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News Article | May 25, 2017
Site: www.eurekalert.org

The protein tags that adorn immune cells and engage with receptors to promote inflammation in the body's endothelial tissues are not what they were thought to be. A KAUST investigation has identified the true surface proteins expressed by T-cells that mediate this molecular liaison, a finding that could help scientists control inflammation that has gone haywire. "This has significant implications for developing targeted therapies to combat inflammatory diseases such as psoriasis and rheumatoid arthritis," says Jasmeen Merzaban, a biochemist at KAUST who led the research. The receptor with which the surface proteins on T-cells interact is known as E-selectin. This 'cell adhesion molecule' is expressed by tissues that line the inner surface of blood vessels: it acts as a kind of Velcro that clings to T-cells when the endothelium needs to fight off infections from bacteria or viruses. The trouble is that E-selectins can also trigger inflammation when there are no such microbial invaders. These aberrant inflammatory signals can cause autoimmune diseases. However, blocking the hitching of E-selectin to T-cells could help reverse that problematic immune reaction. For more than a decade, researchers knew of only two surface proteins expressed by T-cells that could serve as binding partners, or ligands, for E-selection. Yet, mouse studies had shown that reducing expression of these two proteins -- PSGL-1 and CD43 -- was not sufficient to eliminate the crosstalk between E-selectin and T-cells. That suggested to Merzaban that some other E-selectin ligands might be at play. She and her graduate students, Amal Ali and Ayman Abuelela from KAUST's Biological and Environmental Science and Engineering Division, used a mass spectrometry approach to identify the full repertoire of E-selectin ligands expressed by T-cells. They detected 10 such proteins, one of which they explored in greater detail owing to its known function as an E-selectin ligand expressed by blood stem cells, the precursors of T-cells. This protein, called CD44, is also expressed on the surface of both 'helper' and 'killer' T-cells, where it binds E-selectin, the researchers found. Merzaban and her team had discovered a third E-selectin ligand. But, as it turned out, not all these ligands contribute to T-cell tethering. The researchers knocked down the expression of all three ligands, individually and in combination. They discovered that CD44 -- not CD43 -- worked with PSGL-1 as the E-selectin ligands implicated in inflammation. They confirmed the clinical relevance of these findings by looking at T-cells isolated from patients with psoriasis, a common inflammatory skin condition -- which means that "targeting these ligands could be a viable option to treat skin diseases," says Ali.


The catalyst rearranges propane, which contains three carbon atoms, into other molecules, such as butane (containing four carbons), pentane (with five carbons) and ethane (with two carbons). "Our aim is to convert lower molecular weight alkanes to valuable diesel-range alkanes," said Manoja Samantaray from the KAUST Catalysis Center. At the heart of the catalyst are compounds of two metals, titanium and tungsten, which are anchored to a silica surface via oxygen atoms. The strategy used was catalysis by design. Previous studies showed that monometallic catalysts were engaged in two functions: alkane to olefin and then olefin metathesis. Titanium was chosen because of its ability to activate the C-H bond of paraffins to transform them to olefins, and tungsten was chosen for its high activity for olefin metathesis. To create the catalyst, the team heated silica to remove as much water as possible and then added hexamethyl tungsten and tetraneopentyl titanium, forming a light-yellow powder. The researchers studied the catalyst using nuclear magnetic resonance (NMR) spectroscopy to show that the tungsten and titanium atoms lie extremely close together on the silica surfaces, perhaps as close as ≈0.5 nanometres. The researchers, led by the Director of the center Jean-Marie Basset, then tested the catalyst by heating it to 150°C with propane for three days. After optimizing the reaction conditions— for example, by allowing the propane to flow continuously over the catalyst—they found that the main products of the reaction were ethane and butane and that each pair of tungsten and titanium atoms could catalyze an average of 10,000 cycles before losing their activity. This "turnover number" is the highest ever reported for a propane metathesis reaction. This success of catalysis by design, the researchers propose, is due to an expected cooperative effect between the two metals. First, a titanium atom removes hydrogen atoms from propane to form propene and then a neighboring tungsten atom breaks open propene at its carbon-carbon double bond, creating fragments that can recombine into other hydrocarbons. The researchers also found that catalyst powders containing only tungsten or titanium performed very poorly; even when these two powders were physically mixed together, their performance did not match the cooperative catalyst. The team hopes to design an even better catalyst with a higher turnover number, and a longer lifetime. "We believe that in the near future, industry can adopt our approach for producing diesel-range alkanes and more generally of catalysis by design," said Samantaray. Explore further: A new catalyst to transform propane into propene More information: Manoja K. Samantaray et al. Unearthing a Well-Defined Highly Active Bimetallic W/Ti Precatalyst Anchored on a Single Silica Surface for Metathesis of Propane, Journal of the American Chemical Society (2017). DOI: 10.1021/jacs.6b12970


News Article | May 29, 2017
Site: www.sciencedaily.com

By observing the soot particles formed in a simple flame, researchers at KAUST have developed a computational model capable of simulating soot production inside the latest gasoline automobile engines. Although today's passenger vehicle engines are cleaner than ever before, their exhaust can still contain significant numbers of nanoscopic soot particles that are small enough to penetrate the lungs and bloodstream. This new computer model should help car makers improve their engines to cut soot formation. Gasoline engines are not traditionally associated with soot -- it's a problem usually linked with diesel vehicles. But over the last decade, to boost fuel efficiency, manufacturers have made their gasoline engines more diesel-like, adopting "direct injection" technology that sprays fuel directly into the engine cylinder. "Sometimes you get fuel-rich pockets where there's not enough air for complete combustion or sometimes the fuel hits the cylinder wall and forms a pool fire," said S. Mani Sarathy from the KAUST Clean Combustion Center, who co-led the work. Both of these scenarios generate soot. Working out how to minimize soot is a challenge because it is difficult to see inside an engine cylinder as fuel combustion takes place. Sarathy and his coworkers tackled the problem by burning a chemically simplified "gasoline surrogate" mixture in an experimental setup called a counterflow diffusion flame. By shining lasers into this open flame, they could monitor soot and its precursors as the fuel burns. "These experiments have been done previously with gaseous fuels, but this is the first time they have been done with gasoline-relevant liquid fuels," Sarathy said. The team varied the composition of the fuel and observed particle production to build a model of the basic chemical reactions through which soot particles form and grow. "Once we have this basic kinetic model that works well in simple flames, we can utilize the model in an engine simulation," Sarathy explained. An engine combustion simulation is essentially an ensemble of many tiny flamelets, which are combined to give a complete picture of how soot is formed in an engine. Car makers could use Sarathy's model in their own simulations to test whether changes, such as altering engine geometry or the timing of fuel injection, might cut soot production. "We also have industrial partners that utilize the model to see how different fuels and engine combustion strategies affect soot production," Sarathy said. For future engine designs, the model will help manufacturers minimize soot before the engine ever rolls off the production line.


KAUST and Thermo Fisher Scientific Open Center of Excellence in Electron Microscopy


KAUST and Thermo Fisher Scientific Open Center of Excellence in Electron Microscopy


KAUST and Thermo Fisher Scientific Open Center of Excellence in Electron Microscopy


KAUST and Thermo Fisher Scientific Open Center of Excellence in Electron Microscopy


News Article | May 10, 2017
Site: www.prnewswire.co.uk

KAUST and Thermo Fisher Scientific Open Center of Excellence in Electron Microscopy


THUWAL, Saudi Arabia, May 10, 2017 /PRNewswire/ -- King Abdullah University of Science and Technology (KAUST) and Thermo Fisher Scientific Inc. held an opening ceremony on May 9 for the Electron Microscopy Center of Excellence at the KAUST campus in Thuwal, Saudi Arabia. This new center builds upon the long-standing partnership between KAUST and Thermo Fisher, and will focus on excellence in instrument performance and R&D collaboration. To view the Multimedia News Release, please click: https://www.multivu.com/players/uk/8101851-kaust-thermo-fisher-electron-microscopy/ The Center of Excellence aims to offer KAUST scientists and collaborators exploration and experimentation capabilities through Thermo Fisher's leading electron microscopy platform. Industry partners located in the KAUST Research and Technology Park will also benefit from proximity to Thermo Fisher's deep application knowledge in materials science. "We have enjoyed a long history with KAUST and look forward to continued collaboration and technology advancement as part of this new Center of Excellence," said Michael Shafer, president, materials and structural analysis, Thermo Fisher. "By gaining access to the latest characterization techniques, hardware and software available on the market, KAUST will have the opportunity to advance scientific research in the areas of chemistry and catalyst research, nanoparticles and life sciences." Dr. Justin Mynar, director of the KAUST Core Laboratories and Major Facilities said, "This center embodies the mission of our strategic partnership with Thermo Fisher to achieve our common goals in the advancement of high-performance imaging technologies. Our collaboration seeks to elevate the experimental capabilities and capacity in the Electron Microscopy Center of Excellence to provide our students, faculty, researchers and partners an array of scientific opportunities and advantages for the first time in Saudi Arabia." The center's opening ceremony included the official commissioning of the FEI Titan Themis Z scanning transmission electron microscope (S/TEM), the most advanced analytical transmission electron microscope commercially available to date and the first to be installed in the world. Materials scientists use the Titan Themis Z to understand relationships between a material's larger-scale physical properties and its atomic-scale composition and structure. This system joins other highly advanced electron microscopy systems already installed at the center, including a total of 16 electron microscopes from Thermo Fisher. This Center of Excellence is the first implementation in a strategy by KAUST to build long-term partnerships with major instrument suppliers. It will serve as a model for future opportunities to provide state-of-the-art research facilities, training and services to KAUST users and collaborators across the Kingdom of Saudi Arabia. About King Abdullah University of Science and Technology (KAUST) KAUST advances science and technology through distinctive and collaborative research integrated with graduate education. Located on the Red Sea coast in Saudi Arabia, KAUST conducts curiosity-driven and goal-oriented research to address global challenges related to food, water, energy and the environment. Established in 2009, KAUST is a catalyst for innovation, economic development and social prosperity in Saudi Arabia and the world. The university currently educates and trains over 900 master's and doctoral students, supported by an academic community of 150 faculty members, 400 postdocs and 300 research scientists. With 100 nationalities working and living at KAUST, the university brings together people and ideas from all over the world. Visit http://www.kaust.edu.sa for more information. Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Through our premier brands - Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services - we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit http://www.thermofisher.com .


News Article | May 9, 2017
Site: phys.org

"How much can you understand and repair a car if you don't have a detailed picture of what is going on under the hood?" said KAUST Associate Professor Stefan Arold. "Proteins are life's workhorses: their function and dysfunction both create life and end it. Each protein's amino acid sequence folds into a particular 3-D structure that is required to support its function. If you want to understand, affect or engineer a protein's function, you need to know its 3-D structure," he explained. The process to determine that structure begins by purifying and crystallizing the protein under investigation. The protein crystal is then bombarded by extremely powerful X-rays, which diffract in various directions, giving an indication of its structure. Researchers then apply "molecular replacement," which compares the target protein crystal to the 3-D structure of other known similar proteins. But for the researchers to compare their protein with similar ones, first they need to know how its amino acids are arranged. ContaMiner can help researchers determine if they are even looking at the right protein to begin with. "The protein we crystallized might not be the protein we thought it was but instead an unknown contaminant," explained Arold. Protein-based contaminants can, more often than previously thought, get crystallized instead of, or in addition to, the protein under study. These might come from the organism that originally produced the protein or occur during the purification or crystallization process. "Scientists often waste months of work before they identify the error and the identity of the protein contaminant that they had unintentionally crystallized," said Arold. Arold's team has worked tirelessly to compile a preliminary database, called ContaBase, of 62 known contaminants. "Contaminants were a known but under-appreciated problem because many cases went undetected," said Arold. Even in cases where contaminants are finally identified, this information often goes unpublished since the experiment was considered a failure. Often researchers report issues of contamination in online forums rather than peer-reviewed publications. "Because of this, nobody had a good idea of how many and which contaminants might occur and crystalize," he continued. ContaMiner changes this. Now, researchers can submit their X-ray diffraction data to the program, which compares it with an updateable database of known contaminants. "If a contaminant is present, ContaMiner can typically detect it in only 5-15 minutes," said Arold. Several hundred researchers have used the program since it was first described in late 2016 in the Journal of Applied Crystallography. Many from the crystallography community have helped update ContaBase to now include 71 contaminants. "It's an ongoing community effort," said Arold. ContaMiner has also been selected to be included in an online server, called CCP4, which is a highly selective collection of software related to structural biology and is the most widely used resource worldwide, explained Arold. While having international impact, Arold and his team also play a vital role in the local scientific community through their unique set of skills. The KAUST team combines expertise in molecular biology, biochemistry, biophysics, bioinformatics and computation to investigate protein structures and function. It is the only group involved in structural biology in the kingdom and, under the supervision of structural biologist Stefan Arold, it is also setting up important local collaborations. Currently they are collaborating with researchers at King Fahd Specialist Hospital and Research Centre to identify gene mutations that cause diseases in the Saudi population. Arold uses his expertise, together with computational modeling, to understand why specific mutations cause protein malfunctions. "It is intriguing how much harm can be caused by a single mutation" he said. "It also gives us a glimpse of the unimaginable sophistication and complexity of our bodies. Arold and his team also recently worked with KAUST plant scientist Mark Tester and a diverse international team to understand the molecular basis for the production of toxic compounds, called saponins, in some but not all quinoa strains. "Does the region need more structural biologists?" asked Arold. "In my biased opinion, of course yes. In particular, experts in nuclear magnetic resonance spectroscopy, which is highly complementary to X-ray crystallography." He also advocates that biologists develop more awareness of the importance of structural biology for their research. "Wisely, KAUST has invested heavily in structural biology; and biological imaging in general is clearly an area of priority. We have outstanding resources, such as 700 and 950 megahertz nuclear magnetic resonance imaging spectrometers and the TITAN KRIOS electron microscope. And although I am currently the only structural biologist, I might not be alone for much longer," Arold said. Negotiations are already underway to bring more talent to the institution. Explore further: Study gives clues to causes of Motor Neurone Disease and Parkinson's Disease More information: Arnaud Hungler et al. and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants, Journal of Applied Crystallography (2016). DOI: 10.1107/S1600576716014965

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