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Jamboree/Project Abstract/Team Abstracts
From 2009.igem.org
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| + | ===[[Team:Aberdeen_Scotland | Team Aberdeen_Scotland:]] A Synthetic Biology Approach to Pipe Repair: The Pico-Plumber=== | ||
| + | Damage to inaccessible pipe systems, such as computer cooling circuits, is difficult to rectify. An Escherichia coli synthetic biology circuit for pipe repair was designed. Pipe breach detection and the restoration of pipe integrity were implemented through exploitation of chemotaxis, and cell lysis that releases a two-component protein-based glue (lysyl oxidase and tropoelastin). Control was achieved using an AND gate with quorum sensing and the lac inducer IPTG (released from the breach) as inputs. Deterministic and stochastic models of the genetic circuit, integrated with an agent-based model of E.coli cells, were used to define the effective radii of cell migration and timing of lysis. Constructed AND gate, quorum sensing and lysis timing modules were experimentally tested. The two-component glue concept was successfully validated using in vitro alpha-omega complementation of beta-galatosidase activity. Finally, a proposal for an igem.org-based parameter database was developed to aid the rapid identifation of BioBricks parameter values. | ||
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| + | ===[[Team:Alberta | Team Alberta:]] A Synthetic Biology Tool Kit for Artificial Genome Design and Construction=== | ||
| + | The creation of simplified artificial cells with specialized functions, along design principles that are compatible with the goals of synthetic biology, requires advances in two key areas. In Silico modelling tools are needed to assess the performance of artificial networks prior to assembly. Genome biofabrication must achieve rates well beyond existing methods using a modular design so that the extent to which natural systems can be made artificial can be tested. We have taken our first steps towards these goals by directing our efforts to the rational refactoring of the E. coli genome. Using flux balance analysis we have identified 117 new genes that may be essential for survival. We have developed and validated a rapid, modular biofabrication method (BioBytes) and have produced BioBytes for 150 of our 447 essential gene list. We have also built a Lego Mindstorm-based DIY biofab robot and extended the concept to a BioFab-on-a-chip prototype. | ||
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| + | ===[[Team:ArtScienceBangalore | Team ArtScienceBangalore:]]=== | ||
| + | We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase.E. coli, does not bear a gene that codes for this enzyme. We have expressed this gene in different strains of E. coli. Geosmin is responsible for producing the earthy smell when rain falls after a dry spell of weather. | ||
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| + | ===[[Team:Bay_Area_RSI | Team Bay_Area_RSI:]] Breast cancer cell targeting phage=== | ||
| + | Breast cancer is the second most common type of cancer diagnosed in women. RNAi has proven to be an effective mechanism in the silencing of oncogenes. Therefore, we have attempted to build a viable system for the delivery of RNAi into breast cancer cells. First, we inserted a shRNA sequence coding for the Raf-1 protein into an AAV cassette containing two ITR's, allowing it to reproduce itself in mammalian cells. This cassette was inserted into our chosen vector, the filamentous bacteriophage FUSE-55. An antibody sequence was then added to the phage plasmid near the coat protein sequence in order to target HER2. As an additional feature, we have fused Silicatein and Silintaphin to mStrepavidin, which will bind to a protein tag in the coat, forming silicate structures on the coat of the phage, thereby reducing the immunotoxicity of the bacteriophage in vivo. | ||
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| + | ===[[Team:BCCS-Bristol | Team BCCS-Bristol:]] VESECURE=== | ||
| + | Directed delivery of specific proteins into cells would have dramatic consequences for drug delivery and expand the horizons of synthetic biology into the multicellular domain via discrete, targetted communication. Gram-negative bacteria naturally produce outer member vesicles (OMVs): spherical, bilayered proteolipids from 20-200nm in diameter. OMVs carry outer membrane, periplasmic and cytoplasmic proteins, DNA, RNA and other biological molecules. They protect their cargo from the extracellular environment and deliver it to a multitude of target cells via membrane fusion. We investigate the possibility of allowing the secretion of any protein in OMVs via fusion with novel, non-toxic partners enhanced in OMVs, using a novel Bioscaffold compatible with the current assembly standard. A new version of the award winning BSim software has been developed to study applications at the population level such as communication. The ultimate goal is to create a safe and standardised system for directed delivery of proteins into cells. | ||
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| + | ===[[Team:Berkeley_Software | Team Berkeley_Software:]] Eugene, Spectacles, and Kepler: Managing Synthetic Biology Device Development=== | ||
| + | Three crucial activities in synthetic biology are the creation of standardized parts, the construction and specification of devices from these parts, and the automatic assembly of these devices. Each of these activities requires software tools. Tools give users access to data as well as provide algorithmic support and abstraction to design large scale systems. We have created three software tools for these tasks. The first is a domain specific language called Eugene for the specification of biological constructs and rules for their creation. The second contribution is a visual design environment for device creation called Spectacles. Finally, we have created workflows for the Kepler design environment. This work is integrated within the Clotho design framework. We show that together they offer a powerful solution to the problems of today while also providing a path to the more exotic design activities of the future. | ||
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| + | ===[[Team:Berkeley_Wetlab | Team Berkeley_Wetlab:]] Automated assembly of cell surface display devices=== | ||
| + | The University of California Berkeley iGEM team has developed an automated approach to large-scale parts assembly that is accurate, high-throughput, reduces labor, and decreases cost. As a test bed for our system we have chosen to explore novel applications of cell surface display within Escherichia coli, the gold standard organism for bacterial engineering. Displaying peptides and proteins on a cell's surface is difficult, and many attempts may have to be made to generate a given functional protein. By automatically generating and testing a large set of diverse proteins paired with various display methods, we can search a large design space and develop guidelines for rational design of projects involving surface display. | ||
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| + | ===[[Team:BIOTEC_Dresden | Team BIOTEC_Dresden:]] Temporal and spatial control of protein synthesis by in vitro recombination inside picoliter reactors=== | ||
| + | Manufacturing functionalized proteins in vitro poses a challenge, as it requires coordinated molecular assemblies and multi-step reactions. In this project we aim to control, over time and space, the production of proteins tagged with a silver-binding peptide for in situ silver nanoparticle nucleation inside microdroplets generated by microfluidic devices. Combining a transcription-translation system with protein coding genes and a recombination logic inside microdroplets provides spatial control. Moreover, in the microfluidic chamber we can pinpoint the beginning of synthesis, and easily track and isolate the droplets. Site-specific recombination generates a molecular timer for temporal control of protein synthesis. Unlike transcriptional regulation, this method gives true all-or-none induction due to covalent modification of DNA by Flp recombinase. Determining the transfer curve of inter-FRT site distance versus average recombination time allows the onset of gene expression to be predicted. We then apply this Flp reporter system as a powerful PoPS measurement device. | ||
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| + | ===[[Team:Bologna | Team Bologna:]] T-REX: Trans-Repression of Expression. A BioBrick gene-independent control of translation=== | ||
| + | The project aims to realize a device with standard biological parts for the post-transcriptional control of gene expression, regardless of the gene sequence to be silenced. We designed the T-REX device, composed of two non-coding DNA sequences: the TRANS-repressor and the CIS-repressing parts. TRANS-repressor acts as a silencer of CIS-repressing RNA target. This target includes a region complementary to the TRANS-repressor sequence antisense, ends with RBS, and is assembled upstream of the coding sequence to be silenced. Upon binding of TRANS-repressor and CIS-repressing RNAs, the access to RBS by ribosomes is hampered, silencing translation. Accordingly, the amount of TRANS-repressor controls the translation rate of the regulated gene. The TRANS-repressor sequence was determined by a computational analysis performed to minimize the interference with the genomic mRNAs and to maximize the base-pairing interaction to the CIS-repressing RNA. The T-REX device is proposed as a universal and fast switch in synthetic gene circuits. | ||
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| + | ===[[Team:British_Columbia | Team British_Columbia:]] Development of a modular, analog E. coli biosensor=== | ||
| + | To date, efforts to design a whole-cell biosensor capable of detecting levels of one or more biological inputs and responding in an analog mode has been elusive. We have designed a system of synthetic constructs implemented in an E. coli chassis that will allow detection of continuously varying levels of a single metabolic input and report on the concentration with qualitative output depending on threshold levels of the input. Our system design utilizes RNA-level hairpin hybridization and antisense technologies linked to various reporters. Because our approach is modular and does not depend on either endogenous protein processing or exogenous RNA, we envision that such a system could find applications in many different fields, including environmental sensing, detection of diagnostic of therapeutic biomarkers, and systems biology. | ||
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| + | ===[[Team:Brown | Team Brown:]] Engineering Staphylococcus Epidermidis to Secrete Recombinant Histamine Binding Protein in Response to Changing Histamine Concentration=== | ||
| + | The 2009 Brown iGEM Team aims to treat allergic rhinitis (hay fever) by engineering Staphylococcus epidermidis to secrete a histamine-binding protein, rEV131, in response to elevated histamine concentrations during an allergic attack. rEV131 was cloned from a species of tick, Rhipicephalus appendiculatus. We are putting the rEV131 gene into an endogenous element of human nasal flora, Staphylococcus epidermidis. rEV131 will have a secretion tag specific for S. epidermidis. To synchronize rEV131 production with elevation of histamine concentration, we are computationally designing a novel histamine receptor. This histamine-responsive receptor will induce expression of rEV131. Although S. epidermidis is a non-pathogenic species, when it reaches a certain population threshold it produces potentially hazardous biofilms. To mitigate this concern, we have engineered safety measures that prevent excessive growth by repurposing S. epidmidis’ natural population sensor to cue each cell’s "suicide" when a population has reached a dangerous size. | ||
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| + | ===[[Team:BLANK | Team BLANK:]] | ||
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===[https://2009.igem.org/Team:TUDelft Team TU Delft:] Bacterial Relay Race=== | ===[https://2009.igem.org/Team:TUDelft Team TU Delft:] Bacterial Relay Race=== | ||
In our project, we aim at creating a cell-to-cell communication system that allows the propagation of a set of instructions coded on a plasmid, and not just binary information as in quorum sensing. To achieve this goal, we have designed a communication system based on three different modules: a conjugation system, a time-delay genetic circuit, and a self-destructive plasmid.<br> | In our project, we aim at creating a cell-to-cell communication system that allows the propagation of a set of instructions coded on a plasmid, and not just binary information as in quorum sensing. To achieve this goal, we have designed a communication system based on three different modules: a conjugation system, a time-delay genetic circuit, and a self-destructive plasmid.<br> | ||
Revision as of 15:18, 2 October 2009
Team Aberdeen_Scotland: A Synthetic Biology Approach to Pipe Repair: The Pico-Plumber
Damage to inaccessible pipe systems, such as computer cooling circuits, is difficult to rectify. An Escherichia coli synthetic biology circuit for pipe repair was designed. Pipe breach detection and the restoration of pipe integrity were implemented through exploitation of chemotaxis, and cell lysis that releases a two-component protein-based glue (lysyl oxidase and tropoelastin). Control was achieved using an AND gate with quorum sensing and the lac inducer IPTG (released from the breach) as inputs. Deterministic and stochastic models of the genetic circuit, integrated with an agent-based model of E.coli cells, were used to define the effective radii of cell migration and timing of lysis. Constructed AND gate, quorum sensing and lysis timing modules were experimentally tested. The two-component glue concept was successfully validated using in vitro alpha-omega complementation of beta-galatosidase activity. Finally, a proposal for an igem.org-based parameter database was developed to aid the rapid identifation of BioBricks parameter values.
Team Alberta: A Synthetic Biology Tool Kit for Artificial Genome Design and Construction
The creation of simplified artificial cells with specialized functions, along design principles that are compatible with the goals of synthetic biology, requires advances in two key areas. In Silico modelling tools are needed to assess the performance of artificial networks prior to assembly. Genome biofabrication must achieve rates well beyond existing methods using a modular design so that the extent to which natural systems can be made artificial can be tested. We have taken our first steps towards these goals by directing our efforts to the rational refactoring of the E. coli genome. Using flux balance analysis we have identified 117 new genes that may be essential for survival. We have developed and validated a rapid, modular biofabrication method (BioBytes) and have produced BioBytes for 150 of our 447 essential gene list. We have also built a Lego Mindstorm-based DIY biofab robot and extended the concept to a BioFab-on-a-chip prototype.
Team ArtScienceBangalore:
We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase.E. coli, does not bear a gene that codes for this enzyme. We have expressed this gene in different strains of E. coli. Geosmin is responsible for producing the earthy smell when rain falls after a dry spell of weather.
Team Bay_Area_RSI: Breast cancer cell targeting phage
Breast cancer is the second most common type of cancer diagnosed in women. RNAi has proven to be an effective mechanism in the silencing of oncogenes. Therefore, we have attempted to build a viable system for the delivery of RNAi into breast cancer cells. First, we inserted a shRNA sequence coding for the Raf-1 protein into an AAV cassette containing two ITR's, allowing it to reproduce itself in mammalian cells. This cassette was inserted into our chosen vector, the filamentous bacteriophage FUSE-55. An antibody sequence was then added to the phage plasmid near the coat protein sequence in order to target HER2. As an additional feature, we have fused Silicatein and Silintaphin to mStrepavidin, which will bind to a protein tag in the coat, forming silicate structures on the coat of the phage, thereby reducing the immunotoxicity of the bacteriophage in vivo.
Team BCCS-Bristol: VESECURE
Directed delivery of specific proteins into cells would have dramatic consequences for drug delivery and expand the horizons of synthetic biology into the multicellular domain via discrete, targetted communication. Gram-negative bacteria naturally produce outer member vesicles (OMVs): spherical, bilayered proteolipids from 20-200nm in diameter. OMVs carry outer membrane, periplasmic and cytoplasmic proteins, DNA, RNA and other biological molecules. They protect their cargo from the extracellular environment and deliver it to a multitude of target cells via membrane fusion. We investigate the possibility of allowing the secretion of any protein in OMVs via fusion with novel, non-toxic partners enhanced in OMVs, using a novel Bioscaffold compatible with the current assembly standard. A new version of the award winning BSim software has been developed to study applications at the population level such as communication. The ultimate goal is to create a safe and standardised system for directed delivery of proteins into cells.
Team Berkeley_Software: Eugene, Spectacles, and Kepler: Managing Synthetic Biology Device Development
Three crucial activities in synthetic biology are the creation of standardized parts, the construction and specification of devices from these parts, and the automatic assembly of these devices. Each of these activities requires software tools. Tools give users access to data as well as provide algorithmic support and abstraction to design large scale systems. We have created three software tools for these tasks. The first is a domain specific language called Eugene for the specification of biological constructs and rules for their creation. The second contribution is a visual design environment for device creation called Spectacles. Finally, we have created workflows for the Kepler design environment. This work is integrated within the Clotho design framework. We show that together they offer a powerful solution to the problems of today while also providing a path to the more exotic design activities of the future.
Team Berkeley_Wetlab: Automated assembly of cell surface display devices
The University of California Berkeley iGEM team has developed an automated approach to large-scale parts assembly that is accurate, high-throughput, reduces labor, and decreases cost. As a test bed for our system we have chosen to explore novel applications of cell surface display within Escherichia coli, the gold standard organism for bacterial engineering. Displaying peptides and proteins on a cell's surface is difficult, and many attempts may have to be made to generate a given functional protein. By automatically generating and testing a large set of diverse proteins paired with various display methods, we can search a large design space and develop guidelines for rational design of projects involving surface display.
Team BIOTEC_Dresden: Temporal and spatial control of protein synthesis by in vitro recombination inside picoliter reactors
Manufacturing functionalized proteins in vitro poses a challenge, as it requires coordinated molecular assemblies and multi-step reactions. In this project we aim to control, over time and space, the production of proteins tagged with a silver-binding peptide for in situ silver nanoparticle nucleation inside microdroplets generated by microfluidic devices. Combining a transcription-translation system with protein coding genes and a recombination logic inside microdroplets provides spatial control. Moreover, in the microfluidic chamber we can pinpoint the beginning of synthesis, and easily track and isolate the droplets. Site-specific recombination generates a molecular timer for temporal control of protein synthesis. Unlike transcriptional regulation, this method gives true all-or-none induction due to covalent modification of DNA by Flp recombinase. Determining the transfer curve of inter-FRT site distance versus average recombination time allows the onset of gene expression to be predicted. We then apply this Flp reporter system as a powerful PoPS measurement device.
Team Bologna: T-REX: Trans-Repression of Expression. A BioBrick gene-independent control of translation
The project aims to realize a device with standard biological parts for the post-transcriptional control of gene expression, regardless of the gene sequence to be silenced. We designed the T-REX device, composed of two non-coding DNA sequences: the TRANS-repressor and the CIS-repressing parts. TRANS-repressor acts as a silencer of CIS-repressing RNA target. This target includes a region complementary to the TRANS-repressor sequence antisense, ends with RBS, and is assembled upstream of the coding sequence to be silenced. Upon binding of TRANS-repressor and CIS-repressing RNAs, the access to RBS by ribosomes is hampered, silencing translation. Accordingly, the amount of TRANS-repressor controls the translation rate of the regulated gene. The TRANS-repressor sequence was determined by a computational analysis performed to minimize the interference with the genomic mRNAs and to maximize the base-pairing interaction to the CIS-repressing RNA. The T-REX device is proposed as a universal and fast switch in synthetic gene circuits.
Team British_Columbia: Development of a modular, analog E. coli biosensor
To date, efforts to design a whole-cell biosensor capable of detecting levels of one or more biological inputs and responding in an analog mode has been elusive. We have designed a system of synthetic constructs implemented in an E. coli chassis that will allow detection of continuously varying levels of a single metabolic input and report on the concentration with qualitative output depending on threshold levels of the input. Our system design utilizes RNA-level hairpin hybridization and antisense technologies linked to various reporters. Because our approach is modular and does not depend on either endogenous protein processing or exogenous RNA, we envision that such a system could find applications in many different fields, including environmental sensing, detection of diagnostic of therapeutic biomarkers, and systems biology.
Team Brown: Engineering Staphylococcus Epidermidis to Secrete Recombinant Histamine Binding Protein in Response to Changing Histamine Concentration
The 2009 Brown iGEM Team aims to treat allergic rhinitis (hay fever) by engineering Staphylococcus epidermidis to secrete a histamine-binding protein, rEV131, in response to elevated histamine concentrations during an allergic attack. rEV131 was cloned from a species of tick, Rhipicephalus appendiculatus. We are putting the rEV131 gene into an endogenous element of human nasal flora, Staphylococcus epidermidis. rEV131 will have a secretion tag specific for S. epidermidis. To synchronize rEV131 production with elevation of histamine concentration, we are computationally designing a novel histamine receptor. This histamine-responsive receptor will induce expression of rEV131. Although S. epidermidis is a non-pathogenic species, when it reaches a certain population threshold it produces potentially hazardous biofilms. To mitigate this concern, we have engineered safety measures that prevent excessive growth by repurposing S. epidmidis’ natural population sensor to cue each cell’s "suicide" when a population has reached a dangerous size.
=== Team BLANK:
Team TU Delft: Bacterial Relay Race
In our project, we aim at creating a cell-to-cell communication system that allows the propagation of a set of instructions coded on a plasmid, and not just binary information as in quorum sensing. To achieve this goal, we have designed a communication system based on three different modules: a conjugation system, a time-delay genetic circuit, and a self-destructive plasmid.
Cell-to-cell communication systems are important because, in most synthetic biology applications, the desired tasks are generally accomplished by a population of cells, rather than by a single cell. The proposed communication system could be used for creating a distributed sensors network, or it could help to better understand and possibly reduce antibiotic resistance in bacteria.
Furthermore, we have conducted a survey to study the perception on synthetic biology and related ethical issues, among iGEM participants, students and supervisors. We have focused on the top-down and bottom-up approaches as applied to biology.
Team Groningen: Heavy metal scavengers with a vertical gas drive
Heavy metal pollution of water and sediment endangers human health and the environment. To battle this problem, a purification strategy was developed in which arsenic, zinc or copper are removed from metal-polluted water and sediment. In this approach Escherichia coli bacteria accumulate metal ions from solutions, after which they produce gas vesicles and start floating. This biological device encompasses two integrated systems: one for metal accumulation, the other for metal-induced buoyancy. The uptake and storage system consists of a metal transporter and metallothioneins (metal binding proteins). The buoyancy system is made up of a metal-induced promoter upstream of a gas vesicle gene cluster. This device can be changed to scavenge for any compound by altering the accumulation and the induction modules. The combination of both systems enables the efficient decontamination of polluted water and sediment in a biological manner.
Team PKU_Beijing: Conditioned Reflex Mimicking in E.coli
We are engineering our E. coli cells to process the correlation information of two enviornmental signal, similar to the process of conditioning in higher orgamisms. We have constructed and tested a series of AND gates which can sense the two signals: the conditioned and unconditioned stimuli. With the presence of both signals, the AND gate outputs a repressor protein and then changes the state of the bistable switch, which acts as a memory module. In this way, our E. coli cells can convert the information about the concurrence of the two signals into its memory. After the memory module is switched and given the "conditioned stimulus", the E. coli cells will pass the information to the reporter module and thus exhibit the "conditioned response."
