R (2014): Aerobic Methanotrophic Communities in Red Sea Brine-Seawater Interfaces. Frontiers in Microbiology, 5:487. doi: 10.3389/fmicb.2014.00487

  • Mustafa GA, Abdel-Gawad A, Mahmoud, A, Siam, R (2014): Egypt’s Red Sea Coast: Phylogenetic analysis of cultured microbial consortia in industrialized sites. Frontiers in Microbiology, 5:363. doi: 10.3389/fmicb.2014.00363
    Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang  G, Hikmawan T, Guan Y, Antunes, A, Siam R, El-Dorry H, Bajic VB and Stingl, U (2014): Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. ISME Journal. 2014 Aug 8. doi: 10.1038/ismej.2014.137.
    Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, Stingl U, Archer JAC, Jankovic BR, Sogin M, Bajic VB, El-Dorry H (2014): Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS ONE. 2014 Jun 12;9(6):e97338. doi: 10.1371/journal.pone.0097338.
    Demian P, Horton KC, Kajon A, Siam R, Hasanin AM, Elgohary Sheta A, Cornelius C, Gaynor AM. (2014) “Molecular identification of adenoviruses associated with respiratory infection in Egypt from 2003 to 2010.” BMC Infect Dis. 14(1):50.

  • Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB, Siam R, El-Dorry H. (2013). A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. J Biol Chem. 2013 Nov 26. [Epub ahead of print]
  • Mohamed YM, Ghazy MA, Sayed A, Ouf A, El-Dorry H, Siam R. (2013) “Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool”. Scientific Reports 3, Article number: 3358 doi:10.1038/srep03358
  • Thompson LR, Field C, Romanuk T, Ngugi D, Siam R, El Dorry H, Stingl U. (2013). Patterns of ecological specialization amongst microbial populations in the Red Sea and diverse oligotrophic marine environments. Ecol Evol. 3(6):1780-97. doi: 10.1002/ece3.593.
  • Siam R, Mustafa GA, Sharaf H, Moustafa A, Ramadan AR, et al. (2012). Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools. PLoS ONE 7(8): e42872. doi:10.1371/journal.pone.004287
  • Antunes A, Alam I, El Dorry H, Siam R, Robertson A, Bajic VB, Stingl U. (2011). Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake. Journal of Bacteriology. 193(17):4551-2.
  • ElHefnawi M, Hassan N, Kamar M, Siam R, Remoli AL, El-Azab I, AlAidy O, Marsili G, Sgarbanti M. (2011). The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus. Bioinformatics. 15; 27(24):3364-70.
  • ElHefnawi M, Alaidi O, Mohamed N, Kamar M, El-Azab I, Zada S, Siam R. (2011). Identification of novel conserved functional motifs across most Influenza A viral strains. Virology Journal. 27;8:44.
  • Siam, R., Harada, R., Cadieux, C., Battat, R., Vadnais, C., Nepveu, A. (2009). Transcriptional activation of the Lats1 tumor suppressor gene in tumors of CUX1 transgenic mice. Mol Cancer. 5(8):60.
  • Spencer, W., Siam, R., Ouimet, M.C., Bastedo, D.P., Marczynski, G.T. (2009). CtrA, a global response regulator uses a distinct second category of weak DNA binding sites for cell cycle transcription control in Caulobacter crescentus. Journal of Bacteriology. 191(17):5458-70.
  • Gendoo, D.M.A., El-Hefnawi, M.M., Werner, M., Siam, R. (2008). Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions. Virology Journal. 5:91-101.
  • Siam, R., Gómez, E.B., Forsburg, S.L. (2007). Schizosaccharomyces pombe Rad4/Cut5 protein modification and chromatin binding changes in DNA damage. DNA Cell Biology. 26(8):565-75.
  • Siam, R., Dolan, W.P., Forsburg, S.L. (2004). Choosing and using S. pombe plasmids. Methods. 33:189-98.
  • Siam, R., Brassinga, A.K.C., Marczynski G.T. (2003). A dual binding site for integration host factor and the response regulator CtrA inside the Caulobacter crescentus replication origin. Journal of Bacteriology. 185: 5563-5572.
  • Siam, R. and Marczynski, G.T. (2003). Glutamate at the phosphorylation site of response regulator CtrA provides essential activities without increasing DNA binding. Nucleic Acids Research. 31 (6): 1775-1779.
  • Brassinga, A.K.C., Siam, R., McSween, W., Winkler, H., Woods, W., Marczynski G.T. (2001) Conserved response regulator CtrA and IHF binding sites in the proteobacteria Caulobacter crescentus and Rickettsia prowazekii chromosomal replication origins. Journal of Bacteriology, 184: 5789-5799.
  • Brassinga, A.K.C., Siam, R., Marczynski G.T. (2001). Conserved gene cluster at replication origins of Caulobacter crescentus and Rickettsia prowazekii. Journal of Bacteriology, 183:1824-1829.
  • Siam, R. and Marczynski, G.T. (2000). Cell cycle regulator phosphorylation stimulates two distinct modes of binding at a chromosome replication origin. The EMBO Journal, 19:1138-1147.

Rania Siam

Group Leader

  • 2002 - 2003: Postdoctoral Fellow. The Salk Institute for Biological Studies, La Jolla, CA. Molecular and Cell Biology Laboratory
  • 2001: Postdoctoral Fellow. The Scripps Research Institute, La Jolla, CA, Molecular and Experimental Medicine 
  • 2001: PhD McGill University, Montreal, Canada. Microbiology and Immunology
  • 1993: MBBCH. Ain Shams University, Faculty of Medicine, Cairo, Egypt

Rehab Abdallah

Postdoctoral researcher/Senior researcher 

  • 2018: PhD in Microbiology (Max Planck Institute for Terrestrial Microbiology/ Philipps University Marburg) 
  • 2012: MScs in Biotechnology (the American University in Cairo) 
  • 2008: BScs in Biotechnology (Montana State University)


  • Abdallah R. Z., Wegner C.E., Liesack W., Community transcriptomics reveals drainage effects on paddy soil microbiome across the three domains of life, 2019, Soil Biology and Biogeochemistey 132, 131-141
  • Kopf A., Bicak M., Kottmann R., Schnetzer J., Kostadinov I., Lehmann K., Fernandez-Guerra A., Jeanthon C., Rahav E., Ullrich M., Wichels A.,Gerdts G, Polymenakou P., Kotoulas G., Siam R., Abdallah R. Z., et al., The ocean sampling day consortium, 2015, Gigascienc 4 (1), 27
  • Johnson C. B., Shaik R., Abdallah R., Vitha Z., Holzenburg A., FtsZ1/FtsZ2 turnover in chloroplasts and the role of ARC3, 2015, Microscopy and Microanalysis 21 (2), 313-323
  • Abdallah R. Z., Adel M., Ouf A., Sayed A., Ghazy M. A., Alam I., Essack M., Lafi F.F., Bajic V.B., El-Dorry H., Siam R., Aerobic methanotrophic communities at the Red Sea brine-seawater interface, 2014, Frontiers in microbiology 5, 487
  • Project: Red Sea Extremozymes

Amged Ouf

Genomic Specialist

  • 2000: BSc (Biochemistry, Science) Ain Shams University


  • Mohamed, Yasmine M., Mohamed A. Ghazy, Ahmed Sayed, Amged Ouf, Hamza El-Dorry, and Rania Siam. "Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool." Scientific reports 3 (2013).
  • Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB. 2013. A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. Journal of Biological Chemistry:jbc. M113. 493429.

Ahmed El Hosseiny​

Bioinformatics Analyst, Biology Department

  • 2010: Diploma (Bioinformatics) Information Technology, Information Technology Institute (ITI)
  • 2007: BSc (Biotechnology) Agricultural Sciences (English Section), Faculty of Agriculture, Cairo University, Egypt

Shimaa Farag

Research Assistant

  • 2013: MSc Microbiology, Microbiology Department, Faculty of Science, Minia University
  • 2019: BSc Microbiology, Microbiology Department, Faculty of Science, Minia University


  • Ahmed, S.F., Mehanni, M.M. and Abdel-Hamid, A.M. Isolation and characterization of thermophilic, cellulose-degrading Streptomyces griseorubens SH15 strain from agricultural waste compost in Egypt., J Ecosys Ecograph 2018, Volum:8 DOI:10.4172/2157-7625-C2-035.
  • Project: Red Sea Extremozymes

Mohamed N. Malash

Current research project: Detection and characterization of novel extremophilic peptidoglycan hydrolases in metagenomes of hydrothermal vents.

  • 2009: MSc Genetic Engineering and Biotechnology: Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), Menofia University – Sadat city, Egypt


  • S.H. Hassanein, M.I. Nasr, R.M. Abd El-Aziz, A.F. Elbaz, and M.N. Malash (2009) Induction of Cephalosporin C inCephalosporium acremonium Using U.V. Light and Selection of a Mutant that Showed Highest Fermentation Capability. Minufiya J. Agric. Res. 34(1):35-55
  • A.M. Michael and M.N. Malash (2015) A Validated Assay of Urease Enzyme in Different Sources Using Silver Nanoparticles. Food Anal. Methods. 8(10):2482-2486 (DOI: 10.1007/s12161-015-0139-1)

Sarah Sonbol

PhD Student

Current research project: Metagenomic analysis of integrons in Siwa water samples

  • 2014: MSc (Biotechnology) AUC, Cloning, expression and preliminary characterization of a novel nitrilase from the Red Sea, Atlantis II Deep Brine pool using a metagenomic approach
  • 2007: BSc (Pharmacy) Ain Shams University


Sonbol S, Ferreira AJ, Siam R, 2015. A novel nitrilase isolated from the Red Sea Atlantis II brine pool with unique thermostability profile and selected heavy metal tolerance. BMC Biotechnology submitted

Oduwole Iyanu Mumeen

MSc Student

  • BSc Biochemistry (2016), Olabisi Onabanjo University (OOU) Ago Iwoye
  • Project: Novel ligases from the Red Sea brine pool

Graduate Students Supervised/Co-supervised (Graduated)

MSc Thesis Supervisor

  • Mona Kamal Said Abdelaziz (2013) “Molecular variation of the tumor suppressor gene LATS1 in urinary bladder cancer and colon cancer in Egyptian patients”
  • Lotaief, Mohamed Mohamed (2012) “CRISPR diversity in brine pools of the Red Sea: a comparative study of clustered regularly interspaced short palindromic repeats from the Red Sea metagenomes”
  • Ibrahim Farouk Farag (2012) - PhD student Oklahoma State University “Exploring the Biodiversity of Anammox in Atlantis II and Kebrit Brine Pools’ Interfaces”
  • Yasmine Moustafa Mohamed (2012) “Identification and characterization of a novel thermohalophilic esterase from the Red Sea; Atlantis II brine pool”
  • Ghada Mustafa (2012) - PhD student AUC "Unique biodiversity of the Red Sea brine floor revealed by comparative taxonomic analysis of ATLANTIS II and DISCOVERY DEEP brine sediments" 
  • Nardine Marsis (2011) - PhD student Texas A&M "Microbial and chemical profiles of sediments isolated from ATLANTIS II and DISCOVERY deep brine pools in the Red Sea" 
  • Rehab Abdallah (2011) - Research assistant AUC "Exploring the aerobic methanotrophs community in the Red Sea Atlantis II deep brine area" 
  • Peter Refki (2009) - PhD student University of Lyon - France “Molecular Variation of the Tumor Suppressor Gene LATS1 in Diverse Cancer Tissues”

MSc Thesis Co-Supervisor

  • Ossama Mohamed Salah El-Dien El-Sayed Ibrahim (2012) - PhD student Ecole Polytechnique Federale De Lausanne ““Structure-Function Analysis of a Neuron-Specific Vesicular ATPase in Neurotransmission”
  • Nadine Khedr (2012) "Molecular characterization of neuraminidase surface proteins of Influenzavirus B isolates from Egypt, 1999-2008" 
  • Dina Abdel Azeem (2011) - Graduate student London School of Economics "Bacterial Production of Human Discoidin Domain Receptor 2 (DDR2) Kinase and Its Gatekeeper Mutants to Assess Activation By Phosphorylation" 
  • Nada El-Ayouty (2011) "Characterization of the bacterial gut fauna of Phlebotomus papatasi: Culture dependent vs. culture independent techniques" 
  • Pola Demian (2011) - Researcher U.S. Naval Medical Research Unit 3 "Characterization of variant strains of respiratory adenoviruses isolated in Egypt from 2003 to 2010" 
  • Lamyaa Shaban (2010) “Molecular Characterization of Vibrio cholerae Isolates from African Countries”
  • Lobna Mourad (2010) - PhD student AUC “Molecular Characterization of Extended-Spectrum- "-Lactamases (ESBL) Producing Klebsiella pneumoniae and Escherichia coli Among Hospitalized Patient