Day 1 :
Keynote Forum
Emmanuel Mic. Drakakis
Imperial College London, UK
Keynote: Ultra low power cytomimetic VLSI circuits: Synthesis method & proof-of-concept results
Time : 09:30-09:55
Biography:
Emmanuel Mic. Drakakis received the B.Sc. degree (1st Class Honours) in Physics and the M.Phil. degree (1st Class Honours) in Electronic Physics and Radioelectrology from Aristotle University of Thessaloniki, Macedonia, Greece, and the Ph.D. degree in analogue IC design from the Department of Electrical and Electronic Engineering at Imperial College London, U.K. under the supervision of Dr. Alison Payne. During his PhD he was sponsored by the Micro-Electronics Research Center of LM Ericsson-Stockholm (one of eight in the world at the time). Currently he is Reader in Bio-Circuits and Systems in the Department of Bioengineering at Imperial College London. In the Department of Bioengineering he has founded the Bioinspired VLSI Circuits and Systems Group whose research focuses on “Circuits for and from Biology”. He has authored or co-authored a large number (>120) of peer-reviewed journal and conference papers and several book chapters. Dr. Drakakis has received many prizes for research excellence and is involved in several cross-disciplinary research projects. In the past he has served as Guest Ass.Editor for IET El.Letters and as Subject Editor for the International Journal of Electronics – Taylor & Francis. He has also served as an Associate Editor in IEEE publications, including TCAS1 and TCAS2. He is currently an Associate Editor for IEEE Transactions on Biomedical Circuits and Systems and an Associate Editor for Frontiers in Neuromorphic Engineering.
Abstract:
The physics-dictated sub-threshold operation of MOS transistors can lead to ultra-low-power designs but is also governed by a challenging exponential characteristic. This talk will elucidate how to view such a non-linearity as an asset and how to exploit it by treating it as a powerful computational primitive which can lead to the systematic realisation of non-linear dynamics dictated by biology. We will present a method for the systematic implementation of ultra low power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. Several examples of systematic computation of non-linear cellular and molecular dynamics by means of ultra-low-power microelectronic cytomimetic circuits will be elaborated: glycolytic oscillations, nonlinear intracellular calcium oscillations and a gene-protein regulatory system model. Proof-of-concept results from a 1 microwatt cytomimetic prototype chip emulating the complex non-linear mammalian cell cycle dynamics will be reported.
Keynote Forum
Peter L. Nagy
Columbia University, USA
Keynote: Integration of next-generation sequencing data with analytical chemistry, structural biology and cell biology
Time : 09:55-10:20
Biography:
Peter L. Nagy received his MD degree from the University of Pecs, Hungary in 1989. His interest to pursue a career as a physician scientist led him to Purdue University where he earned his Ph.D. in Biochemistry.He worked under the mentorship of Dr. Howard Zalkin and made important discoveries relating to C1-metabilism in bacteria. Subsequently he completed Anatomic and Molecular Genetic Pathology training and Stanford University as well as postdoctoral training in Michael Cleary’s laboratory. He was the first to purify and functionally characterize the Set1 histone methyltransferase complex from S. cerevisiae in collaboration with Dr. Roger Kornberg. He co-developed the FAIRE method with Jason Lieb allowing physical fractionation of chromatin based on formaldehyde crosslinkability. Currently he leads a research laboratory investigating the role of transcriptional defects in neurodegenerative diseases, such as AOA2 and ALS4, and is director of the clinical next-generation sequencing facility in the Laboratory of Personalized Genomic Medicine at Columbia University Medical Center in the Department of Pathology and Cell Biology.
Abstract:
Next-generation sequencing in the clinical practice allows for a critical review of the literature describing the pathogenicity of specific mutations or the disease relatedness of specific genes and also provides an important discovery tool for new disease genes and disease causing mutations. Because of the large volume and complex nature of the data obtained from large panels and whole exome sequencing testing, the management of the data in a transparent, yet powerful analytical framework is key to a successful clinical operation. Population allele frequency, data from parents and precise, yet concise phenotypic description are the cornerstone for successful clinical evaluation of the pathogenicity of variants identified. The full potential for discovery of new disease associated genes and disease causing mutations can only be realized if there is a tight collaborative effort between the clinicians performing the interpretation and structural biologists and analytical chemists and cell biologists who can help predict and verify the effects of variants identified. My presentation will focus on the need to foster and strengthen this multidirectional information flow. I will review the resources that are already available and propose ways to improve them through integrating new data types or design of more user-friendly interfaces.
- Track 1: Genomics and Bioinformatics, Track 2: Integrative Computational Biology, Track 3: Drug Discovery and Integrative Biology
Location: Valencia B, Melia Valencia
Chair
Jeffrey Zheng
Yunnan University, China
Co-Chair
Dang Duong Bang
Technical University of Denmark, Denmark
Session Introduction
Jeffrey Zheng
Yunnan University, China
Title: Variant maps to identify coding and non-coding DNA sequences of genomes selected from multiple species
Time : 10:25-10:45
Biography:
Jeffrey Zheng has completed his PhD in 1994 from Monash University. He is the Professor and Head at the Department of Information Security, School of Software, Yunnan University from 2004. He has published more than 200 papers in national and international conferences, reputed journals and serving as an Editorial Board Member of Information Acquisition. He is active working on exploring mysteries of coding and non-coding DNA/RNA mechanism to use variant logic construction.
Abstract:
In recent years, many DNA sequencing projects are developed on cells, plants and animals over the world into huge DNA databases. Researchers notice that mammalian genomes encode thousands of large non-coding RNAs (lncRNAs), interact with chromatin regulatory complexes, and are thought to play a role in localizing these complexes to target loci across the genome. It is a challenge target using higher dimensional tools to organize various complex interactive properties as visual maps. In this talk, Variant maps are uesd to provide models and experiment results using visual representation techniques to distinguish multiple species – Salmonella, Caenorhabditis elegans, Arabidopsis, Pan troglodytes and human genomes between coding and non-coding sequences selected. Our model uses probability measurements on the DNA sequences to separate coding and non-coding regions respectively to generate visual patterns to identify different sequences. Sample 2D maps are listed and their characteristics are illustrated under controllable environment. Visual results are analyzed to explore their intrinsic properties on selected multiple species of genome sequences.
Lidia Gardner
The University of Tennessee Health Science Center, USA
Title: Importance of Apolipoproteins in MS
Time : 10:45-11:05
Biography:
Lidia Gardner is an Associate Professor in the Department of Neurology at the University of Tennessee Health Science Center. She leads a research program in Multiple Sclerosis at Memphis Veterans Administration Medical Center. Dr. Gardner has extensive experience in biochemistry and molecular biology, basic and clinical research. She is published in leading biomedical journals. She is currently serving on the Institutional Animal Care and Use Committee. Dr. Gardner received an MBA from the University of Memphis and a Ph.D. from the Russian Academy of Sciences in Cell Biology and completed her postdoctoral studies at the University of Tennessee Health Science Center.
Abstract:
Multiple sclerosis (MS) is a multifaceted disease of the central nervous system. We discovered that progressive MS patients have lower levels of apolipoprotein A-I (ApoA-I) in serum and plasma compared to healthy age-matched controls or relapsing remitting patients. Apolipoproteins play important roles in cholesterol transfer and lipid metabolism in the central nervous system. Our data indicate that ApoA-I levels decline with disease progression. Therefore increasing ApoA-I levels might be beneficial for MS patients. We examined the role of ApoA-I in a mouse model of MS - Experimental Autoimmune Encephalomyelitis (EAE). ApoA-I deficient female mice (C57Bl/6-Tg(ApoA1)1Rub/J) demonstrated a higher incidence and severity of the EAE in comparison to the wild type control mice (C57Bl/6J). EAE was accompanied by an increase in cytokines (INF-gamma, TNF-alpha, TGF-ß, IL-2, IL-23) and T cell differentiation into CD25+/Foxp3+ T cells in these animals. To further investigate the role of ApoA-I in MS, we have treated mice with GW3965, an orally active liver X receptor (LXR) agonist. The LXR form heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism. We found that mice treated with GW3965 had a lower disease incidence, EAE scores and cytokine expression compared to mice with regular EAE. Variation of ApoA-I levels correlated with disease incidence and severity. Our studies indicate that LXR activation resulted in increased ApoA-I production in the liver and in the spinal cord of experimental animals. Further investigation into the mechanisms of ApoA-I formation and disease-associated loss might lead to novel therapies in MS.
Cuong Cao
Queen’s University Belfast, United Kingdom
Title: Metamaterials-based label-free nanosensor for conformation and bioaffinity sensing
Time : 11:20-11:40
Biography:
Cuong Cao is currently a Lecturer in Advanced Micro- and Nanodiagnostics within Institute for Global Food Security, Queen’s University Belfast, UK. His research interest includes exploration and exploitation of multifunctional micro- and nanostructures, plasmonics-based biosensing platforms (SPR, LSPR, SERS), and integrated point-of-care analyses with a particular emphasis on detecting and identifying pathogens, biomarkers, food and environment toxins.
Abstract:
Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding of their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance (LSPR) have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. In this presentation, we demonstrate that plasmonic metamaterials consisting of periodic arrays of artificial split-ring resonators (SRRs) can enable capabilities of both sensing and fingerprinting of biomolecules. By engineering geometry of individual SRRs, LSPR frequency of the metamaterials could be tuned to visible-near infrared regimes such that it allows parallel acquisition of optical transmission and highly SERS spectra from large functionalized SRR arrays. This will provide the basis for the development of a dual detection platformthat can simultaneously probe conformational states and binding affinity of biomolecules, e.g. G-quadruplexes, in different environments. We further present the use of the metamaterials for fingerprinting and detection of arginine-glycine-glycine domain of nucleolin, a cancer biomarker which specifically binds to a G-quadruplex, with the picomolar sensitivity. The dual-mode nanosensor will significantly contribute to unraveling the complexes of the conformational dynamics of biomolecules as well as to improving specificity of biodetection assays.
Bakovic Marica
University of Guelph, Canada
Title: The phospholipid enzyme CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) is a new target for oxidative stress therapy and ischemia
Time : 11:40-12:00
Biography:
Marica Bakovic completed BSc in Chemistry and PhD in Biological Chemistry at the University of Alberta. She received post-doctoral awards from Medical Research Council and Alberta Heritage Foundation. Before coming to the University of Guelph, she worked in the area of molecular and cell biology of lipid metabolism at the Faculty of Medicine, University of Alberta. Currently, she is Professor in the Department of Human Health and Nutritional Sciences at the University of Guelph. Dr. Bakovic has a long-lasting interest in nutrition and metabolism, especially in the area of regulation of membrane phospholipids, fatty acids, and methyl-group donors.
Abstract:
It is well-known that is beneficial to transiently block respiration during ischemia/reperfusion; however there is an unmet clinical need for discovering new compounds and targets that can inhibit the respiration. We established that the ‘over-the-counter’ anti-histaminergic drug Meclizine could inhibit mitochondrial respiration (uncoupling the OXPHOS) by elevating the levels of phosphoethanolamine, an intracellular metabolite in phospholipid biosynthesis and the exclusive substrate of Pcyt2. That phosphoethanolamine was the only elevated intermediate (35-fold) during the inhibition of respiration with Meclizine strongly directed towards Pcyt2 as the drug target. The extensive metabolic studies as well as studies on recombinant Pcyt2 protein provided strong evidence for direct inhibition of Pcyt2 with Meclizine. The impact of our discovery is not only how to expand the future use of Meclizine but also to offer the first inhibitor for the CDP-ethanolamine Kennedy pathway, to continue to investigate the regulation of the membrane phospholipid synthesis and the basic function of Pcyt2. This is the first time to be demonstrated that the membrane biogenesis impacts mitochondrial OXPHOS and that the inhibition of the CDP ethanolamine pathway at the level of Pcyt2 is protective under pathological conditions of oxidative stress and ischemia.
Dang Duong Bang
Technical University of Denmark, Denmark
Title: Towards a total integrated Lab-on-a-chip system for food safety
Time : 12:00-12:20
Biography:
Dang Duong Bang received his MSc (1990) and PhD (1995) in Molecular Biology from Leiden University, Leiden, The Netherlands. Since 1998 he worked as aresearch scientist at National Veterinary Institute and was promoted as senior scientist and leader of Laboratory of Applied Micro and Nanotechnology (LAMINATE) at National Food Institute Technical University of Denmark (2002). He was promoted as professor at National Food Institute, Technical University of Denmark in 2014. His research focuses on host-bacterial pathogens interaction and applied micro-nanotechnology for rapid detection and identification of pathogens (virus and bacteria). He has worked on several EU and national projects on development of Lab-on-a-chip systems for DNA analysis. These include: DNA array for detection of pathogens (Campylobacterspp, Salmonellaspp, Avian Influenza etc…),solid phase PCR array for early detection of Colon cancer, magnetic, nano and biosensor for sample preparation and nucleic acid isolations and development of total integrated Lab-on-a-chip PCR based systems for on line, at site rapid detection and identification of pathogens (virus and bacteria) in food and animal productions chains as well as in clinical diagnostics.
Abstract:
More than 200 known diseases transmitted through food and food products. In 2011, USA Center Diseases Control and Prevention (CDC) estimated that 1 in 6 Americans (48 million people) get sick with food borne diseases, resulting in 128,00 hospitalization and 300 deaths. The the globalization of agro-food trade is becoming more and more elongated. Foods move across borders and continents in shorter time frames. Consequently, contaminated foods have often been consumed before authorities. Conventional culture methods have been the main workhorses for food safety control, they are expensive, time consuming require sample treatment and inability for onsite testing therefore establishing traceability via cost-efficient rapid and accurate methods for detecting of foodborne pathogens in the entire food chain are urgent need. Micro-fabrication and miniaturisation of biological assays in a so call Lab-on-a-Chips (LOCs) have well known advantages such as greatly reduced reagents consumption, shorter times, faster mixing, high automation, high-throughputs, all leading to reduction of costs .LOCs have been applied in many different contexts (genomics, proteomics, cellomics, immunology etc). However, the fully integrated Lab-Chip remains the main challenge. Recently, via number of national and EU funded projects different total integrated LOC systems for at site rapid detection and identification of food-borne pathogens were developed at DTU. By integrating all the steps from on chip PCR reagents storage, sample preparation to PCR detection in the LOC systems, the pathogens can be on-line or at site rapid detection and identification at sub-species.
Normi Mohd Yahaya
Universiti Putra Malaysia, Malaysia
Title: Hypothetical proteins: Can they be the next drug targets?
Time : 12:20-12:40
Biography:
Normi M. Yahaya has completed herPhD at the age of 25 years from RIKEN Institute and Universiti Sains Malaysia in Molecular Genetics specializing on protein engineering under the RIKEN-Asia Joint Graduate School Program.She later pursued her postdoctoral training in the area of structural biology, specifically in protein nuclear magnetic resonance (NMR) in Institut National Polytechnique de Lorraine, Nancy, France under Center National de la Recherche Scientifique (CNRS). She has won several awards of merit including PACIFICHEM 2010, Young Scholar Award and being one of the Selected Young Scientists for the 60th Meeting of Nobel Prize Winners with Young Scientists in Lindau, Germany.
Abstract:
Hypothetical proteins, also known as orphan proteins, can be found across all genomes of all taxa of life. Despite their considerable number in any given genome, their functional presence and significance is rarely investigated due to their sequence and structural dissimilarity to well-characterized proteins. This further poses challenges on the right approach to be adopted and streamlined when studying these proteins. Using a combination of both genomics and bioinformatics approaches, we streamlined our efforts in mining for hypothetical proteins which are deemed functionally significant, specifically of medical relevance, to be used as potential drug targets in the future. Using the locally isolated Bacillus lehensis G1 alkaliphile as a model, 1,202 hypothetical proteins encoded by its genome were thoroughly analysed using several bioinformatics tools to determine their sequence identity, the presence of functional domains, cellular localization, metal-binding properties, among many others. A hypothetical proteins cluster was accordingly developed based on these data and several hypothetical proteins deemed to be involved in significant processes such as metal-trafficking and antibiotics-degradation/resistance were identified from the cluster. Prediction on their structures, functions and mechanisms were subsequently achieved via in silico protein modelling and docking approaches. Results obtained from this integrated study do reveal that the selected hypothetical proteins have high possibility in carrying our metal-to-protein trafficking and conferring antibiotics-resistance. Such case studies on these orphan proteins highlighted in this present work point to the interesting and very promising notion of using them as the next potential drug targets.
Anders Wolff
Technical University of Denmark, Denmark
Title: Lab-on-a-chip system with integrated sensors for 3D tissue engineering applications
Time : 12:40-13:00
Biography:
Anders Wolff is head of the BioLabChip group at the Department of Micro and Nanotechnology at the Technical University of Denmark: His received his MSc in Chemical Engineering from DTU in 1993 and his PhD in Biochemical Engineering from Delft University of Technology (Delft, The Netherlands) in 1997. He joined the Department for Micro and Nanotechnology (now DTU Nanotech) in 1998. In 2000 he was promote to associated professor and leader of the Cell Handling Group (now BioLabChip group) at DTU Nanotech. Hisresearch focus on various microsystems for cell analysis that included chip flow cytometers with integrated optics, dielectrophoresis for cell handling, sorting and sample preparation, PCR chip, and integrated microsystem for sample preparation and DNA amplification. In recent years his group has also worked on scaffolds for tissue engineering and bioartificial organs.
Abstract:
Organ transplantation is often the primary life-saving medical approach for treatment of several diseases. However, limitations in this procedure such as shortage of donor organs and tissue rejection have motivated research into the development of bio-artificial organs as an alternative approach. Development of a novel, modular, microfluidic lab-on-a-chip system is presented, which is designed to engineer liver tissue in an in vivo mimicking environment. The system incorporates smart bioreactors, designed to support a 3D porous scaffold with embedded cells and integrated sensors for monitoring the development of the tissue. Each bioreactor is designed to accommodate a microporous scaffold having dimensions of 5 x 5 x 5 mm3 and includes spatially distributed bio-impedance based sensors which penetrate the scaffold for real time monitoring of the distribution, proliferation and viability of cells under continuous perfusion conditions. To enable delivery of nutrients and removal of tissue culture waste products, the system also incorporates peristaltic pumps, motors and reservoirs. An array of eight bioreactors are included, to enable parallel tissue culture experiments for optimization of parameters such as flow rate, and to allow screening of various stem cell differentiation factors. The system components are fabricated using a combination of 3D rapid prototyping and microfabrication techniques. Proof of principle is demonstrated by culturing liver cancer cell line (HepG2 cells) in porous scaffolds based on polymers such as PDMS, gelatin, and polylactic acid.
The robust and versatile microfluidic platform presented in this work has a huge potential for 3D tissue engineering applications. The novelty of the device is in the employment of combined micro sensing and polymer scaffold engineering approaches for 3D organ engineering. The use of integrated non-invasive sensing strategies, overcome limitations in traditionally adopted optical techniques, and enable monitoring of tissue development within otherwise inaccessible areas of a 3D tissue construct.
Ryszard Maleszka
The Australian National University, Canberra
Title: Deciphering the epigenetic code with innovative insect models
Time : 13:00-13:20
Biography:
Ryszard Maleszka received his MSc and a PhD in Genetics from the University of Warsaw and has done postdoctoral work at the National Research Council of Canada before moving to Australia in 1987. He is spearheading a research theme called ‘From Molecules to Behaviour’ that uses invertebrate model systems to study the genotype to phenotype link, and to understand how epigenetic networks contribute to environmentally-driven phenotypic plasticity. He is a member of several genomic consortia and advisor to genomic databases. He authored over 135 articles and book chapters including a number of landmark papers in Science and Nature.
Abstract:
The modern field of epigenetics is driven by a deluge of raw sequencing data that reveal a very complex portrait of epigenomic dynamics operating at multiple levels, interacting with each other and remaining in a constant flux. We and others have recently discussed this multifaceted and versatile regulatory network in the context of an epigenetic code as a prime driver of organismal complexity, robustness, plasticity and disease development. We proposed that by providing organisms with a large repertoire of alternative functional interactions, the epigenetic code increases their adaptability to unforeseen environments.But how do we evaluate what these chemical modifications mean in a functional context?How environment is linked to the genome and how external cues are translated into cellular responses via epigenomic changes? When do these changes go above threshold and guide organisms into another direction, such as an alternate developmental trajectory? How does malfunctioning of epigenetic mechanisms result in diseases? To what extent sequence variants such as single nucleotide polymorphism (SNPs) affect epigenomic marks? We are using the social honey bee to develop a framework for explaining the functional significance of environmentally-driven epigenetic modifications in genomic DNA. Specifically, we aim to obtain empirical evidence supporting the idea that epigenomic dynamics is not only influenced by polymorphic changes in DNA, but sequence variants may be necessary to ensure the high level of flexibility of the epigenetic code. We also aspire to shed light on the effects of nutrition on methylation and gene splicing and to determine if the enzymatic machinery implicated in adding/removing epiegenetic marks has sequence specificity.
Maria-João R. P. Queiroz
University of Minho, Portugal
Title: Synthesis and evaluation of new thienopyrimidine/pyridine derivatives as antitumoral and/or antiangiogenics
Time : 14:00-14:20
Biography:
Maria-João Queiroz has completed her first degree in Pharmaceutical Sciences in the University of Porto-Portugal (1986), PhD in Organic Chemistry (1993) in the University of Minho- Portugal and carried out postdoctoral studies in the University of Metz-France (1994). She is Coordinator Researcher since June 2009 and she was the director of the Chemistry Research Centre of the University of Minho from January 2010 to March 2015. She has published more than 110 papers in reputed journals of Organic Chemistry and Medicinal Chemistry and attended to more than 150 conferences around the world. She was also the responsible of several financed projects in Medicinal Chemistry, coordinating different teams.
Abstract:
New thieno[3,4-d]pyrimidines and thieno[3,2-b]pyridines were prepared, fully characterized, and evaluated as antitumor compounds against various human tumor cell lines and/or as antiangiogenics using HUVECs (Human Endothelial Vein Umbilical Cells) that express the VEGFR2 (Vascular Endothelium Growth Factor Receptor-2) which is a trans-membrane tyrosine kinase receptor involved in angiogenesis. Some of our compounds were shown to be active against several human tumor cell lines with low to moderate IC50 values and for the most promising compounds the effects on the cell cycle profile and the induction of apoptosis were studied. The toxicity of these compounds was also studied using a primary porcine liver cell culture established by our group. Some of the compounds prepared, suggested by rational design, were shown to be inhibitors of the phosphorylation of the intracellular domain of tyrosine kinase of the VEGFR2. This mechanism of action of the evaluated anti-proliferation of HUVECs by the BrdU assay in the presence of the compounds was confirmed using western Blott.
Hector Ricardo Galvan Garcia
Dermatology Hospital, Mexico
Title: Onychomycosis: 1064-nm Nd: YAG q-switch laser treatment
Time : 14:20-14:40
Biography:
Hector Ricardo Galvan Garcia has completed his MD at the age 25 years from Guadalajara University and Postdoctoral studies from Institute of Dermatology of Jalisco. He is Director of Hospital Dermatology Dermoquirurgica in Jalisco, Mexico and has published more than 20 papers in reputed journals and serving as an Editorial Board Member of repute.
Abstract:
Laser treatment of onychomycosis is a quick and easy method without complications. Two hundred patients with a KOH (25%) and glycerol (5%) (1 hour at 51-54 °C) for lipid emulsification, and mycological structures were identified under 3400x magnification(+) , onychoscopy (jagged edge and longitudinal striae, positive), confirmed clinical diagnosis of onychomycosis were included in the present study( patients of all ages who had not previously received any type of treatment were included). All of the patients were treated in a single session (with a 1064-nm neodymium-doped yttrium-aluminum garnet (Nd:YAG)q-switch laser (600 mJ 3Hz. Spot 3 mm). There was a 100% clinical response rate within the 18-month follow-up period with no side effects. Thus, this method is proposed as a novel and safe method for the treatment of this ungual pathology, in all of its clinical manifestations, including in the hands and feet and all age groups, without side effects.
Gulacti Topcu
Bezmialem Vakif University, Turkey
Title: Natural cholinesterase inhibitors isolated from anatolian plants
Time : 14:40-15:00
Biography:
Gulacti Topcu obtained her PhD in 1985fromFaculty of Pharmacy at Istanbul University on natural product chemistry, and workedat the University of Illinois at Chicago, College of Pharmacy in the Department of Medicinal Chemistry and Pharmacognosyas a post-doc between 1986-88. She became a full Professor in Organic Chemistry, specifically in Phytochemistry in 1999. Since 2011, she is the Dean of Faculty of Pharmacy, Bezmialem Vakif University at Istanbul. She has published more than 165 papers in reputed journals with more than 2400 citations (h-index:27). She has been serving as the Editor-in Chief of the “Records of Natural Products” which is a SCI journal.
Abstract:
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, accompanied by dementia, which affects about 38million people worldwide by 2014. The pathogenesis of AD is fairly complex, and besides genetic factors, environmental factors may play important role. Since the cholinergic system plays an important role in the regulation of learning and memory processes, it has been targeted for the design of anti-Alzheimer's drugs. Cholinesterase inhibitors enhance cholinergic transmission directly by inhibiting cholinesterase enzymes, particularly acetylcholinesterase. However, both AChEBuChEenzymes may play an important role in amyloid β aggregation during the early stages of senile plaque formation. The major AD therapeutics available on the market are acetylcholinesterase inhibitors; tacrin, donepezil, rivastigmin and galanthamine besides an NMDA receptor antagonist memantine. But, none of them can provide a satisfactory cure for Alzheimer's disease. Therefore, there is an immediate requirement more efficient drugs than ones prescribed by the physcians at the moment. In our ongoing studies on natural products in drug discovery, we have investigated potential anti-cholinesterase compounds isolated from several plant families. Among them, terpenoids, particularly abietanediterpenoids take an important place in both prevention and treatment of AD, as well as some flavonoids and other phenolics. In this study, a number of compounds including a series terpenoids, flavonoids and a few phenolics isolated from namely Anatolian Lamiaceae family plants have been assayed for anticholinesterase activity tests besides antioxidant and antiradical properties in vitro. The compounds which showed at least 50% inhibition against one of the cholinesterase enzymes at 200 microM were tested in five concentrations to determine their IC50 values.
Xiangqun Xu
Zhejiang Sci-Tech University, China
Title: Approaches for stimulating white rot fungi to accumulate bioactive polyphenols and flavonoids
Time : 15:00-15:20
Biography:
Xiangqun Xu received the BSc degree in Biochemistry from Xiamen University, Xiamen, China, MSc degree in Biochemistry from Zhejiang Medical University, Hangzhou, China, and PhD degree in Biomedical Engineering from Keele University, Keele, UK. She was engaged in Postdoctoral training in Biomedicine in Institute of Biotechnology, Cranfield University, UK. She is currently a Professor in Biotechnology and Biochemical Engineering at Zhejiang Sci-Tech University, Hangzhou. Her current research interests include secondary metabolism of microorganisms and plants, natural products, medicinal mushroom polysaccharides and polyphenols/flavonoids, and medical imaging. She has published more than 50 reputed papers.
Abstract:
Polyphenols particularly flavonoids are important secondary metabolites from the medicinal mushroom Inonotus obliquus. Both the rarity of I. obliquus (white-rot fungus) fruit body and the low efficiency of current method of submerged fermentation lead to a low yield of polyphenols. I. obliquus grown in submerged culture could produce anti oxidative polyphenols. We developed the lignocellulose degradation and stimulatory agent-based approaches for enhancing the simultaneous accumulation of I. obliquus exo-polyphenols (EPC) and endo-polyphenols (IPC). Lignocellulose degradation increased the production and antioxidant activity of extra- (EPC) and intra-cellular (IPC) phenolic compounds. The production of EPC and IPC was significantly enhanced by wheat straw, rice straw, corn stover, sugarcane bagasse and peanut shells. Both of the EPC and IPC extracts from the lignocelluloses containing media showed a higher DPPH radical-scavenging activity than those from the control. The highly active polyphenols/flavonoids such as epicatechin-3-gallate (ECG) and epigallocatechin-3-gallate (EGCG) and phelligridin G significantly increased. Davallialactone and inoscavin B in the EPC extracts were generated in large amounts in the lignocellulose media but not found in the control medium. Linoleic acid was the most effective out of the 17 tested stimulatory agents, the majority of which increased the EPC and IPC production. The addition of linoleic acid resulted in 7, 14 and 10-fold of increase (p<0.05) in the production of EA-EPC (EPC extracted by ethyl acetate), NB-EPC (EPC extracted by n-butyl alcohol) and IPC and significantly increased the production of ferulic acid, gallic acid, ECG, EGCG, phelligridin G, inoscavin B and davallialactone. The EA-EPC, BA-EPC and IPC from the linoleic acid-containing medium had significantly (p<0.05) stronger scavenging activity against DPPH radicals which was attributed to the higher content of these bioactive polyphenols and flavonoids. The combination effect of lignocellulose degradation and stimulatory agents was evident.
Zhonglin Tang
Chinese Academy of Agricultural Sciences, China
Title: Systematic identification and characteristics of long non-coding RNAs in pigs
Time : 15:20-15:40
Biography:
Zhonglin Tang has completed his PhD from Huazhong Agricultural University and Postdoctoral studies from Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS). He is the PI of Agricultural Genome Institute at Shenzhen, CAAS. His field of interest is functional genomics and expression regulation of skeletal muscle in pig and mouse. He has published more than 44 papers in reputed journals and has been serving as an Editorial Board Member of repute.
Abstract:
The long non-coding RNAs (lncRNAs) are non-protein coding RNAs and involve in a variety of biological processes. Pig (Susscrofa) is an important farm animal and ideal biomedical model. In this study, we performed a genome-wide scan of lncRNAs in pig. Based on strand-specific RNA-Seq data, a computational method was used to identify 96,314 novel lncRNAs candidates in pig genome which included 39,528 large intergenic ncRNAs (lincRNAs), 180 nature antisense transcripts and 56,606 intronic ncRNAs. Novel lncRNAs show fewer exon number, shorter transcripts length, lower GC content, expression and conservation level, higher SNP density than protein-coding transcripts. To validate the result, we perform RT-PCR to detect selected lncRNAs. Expression analysis of 5 abundant lncRNAs was conducted by quantitative PCR (qPCR) in 9 tissues of Landrace pigs in 160 days post-coitus (dpc). We first performed identification and characterization of pig lncRNAs using strand specific RNA sequencing. Our study significantly expanded the number of pig lncRNAs in non-protein coding RNA database and provided important information for functional studies.
- Workshop: Creative Approaches for Computational Genomics
Location: Valencia B, Melia Valencia
Session Introduction
Jeffrey Zheng
Yunnan University, China
Title: Creative approaches for computational genomics
Time : 15:55-16:55
Biography:
Jeffrey Zheng has completed his Ph.D in 1994 from Monash University. He is the Professor and Head at the Department of Information Security, School of Software, Yunnan University from 2004. He has published more than 200 papers in national and international conferences, reputed journals and serving as an editorial board member of Information Acquisition. He is active working on exploring mysteries of coding and non-coding DNA/RNA mechanism to use variant logic construction.
Abstract:
Associated with advanced next generation of sequencing technologies to capture various variations on cancers & diseases, huge amount of genomic sequences are ensembled & collected in worldwide databases. There are urgent requirements for modern genomic analysts to apply advanced tools & technologies to index, retrieve, visualize & search genomic sequential information more conveniently. This workshop organizes a group of creative researchers & students together to discuss the state of the arts technologies in addition to exploring new schemes for computational genomics. All levels of approaches are encouraged on the concepts, ideas, models, tools, packages and practices of computational methods for the identification and characterization of functional elements & components from DNA sequence data. The primary target of this workshop is the theory and practice of algorithms in computational genomics, with the goals of using current methods for biological discovery and developing creative algorithms & approaches. This workshop focuses on approaches for extracting and organizing information from similarity aspects on indexing & clustering of protein and DNA sequences through sequence database searches, feature measurements & visualizations. Additional topics include: *Disease sequences: cancer, infectious diseases, cardiovascular disease and psychiatric dysfunctions *Coding & non-coding RNA/DNA sequencing data *Novel ideas & models to identify functional components of genomic variations *Randomness measurements & visualizations *Generation & simulation mechanism on pseudo RNA/DNA sequences *Geometric & topological invariant measurements *Mathematical modelling on variations *Probability & statistical analysis *Combinatorial & permutation models *Efficient computational schemes on clustering genomic sequences *Content-based genomic sequence indexes & retrievals *Integration of genetic and sequence information in genomic databases *Genome browsers and feature visualizations