Day 2 :
Keynote Forum
Davide De Lucrezia
Explora Biotech Srl, Italy
Keynote: Empowering computer-assisted biological design by using in vivo characterized standard biological parts
Time : 10:00-10:45
Biography:
Davide De Lucrezia is currently the CEO of Explora Biotech Srl, a biotech dynamic company he co-founded in 2006. He graduated in 2004 in Biology at the University of Rome “Roma Tre” and pursued a PhD degree in Biochemistry in 2009. Over the years, he has served as Operative Coordinator of the LivingTech Lab at the European Centre for Living Technology (Venice, Italy), Head of the Pharmacokinetics and Metabolomics Unit at San Raffaele Hospital in Rome, Staff Scientist at Polyphor AG (Switzerland), and Research Technician at the Swiss Federal Institute of Technology of Zurich. He wrote several papers published in international peer-reviewed journals and books for both specialized and general audience and is the inventor of 2 patents.
Abstract:
With synthetic biology, we can now design and construct new biological parts, devices and systems in a rational and systematic way. The application of forward engineering approach to biology necessarily requires the implementation of two fundamental design principles: 1) the use of standardized biological parts; and 2) the development of multi-scale predictive models to aid system engineering design. The author will report the latest results of our ongoing efforts to develop a comprehensive and highly integrated toolkit to exploit the full potential of synthetic biology based on: Comprehensive in vivo characterization of BioBricks and devices within the context of the host organism and under variable experimental settings to achieve a context-related description of part/device dynamics and performance; Development of a computer aided design tools (CAD) for biological engineering capable to support both design and simulation on multiple hierarchical levels. The hallmark is the deployment of a modeling platform that allow the multi-scale description of biological systems combining currently available algorithms and exploiting different modeling paradigms (e.g. continuous-deterministic models, probabilistic graphical models, discrete dynamical networks, P-systems) according to the scale under investigation.
- Systems and Synthetic Biology | Systems Biology| Computational Systems Biology | Industrial Systems and Synthetic Biology| Metabolomics| Bio-Sensors and Bio-Electronics| Biology Engineering
Location: Forum 12
Session Introduction
Ralf Takors
University Stuttgart, Germany
Title: Escherichia coli HGT – A novel high glucose throughput chassis especially designed for typical production conditions in large scale based on comprehensive systems biology studies
Time : 10:45-11:15
Biography:
Ralf Takors completed his PhD in Biochemical Engineering in 1997 and received Habilitation in Metabolic Engineering in 2004, both at Forschungszentrum Jülich GmbH and RWTH Aachen. He has worked at the Evonik Industries till 2009, where he was responsible for bioprocess development, metabolic engineering and systems biology research. In 2009, he became the Head of the Institute of Biochemical Engineering at the University Stuttgart. Research interests are Systems Metabolic Engineering and Synthetic Biology for the development of novel bioprocesses.
Abstract:
Sooner or later novel processes with recombinant producers should find their way from the labs to large-scale fermenters to commercialize the product. However, successful scale-up is often hampered by harsh production conditions which expose the strains to frequently changing substrate supply due to technical limits of mixing. In a series of systems biology experiments, metabolic and transcriptional responses of E. coli to large-scale conditions were studied. Short- and long-term consequences of changing glucose and nitrogen availabilities were investigated. Applying typical mixing times of 110 seconds, more than 600 genes were found to be frequently up- and down regulated. Accordingly, cellular maintenance demands increased by 40 to 50% which was identified by measurements and by systems modeling and which created a list of gene candidates for smart genome reduction. ppGpp, the alarmone of stringent response, turned out to be protagonist of the observed regulation programs. Engineering of key genes of the stringent response together with modulations in central metabolism finally yielded E. coli HGT. The strain shows 10 fold increased glucose uptake rates (compared to the native maintenance demands) under resting or slow growth conditions which are a preferred production scenario. The surplus of glucose uptake is available as pyruvate to enable likewise utilization which is why E. coli HGT represents a novel chassis for the production of pyruvate derived products in large-scale.
Betty Lee
Non-Proliferation and Treaty Compliance, US Department of Commerce, USA
Title: Biosecurity and how export controls impact the life sciences
Time : 11:30-12:00
Biography:
Betty Lee has a PhD from Dartmouth Medical School, USA and MS in Clinical Chemistry from the University of Windsor, Canada. She has done his second MS Biochemistry from LSU Medical Center, USA. She completed her Post-doctoral training at the National Institutes of Health, USA. She is currently working as a Licensing Officer with the US government. She educates industries and academia about the Export Administration Regulations (EAR) and participates in outreach. In addition, she participated in the policy review of the Executive Order titled “Optimizing the security of biological select agents and toxins in the United States” signed by President Obama on July 2, 2010
Abstract:
Balancing biosecurity and legitimate life science research has become a priority in recent years. The rise of biotechnology and informatics has made rapid advances in the 21st century. Such a convergence of biology and technology increases the pace of biological findings and the emergence of new technologies. Emerging technologies that could be used for biological warfare poses a formidable challenge because of the unpredictable nature of science. Dual use research in the life sciences requires some oversight by the government and funding agencies. The published results of scientific research could be used to improve health or agricultural products or they could be used to enable bioterrorism. Life Sciences research is conducted increasingly in an interdisciplinary and international environment. Informatics, systems biology, nanotechnology, and synthetic biology are at the forefront of such endeavors. Oversight of such research is essential to continue the free exchange of information and also balance the national security concerns. One of the tools that are at the nexus of biosecurity and life sciences is export control. The session will provide an overview of the biological agents (viruses, bacteria and toxins), genetic elements (DNA, plasmids, vectors) which are currently controlled on the Australia Group Control List and Commerce Control List for exports. The Australia Group is an informal forum of countries which seeks to ensure that exports do not contribute to the development of chemical or biological weapons. Topics of discussion will include deemed exports, fundamental research and technology transfer.
Erchin Serpedin
Texas A&M University, USA
Title: A robust PCA algorithm for metagenomic biomarker detection
Time : 12:00 -12:30
Biography:
Erchin Serpedin is currently a Professor at Texas A&M University in College Station, TX. He is the author of more than 140 journal papers, 250 conference papers, and 4 books. His research interests lie in the areas of computational biology, systems biology, signal processing and machine learning
Abstract:
We propose a novel consistency-classiï¬cation framework that enables the assessment of consistency and classiï¬cation performance of a biomarker discovery algorithm. The proposed evaluation protocol is based on random resampling those models the variation in the experiment size. The metagenomic data matrix is modeled as a superposition of two matrices. The ï¬rst matrix is a low-rank matrix that depicts the abundance levels of the irrelevant bacteria. The second matrix is a sparse matrix that describes the abundance levels of the bacteria that are differentially abundant between different phenotypes. We propose a novel Robust Principal Component Analysis (RPCA) based biomarker discovery algorithm to recover the sparse matrix. RPCA is a multivariate feature selection approach that processes the features collectively rather than individually. Comprehensive comparisons of RPCA with the state-of-the-art algorithms on two realistic datasets show that RPCA consistently outperforms the existing state-of-the-art algorithms in terms of classiï¬cation accuracy and reproducibility performance. Thus, the proposed RPCA-based biomarker detection algorithm provides a high reproducibility performance irrespective of the complexity of the dataset and the number of selected biomarkers. RPCA selects also biomarkers with quite high discriminative accuracy. Therefore, RPCA appears to represent a very consistent and accurate methodology for selecting taxonomical biomarkers in microbial populations.
Maria A Ragusa
University of Palermo, Italy
Title: Metallothionein family in sea urchin: Genes and their expression during embryo development and following exposure to stressors
Time : 12:30-13:00
Biography:
Maria A Ragusa has completed her PhD in Cellular and Developmental Biology and Post-doctoral studies from Palermo University. She is an Assistant Professor of Molecular Biology at the University of Palermo (Italy). She has published more than 15 peer reviewed papers in reputed international journals and has been serving as peer reviewer for many international journals. Her research work comprises gene transcription regulation during embryo development and early molecular defense strategies activated by embryos in response to exposition to stress agents. Recently, she also studied the effects of HPV infection on semen
Abstract:
Echinoderms represent a very fascinating phylum belonging to deuterostome superphylum, including also hemichordates, tunicates and vertebrates. Among echinoderms, sea urchin species are studied worldwide as excellent model organisms for the study of developmental biology, and are suitable as bioindicators. During a study on the defense strategies activated by Paracentrotus lividus sea urchin embryos in response to CdCl2, we isolated five metallothionein (MT) cDNAs. Two of the five MT genes were constitutively expressed, whereas the other three genes appear to be specifically switched-on in response to cadmium treatment. With the aim of better understanding the evolutionary relationships, functional variety, and the utilization of MTs during development, the gene organization of P. lividus MTs was analyzed and their mRNA expression patterns were unveiled. Particularly, we determined the expression profiles and the spatial patterns of MT transcripts during development and after metal and antimicrobial drug treatments. MTs show a high polymorphism both in sequence/structure and expression pattern. In the light of our findings it seems reasonable to consider MT7 and MT8 as the major variants associated with physiological functions, playing their major roles in metal homeostasis and redox activity in ecto-, meso- and endo-dermal tissues. On the other hand, a metal detoxification role can be attributed to MT4, 5, and 6, particularly important in mesenchyme cells for the skeletogenic pathway. Since differences not only between the two classes occur, each isoform would correspond to a more definite physiological function. For these interesting results we started to study the mechanisms that control MT gene expression in sea urchin embryogenesis.
- Presentation on Tecan Group Ltd
Location: Forum 12
Session Introduction
Guido Cimoli
Tecan Group Ltd., Germany
Title: Automation and Synthetic Biology simplifying complexity
Time : 14:00-14:30
Biography:
Guido Cimoli completed his Master’s degree in Biology at University of Genoa and worked as a Researcher at National Cancer Institute. He completed his PhD in Molecular Pharmacology at University of Pavia. He worked as a Bio-pharma Application Specialist and Project Leader at Tecan Group Ltd., from February 2004 to December 2007. He is currently responsible for the sales development for automation in Europe and Middle East.
Abstract:
In the last few years, the branch of biology (or of engineering, as some says) called synthetic biology has definitely taken the center of the stage. This oxymoronic branch is quickly spreading from agriculture to medicine, from students to Nobel Prize laureates, from engineers to molecular biologist and at every step increasing sophistication and complexity. The complexity stems both from intrinsic sophistication of the biological circuits that wants to be mimicked or created and also from the large amount of steps that have to be physically performed to transform an in silico circuit to a real, organic one. While the complexity at scientific level can be only tamed by continuous development of knowledge (and its spreading) and the development of more powerful software and deeper databases, the complexity at practical level can be tremendously decreased by the introduction of automation procedures. Automating tasks which requires high manual skills while being of limited intellectual complexity (think of separating interphases), or tasks that requires extremely high precision and management of ultra-low volumes (think of low volumes qPCR), or highly repetitive ones and at high frequency (think of colony picking or screening) can only improve the outcome with respect to manual performance. Automation does not only improve the quality of the data esults of a given task but can also bring other advantage like freeing skilled personnel for more important tasks, reduce burden of labor, scale up processes, standardize operations within the laboratory, examples will be given in the presentation.
- Young Research Forum
Location: Forum 12
Session Introduction
Lenka Dohnalová
University of Chemical Technology, Czech Republic
Title: Microbiome contribution and metabolite intervention in post-dieting weight regain
Time : 14:30-14:55
Biography:
Lenka Dohnalová has completed her BSc from University of Chemical Technology Prague, where she is currently completing her Master’s studies. She spent 1.5 years as a visiting student in the lab of Eran Elinav at the Weizmann Institute of Science, where she investigated the role of the intestinal microbiome in metabolism and immunity.
Abstract:
Despite the effectiveness of commonly used dietary weight reduction strategies, the majority of dieters fail to maintain the reduced weight in the long run. Recently, we uncovered a contribution of the intestinal microbiome to post-dieting weight regain by flavonoid-mediated regulation of energy expenditure. We identified a stable microbial composition that persists after obesity and promotes faster weight regain after high-fat diet (HFD) re-exposure. Furthermore, we demonstrated that fecal microbiome transplantation as well as flavonoid supplementation ameliorates the secondary weight gain. Additionally, we developed a machine leasing-based algorithm based on 16S rRNA data for the accurate prediction of weight-regain. Our data therefore suggest a possible implication of microbiome and metabolome in the personalized prediction and treatment of post-dieting weight regain.
Qiang Yan
Virginia Commonwealth University, USA
Title: Modularization strategies in metabolic engineering Serratia marcescens for N-acetylneuraminic acid production
Time : 14:55-15:20
Biography:
Qiang Yan is a PhD candidate working under the supervision of Dr. Stephen S Fong in the Department of Chemical and Life Science Engineering, Virginia Commonwealth University (VCU). His research interest focused on using molecular genetic techniques, synthetic biology and computational models to design modify and improve organism as workhorse to solve real-world problems.
Abstract:
Annually, large amounts of waste material are generated from seafood (crab, shrimp and lobster shells) that typically go to landfills with high expense (e.g. $150/ton in Australia). The biopolymer chitin makes up ~40% total weight of such waste and it can potentially be used as a sustainable feedstock for value-added products. In this study, we developed a consolidated bioprocess to produce N-acetylneuraminic acid (NeuNAc) directly from chitin using the chitinolytic organism Serratia marcescens by developing and implementing genetic engineering tools to modify S. marcescens. Starting from RNA sequencing data, 10 native promoters of varying strength were identified and characterized using a fluorescent reporter gene (sfGFP). Two heterologous genes (N-acetylglucosamine isomerase and NeuNAc lyase) were introduced in S. marcescens, and expression was transcriptionally controlled using three different strength promoters (high-high, medium-medium, and low-low). An initial 34.8 mg/L NeuNAc was produced under a high-high promoter combination. Improvements to NeuNAc were conducted by changing expression strength of the two heterologous genes to balance metabolic flux. Using a high strength promoter for the isomerase and a medium strength promoter for the lyase improved both NeuNAc production (1.42-fold) and growth (2.57-fold). Further improvements were tested by characterizing the kinetics of each heterologous enzyme and implementing alternative genes. Swapping N-acetylglucosamine isomerase gene did not show any improvement in production; however, swapping the second-step reversible NeuNAc lyase (nanA) to an irreversible NeuNAc synthase (neuB) improved NeuNAc production (3.25-fold). Overall, we identified and characterized promoter sequences that can be used for genetic engineering of S. marcescens and have implemented the tools to demonstrate and improve production of NeuNAc.
- Poster Presentations
Location: Forum 12
Session Introduction
Albert Jeltsch
University Stuttgart, Germany
Title: Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic loci
Time : 15:20-15:35
Biography:
Albert Jeltsch finished his PhD on Restriction Endonucleases at University Hannover in 1994. Afterwards, he started working on DNA Methyltransferases at Justus-Liebig University Giessen and at the Jacobs University Bremen. Since 2011, he is a Professor of Biochemistry at the University Stuttgart. He is the recipient of the Gerhard-Hess award (DFG) and BioFuture award (BMBF). He has long standing expertise in the biochemical study of DNA and protein methyltransferases, methyl lysine reading domains and in rational and evolutionary protein design. His work has been published in >200 publications in peer reviewed journals and is in the editorial boards of several journals
Abstract:
Investigation of the fundamental role of epigenetic processes depends on the development of methods, which enable live-cell detection of epigenetic modifications with locus-specific resolution. Here, we address this urgent technological demand by developing four modular fluorescence complementation-based epigenetic biosensors for live cell microscopy applications. In these tools, we combine the high DNA sequence specificity of engineered anchor proteins, with the great versatility of chromatin reading domains as natural detector modules for the recognition of target epigenetic marks. Simultaneous readout of DNA sequence and epigenetic mark is detected as reconstituted fluorescent signals that arise upon binding of the anchor and detectors modules in close spatial proximity, within the nuclei of living cells. With this approach we could directly detect DNA methylation and histone 3 lysine 9 trimethylation at defined, endogenous genomic sites, in several mouse and human cell lines. Furthermore, we could follow dynamic changes in these marks with locus-specific resolution upon drug treatment or induction of epigenetic enzymes. We anticipate that this versatile technology will play an important role in improving our understanding of how specific epigenetic signatures are set, erased and maintained during embryonic development or the onset of diseases.
Yuquan Xu
Biotechnology Research Institute, China
Title: Insights into the combinatorial biosynthesis and tailoring of fungal polyketides
Biography:
Yuquan Xu has completed his PhD from China Agricultural University and postdoctoral studies from University of Arizona and University of California, San Diego. His research fouses on combinatorial biosynthesis of fungal polyketides. He has published more than 23 papers in reputed journals.
Abstract:
Combinatorial biosynthesis aspires to exploit the incorporation of different microbial anabolic pathways to engineer the synthesis of new chemical entities. The modular enzymes composed by functionally independent domains, e.g., polyketide synthases (PKS), are suitable test case for the modularization of secondary metabolic pathways into “build–couple–pair” synthetic schemes. Fungal benzenediol lactones (BDLs) polyketides provide an opportunity for combinatorial biosynthesis. Fungal BDLs are important pharmacophores with wide-ranging bioactivities, and their biosynthesis involves a pair of collaborating iterative polyketide synthases (iPKSs): A highly reducing iPKS (hrPKS) with product that is further elaborated by a non-reducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Co-expressing random heterocombinations of hrPKSs and nrPKSs from different BDL biosynthetic pathways in Saccharomyces cerevisiae lead to the one-pot, one-step combinatorial biosynthesis of structurally diverse polyketides. In addition, the chemical diversity was further increased using heterologous tailoring enzymes such as glycosyltransferase and methyltransferase. Through heterologous expression and domain recombination to create hybrid enzymes, the product template (PT) domains in fungal nrPKSs that catalyze the first-ring cyclization of the benzenediol moiety can be used heterologously to create unnatural products with different polyketide folding modes. This folding mode difference can be programed by reshaping the cyclization chamber of a PT domain by only three selected point mutations. In addition, unnatural products can be generated via shuffling the nrPKS subunit if carefully tune the selectivity of the starter unit (SAT) and the TE domain. Our work provides a biosynthetic tool to generate unnatural polyketides as an unexplored source of chemical diversity and novelty, ready to be exploited for drug discovery, and these results demonstrated the potentials of combinatorial biosynthesis to produce new product with structure variety when considering the rules of enzyme activity and selectivity, shedding lights to further engineer the metabolic pathways in fungi.