DATE: Wednesday, October 24, 2018
TIME: 12:00 PM - 01:00 PM
LOCATION:Building 2 - Level 5 - Room 5209
Abstract: Structural insights into biological molecules such as proteins at atomic detail help us understand their properties, functions, interactions and regulation. This allows us to understand biological processes at the molecular and cellular level. Cryo electron microscopy of vitrified biological macromolecular complexes allows obtaining structural insight in near-native conditions. Moreover, the method is most suitable for studying macromolecular complexes with multiple interacting subunits in multiple conformations. Thus besides resolving structures of individual components (subunits), we also learn about the way the molecular machinery is built and how it works. Some examples from ongoing projects in Arold lab e.g. Cdc48A – the plant unfoldase/degradation machinery will illustrate the power of cryo electron microscopy for studying these molecular machines.Bio:Dr. Bilal Qureshi I am a biophysicist by training and I investigate fundamental processes of life at molecular level. I employ methods like x-ray diffraction or single-particle cryo electron microscopy to obtain structures of biological macromolecules. Moreover, I investigate interactions of these molecules by biophysical and biochemical methods to understand the underlying molecular mechanisms for basic cellular processes such as signal-transduction, protein trafficking and enzyme regulation etc. Besides, I produce engineered molecules with predicted properties to further corroborate my findings. My research has impact in basic sciences as well as for drug development.
DATE: Tuesday, October 30, 2018
TIME: 02:00 PM - 03:00 PM
LOCATION:Auditorium between Bldg 2&3 - Level 0 - Room 0215
Advisor: Professor Mark TesterBio:Mariam Awlia was born in Jeddah, Saudi Arabia. She received her Bachelor of Science degree in Biochemistry from University College London (UCL) and Masters degree in Bioscience from King Abdullah University of Science & Technology (KAUST). She is now a PhD candidate in Plant Science at KAUST with a specialisation in plant salinity tolerance under the supervision of Prof. Mark Tester. Research Interests:She is interested in understanding the mechanisms of salinity tolerance in plants; an area of importance to agriculture and environmental sustainability. More specifically, her work examines the osmotic component of salinity tolerance (the shoot ion independent tolerance), which is the earliest response to salt stress and is mainly related to changes in growth rate, leaf temperature (stomatal closure) and photosynthetic activity.
DATE: Wednesday, October 31, 2018
TIME: 03:00 PM - 04:00 PM
Speaker 1: Razan Yahya, PhD StudentTitle: Airborne Prokaryote and Virus abundance over the Red SeaAbstract:Aeolian dust exerts a notable influence on atmospheric and oceanic conditions and human health, particularly in arid and semi-arid regions like Saudi Arabia. Dust is often characterized by its mineral and chemical composition, but there is a microbiological component of natural aerosols which has received comparatively little attention. Moreover, the amount of materials suspended in the atmosphere is highly variable from day to day. Thus, knowing the loads of dust and suspended microbes and its variability over the year is essential to understand the possible effects of dust on the Red Sea ecosystem. Here, we present the first estimates of dust and microbial loads at a coastal side on the Red Sea over a two-year period supplemented with information from dust samples collected along the Red Sea in offshore water and their variability. Weekly average dust loads in a coastal site on the red sea ranged from 4.63 to 646.11 µg m-3, while the abundance of airborne prokaryotic cells and viral particles ranged from 37,976 to 1,168,792 cells m-3 and from 69,615.5 to 3,104,758 particles m-3, respectively. These are the first estimates of airborne microbial abundance that we are aware of in this region. The large number of dust particles and suspended microbes found in the air indicates that airborne microbes may have a large impact on our health and that of the Red Sea ecosystem.
Speaker 2: Nojood Aslismail, PhD StudentTitle: Functional Metagenomics of the Global Dust Belt Microbiome over the Red SeaAbstract:Atmospheric dust loads are concentrated in a broad region extending from the west coast of North Africa, through the Middle East, into Central Asia (approximately 10 to 30 oN) deemed the “global dust belt". The Red Sea is the only Sea, in addition to the shallow Arabian Gulf, fully contained within the “global dust belt”, receiving about 6 x106 metric tons of dust, mostly contributed by the Sahara Desert and the Arabian Desert, annually. Current understanding of the airborne microbiome focusses on quantifying loads and fluxes and characterizing the identity of the microorganisms transported. However, the ability of microorganisms to survive in harsh environment the atmosphere represents (e.g. high UV radiation and desiccation) is poorly understood, but must be controlled by a set of functions conferring resistance to these microorganisms. Our main goal is to interrogate the Aeolian metagenomes to detect a parsimonious set of genes coding for functions hypothesized to play a significant role in allowing airborne microorganisms to survive atmospheric transport. A total of 0.0677 Tbp of DNA were sequenced, with a total of 5,632,449 unique predicted genes, with a yield of 30.9 x 106 genes per Tb pair of DNA sequenced. Two-thirds (69.24%) of the genes were assigned to bacteria, followed by eukaryotic genes (2.76%), archaeal genes (0.75%), and viral genes (0.24%). We specifically explored the presence of genes related to mechanisms reported to improve survival and transport during the airborne phase (aerosolization, chemotaxis, aerotaxis, sporulation, germination, biofilm formation, DNA repair), thereby facilitating an airborne lifestyle, or may impact on organisms (antibiotic resistance, pathogenicity), or perform important functions (e.g. nitrogen fixation) in the receiving environment.Here we provide a first assessment of the functional genomics of the Aeolian microbiome in the “global dust belt”.
DATE: Wednesday, November 07, 2018
Abstract:Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an analogy to an increase in the local viscosity due to the presence of the protein residues. This explanation denies the opposite effect of fluorescence quenching. Here, we present a modified perspective for understanding PIFE’s mechanism. We also describe a novel phenomenon that we name ‘protein-induced fluorescence quenching’ (PIFQ), which exhibits an opposite effect of PIFE. Our characterization of these two fluorescence modulations reveals that the initial fluorescence state of the mediator (DNA) determines whether this mediator-conjugated dye undergoes through PIFE or PIFQ, upon protein binding. This key role of the mediator DNA, which was never characterized to this day, enabled us to provide a protocol for the experimental design for obtaining, ‘on-demand’, either PIFQ or PIFE. This work will have a profound impact on the interpretation of PIFE results and will remove the arbitrary nature of its experimental design. It will also allow for proper integration of PIFE and PIFQ with existing bulk and single molecule fluorescence techniques in studying the mechanisms of nucleic acids binding proteins.
Bio:Vlad-Stefan Raducanu graduated from the Faculty of Physics, University of Bucharest, Romania. His bachelor’s degree thesis was in Theoretical Physics on the subject of “Coherent quantum states of electrons in uniform static magnetic fields”. During his bachelor’s degree studies, he came in contact with Biophysics and Biochemistry, to which he was attracted immediately. With the desire to gain more knowledge of Biology he joined KAUST for a master’s degree in Bioscience. During his master’s he joined Professor’s Samir Hamdan laboratory, in which he later continued up to date as a Ph.D. student. His focus is in understanding different processes involved in DNA Repair and Replication, through a variety of Biophysical and Biochemical methods, with an emphasis on fluorescence tools.
DATE: Thursday, November 08, 2018
TIME: 10:00 AM - 11:00 AM
LOCATION:Building 2 - Level 5 - Room 5220
PhD Advisor: Professor Satoshi HabuchiAbstract:Researches on Hematopoietic Stem Cell (HSC) have been expanding that leads to an increase in our understanding of HSC normal behaviors and abnormal alterations. One of the most important issues in the research on HSCs is to understand the mechanism of the homing process of these cells to settle in its niche in the bone marrow and establish the production of various blood cell types after bone marrow transplantation. The cells first must come in contact with the endothelial cells. This contact is known as adhesion and occurs through a multi-steps paradigm ending with transmigration to the bone marrow niche. The initial step of the homing, tethering and rolling of HSC, is mediated by P- and E-Selectins present on endothelial cell surface through their interactions with the ligands expressed on the surface of HSC. Thus, understanding the adhesion process and its contribution for efficient HSCs homing will have great impact on HSC therapy. The selectin – ligands interaction has been intensively studied using in vivo and in vitro approaches. However, the molecular mechanism involved by HSCs at single molecule level is poorly understood. Here in this study, a novel experimental method to unravel the molecular mechanisms of the Selectin-ligands interactions in vitro at the single molecule level is developed by combining microfluidics, epi-fluorescence microscopy and live cells. In this work, the new single-molecule imaging technique enabled us to directly visualize the nanoscale spatiotemporal dynamics of the membrane protein-ligand interactions under conditions of shear stress acting on the cells at the molecular level in real time. Using this method, we revealed that selectin ligands on membrane-tethers and slings show unique spatiotemporal dynamics that is distinct from those on the cell body. We demonstrated that the membrane tethers are formed from single microvilli on the cells, which provides a mechanism to spatially localize selectin ligands, PSGL-1 and CD44 on the tethers and slings. We also demonstrated that the selectin ligands show fast diffusional motion along the tethers and slings compared with that on the cell body due to the detachment of cell membranes from actin cytoskeleton during the formation of the tethers. Our results suggest that the spatial confinement of the selectin ligands together with the fast scanning of a large area by the selectin ligands increase the efficiency of selectin-ligands interaction during the rolling, resulting in slow and stable rolling of the cell on selectin. Our findings contribute significantly to molecular level understanding of the initial step of HSCs. This single-molecule imaging technique that we developed in this study will find wide applications in the molecular-level studies on cell-cell interactions including cancer cell metastasis. Bio:Working with human cells and in particular blood cells either in normal or in disease states, is an area of interest for me. I have studied pathology and granted a bachelor degree in Medical Laboratory Technology with excellent GPA and first honor from king Abdullaziz University in Jeddah, Saudi Arabia where I have studied different subjects in the medical field but the most attractive for me was Hematology and in particular hematopoietic stem cell. I have joined KAUST and received a Master degree in Biosciences. During the past five years, I was working with human cells in particular characterizing the homing process of hematopoietic stem cell homing after bone marrow transplantation. I have a great enthusiasm to continue my work in the field of hematopoietic stem cell either normal or cancers. Before joining KAUST, I was working in Saudi Aramco as a COOP-trainee for one year in Saudi Aramco Medical Services in Dhahran, Saudi Arabia.
DATE: Wednesday, November 14, 2018
Abstract:Currently, there is a tremendous effort on the development of biomedical devices in healthcare industry for the early diagnosis, prevention or treatment of chronic disease such as diabetes or cardiovascular disease. With the evolution of microelectronics industry and their direct implementation in the biomedical arena, innovative tools and technologies have come to the fore enabling more reliable and cost-effective treatment. During the last decade, conducting polymers have attracted special attention due to their unique set of features such as combined ionic and electronic conduction, soft nature and ease in processability rendering them an ideal alternative to the inorganic materials used for electrophysiological applications. Driven by the technological demands for low-cost and large area electronics, in this seminar I will focus on the integration of the conducting polymer Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) with additive printing technologies toward the realization of high performances biomedical devices.Bio:Eloise did her masters in Grenoble INP-Pagora and her PhD in Ecole des Mines de Saint Etienne in France. She is postdoctoral fellow in Prof. Khaled Salama’s group and also in collaboration with Prof. Inal and Prof. Baran. Eloise’s current research focuses on the fabrication of printed autonomous biosensors for monitoring human metabolites. She aims to develop cutaneous, minimally invasive and conformable sensors mounted on the skin.
DATE: Wednesday, November 21, 2018
About:My research interests lie in the broad fields of materials science, bioscience, physical chemistry and organic electronics. Since the beginning of my research career in April 2011, I worked on the development of various electronic and electrochemical devices based on conducting polymers. The last 18 months as a post-doc at KAUST, I am studying how these materials conduct electrons and ions and exploiting their use in novel organic electrochemical devices for bioelectronic applications. To this end, I have developed a methodology to define the efficiency of ionic doping in conducting polymers and studied extensively the mechanisms of operation of organic electrochemical transistors. Furthermore, I studied how different biomolecules, such as cells, enzymes and lipid bilayers, interact with conducting polymers and assisted my teammates to develop organic electrochemical devices for ultra-sensitive detection of metabolites. Currently, I am developing a wireless, photosensitive device that can be used to stimulate electroactive cells, i.e. neurons, by shining low intensity, visible light on it. Previously, as a PhD student, post-doc and senior researcher in Cyprus University of Technology (CUT), I have developed functional electrodes for organic and hybrid solar cells. Through an in depth investigation on material properties, processing and device physics, I designed solution-based functional materials, dealing with issues related to device initial efficiency, long-term stability and product development targets.
DATE: Wednesday, November 28, 2018
Abstract:Striga hermonthica is a root parasitic plant that infests cereals, decimating yields, particularly in sub-Saharan Africa. For germination, Strigaseeds require host-released strigolactones that are perceived by the family of HYPOSENSITIVE to LIGHT (ShHTL) receptors. Inhibiting seed germination would thus be a promising approach for combating Striga However, there are currently no strigolactone antagonists that specifically block ShHTLs and do not bind to DWARF14, the homologous strigolactone receptor of the host. Here, we show that the octyl phenol ethoxylate Triton X-100 inhibits S. hermonthica seed germination without affecting host plants. High-resolution X-ray structures reveal that Triton X-100 specifically plugs the catalytic pocket of ShHTL7. ShHTL7-specific inhibition by Triton X-100 demonstrates the dominant role of this particular ShHTL receptor for Striga germination. Our structural analysis provides a rationale for the broad specificity and high sensitivity of ShHTL7, and reveals that strigolactones trigger structural changes in ShHTL7 that are required for downstream signaling. Our findings identify Triton and the related 2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]acetic acid as promising lead compounds for the rational design of efficient Striga-specific herbicides.Bio:M.Tech in Biotechnology, IIT Madras, India (2008).PhD, National University of Singapore, Singapore (2013) in Biophysical Characterization of proteins involved in cell signaling. Post-doctoral fellow at StruBE lab, Professor Stefan Arold, KAUST (2013 – 2018).Research Scientist at StruBE lab, Professor Stefan Arold, KAUST (2018 - Present).