DATE: Tuesday, October 22, 2019
TIME: 09:00 AM - 10:00 AM
LOCATION:Building 3 - Level 5 - Room 5220
Abstract: Wnt3 is a member of the Wnt signalling protein family, which comprises a set of lipid-modified signalling molecules that act by binding to receptors of the Frizzled family via the co-receptor LRP5/6. Wnt proteins can act over short distances (auto- and paracrine signalling) and over long distances as expected for a classical morphogen. Wnt3 has two putative lipidation sites, C80 and S212. Wnt lipidation is assumed to be important in Wnt localization in the membrane, in secretion and in receptor binding. This raises multiple questions about the way Wnt3 functions. First, the source and sink for Wnt3 as a morphogen have to be identified. Second, as a lipidated protein, involved in autocrine signalling, it is localized to the plasma membrane. However, Wnt3 and Fzd1 localization within the membrane and the localization dependence on the lipid modifications are not known. Third, as a protein, involved in short range paracrine or long range signalling, Wnt3 is secreted and requires transport to reach target cells, despite its hydrophobic nature due to lipid modifications. However, the transport mechanism has not been determined and the interstitial spaces have not been mapped. Finally, the binding of Wnt3 to its target Frizzled receptors needs to be quantified. To start answering these questions, we have used a combination of fluorescence microscopy and spectroscopy techniques to measure Wnt3 characteristics in live zebrafish embryos. The identification of source and target cells as well as the mapping of the interstitial spaces were achieved by confocal and light sheet fluorescence microscopy. The measurement of Wnt3 membrane localization, diffusion within the interstitial spaces, and interaction with Fzd1 receptors were accomplished by fluorescence correlation spectroscopy (FCS) modalities that allow measuring the dynamics of molecules with high temporal resolution and single molecule sensitivity. Our results give a preliminary outline of Wnt3 action, starting from source cells, transport through interstitial spaces, and binding to its receptors on target cells. Biography: Thorsten Wohland studied Physics at the Technical University of Darmstadt and the University of Heidelberg in Germany from 1989-1995. He completed his diploma thesis in physics at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, where he worked on the influence of light polarization on the forces in optical tweezers under the supervision of Ernst H.K. Stelzer. In 1997 he joined the research group of Prof. Horst Vogel at the Swiss Federal Institute of Technology in Lausanne (ETHL/EPFL), Switzerland. In the year 2000 he obtained his doctoral degree in the field of biophysics for the study of theoretical and practical aspects of fluorescence correlation spectroscopy (FCS) and its application to integral membrane proteins. Following another two years in the group of Richard N. Zare at Stanford in the USA working on single molecule detection and protein immobilization he started as Assistant Professor at the NUS in June 2002. At NUS he developed several new fluorescence correlation spectroscopy methods, imaging total internal refelection fluorescence correlation spectroscopy (ITIR-FCS), single plane illumination microscopy FCS (SPIM-FCS), and single wavelength fluorescence cross-corrleation spectroscopy (SW-FCCS), which allowed for the first time to take correlation images of live cells and quantitatively measure affinity constants of bimolecular interactions in live organisms, respectively. His current research aims at the integration of fluorescence microscopy and spectroscopy to yield quantitative microscopy methods that can extract information with high spatial and temporal resolution and the application of these methods to biological problems.
DATE: Thursday, October 24, 2019
TIME: 09:00 AM - 11:00 AM
LOCATION:Building 2 - Level 5 - Room 5209
PhD Advisor: Professor Mark TesterAbstract:Salt stress severely constrains plant performance and global agricultural productivity. 5% of arable land, 20% of irrigated areas and 98% of water reserves worldwide are saline. Improving the salt tolerance of major crop species will help attenuate yield losses and expand irrigation opportunities and provide in situ relief in areas where poverty, food and water scarcity are prevalent. Increasing the salt tolerance of crops with high commercial and nutritional value, such as tomato (Solanum lycopersicum), will provide particularly significant economic and health benefits. However, salt tolerance is a complex trait with a limited genetic repertoire in domesticated crop varieties, including tomato, frustrating attempts to breed and engineer tolerant crop varieties. Here, a genome-wide association study (GWAS) was undertaken, using the rich genetic resources of the wild, salt tolerant tomato Solanum pimpinellifolium and the latest phenotyping technologies to identify traits that contribute to salt tolerance and the genetic basis for variation in those traits. A panel of 220 S. pimpinellifolium accessions was phenotyped, focusing on image-based high-throughput phenotyping over time in controlled and field conditions in young and mature plants. Results reveal substantial natural variation in salt tolerance over time across many traits. In particular, the use of unmanned aerial vehicle (UAV)-based remote sensing in the field allowed high-resolution RGB, thermal and hyperspectral mapping that offers new insights into plant performance in the field, over time. To empower our GWAS and facilitate the identification of candidate genes, a new S. pimpinellifolium reference genome was generated, 811Mb in size, N50 of ~76kb, containing 25,970 annotated genes. Analysis of this reference genome highlighted potential contributors to salt tolerance, including enrichments in genes with stress response functions and a high copy number of the salt tolerance-associated gene inositol-3-phosphate synthase (I3PS). Initial genotyping-by-sequencing results for the S. pimpinellifolium panel identified 1054 SNPs. GWAS identified several loci associated with salt tolerance traits, e.g. a locus on chromosome 6 for salt tolerance index (S/C) for yield in the field, but the limited number of SNPs restricted our ability to generate a tractable list of candidate genes. A recently completed full genome re-sequencing of the panel, along with a newly available S. pimpinellifolium reference genome with N50 of ~11Mb, will serve to identify a significantly larger number of SNPs and enable a more insightful GWAS. The increased genetic resolution will facilitate the identification of candidate salt tolerance genes. Further research including gene validation, breeding, genetic modification and gene editing experiments will drive the development of new salt tolerant tomato cultivars.
TIME: 11:00 AM - 12:00 PM
LOCATION:Auditorium between Bldg 4&5 - Level 0 - Room 0215
PhD Advisor: Professor Carlos M. DuarteAbstract: Marine macrophytes offer a promising nature-based solution to climate change mitigation, as they sequester carbon in their living biomass and in their coastal sediments. Estimation of the macrophyte organic carbon contribution to coastal sediments is key for understanding the sources of blue carbon sequestration, and for establishing adequate conservation strategies. Nevertheless, identification of marine macrophytes has been challenging and current estimations are uncertain. In this dissertation, eDNA-based methods were used to fingerprint marine macrophytes and estimate their contribution to the organic pool accumulated in blue carbon habitats; these estimations were similar to traditional estimations of organic carbon based on stable isotopes. Thus, eDNA offers an unprecedent taxonomic discrimination, and resolve the contribution of marine macrophytes to the organic pools in blue carbon sediments.
TIME: 03:00 PM - 05:00 PM
LOCATION:Auditorium between Bldg 2&3 - Level 0 - Room 0215
PhDAdvisor: Professor Mark TesterAbstract:Increasing salinity is a worldwide problem, but the knowledge on how salt enters the roots of plants remains largely unknown. Non-selective cation channels (NSCCs) have been suggested to be the major pathway for the entry of sodium ions (Na+) in several species. The hypothesis tested in this research is that PQ loop (PQL) proteins could form NSCCs in the plasma membrane, mediate some of the Na+ influx into the root and thus contribute to toxic ion accumulation and the inhibition of growth in saline conditions. This is based on previous preliminary evidence indicating similarities in the properties of NSCC currents and currents mediated by PQL proteins, such as the inhibition of an inward cation current mediated by PQL proteins by high external calcium and pH acidification. PQL family members belonging to clade one in Arabidopsis and barley were characterized using a reverse genetics approach, electrophysiology and high-throughput phenotyping. Expression of AtPQL1a and HvPQL1 in HEK293 cells increased Na+ and K+ inward currents in whole cell membranes. However, when GFP-tagged PQL proteins were transiently overexpressed in tobacco leaf cells, the proteins appeared to localize to intracellular membrane structures. Based on q-RT-PCR, the levels of mRNA of AtPQL1a, AtPQL1b and AtPQL1c is higher in salt stressed plants compared to control plants in the shoot tissue, while the mRNA levels in the root tissue did not change in response to stress. Salt stress responses of lines with altered expression of AtPQL1a, AtPQL1b and AtPQL1c were examined using RGB and chlorophyll fluorescence imaging of plants growing in soil in a controlled environment chamber. Decreases in the levels of expression of AtPQL1a, AtPQL1b and AtPQL1c resulted in larger rosettes, when measured seven days after salt stress imposition. Interestingly, overexpression of AtPQL1a also resulted in plants having larger rosettes in salt stress conditions. Differences between the mutants and the wild-type plants were not observed at earlier stages, suggesting that PQLs might be involved in long-term responses to salt stress. These results contribute towards a better understanding of the role of PQLs in salinity tolerance and provide new targets for crop improvement.
TIME: 03:00 PM - 04:00 PM
Bio:Hugo de Boer is a professor in biosystematics at the University of Oslo in Norway. In Oslo he leads a research group that uses molecular techniques to identify plants as well as other organisms. In research they use anything from soil eDNA, aquatic eDNA, gut and faecal DNA for diet analysis, ancient and sedimentary ancient DNA to elucidate what species occur in forests, effectiveness of biodiversity restoration, illegal wildlife trade, reconstruct past vegetations, trophic interactions and food webs, allergic pollen and invasive species.”https://www.plantid.uio.no/https://www.nhm.uio.no/english/about/organization/research-collections/people/hugode/Abstract:In eastern Mediterranean countries and the Middle East, orchids are collected from the wild for the production of salep, a beverage made of dried orchid tubers. This traditional use is widespread and increasing in popularity, and terrestrial orchids are wild harvested from Albania to Iran. Understanding what species are affected by this trade and where they are sourced from is a difficult challenge as traded tubers lack characteristics for morphology-based identification. In a series of ethnobotanical studies using high-throughput sequencing based molecular identification we shed light on this trade in CITES-listed species and its implications for conservation. Investigations focused on collectors, cross-border traders, market vendors, and salep drink and ice-cream retailers in Greece, Turkey, Iraq and Iran. Understanding the species diversity and provenance of salep orchid tubers enables elucidation of the chain of commercialization of endangered species back to the harvesters and their natural habitats, and allow for targeted efforts to protect or sustainably use wild populations of these orchids. Join me for an investigate venture into orchids local food in the Eastern Mediterranean and the Middle East.
DATE: Monday, October 28, 2019
TIME: 12:00 PM - 01:00 PM
LOCATION:Building 3 - Level 5 - Room 5209
Abstract:Proteins are one of the most important biomolecules, which perform various functions within organisms. Understanding protein functions is an indispensable part of biological researches. In this talk, I will focus on studying the functions of two important kinds of proteins: enzymes, which catalyze chemical functions within organisms, and RNA binding proteins (RBP), which regulate transcription and translation. As for enzymes, I will introduce our work in developing novel methods, based on deep learning, to predict enzyme functions by annotating EC numbers utilizing only sequence information. In terms of RBP, I will discuss our recent work of developing a deep learning framework to predict binding preference of RNA constituents on protein surface, whose predictions have been verified by both in vitro and in vivo experiments, including RNAcompete, Immunoprecipitation, and siRNA Knockdown. Bio:Yu Li is a PhD student of KAUST, majoring in Computer Science (CS), under the supervision of Prof. Xin Gao. He is a member of Computational Bioscience Research Center (CBRC). His main research interest is developing novel computational methods and algorithms, mainly deep learning methods, for solving biological problems and understanding the principles behind the bio-world. He obtained MS degree in CS from KAUST at 2016. Before that, he got the Bachelor degree in Bioscience from University of Science and Technology of China (USTC).
DATE: Thursday, October 31, 2019
TIME: 01:30 PM - 02:30 PM
PhD Advisor: Professor Stefan AroldAbstract:The focal adhesion kinase (FAK) and the protein tyrosine kinase 2-beta (PYK2) are two closely related non-receptor tyrosine kinases that link cell adhesion, migration and proliferation, and thus also promote cancer cell invasiveness. FAK and PYK2 have the same domain structure (comprising the FERM, kinase and FAT domains) and possess several overlapping functions, however their cellular roles can be different or even opposing. In particular, PYK2 can be activated by calcium, and has important functions in the brain and neurodegenerative disease. The molecular basis for calcium-based activation of PYK2 is unclear and controversial. In this work we combined biophysical and structural methods to determine the molecular basis for calcium-sensing in PYK2. For this, we investigated the least-studied region of these kinases, namely the long linker (KFL) region between the kinase and FAT domains. This linker is only ~20% conserved between FAK and PYK2, and, therefore, is a prime candidate for causing their differential properties. We find that the linker harbors a helical segment, which is conserved in both FAK and PYK2, and contributes to their dimerization (an important step in their activation). Helix-flanking regions differ between both proteins, and we show that these of PYK2 create a non-canonical dimeric binding site for calcium-bound calmodulin. Calmodulin-binding is synergistic with linker dimerization in PYK2, explaining how calcium influx can be translated into activation of PYK2. Collectively, our work clarifies the capacities for FAK and PYK2 to receive, process and transduce cellular signals, and may provide new opportunities for targeted therapeutic intervention. Bio:Afaque is a
PhD candidate in the research group of Prof. Stefan Arold investigating
the structural and functional basis of focal adhesion proteins to
understand their role in promoting cancer cell invasiveness. His
research combines experimental methods (biophysics and structural
biology) with computational methods (molecular dynamics and
bioinformatics). He received his Master of Science (Bioinformatics) and
Bachelor of Science (Biotechnology) from the University of Mumbai,
DATE: Tuesday, November 05, 2019
LOCATION:Building 2 - Level 5 - Room 5220
Abstract:Synthetic biologists try to refacture biological complexity into exchangeable parts and plug-and-play devices for reliable and predictive engineering. Proteins are the most versatile among the various biological building blocks. Yet, proteins have, traditionally, been considered too complex for the “let’s pull this apart and put it somehow back together” approach of synthetic biologists. This is now changing. I will review the most important methods for protein engineering and how these fit into (and benefit from) modern synthetic biology design-build-test workflows. Key technologies discussed will be gene synthesis, molecular modelling and protein design, laboratory automation as well as cell-free expression systems. Bio:Raik studied Biochemistry in Leipzig, performed his PhD research in computational biology at the Pasteur Institute in Paris and then returned to the wet lab bench for postdoctoral studies in protein bioengineering at the CRG in Barcelona and the IRIC in Montreal. He is now a research scientist at BESE and CBRC. His main research interests deal with protein-protein interactions, molecular modelling and how we can use proteins and protein domains as building blocks in the engineering of more complex and useful systems.