International Synthetic and Systems Biology Summer School
Biology meets Engineering and Computer Science
15 - 19 June 2014, Taormina - Sicily, Italy
Recent advances in DNA synthesis have increased our ability to build biological systems. Synthetic Biology aims at streamlining the design and synthesis of robust and predictable biological systems using engineering design principles. Designing biological systems requires a deep understanding of how genes and proteins are organized and interact in living cells: Systems Biology aims at elucidating the cellular organization at gene, protein and network level using computational and biochemical methods.
The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion course on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for doctoral students, early career researches and industry leaders. Participants will also have the chance to present their results, and to interact with their peers, in a friendly and constructive environment.
- April 18, 2014: Program of the Summer School - Draft 0.4 - April 18, 2014.
- April 11, 2014: Satellite Meeting:
3rd International Synthetic Yeast Genome (Sc2.0) Meeting, Friday, June 20, 2014 - Jef D. Boeke, Giuseppe Nicosia and Giovanni Stracquadanio.
The Synthetic Yeast Genome Project (Sc2.0) is synthesizing and constructing a modified version of the S. Cerevisiae genome to test biological questions and give new functions. For this one day meeting we will be bringing those around the world involved in the Sc2.0 project together in beautiful Taormina to discuss progress on the synthetic S. cerevisiae genome and opportunities to use the strains and tools of the project. Related topics in synthetic and systems biology will also be discussed. This meeting is open to all interested in Sc2.0 and we encourage you (and your colleagues) to register if you'd like to attend.
- April 3, 2014: The Summer School will start June 15th at 9:00am and it will end June 19th at 20:00.
- March 31, 2014: We are pleased to inform that we received more than 200 applications! We thank all the applicants for their interest in the school, and we are looking forward to see you in Taormina!
- March 27, 2014: Scientists build First Synthetic Yeast Chromosome (Science Vol. 344 no. 6179 pp. 55-58), Synthetic Yeast researchers, Jef Boeke & Joel Bader, will be lecturing at SSBSS2014
- March 11, 2014: Workshop on "Biosensors and Synthetic Circuits in Mammalian Cells" by Velia Siciliano and Liliana Wroblewska MIT, USA.
- February 19, 2014: New Speaker! Joel Bader, Johns Hopkins University, USA
- February 15, 2014: For the applications received from February 16 to March 31 the organizing committee will send the corresponding notification by April 10. Applicants that need a early notification (e.g., for travel grant applications) must contact the SSBSS 2014 Organizing Committee via email: email@example.com
- February 15, 2014: To the 123 applicants that submitted the application form by February 15th, the organizing committee will send the notification by March 1st (as reported in the first call for participation).
- February 15, 2014: We are pleased to inform that we received more than 120 applications and, due to many requests, we are extending the application deadline to March 31, 2014. For this reason, we will have up to ~150 slots for selected and motivated students. We thank all the applicants for their interest in the school, and we are looking forward to see you in Taormina!
- February 15, 2014: We received more than 120 applications and 50 abstracts/posters. We thank you very much all the applicants and presenters for this great participation to the SSBSS 2014!
- January 30, 2014: Reduced registration fees thanks to the generous support of our sponsors.
December 29, 2013: Co-located Event: The 3rd International Synthetic Yeast Genome (Sc2.0) Meeting will be held in Taormina Friday June 20, 2014 from 9:00 AM to 8:00 PM.
Previous edition: The 2nd International Synthetic Yeast Genome (Sc2.0) Consortium Meeting Johns Hopkins University and Imperial College London Friday, July 12, 2013 from 9:00 AM to 8:00 PM (GMT) London, United Kingdom, co-located event at SB 6.0.
List of Speakers
- Uri Alon, Weizmann Institute of Science, Israel
- Joel Bader, Johns Hopkins University, USA
- Jef Boeke, Johns Hopkins University, USA
- Jason Chin, MRC - Cambridge, UK
- Paul Freemont, Imperial College London, UK
- Farren Isaacs, Yale University, USA
- Tanja Kortemme, University of California San Francisco, USA
- Giuseppe Nicosia, University of Catania, Italy
- Sven Panke, ETH, Switzerland
- Rahul Sarpeshkar, MIT, USA
- Velia Siciliano, MIT, USA
- Giovanni Stracquadanio, Johns Hopkins University, USA
- Ron Weiss, MIT, USA
- Liliana Wroblewska MIT, USA
Lecture I: Elementary Circuits in Biology
To understand biological systems, our lab has defined "network motifs": basic interaction patterns that recur throughout biological networks, much more often than expected at random. The same small set of network motifs appears to serve as the building blocks of the circuitry that processes information from bacteria to mammals. Specific network motifs may be universal building blocks of biological computation. We experimentally studied the function of each network motif in the bacterium E. coli using dynamic fluorescent measurements from living cells. Each network motifs can serve as an elementary circuit with a defined function: filters, pulse generators, response accelerators, temporal-pattern generators and more. Evolution seems to have rediscovered the same motifs again and again, perhaps because they are the simplest and most robust circuits that perform these information-processing functions.
Lecture II: Evolution and Optimality of Gene Circuits
Organisms, tissues and molecules often need to perform multiple tasks. But usually no phenotype can be optimal at all tasks at once. This leads to a fundamental tradeoff. We study this using the concept of Pareto optimality from engineering and economics. Tradeoffs lead to an unexpected simplicity in the range of optimal phenotypes- they fall on low dimensional shapes in trait space such as lines, triangles and tetrahedrons. At the vertices of these polygons are phenotypes that specialize at a single task. We demonstrate this using data from animal and fossil morphology, bacterial gene expression and other biological systems.
- Lecture I: Elementary Circuits in Biology
Lecture I: Network Remodeling during Development and Disease
Biological networks change in response to genetic and environmental cues. Changes are reflected in the abundances of biomolecules, the composition of protein complexes, and other descriptors of the biological state. Methods to infer the dynamic state of a cell would have great value for understanding how cells change over time to accomplish biological goals. We describe methods that predict the dynamic state of protein complexes in a cell, combining dynamic information from mRNA transcript profiling with underlying protein-protein interaction networks.
Lecture II : Gene and Pathway Analysis of Genome-wide Association Studies
While most genome-wide association studies are based on analysis of individual variants, the causal variants often cluster in a small set of genes. We describe Bayesian methods that exploit gene-based and pathway-based clustering to improve the search for disease-related genetic variation.
- Lecture I: Network Remodeling during Development and Disease
Lecture I: Genome Design and Synthesis
Genome Design and Synthesis strategies vary considerable. Most of the published work on genome synthesis involves resynthesis of the native or near-native genome of bacteria. In this case, the design considerations are rather minimal and the major challenges involved have to do with design of an assembly strategy that is effective. Hierarchical strategies involve going from 10s of bases in oligonucleotides up to several megabases of dsDNA. A wide variety of methods have been described that can be used to assemble DNA and the details of these methods have significant impacts on speed of synthesis, cost of synthesis, and accuracy of synthesis. Innovative methods have been described that operate at all different levels of the assembly hierarchy. When more radical designs that deviate from that of wild-type genomes are considered, appropriate design software tools are needed. Our group has focused on genome editing software which takes advantage of well-developed browser platforms for visualizing genome features, and adapting them to genome editing. A variety of design features were somewhat arbitrarily selected for incorporation into Sc 2.0, the synthetic yeast genome. These, as well as possible future more aggressive designs under consideration will be discussed, as will interesting targets for future genome synthesis projects.
Lecture II: Combinatorial DNA Assembly methods and their Applications
A wide variety of pathways are available for engineering to make useful products or encode interesting behaviors in cells and organisms. As more and more complex pathways and gene networks are discovered and dissected, more and more efficient means of assembling pathways are needed. Even more importantly, libraries of these, in which the promoter strength or host of origin for the coding sequences can be systematically varied are especially valuable. Methodologies and strategies for accomplishing this are discussed, incorporating Golden Gate, MoClo, Gateway cloning, and combinations of such methods will be discussed. Examples of pathway optimization will also be reviewed.
- Lecture I: Genome Design and Synthesis
Lecture I: Reprogramming the Genetic Code
The information for synthesizing the molecules that allow organisms to survive and replicate is encoded in genomic DNA. In the cell, DNA is copied to messenger RNA, and triplet codons (64) in the messenger RNA are decoded - in the process of translation - to synthesize polymers of the natural 20 amino acids. This process (DNA RNA protein) describes the central dogma of molecular biology and is conserved in terrestrial life. We are interested in re-writing the central dogma to create organisms that synthesize proteins containing unnatural amino acids and polymers composed of monomer building blocks beyond the 20 natural amino acids. I will discuss our invention and synthetic evolution of new 'orthogonal' translational components (including ribosomes and aminoacyl-tRNA synthetases) to address the major challenges in re-writing the central dogma of biology. I will discuss the application of the approaches we have developed for incorporating unnatural amino acids into proteins and investigating and synthetically controlling diverse biological processes, with a particular emphasis on understanding the role of post-translational modifications
Lecture II: Reprogramming the Genetic Code - part II
- Lecture I: Reprogramming the Genetic Code
Lecture I: Foundational Technologies for Synthetic Biology - from DNA Assembly to Part Characterisation
Synthetic biology is an application-focused field attempting to apply a systematic engineering approach to the design of new biological systems at the molecular level primarily using DNA. Notable progress has been made in the implementation of synthetic genetic circuits in living-systems that mimic functions such as switches, oscillators, timers, pulse generators, band-pass filters and logic gates (1,2). These genetic circuits are anticipated to enable the engineering of biological systems to a complexity previously unattainable. Over the past decade synthetic biology has aided the development of novel biological systems for a range of applications from bacteria that seek and destroy herbicides to the biosynthesis of valuable drugs (3, 4). To accelerate the development of the field many groups are establishing foundational technologies, which can be used across a wide range of applications. Within the Centre for Synthetic Biology and Innovation at Imperial College London (CSynBI; www.imperial.ac.uk/syntheticbiology) we are developing a series of platform technologies to enable the systematic design assembly and testing of synthetic biology designs including integration into an information system. I will describe recent developments in CSynBI on high throughput in vivo part characterization and the automated production of datasheets as well as new approaches in combinatorial DNA assembly. I will also describe our recent in vitro platform for the rapid characterization of DNA regulatory elements using a cell free system (5).
Lecture II: Synthetic biology designs for biosensor applications
Biosensors generally can be used to monitor parameters of interest or target analytes and in part they involve a biological component. Early biosensors started when techniques for immobilising enzymes onto solid supports were first developed (1). The relatively recent discovery of bioluminescent (e.g. luciferase) and fluorescent (e.g. green fluorescent protein, GFP) proteins has provided a convenient mechanism for visualising gene expression and protein synthesis in cells and has lead to their use as reporter proteins. By utilizing such constructs, whole cell biosensors have been developed for example to specifically detect certain compounds or act as indicators to monitor cell growth and fitness (2,3). Biological organisms naturally monitor their environment and react accordingly with highly evolved detection and sensing systems, which can now be refactored at the genetic level for specific biosensor applications. One overall aim of synthetic biology is to harness nature's toolbox by fusing molecular biology and engineering disciplines and thus the field of biosensor design and construction has been a major focus for synthetic biologists (4-8). In this lecture I will describe the principles behind biosensor design using synthetic biology approaches providing exemplars to illustrate these principles. I will also present recent data from my groups on developing synthetic biology biosensors for healthcare applications and show how additional societal implications can be integrated into biosensor designs.
- Lecture I: Foundational Technologies for Synthetic Biology - from DNA Assembly to Part Characterisation
Lecture I : Genome engineering technologies for rapid editing & evolution organisms
The growing availability of whole genome sequence data sets generated by massively parallel sequencing permits detection of potential associations between genotype and phenotype. These advances motivate the development of high throughput genome editing technologies to systematically elucidate the causative mutations underlying important phenotypes. Similarly, expanding protein and RNA structure databases provide a valuable resource for researchers seeking to engineer macromolecules with new binding specificities. Finally, as complex metabolic networks controlling the flow of biomolecules through cells are elucidated, efforts to alter native metabolism for engineered biosynthesis of desired compounds are rapidly growing in basic research and industrial biotechnology. I will discuss the development of high-throughput and automated methodologies for precise manipulation of genomes. Multiplex automated genome engineering (MAGE) simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Conjugative assembly genome engineering (CAGE) facilitates the large-scale assembly of many modified genomes. These methods treat the chromosome as both an editable and evolvable template and are capable of fundamentally re-engineering genomes from the nucleotide to the megabase scale. I will present applications of MAGE to generate combinatorial genomic variants from a complex pool of synthetic DNA to diversify target genes in order to optimize biosynthetic pathways. The growing toolbox for genomic engineering will be discussed.
Lecture II: Design, construction & function of genomically recoded organisms
The conservation of the genetic code, with minor exceptions, enables exchange of gene function among species, viruses and across ecosystems. Fundamental changes to the genetic code could significantly enhance our understanding of the origins of the canonical code and reveal new subtleties of how genetic information is encoded and exchanged. Modifying the canonical genetic code could also lead to orthogonal biological systems with new properties. I will discuss the construction of a genomically recoded organism (GRO). In the GRO, all known UAG stop codons in Escherichia coli MG1655 were replaced with synonymous UAA codons, which permitted the deletion of release factor 1 and reassignment of UAG translation function. This GRO exhibited improved properties for incorporation of nonstandard amino acids that expand the chemical diversity of proteins in vivo. The GRO also exhibited increased resistance to T7 bacteriophage, demonstrating that new genetic codes could enable increased viral resistance.
- Lecture I : Genome engineering technologies for rapid editing & evolution organisms
Lecture I: Computational protein design - principles, challenges and progress
Lecture II: Design of reprogrammed and new functions - from proteins to cells
Lecture I: Biological Circuit Design by Pareto Optimality
Lecture II: Programming Living Molecular Machines for Biofuel Production
- Lecture I: Biological Circuit Design by Pareto Optimality
Lecture I: Synthetic Biology of Cell free Systems
The use of parts of cells, specifically enzymes, has a long tradition in therapy, diagnostics and particular chemical synthesis. One of the most attractive feature of enzymes as biological catalysts is that they all have been engineered by nature to operate at comparable environmental conditions. This is a major difference to chemistry and enables the coordinated operation of a cascade of enzymes concomitantly in one vessel, opening ways to efficiently conduct complex chemistry and circumventing thermodynamic challenges. Synthetic biology allows constructing such systems with an unprecedented degree of scope and ease. We will illustrate the potential of the approach by discussing the generation of large enzyme systems for the production of fine chemicals. Furthermore, we will discuss an engineering approach to optimizing such systems based on advanced on-line MS-analytics and design of experiments.
Lecture II: Exploiting Engineered Cell-Cell Communications in Large Scale Biotechnology
Synthetic biology brings with it a drastic increase in the scope of experimental operations, which it typically accommodated by a tendency to miniaturize and parallelize experimentation. While this is relatively straight forward for in vitro approaches such as DNA assembly, suitable approaches are less clear when interaction of living cells is required. We will discuss recent efforts of our laboratory to develop nanoliter-sized cultivation systems and their resulting applications to high-throughput screening strategies in the fields of fluorescent protein engineering, vitamin production, and engineering of novel antibiotics.
- Lecture I: Synthetic Biology of Cell free Systems
Lecture I: Analog versus Digital Computation in Biology
The fundamental laws of noise in gene and protein expression set limits on the energy, time, space, molecular count, and part-count resources needed to compute at a given level of precision in the cell. Based on these laws, we conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation in the cell. Hence, synthetic and natural circuits in cells must use analog, collective analog, probabilistic, and hybrid analog-digital computational approaches to function; otherwise, even relatively simple computations in cells like addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. A deep connection between analog circuits and cell biology enables us to also engineer synthetic analog computation in cells efficiently.
Lecture II: Analog Synthetic and Systems Biology
The deep connection between analog circuits and cell biology arises because there are astounding similarities between the equations that describe noisy electronic flow in sub-threshold transistors and the equations that describe noisy molecular flow in chemical reactions, both of which obey the laws of exponential thermodynamics. Based on these similarities, we have engineered logarithmic analog computation in living cells with less than three transcription factors, almost two orders of magnitude more efficient than prior digital approaches. In addition, highly computationally intensive noisy DNA-protein and protein-protein networks can be rapidly simulated in mixed-signal supercomputing chips that naturally capture their noisiness, dynamics, and loading interactions at lightning-fast speeds. Such an approach may enable large-scale design and analysis in synthetic and systems biology that is faithful to how messy analog biology works, quite different from clean, well-defined digital design.
- Lecture I: Analog versus Digital Computation in Biology
Lecture I: Minimal Genomes: High-Throughput Sequencing, Statistical Methods and Physics Models to Unveil Minimal Yeast Chromosomes Compatible with Life
Lecture II: Computational Tools for Genome editing, Combinatorial Assembly and Workflow Tracking
- Lecture I: Minimal Genomes: High-Throughput Sequencing, Statistical Methods and Physics Models to Unveil Minimal Yeast Chromosomes Compatible with Life
Lecture I: Synthetic Biology: From Parts to Modules to Systems
Lecture II: Mammalian Synthetic Biology: Scientific and Therapeutic Applications
- Lecture I: Synthetic Biology: From Parts to Modules to Systems
- Workshop on "Biosensors and Synthetic Circuits in Mammalian Cells"
- I. Principles of Circuit Design in Mammalian cells
- II. Mammalian in vivo Biosensors
- III. Circuits based on RNA Regulation
- IV. Targeted Genomic Integration of Circuits
- Workshop on "Biosensors and Synthetic Circuits in Mammalian Cells"
- Giuseppe Nicosia, University of Catania, Italy
- Joel Bader, Johns Hopkins University, USA
- Jole Costanza, University of Catania, Italy
- Barbara Di Camillo, University of Padova, Italy
- Markus Herrgard, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
- Heiko Muller, Italian Institute of Technology, Italy
- Giuseppe Narzisi, Cold Spring Harbor Laboratory, USA
- Wieslaw Nowak, Nicholas Copernicus University, Poland
- Elisa Pappalardo, Johns Hopkins University, USA
- Gianna Maria Toffolo, University of Padova, Italy
- Renato Umeton, MIT, USA
- Luca Zammataro, Italian Institute of Technology, Italy
- Student Application: March 31, 2014
- Notification Acceptance: April 10, 2014
- Oral/Poster Submission: March 31, 2014
- Notification of Decision for Oral/Poster Presentation: May 15, 2014
- Early Registration: April 30, 2014
- Late Registration: After April 30, 2014
The school will be open up to
100 150 qualified, motivated and selected students. Undergraduate and graduate students, post-docs, research fellows and industrial professionals are encouraged to apply. School fees will be 450 Euro for undergraduate and graduate students, 550 Euro for post-docs and research fellows and 650 Euro for all other participants. Fees will cover lectures, course materials, coffee breaks, social tours and Wi-Fi Internet Connection.
The School will involve a total of 28-32 hours of lectures, the final achievement will be equivalent to 7-8 ECTS points (ECTS grading scale).
Applications should be received before March 31, 2014. Applicants will receive notification of acceptance by April 10, 2014.
Short Talk and Poster Submission
Students may submit a research abstract for presentation. School directors will review the abstracts and will recommend for poster or short-oral presentation. Abstract should be submitted by March 31, 2014. The abstracts will be published on the electronic hands-out material of the summer school.
Leonardo Design Systems
Venue and Accommodation
SSBSS will be hosted in Taormina (Google Map) at the venue "Hotel Villa Diodoro" that offers 2 main conference rooms, 5 meeting rooms and an open terrace for coffee breaks. The plenary room can to accommodate more than 250 people. All the rooms are equipped with Wi-Fi connection.
The Secretarial and conference facilities: Direct-dial telephone, Fax-PC, WI-FI/ADSL lines, Production room, Photocopier, Conference speaker system, Portable microphones, Light dimming, Overhead projector, Flip chart, Slide projector, Movie projector, Laser pointer, Podium, Stage-Catwalk, Post congress, Transfer to/from Catania International Airport.
Plenary talks and introductions to the poster sessions will be held in one of the main conference rooms while the actual poster sessions will be held in the other main room.
Hotel Villa Diodoro
Via Bagnoli Croci 75
98039 Taormina, Messina, Italy
T: +39 0942 2 33 12
F: +39 0942 2 33 91
Travel to Taormina
Catania Fontanarossa "Vincenzo Bellini" International is the nearest and most convenient airport at some km. 55 from Taormina. It features several flights from the major Italian cities such as Milan Malpensa, Rome, Naples, Venice, etc and many international direct flights from important European cities such as Bruxelles, Munich, Barcelona, Athens, Malta and many more. Lots of charter flights from all over the world land to Catania too.
From Catania airport you can reach Taormina in one-hour drive by very convenient direct highway A18 (direction Messina, exit TAORMINA). Direct bus to Taormina centre are available at 08.30 - 11.30 - 13.30 - 16.30 - 18.30 - 20.30 every day. By Taxi about 1 hour.
Taormina's railway station is considered one of Italy's most beautiful for its elegant charming Sicilian Liberty style decor; every train arriving from Northern Italy to Sicily stops here.
One has a large choice of trains, from de-luxe Eurostar down to simple but very efficient "Espresso train" normally departing from Milan, Turin and Rome through Naples and the Amalfi & Capri area.
Taormina offers a wide choice of Hotels, B&B, Apartments and Hostels. At the following links you can find some other kinds of accommodations:
Some Hotels in Taormina
- Hotel San Domenico *****L
- Hotel Imperial *****
- Hotel Villa Diodoro ****
- Hotel Villa Ducale ****
- Hotel Villa Paradiso ****
- Hotel Villa Carlotta ****
- Hotel Monte Tauro ****
- Hotel TaoDomus ***
- Hotel Villa Schuler * **
- Hotel Isabella ***
- Hotel La Pensione Svizzera ***
- Hotel Del Corso ***
- Hotel Vittoria **
- Hotel Elios **
- Hotel Condor **
- Hotel Soleado **
- Hotel Villa Astoria *
Bed & Breakfast in Taormina
Apartments in Taormina
- Taormina City Center
- Only Apartments - Taormina
- Residence Circe - Taormina
- Residence Agrumi - Taormina
- Apartments Taormina