Marine Metagenomics activities at KAUST General introduction of science in Middle East

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1 Marine Metagenomics activities at KAUST General introduction of science in Middle East Dr. Rimantas Kodzius September 19 th, 2014 Nagahama, The Genetics Society of Japan (GSJ) meeting

2 Overview Renaissance of Middle East countries King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Center (CBRC) The Red Sea as a source for our research Pipeline for the research platform Comparative Genomics and Genetics (CGG) laboratory Summary Acknowledgements KAUST King Abdullah University of Science and Technology 2

3 About Dr.Rrimantas KODZIUS PhD in 2002, studied/ worked in 10 countries: Lithuania, Austria, Germany, Switzerland, Sweden, Japan, Australia, Singapore, Hong Kong and Saudi Arabia Publications in Science, Nature Genetics, Nature Methods KAUST King Abdullah University of Science and Technology 3

4 The Golden Age of Middle East Due to recent discovery of energy reserves (oil and gas), the Middle East countries take the opportunity to invest into infrastructure, education and research * In Bold countries made most recent progress 1. Bahrain 2. Cyprus 3. Egypt 4. Iran 5. Iraq 6. Israel 7. Jordan 8. Kuwait 9. Lebanon 10. Oman 11. Palestine 12. Qatar 13. Saudi Arabia 14. Syria 15. Turkey 16. United Arab Emirates 17. Yemen 18. Armenia 19. Azerbaijan 20. Georgia 21. (Kazakhstan) 22. Kyrgyzstan 23. Tajikistan 24. Turkmenistan 25. Uzbekistan KAUST King Abdullah University of Science and Technology 4

5 Middle East countries, in recent developments 1. United Arab Emirates New York University of Abu Dhabi 2. Qatar Qatar Foundation leads human, social, and economic development of Qatar 3. Oman 4. Kuwait Kuwait Foundation for the Advancement of Sciences 5. Saudi Arabia KAUST a successful experiment for mixed gender studies 6. (Kazakhstan) Nazarbayev University, president Shigeo Katsu KAUST King Abdullah University of Science and Technology 5

6 King Abdullah University of Science and Technology (KAUST) KAUST is a modern and international university close to the Red Sea, with the focus on Water Food Energy Environment Divisions Biological and Environmental Sciences and Engineering (BESE): 132 students Computer, Electrical and Mathematical Sciences and Engineering (CEMSE): 223 students Physical Science and Engineering (PSE): 245 students From total 740 students there are 189 MS and 505 PhD students KAUST King Abdullah University of Science and Technology 6

7 Work specificities in Middle East/ I Incentives Tax free salary (Free) food, (free) housing, free electricity, free water, free internet, free use of gym Proximity of Red Sea recreational activities such as diving, snorkel, fishing New campus and grant support to realize scientific dreams International professors/ students Schools, everything else within campus 24/7 security around the clock KAUST King Abdullah University of Science and Technology 7

8 Work specificities in Middle East/ II Issues Difficulties getting people and equipment for the labs (time could be easily 6 months) need proper planning and follow up Remote location Adaptation to hot weather (up to 50 C) May 19 th, 2010 Arab News KAUST King Abdullah University of Science and Technology 8

9 Computational Bioscience Research Center (CBRC) Research Centers at KAUST Advanced Membranes and Porous Materials Catalysis Desert Agriculture Clean Combustion Computational Bioscience Geometric Modeling and Scientific Visualization Red Sea Solar and Photovoltaic Engineering Water Desalination and Reuse CBRC: a combination of both experimental research and biocomputational analysis Comparative Genomics and Genetics lab (CGG) is a part of CBRC KAUST King Abdullah University of Science and Technology 9

10 From Environment to Production/ I Design, Modeling, and Development of Microbial Cell Factories (MCF) 1. Collect microbial samples in large scale from diverse environments such as marine, soil, and oil Environmental samples are collected from coastal and offshore areas of the Red Sea, and nucleic acid is extracted directly from the microbial samples 2. Identify desired genes and metabolic pathways in microbe samples using metagenomic analysis and computational modeling Extracted DNA is subjected to Next Generation Sequencing Computational analysis of whole microbe genome and the 3D modeling of their proteins and metabolic networks is performed Desired genes and metabolic pathways are determined KAUST King Abdullah University of Science and Technology 10

11 From Environment to Production/ II Design, Modeling, and Development of Microbial Cell Factories (MCF) 3. Edit and insert desired microbial genes into the genome of a suitable host using genome editing technologies A sophisticated genome editing technology (CRISPR system) is utilized to edit specific sequences of microbe genes to obtain maximum desired properties Using the same technology, the modified microbe genes are inserted at precise locations within the host genome 4. Express desired genes in suitable host for mass production of food, fine chemicals, and energy The host (such as microalgae) transformed with bacterial genes are cultured to produce mass quantities of desired products Metabolic model Single cell sorting Target gene DB Experimental platform for Gene Editing in the cell KAUST King Abdullah University of Science and Technology 11

12 Value / Unit Pipeline: from discovery to production Samples / Extraction / Sequencing In silico Analysis Cell functions No Yes Organism identification Single cell manipulation No Yes Sea water samples DNA extraction NGS Database search Functional prediction Structural prediction Information integration Biological network Judgement of usefulness Gene or Genome editing genomic identification Judgement of usefulness High Triangle value Novel drugs Food Animal feed Outputs Output Oil Low Small Large Quantity KAUST King Abdullah University of Science and Technology 12

13 CGG lab objectives CGG lab is part of CBRC There are two scientific objectives 1) Establish the sampling pipeline 2) Perform basic science experiments For the basic science experiments, we are looking for the new model organisms My interest is in sensory organs (such as chemical and light perception) KAUST King Abdullah University of Science and Technology 13

14 Instrumentation Comparative Genomics and Genetics lab is investing to laboratory instrumentation: Single cell instrumentation Synthetic Biology (Genome Engineering) Examples of the instrumentation: All necessary instruments for molecular biology laboratory Nikon microscopes Ti-U & SMZ25 High speed camera Photron SA-Z Fluigent pulseless microfluidic pumps Five different wavelength lasers KAUST King Abdullah University of Science and Technology 14

15 Summary We take the challenge Helping the country, growing the university Open hands to perform the science We are the University Big plans, big grants CBRC funding next 6 8 years (20 30 million USD) Additionally every professor gets his own funding There are grants to apply (University, KACST, Qatar, etc.) collaboration is encouraged (even multidisciplinary) Bright future, at the same time remain realistic KAUST King Abdullah University of Science and Technology 15

16 Acknowledgements KAUST/ Distinguished professor Takashi Gojobori CCG society for invitation KAUST King Abdullah University of Science and Technology 16