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King Abdullah University of Science and Technology at Thuwal, Kingdom of Saudi Arabia

BE the

March 2011 / Rabi-I 1432 Issue No. 7


Bio-organometallic Catalysis

Explore Explore our neighbor Thuwal

Turn to p. 4–5

Over billions of years, evolution has provided amazing solutions for life’s many challenges. One of these is the group of naturally occurring catalysts – enzymes. These remarkable biocatalysts can be further developed to provide a more environmentally friendly and cost-competitive type of catalysis – becoming a “green” alternative to synthetic chemistry. Unlike the toxic chemicals often associated with industrial catalysis, naturally occurring enzymes can offer unsurpassed selectivity and activity in very mild conditions. The attraction of using this more natural approach has been reflected in the increased global share of biocatalysis in fine chemical production up from 7% in 2000 to over 25% in 2010 and expected to double in the next five years. However, nature’s catalysts still have some weaknesses: there are a limited number of enzymes and they are optimized to work under physiological conditions. The challenge is to mimic the diversity offered by modern synthetic chemistry using biocatalytic methods. At KAUST, Professor Jörg Eppinger and his interdisciplinary research team set out to unite the two scientific worlds of biotechnology and homogeneous catalysis by providing nature with novel tools that capitalize on the advantages of both sciences. New types of catalysts will emerge, which provide the reaction diversity of artificial as well as the selectivity and environmental friendliness of biocatalysts. One huge hurdle has to be overcome. In stark contrast to artificial organometallic catalysts, which require rigorous exclusion of moisture and air, functional biocatalysts often need water and oxygen. Initially, Prof. Eppinger’s research team developed organometallic catalysts motives, highly active in water and air at room temperature. In two recent papers in Green Chemistry, Alexander Marziale, a PhD student in Prof. Eppinger’s group described an efficient protocol for palladium-catalysed Suzuki-Miyaura cross-coupling in these mild conditions to isolate over 50 different pure products by using simple filtration. The publications stirred great interest in the scientific community as they reflect the recent focus on the more sustainable use of resources. What is palladium and what does cross-coupling mean? Cross-coupling is a tool in synthetic chemistry that allows for the artificial formation of bonds between carbon and nonmetal elements. Being able to make such bonds is the basis of nature’s amazing diversity such as flower color, and this Continued on p.2



Two observant KAUST students who spotted a shark that seemed unfamiliar in a Jeddah fish market are authors on a paper currently in press in the journal Zoology in the Middle East. The paper, written jointly with their supervisor, Professor Michael Berumen, describes a "range extension" of this species - previously unknown in the Red Sea. Julia Spaet and Jesse Cochran purchased the shark suspecting that they had chanced upon something unusual, and further examined it back at KAUST to establish that it was indeed a juvenile Pigeye Shark.

With this new finding, there are now 29 species of shark reported to inhabit the Red Sea ranging from small reef sharks (about 1m in length) to whale sharks which can grow up to 18m. These sharks are almost always benign, attacking people rarely and for reasons that no one has been able to establish. Be reassured that statistically, you are more likely to be killed by a coconut falling on your head than by an attack from a shark! This particular specimen was caught on a hand line about 300km south of Jeddah. Sharks actually predate trees, first appearing some 400 million years ago, and they have changed remarkably little since. Their

cartilaginous skeleton not only makes them lighter in weight, but more flexible. Shark teeth seem to have evolved from their dermal denticles – the rough, sharp protrusions that is one of the distinguishing features. Should you choose to run your hand over a shark’s skin, you would find it has a nap – like velvet - smooth as silk in one direction, and well capable of cutting your palm in the other. Teeth vary from species to species: some flat to crush crustaceans for food; others long and pointed to allow smaller fish to be captured; others serrated and triangular so that the shark can tear chunks of flesh from larger prey. The benign whale shark barely has teeth as it feeds by filtering plankton. Unlike most other fishes, salt levels in the blood of sharks are equivalent

to those in salt water and the shark uses urea to regulate the level; bull sharks can actually move from salt water to fresh water by regulating their blood salt levels by increasing diuresis. Unfortunately the urea accumulates in the flesh of shark meat; unless bled immediately it has a noxious taste and smell. Anyone who has visited the Red Sea Research Center’s lab following a shark dissection can attest to this powerful odor! Additionally, mercury levels are such that one 300g shark steak provides the lifetime tolerance limit. That said, sharks are threatened because the cartilage from their fins gives soup an unusual texture considered exquisite by some, thus leading to the disappearance of 85% of species in the South China Sea, for example. By some estimates, something between 1 million and 100 million sharks are harvested globally each year. Continued on p.2


News 1-2

Blue Brain Project 3

Thuwal Tour 4-5

Research 6-7

Community 8



March 2011

Alliteration is a slippery slope. KAUST is a catalyst for connections; collaborations across continents and our own campus and community with the goal of concrete contributions to research, education, and economic development. When KAUST’s 2nd graders joined us for a morning of newspapering, they enjoyed the fun we have with words (and images) as we share with you the excitement of this burgeoning university. With this issue we reluctantly say goodbye to Judy Love-Eastham

The Beacon

(pictured here with the 2nd graders), who has led us at The Beacon since its inception in pursuit of quality, insight, and humanity. We salute her, we thank her, and we will miss her. ‎- THE BEACON Editorial

In Brief The KAUST School Personal Project Fair

Write to us at The Beacon, Issue 7, March 2011. Published by The Communications Department, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Contact Salah Sindi +966 (2) 808-3221, email, or Christopher Sands +966 (2) 808-3228, email © King Abdullah University of Science and Technology. Printed on partially recycled paper.

Organometallic Chemistry continued from p.1

process is used by organic chemists to create pharmaceuticals and other complex everyday materials. While carbon-carbon bonds provide a strong, stable skeleton, linkage to other elements is required for functional molecules. Chemists have built on their knowledge of naturally occurring organic (carbon-based) chemistry to synthesize the medicines or plastics that have become part of daily life. The synthesis of such chemicals/compounds depends on the chemist’s ability to join carbon and nonmetal. Palladium cross-coupling is arguably the most precise and efficient way to synthesize complex molecules: when atoms encounter one another in close proximity on a palladium center, formation of a chemical bond is kick-started. The catalytic properties of a palladium atom are tailored by so called ligands – small molecules that bind to the metal center. Palladium cross-coupling is so fundamental to the synthesis of molecules that the 2010

Nobel Prize for Chemistry was jointly awarded to the three pioneering scientists in this area for work which has facilitated research worldwide as well as the commercial production of molecules used in the electronics and drug industries. The element, palladium, is one of the platinum group metals widely used in automotive catalytic converters or fuel cells. It would seem to be prohibitively expensive, but is so efficient that only 1g is required to produce 1T. This incremental research at KAUST will further allow for this process in water at room temperature. What’s the next step? Prof. Eppinger’s team is targeting the integration of the developed catalyst motive into the framework provided by a protein. Suitable “host” proteins were isolated from extremophilic organisms, which are highly tolerant of heat, acid and/or salt – parameters, which will be important for the application of any catalyst created. The active palladium-based “guest” catalyst

will be introduced by a variety of methods, the most versatile one being to create organisms that use an expanded genetic code. This will enable the introduction of an unnatural amino acid containing the catalyst motive to a living cell. This endeavor was started three months ago in collaboration with the Scripps Research Institute in the USA and the Technische Universität München with support from KAUST’s Global Collaborative Research Program. Currently, Dominik Jantke, a first year PhD student in Prof. Eppinger’s group is in Munich elucidating the crystal structure of an organometallic enzyme hybrid catalyst. When asked whether his research belongs in chemistry or biology, traditionally two distinct university departments, Prof. Eppinger responds, “Nature doesn’t recognize such boundaries.” 

Pigeye shark continued from p.1

The fish market in Jeddah is where local fisherman hawk their wares: these fish are largely caught in the Red Sea though some are imported from Yemen, Oman, and the Gulf Coast. Marine biology master’s students visit such markets (taking tape measures) because the fish they see there mirror to some extent the populations in the Red Sea, whose species are poorly characterized at present. This is a first step to enumerating the diversity of fish species and numbers. As well as recording the size of the shark body, students note the relative size, shape and position of their fins. When they need to further define the species, the shark is taken to KAUST for an intensive examination and dissection where teeth and vertebra are carefully counted. At the same time stomach contents are identified to establish their prey. Why is the discovery of this species in the Red Sea important? Sharks are

apex predators: one of the species at the top of the ocean’s food chain. The removal of such a species causes what is known as a trophic cascade: their prey increases, leading to fewer of the species upon which these feed and so forth – cascading down the food chain. Extensive research in other parts of the world finds major ecological changes associated with humans overfishing top marine predators. The extent of these changes is so severe and complete in most systems that we hardly recognize it as unusual until we find the uncommon location not yet showing major human influences. For coral reefs, such unimpacted systems are always characterized by large, healthy shark populations. Sharks are highly sensitive to human impact, particularly fishing. Their biology predisposes them to this susceptibility in many ways. Notably, sharks reach maturity late in life and breed small litters infrequently after

long gestation periods. The umbilical scar on the identified shark indicated that it was a juvenile suggesting the Red Sea might serve as a nursery habitat for this species; losing such a habitat could have implications for the global pigeye population. In addition, it is acknowledged that preserving biodiversity is vital: scientists are only just beginning to realize what individual species may be able to contribute to areas as diverse as anti-cancer pharmaceuticals and aging studies. There are already examples of modifying shark genes to develop antibodies that in-vitro testing suggests may be effective in diseases such as malaria. As less than 40 published articles on Red Sea sharks exist in total, Julia Spaet hopes to do a multi-faceted population analysis for her PhD. By combining market surveys, longline fishing, camera traps, and studies of potential nurseries, she hopes

to generate an accurate assessment of the structure of the local population. “It is just common sense,” says Spaet, “you can’t protect something if you don’t know that it’s there.” This is fundamental work that can serve as a basis for any future projects in the region. Jesse Cochran plans to supplement Spaet’s population studies with life history studies (age, growth, demography, etc.) and blood chemistry analysis (a more subtle and immediate assessment of an individual’s health). He explains, “The studies work well together. When Julia does her experimental fishing, I can get a blood sample from anything she catches. When she does her market surveys, I can get vertebrae and samples for the life history work.” With their combined efforts and expertise, KAUST will make significant contributions to our understanding of these crucial animals in the Red Sea ecosystem. 

The Pigeye Shark

The Bull Shark

On February 21, twenty-four 10th graders showcased their independently-driven, longterm projects demonstrating the knowledge, skills, and understanding gained during the Middle Years Program (MYP). This culminating activity features several months of research on a topic of their choice, framed within the school’s interdisciplinary lenses of learning. Among the diverse research topics of the Class of 2013 were airplane aerodynamics, teen depression, and snakes of Saudi Arabia. 

KAUST at JEF KAUST is following in the footsteps of Harvard, Stanford and MIT to become the first Saudi academic partner to the Jeddah Economic Forum. 21st Century Transformation is the theme of the 11th annual forum which takes place from March 19-22. Professor Stefan Catsicas will give a luncheon address entitled "Worldwide Technology Trends and KAUST" and KAUST Economic Development are sponsoring a panel discussion which will include presentations by Prof. Jean Marie Basset (Director of Catalysis Research Center), Terry McElwee (Director of Technology Transfer and Innovation), and Amin Al Shibani (VP of Economic Development). 


Organized by IEEE Women in Engineering Affinity Group (Saudi Arabia Western & Eastern Sections of IEEE) in collaboration with KAUST Women in Science & Engineering Committee Date: March 19, 2011 Time: 9am to 5pm

Invited Speakers •

Eng. Meliha Selak, IEEE PES Governing Board, VP Chapters & BC Hydro, Vancouver - My Experience as an Engineer, and How the Profession is Suited to Women

Dr. Boutheina Tlili, Associate Professor of Elec. Eng., R.I.T, Dubai Women in Engineering Training

Dr. Lana El Chaar, Assistant Professor, Elec. Eng. Dept., Petroleum Institute, Abu Dhabi - Engineering Skills to Enhance the Community

Location: R  oom 5209, Building 3

This workshop aims to inspire, engage, encourage, and empower women engineers in Saudi Arabia to enhance networking, advocate women in leadership roles, and help them to overcome the challenges in career advancement in the engineering and science professions.

For more details and to register, email: | Sponsored by IEEE Western & Eastern Saudi Arabia Sections

20 million viewers of the film “Wall Street – Money Never Sleeps” saw six screen shots of Fusion Simulation Project Workshop Report by A. Kritz & D.E. Keyes, 2009. KAUST’s own Prof. David Keyes says it is "perhaps his best-cited paper"! 

Twentieth Century FOX

Cited by Hollywood

Blue Brain Project

March 2011


From left to right: Provost Stefan Catsicas, Henry Markram, President Choon Fong Shih, and Patrick Aebischer

Henry Markram:

Simulating the Human Brain Speaking at the inaugural President’s Distinguished Visiting Speaker Lecture in early February, Prof. Henry Markram remarked that KAUST “is a mind-blowing place.” And Prof. Markram should know. He is a professor of neuroscience and the director of the Blue Brain Project at École Polytechnique Fédérale de Lausanne (EPFL). At KAUST to discuss possible collaborations with faculty members and researchers in the areas of visualization, high performance computing and bioinformatics, Prof. Markram was invited by President Choon Fong Shih to describe his “high-risk, high-return project” to the entire KAUST community. President Shih said, “One of KAUST’s key responsibilities is to facilitate connected minds, to connect our faculty, students, postdocs, and staff with distinguished researchers from near and far, so that they can share their expertise, insights, and perspectives with our community. It is my hope that the President’s Distinguished Visiting Speaker Series will help to create these connections, and I am pleased to welcome Professor Henry Markram to open the series.” While KAUST, with its remarkable facilities and topflight researchers, was mind-blowing to Prof. Markram, his project, as he described it in a captivating lecture complete with dazzling video clips of simulated brain activity, was mind-blowing to the audience. In the Blue Brain Project (so named because an IBM Blue Gene/L supercomputer, a sister to KAUST’s Shaheen, provides its computing power), Prof. Markram and his colleagues in the Brain Mind Institute at EPFL with collaborators from across the world are building a “simulation-based research facility” that has modeled and simulated the neocortical column of a rat’s brain at the cellular level and will seek to model the full human brain. They started by “reverse engineering” the neocortical column, which is a highly evolved microcircuit in the mammalian brain that generates perception. “The holy grail for neuroscience and us to understand the brain is to understand the neocortical column,” explained Prof. Markram.

Based on 15,000 experiments in the wet lab, Prof. Markram and his team systematically modeled the key elements of neurons to determine neuronal composition. “This is not a model that is just based on ideas,” he said. “It is based on data.” Because of its complexity, the neocortical column became for Prof. Markram a “proof of concept” that makes possible the transition to simulating the 100 billion neurons that make up our brains. Of course, no computer is large enough or fast enough to run such a massive simulation. When exascale supercomputing (1000-fold faster than China’s Tianhe-1A supercomputer, currently the fastest computer in the world) has been developed, Prof. Markram will be ready. His project was recently shortlisted to compete to become one of the European Union’s Flagship Initiatives. If successful, the project will be awarded 1 to 3 billion euros over ten years, enough funding for the team to achieve remarkable results and to be poised to take advantage of all advances in computing power and technology. And what will be possible once Prof. Markram has built his model? Many have compared him to the science fiction character Dr. Frankenstein, who created a sentient being in his laboratory that quickly became a terrifying monster. But his goal is not sinister. “At present,” he has written, “a detailed model is the only approach that could produce a list of the most vulnerable circuit parameters, revealing likely candidates for dysfunction and targets for treatment.” Our simulation “could be used to test hypotheses for the pathogenesis of neurological and psychiatric diseases and to develop and test new treatment strategies.” (Nature Reviews Neuroscience 7: 153-159, p.158). With US$2 trillion being spent on brain diseases per year and the world’s population aging, the model will not only save huge amounts of money globally, it will give new hope to the millions of people affected by illnesses ranging from Alzheimer’s disease to Zellweger Syndrome, a deadly condition that damages the deep parts of the brain. 

luding EPFL’s President, l colleagues from EPFL, inc e Prof. Markram and severa collaborations on the Blu KAUST to discuss possible ted visi er, isch Aeb rick ers Pat h faculty memb , initiatives. They met wit er oth as ll we as t jec Brain pro mutual interests in administrators to discuss researchers and academic informatics. mance computing and bio visualization, high perfor cutting-edge sciT is a perfect place to do For Prof. Markram, KAUS quite sure that in ld connections here. “I am ence and he hopes to bui nce and technology one of the leaders in scie ten years, KAUST will be going to be a big is no doubt about it. It is in the world. I think there f. Markram, with doubt about it.” And Pro challenge but there is no human brain iative proposal to fund his his billion-euro Flagship Init . ly understands challenges project in the works, certain tretti, Prof. gis possible. Prof. Pierre Ma Other connections are also d Institute at EPFL, is cur Director of the Brain Min and gue lea col m’s rkra ion Ma in Research Organizat l of the International Bra rently the secretary genera UAE Al Ain University to Aebischer recently visited (IBRO). He and President to support neuroscience to train neuroscientists and T promote IBRO initiatives work that will help KAUS t. IBRO may provide a net Eas dle Mid the in ch of ear ge res explore a broad ran earchers in the region to make connections with res s.  brain research collaboration



March 2011


The Beacon

Point of Interest


1. Thuwal Center 2. Thuwal Park 3. Ruins of the Old Souk 4. Boys' school 5. Thuwal Fisherman Association 6. Girls' school 7. Mosque

Our neighboring municipality, Thuwal, which is part of the Governate of Jeddah in Makkah province, covers an area of approximately 600 square meters and has a population of almost 15,000 people. Historically a fishing village, it was also known for its souk that served not only Thuwal but the surrounding villages and for its sweet water which irrigated the millet farms that were scattered throughout the valley. It is said that the Prophet (peace be upon him) passed by this village in his migration journey to Madinah. Since Thuwal is along the route between Makkah and Madinah and was a good source of water and supplies, it provided an ideal rest stop for pilgrims. The poet Alshareef Barakat Mohammed Barakt mentioned the name of Thuwal in a poem describing his victory over his enemies in the year 912 Hijra (1506 A.D.).


Occupations Fishing and farming were, by virtue of its geographical location, the most predominant occupations among Thuwal residents. The actual time at sea or in the fields is now often outsourced to expatriates who work for indigenous residents or who are offered the land by the ancestral land owners for a small fee. Until five years ago, the main industry in Thuwal was wooden boat building. Thuwal people also engage in some minor crafts such as making household items made of palm The tree leaves, tents and fishing gear. Aljahdali Brand You will still see herds of goats, sheep and camels around the village from time to time. These were certainly more abundant decades ago and, in the past, cattle could be seen – to the extent that the Aljahdali tribe had their own symbol with which they branded their cattle.


8. New Fisherman Corniche and Wharf 9. Old Fisherman Wharf 10. Thuwal Municipality 11. KAUST Beach 12. KAUST Visitor Center

Restaurant 1. Bukhari Restaurant 2. Alsayed Fish and Local Food Restaurant



3. Alsalheyah Fish Restaurant 4. Zum Zum Pakistani Restaurant 5. Mandi Restaurant

Goods & Services 1. Auto repair and spare parts shops

Fishing In the early days many of the fishermen went on long trips to Algeria, Sudan, Somalia and Eritrea aboard big boats called qateera (‫ )قطرية‬or saeeya (‫ )ساعية‬looking for pearls and oysters. These trips involved around 30 people but, once they reached their destination, they’d break up into pairs and dive in smaller boats called alhuwari (‫)اهلواري‬. They would often sell the oysters in the ports along the way and then purchase goods such as spices and fabrics to bring back home to sell in Thuwal and neighboring villages. 8 Other fishermen took shorter trips up and down the western coast where the fish trap areas are. The captain would have selected ten or more sailors to join him on boats called aljarady (‫ )اجلارادي‬or alsawaai (‫ )السواعي‬and he stocked up his boat with alkharj (‫ )اخلرج‬which was the food and supplies for the one or two week trip.

2. Thuwal Souk and Fish Auction 3. Fruit Store 4. Central Market


5. Al Fursan Photo Studio 6. Tailor


At the fish Market one might find:




Farming Over 80% of the land in the eastern part of the Thuwal valley is farmland. Much of the land is ancestral and either farmed by a family member or offered, for a small fee or alkhebr (‫)اخلرب‬, to someone who would like to use the land to grow crops to feed his family. If the harvest is plentiful, he may sell the excess and take the profit after giving 1/5 of the crop to charity or hasana (‫ )حسنة‬on behalf of the owners and heirs of the farm.


The Souk Prior to the reign of King Abdul Aziz, Thuwal was a relatively large port with 10 to 15 boats carrying food products to trade in the local souk and the neighboring areas anchoring there weekly. The skeletal shapes of mud buildings that can still be seen behind the old fish market are surmised to have been the souk built around the time of the foundation of the Kingdom of Saudi Arabia on the site of the original marketplace. In those days you would have found various food items, herbs, dried fish, clothing and crafts made out of palm leaves in the souk. The roaming bedouins would have come and set up their tents near the souk to provide various services, such as fixing broken coffee pots, while their sheep roamed close by. Later concrete buildings took the place of the mud ruins and today mobile phone vendors mingle with the traditional dried fish vendors and bakers. A particular experience not to miss in Thuwal is the old fish market. After 4pm every day it is abuzz with excitement as the auction begins. Sparse at first, the crowd gets thicker as people begin to hear the prices and crane their necks to see the next bundle of fish. Put your hand out quickly when you 4 see the batch you want and, if you were quick enough, they’ll be thrown at your feet. Pay the man, then have them gutted and cleaned right at the market before taking them home for a feast with family and friends. 



March 2011



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What’s in a Name?

s fo rm erl y ca lle d y va lle y bu t it wa arb ne e th er aft d me an s al wa s na me ald aa j (‫ )الد عج‬wh ich Th e vil lag e of Th uw be en att rib ut ed to s ha me na is Th . ‫)ال‬ Al du aij ey ah (‫دعيجية‬ the eye”. of ss ne dali (‫)اجلحديل‬. ck bla “extreme le of Thuwal is Aljah op pe us no ige ind for the families working The main tribal name scendents of Thuwal de of er mb nu a g and their e of havin about their families We have the privileg ask them to tell you to ate sit he n't Do within the University. e. pride in their heritag


Basmah H AlJahdali Admin Assistant, Security HQ


Haitham Aljahdali

Marine Biologist Coastal and Marine Resources Department, Core Labs

Hatem AlJahdali Financial Analyst, Finance Department


Maha Aljahdali Alha

Web designer, Digital Media Division, artment Communications Dep




Ramzi Aljahdali Marine Operational Logistics Officer



March 2011

The Beacon

g n i t a t i l i c a F CBRC:


y r a n i l p i c s i d s an

h c r a e Res

Quite apart from its primary role conducting research in the field of bioinformatics and systems biology, the Computational Bioscience Research Center (CBRC) directed by Professor Vladimir Bajic supports KAUST researchers with one of the most enabling technologies in life sciences today. The computational analysis and modeling of biological and biomedical data derived from genomics, transcriptomics, proteomics and other high-throughput approaches combined with system-level information has become a powerful and essential component of modern life-science research and is establishing itself as a driver of experimental design as well as an analytic and predictive tool. The research activities of the center are defined as two complementary foci. The first is the development of methods, tools, repositories and platforms for data integration and efficient ‘knowledge extraction’ in the biomedical field: a crucial component of what we call bioinformatics and computational biology. The second is the application of these tools to the studies of bioactive components in living cells. The CBRC, through its primary activities, engages in various domains ranging from biology and medicine to biotechnology. Prof. Bajic explains that the very nature of the work demands close transdisciplinary relationships between the experimental biologists and computational scientists to understand the biological context of

the data and so develop tools to perform the appropriate analysis of these large, complex datasets. Similarly, the center works closely with scientists in the Bioscience Core Lab, who generate much of the raw data. In addition to computational and mathematical scientists, the CBRC’s staff of 30 has several members who are experimental biologists utilizing a mix of experimental and computational techniques for their research. The center is also home to over 30 MSc and PhD students. Since its inception, the CBRC has had an exceptional group of faculty with broad expertise including Professor Ken Minneman - a pharmacologist and a former President of the American Society for Pharmacology and Experimental Therapeutics, Professor Tim Ravasi who works in transcriptomics and integrative systems biology and Professor Arnab Pain whose interests lie in pathogen genomics. The center plans to attract additional faculty in 2011. Prof. Bajic that working together with partners such as Profs. Uli Stingl and Christian Voolstra from KAUST’s Red Sea Center as well as with local and international collaborators, builds critical mass and ensures competitiveness at the international level. Within the Kingdom, for example, CBRC is working with Prof. Abdulaziz Al-Swailem and Prof. Mohamed B. Al-Fageeh at King Abdullah City of Science and Technology

(KACST) where the dromedary genome has recently been determined. The CBRC and KACST teams are working to produce a detailed functional annotation of this genome. In addition to its tremendous importance in the Kingdom and the region, the camel is an interesting mammal that exhibits some unique immune system properties. It produces smaller antibodies that hold promise as more penetrating therapeutic agents than larger human antibodies. In his research, Prof. Bajic focuses on the development of approaches for bioinformatic applications using high-performance computing systems. The problems that particularly interest him include reconstruction of biological networks and development of computational models of key cellular responses that will allow for simulation and exploration of cellular reactions in exposure to chemicals and biological agents under different types of conditions. Such ‘virtual cell’ models can serve various purposes including detection of relevant biomarkers of different diseases or conditions, as well as assessment of effects of natural products and drugs using computers. These research tools will be applied in research of the Red Sea extremophiles, the desert microbiome and plants. Three recent results from his research include a new biomarker for ovarian cancer that can significantly improve ovarian cancer detection in collaboration with Prof. Mahesh Choolani from

National University of Singapore, as well as two studies conducted at KAUST on the regulation of gene activation. (Links to these three publications as well as other recent papers, can be accessed by using the QR code on page 7).The group has also developed a number of bioinformatic resources that are provided for public use. Dr. Arnab Pain, an Associate Professor of Bioscience, was attracted to KAUST by the expertise of colleagues in diverse disciplines and by the core laboratory facilities including state-of-the-art genomics, proteomics, imaging and visualization. With over ten years of experience working at the Wellcome Trust Sanger Institute in Cambridge (UK), he is initiating a research program at KAUST that directly complements various research activities of CBRC. His primary focus is to use high-throughput sequencing and other functional genomic technology platforms coupled with bioinformatics tools to understand genetic make-up and dynamics of genome variation in a number of viral, bacterial and protozoan pathogens that have major impact on human, animal and plant health in Saudi Arabia and in other GCC countries. Analyzing large-scale datasets will form the backbone of this research and it is aimed at fostering cross collaboration between biologists and computer scientists within KAUST, the Kingdom, the region, and internationally. Apart from its unique access to the Red Sea,

Research KAUST is compellingly placed to look at infectious disease agents because of its proximity to Makkah, where each Hajj, some 2.5M pilgrims from around the globe gather in a confined space. This offers extraordinary potential for research on genomics-driven infectious disease epidemiology. Despite elaborate and successful efforts by the Saudi Ministry of Health (MoH) to prevent disease transmission, pathogens travel from abroad and within the Kingdom and are transmitted during mass gatherings causing local outbreaks. This offers researchers unique opportunities to look at how pathogens spread during outbreaks and to examine their sources. Working in close partnership with the King Abdullah Medical Research Center (KAIMRC) in Riyadh and Jeddah, and with the MoH, Dr. Pain and his colleagues will be undertaking a major genome variation survey program for diagnostics focusing on the respiratory and gastrointestinal pathogens that cause major health concerns. Dr. Pain will also be working with colleagues from King Saud University to consider genomics-driven management strategies for controlling red palm weevils, a major pest destroying local date palms. By looking closely at the genetic makeup of the microorganisms that populate the gut of the weevil, the team hopes to identify certain traits in the gut bacteria that may provide vital nutrition to the insect. It is hoped that by interfering with these bacteria, weevil populations can be controlled. Computational reconstruction of the metabolic networks will form an important aspect of this work and the expertise within CBRC will be used to translate numbers into biological sense. Benoit Marchand, a computer scientist at CBRC, seconded from Research Computing, is

helping CBRC to parallelize critical bioinformatic algorithms for supercomputing systems at KAUST. Prof. Bajic describes him as an optimization and parallelization computer expert. Dr. Marchand works closely with researchers at CBRC to improve problem solving turnaround time and is the interface between the needs of such researchers and the requirements of KAUST’s supercomputers, Shaheen and Noor. He explains that processing data from a single project (for example the data from CBRC’s collaboration with RIKEN in Japan) could take a lifetime, but by introducing “disruptive” technology to the already extraordinary power of Shaheen, the process can be accelerated by tens of thousands of times. Dr. Marchand’s methods begin when he immerses himself fully in the challenge - imagining what the process is from the point of view of the computer and transposing the way an algorithm operates into an equivalent algorithm in the way the computer “thinks”. By splitting an algorithm into smaller fragments, running subsets and later reassembling the application, he is able to tune it, clean it and further streamline it. All this is done incrementally with results checked for accuracy at every stage: “No stone can be left unturned,” explained Dr. Marchand, “There are no shortcuts, no assumptions and no room for assuming that the obvious might work as expected.” Supercomputers such as Shaheen were originally designed for cryptanalysis and the challenges of bioinformatics are similar, but Dr. Marchand’s interdisciplinary work at KAUST extends to research areas including geophysics and materials science. “Nowhere else in the world do individual faculty each have access to 3-4 teraflops of computing power”, he points out. 

March 2011

Recent publications involving the research being done at the Computational Bioscience Research Center can be accessed using this QR code.

Or visit

LAB GEAR Quick Response Codes (QR Codes)

Bill Press:

Using mathematics to monitor drug efficacy

In an engaging lecture, the President’s Distinguished Speaker, Prof. Bill Press, spoke about how health information (HI) technology could change the way that drug efficacy is monitored in the future. In his role as representative to President Obama’s Council of Advisors on Science and Technology working strategy group, Prof. Bill Press, from University of Texas in Austin, realized that when discussing policies, “Words were going into my ears, and equations were coming through my hands.” This is not surprising given his recent experience in computational biology after some 20 years in astronomy and physics. Prof. Press realized that this new HI technology would allow for comparative effectiveness research (CER) that could nullify the need for expensive randomized clinical trials (CTs), which he demonstrated were often flawed and arguably inherently unethical. Almost inevitably, half of all current CT participants receive an inferior treatment, and there are few clear standards for early termination. He proposes that clinical trial patients would be assigned to one of two treatment groups and by using the “two-armed bandit approach” of decision

analysis, fewer patients will be assigned to the inferior treatment and total costs will kept to a minimum. His CER model will be Bayesian, adaptive and decision-theoretic: all well developed disciplines with an extensive knowledge base. In a Bayesian clinical trial, each new data point refines the conclusion so that the best treatment will predominate - quite rapidly in the case of a substantially more effective treatment - to become the market leader. Initial safety testing would remain imperative, but this method would markedly shorten the time to market for new drugs, reducing the cost and risk to both patient and manufacturer, expanding the market for smaller players and incentivizing the development of new drugs. Further explanation of this methodology can be found in Prof. Press’ publication: There is a further endorsement of this “remarkable contribution to a positive direction for the field of CER” in commentary by Dr. Christine Cassel, President and CEO of the American Board of Internal Medicine. h t t p : / / w w w. n c b i . n l m . n i h . g o v / p m c / a r t i c l e s / PMC2799711/pdf/zpq22037.pdf 


There are two parts to Quick Response (QR) technology: The QR Reader, and the QR code itself. QR codes are essentially barcodes that have information embedded within their black and white patterns. This information can, amongst other things, pass on instructions to your QR Reader to perform set actions such as: visit a webpage, collect contact details, send an SMS or register for an offer. A QR Reader can be anything with a camera that has the supporting software. Examples of these are smartphones, tablet PCs, gaming consoles, etc. Some readers, such as smartphones from Android, Nokia, Blackberry, etc. come with QR software preinstalled, but for those that don’t, there is freely available software to download specifically for your device. Using a QR code can be as simple as taking a picture: select the software on your reader (I use BeeTagg), take the picture of the QR code and the software will perform the instructions within the code. Most recently, for us, the codes we embedded in The Beacon launched your smartphone’s browser and downloaded PDF’s of the posters from the 2011 WEP Poster Session. We like QR codes because they are smart and they cram a lot of information into a very small space — so expect to see them appearing in more KAUST media. If you haven’t tried QR codes, have a look on your device and give it a try. If your device doesn’t have the software preinstalled, do a search for compatible QR Readers online. — Craig Brown, Head of Digital Media



March 2011

The Beacon Photo by: Kumaran Mande

photo of the month

This month’s photo was snapped by Kumaran Mande, a research scientist in the Biosciences Core Laboratories. Kumaran shares, “One of the research areas of KAUST is to study the Red Sea microbial community to identify novel drug compounds . . . this gentleman is out fishing for his own “Novel Compounds” in the Red Sea!” Would you like to see your photo published in The Beacon? Every month we carefully review submissions and choose the one that best captures our attention. Keep them coming! 

The Beacon Staff Gets Younger and Shorter!

Email your photos to

Faculty Appointments Pierre Beaujuge Assistant Professor, Chemical Sciences, CLSE Solar Photovoltaic Engineering Research Center

Alexander Rothenberger Associate Professor Chemical Sciences, CLSE Solar Photovoltaic Engineering Research Center

Suzana Pereira Nunes Associate Professor, Chemical and Biological Engineering, CLSE Water Desalination and Reuse Research Center

Ganesh Sundaramoorthi Assistant Professor, Applied Mathematics & Computational Science, MCSE Geometric Modeling and Scientific Visualization Research Center

Klaus-Victor Peinemann Professor, Chemical and Biological Engineering, CLSE Advanced Membranes and Porous Materials Research Center

Ying Wu Assistant Professor, Applied Mathematics & Computational Science, MCSE

My university Nouf Al-Jabri Nouf came to KAUST in September 2010 as a NESMA scholarship winner. Two months after commencing her master’s program, she received another award. This one was from King Abdulaziz University in recognition of her special status as the first undergraduate female to have undertaken research at its King Fahd Medical Research Center. Nouf has been greatly influenced by two female role models: Saudi medical researcher Dr. Hayat Sindi, who is currently a visiting scholar at Harvard University and Dr. Khawla Al-Kuraya, Director of the

Research Center at King Faisal Specialist Hospital and Research Center. She also feels privileged be working with, and be mentored by, Prof. Niveen Khashab. She is single-minded in her plans for the future. She intends to continue for a PhD at KAUST and continue the research that she started in her undergrad years – to find a drug carrier that will kill cancer cells without harming tissue and is thrilled that KAUST enables her to be able to stay in Saudi Arabia to do so. 

Yu Han When Dr. Yu Han, Assistant Professor, Chemical and Biological Engineering, first heard of KAUST, Singapore press were buzzing about National University of Singapore President, Prof. Choon Fong Shih, moving to Saudi Arabia. He was then a Postdoctoral Fellow at the Institute of Bioengineering and Nanotechnology in Singapore and he saw it as a great opportunity to follow in Prof. Shih’s footsteps. He was a visiting Professor at Imperial College, London for five months prior to coming to KAUST. Then he, his wife and young son moved to Jeddah in July 2009.

Yu has the best of both worlds; his own lab for research on nanoporous materials as well as the opportunity to work with colleagues in the Advanced Membranes and Porous Materials Center on potential membrane applications of his research. “Overall”, he says, “the caliber of KAUST students is better than I expected”. His only regret is that some master’s students decided to pursue their PhD elsewhere; a situation that he understands but hopes will improve as the institution grows. He fully expects that it will. 

Bijesh Manthrakalam Bijesh hails from Kasaragod district of Kerala State in India. Following his high school graduation he became a bus conductor, allowing him time to pursue his passion for politics. Representing the Indian National Congress, he rose quickly in the local party and was elected President of the Panathady Panchayat, retaining that position for five years. To support his family, Bijesh took up landscape gardening and seven years ago he moved from his home in Kerala; first to Bangalore, then Dubai, Abu Dhabi, and finally arriving at KAUST in July 2009.

When he’s not taking care of our gardens at KAUST, Bijesh enjoys playing cricket and volleyball with his workmates and maintains his interest in politics watching news on TV. He talks proudly of his one year old son and his wife who holds an M.A. in political science and is currently studying for her B.Ed. – whom he phones twice a week. When asked what he hopes to be doing in ten years, Bijesh’s smile widens and he says he sees himself settled back home with his family, once again pursuing a political career. 

The Communications Department was buzzing with activity on February 21, when we welcomed 49 second graders to building 16. We enjoyed the children’s infectious curiosity and boundless energy as The Beacon staff led them through a workshop about newspapers. After identifying the parts of a paper, our staff helped each class design their own front page, featuring their quotes about what they have been learning in their communications unit. The students created a headline and photo caption, before sending their personalized Beacon front page to print. In addition to this glimpse into the workings of a real newspaper, these KAUST School students have been engaged in several activities and lessons about the different ways of communicating. One of their field trips involved taking a bus tour around the campus and community, identifying signs and classifying them. Their studies have also included learning more about hieroglyphics, sign language and Skype. 

Accolades Sid Samtaney, a tenth grader at The KAUST Schools, placed first in the Saudi Arabian Intra-Kingdom Activities Conference (SAIKAC) Cross Country event held on January 27 in Dhahran. This event featured about 25 male and female runners in grades 10, 11 and 12 from schools across the Kingdom. In addition to first place in his division and overall, his official time of 8:23 broke the course record for his age group. KAUST was well represented by both our cross country runners, with Matias Lehvaslaiho finishing third in his division for grade 10. The race course covered 3km of undulating terrain of concrete, dirt and grass. Well done to our student athletes! 

March 2011