Team:Lethbridge Canada/parts

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Lethbridge_Canada iGEM
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<span id="title_first">Lethbridge</span>
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<span id="title_second">iGEM Team</span>
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<p id="stmp">Parts</p>
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<a href="#place1" class="stmp">Preprooxyphysin</a>
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<a href="#place2" class="stmp">Protein Convertase I</a>
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<a href="#place3" class="stmp">Synthesis</a>
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Preprooxyphysin
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Neurophysin I is a carrier protein with a size of 10 KDa and containing 90 to 97 aminoacids that is a cleavage product (formed by splitting of a compound molecule into a simpler one) of preprooxyphysin.[1] It is a neurohypophysial hormone that is transported in vesicles with oxytocin, the other cleavage product, along axons, from magnocellular neurons of the hypothalamus to the posterior lobe of the pituitary. Although it is stored in secretory vesicles with oxytocin and released with oxytocin, its biological action is unclear.
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NH2 - Ala - Ala - Pro - Asp - Leu - Asp - Val - Arg - Lys - Cys - Leu - Pro - Cys - Gly - Pro - Gly - Gly - Lys - Gly - Arg - Cys - Phe - Gly - Pro - Asn - Ile - Cys - Cys - Ala - Glu - Glu - Leu - Gly - Cys - Phe - Val - Gly - Thr - Ala - Glu - Ala - Leu - Arg - Cys - Gln - Glu - Glu - Asn - Tyr - Leu - Pro - Ser - Pro - Cys - Gln - Ser - Gly - Gln - Lys - Ala - Cys - Gly - Ser - Gly - Gly - Arg - Cys - Ala - Val - Leu - Gly - Leu - Cys - Cys - Ser - Pro - Asp - Gly - Cys - His - Ala - Asp - Pro - Ala - Cys - Asp - Ala - Glu - Ala - Thr - Phe - Ser - Gln – Arg - OH
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<li class="navigation_project"><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/project" class="strict">Project</a>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/project">Description</a></li>
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                                                <li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/project#video_oxy">Visual Modeling</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/math">Math Model</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/results">Results</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/wikifreeze">Wikifreeze</a></li>
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<li class="navigation_parts decrease_opacity"><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/parts" class="strict">Parts</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/protocols#protocol_header">Protocols</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_march">Notebook: March</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_april">Notebook: April</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_may">Notebook: May</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june">Notebook: June</a></li>
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</ul>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/outreach">Overview</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/presentations">Presentations</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/interviews">Interviews</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/videos">Videos</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/surveys">Parent Surveys</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/novel_study">Novel Study</a></li>
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<li class="navigation_team decrease_opacity"><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/team" class="strict">Team</a>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/team#the_team">The Team</a></li>
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<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/team#the_advisors">The Advisors</a></li>
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<li class="navigation_sponsors decrease_opacity"><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/sponsors" class="strict">Sponsors</a></li>
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<th>Name</th>
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<th>Type</th>
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<th>Length</th>
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<td>&#9829;</td>
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<td>&#9733;</td>
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_J23100">BBa_J23100</a></td>
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<td>Regulatory</td>
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<td>High constitutive promoter</td>
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<td>John Anderson</td>
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<td>35</td>
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<td>&#9829;</td>
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<td>&#9733;</td>
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_J23108">BBa_J23108</a></td>
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<td>Regulatory</td>
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<td>Medium-high constitutive promoter</td>
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<td>John Anderson</td>
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<td>35</td>
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History
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_J23113">BBa_J23113</a></td>
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<td>Regulatory</td>
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<p>
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<td>Medium-low constitutive promoter</td>
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iGEM developed out of student projects conducted during MIT's Independent Activities Periods in 2003 and 2004.[3][4] Later in 2004, a competition with five teams from various schools was held. In 2005, teams from outside the United States took part for the first time.[5] Since then iGEM has continued to grow, with 130 teams entering in 2010.[6]
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<td>John Anderson</td>
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</p>
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<td>35</td>
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Because of this increasing size, in 2011 the competition was split into three regions: Europe, the Americas, and Asia (though teams from Africa and Australia also entered via "Europe" and "Asia" respectively).[7] Regional jamborees will occur during October; and some subset of teams attending those events will be selected to advance to the World Championship at MIT in November.[8]
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In January 2012 the iGEM Foundation was spun out of MIT as an independent non-profit organization located in Cambridge, Massachusetts, USA. The iGEM Foundation supports scientific research and education through operating the iGEM competition.
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For the 2012 competition iGEM expanded into having not only the Collegiate division, but also competitions for entrepreneurs and high school students.
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<td>&#9829;</td>
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<td>&#9733;</td>
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_J23114">BBa_J23114</a></td>
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<td>Regulatory</td>
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<td>Low constitutive promoter</td>
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<td>John Anderson</td>
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<td>35</td>
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<td>&#9829;</td>
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BioBricks
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_J61002">BBa_J61002</a></td>
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<td>Plasmid_Backbone</td>
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<td>EX-Ptet-S-rbs-RFP-P “RFP reporter”</td>
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BioBrick standard biological parts are DNA sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems. BioBrick parts represent an effort to introduce the engineering principles of abstraction and standardization into synthetic biology. The trademarked words BioBrick and BioBricks are correctly used as adjectives (not nouns) and refer to a specific "brand" of open source genetic parts as defined via an open technical standards setting process that is led by the BioBricks Foundation.
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<td>John Anderson</td>
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<td>2948</td>
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BioBrick parts were introduced by Tom Knight at MIT in 2003.[1][2] Drew Endy,[3] now at Stanford, and Christopher Voigt, at MIT, are also heavily involved in the project. A registry of several thousand public domain BioBrick parts is maintained by Randy Rettberg team at http://partsregistry.org. The annual iGEM competition promotes the BioBrick parts concept by involving undergraduate and graduate students in the design of biological systems.
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One of the goals of the BioBricks project is to provide a workable approach to nanotechnology employing biological organisms. Another, more long-term goal is to produce a synthetic living organism from standard parts that are completely understood.[4]
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Each BioBrick part is a DNA sequence held in a circular plasmid; the "payload" of the BioBrick part is flanked by universal and precisely defined upstream and downstream sequences which are technically not considered part of the BioBrick part. These sequences contain six restriction sites for specific restriction enzymes (at least two of which are isocaudomers), which allows for the simple creation of larger BioBrick parts by chaining together smaller ones in any desired order. In the process of chaining parts together, the restriction sites between the two parts are removed, allowing the use of those restriction enzymes without breaking the new, larger BioBrick apart.[5] To facilitate this assembly process, the BioBrick part itself may not contain any of these restriction sites.[1]
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There are three levels of BioBrick parts: "parts", "devices" and "systems".[3] "Parts" are the building blocks and encode basic biological functions (such as encoding a certain protein, or providing a promoter to let RNA polymerase bind and initiate transcription of downstream sequences); "devices" are collections of parts that implement some human-defined function (such as a riboregulator producing a fluorescent protein whenever the environment contains a certain chemical);[6] "systems" perform high-level tasks (such as oscillating between two colors at a predefined frequency).
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Example BioBrick systems honored at previous iGEM competitions include:
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E. coli detector for arsenic that responds with pH change;
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E. coli producer of various scents such as banana or mint;
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human cell line engineered to inhibit excessive response to Toll-like receptor activation, so as to avoid sepsis.
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Two measures for the performance of biological parts have been defined by Drew Endy's team: PoPS or Polymerase per second, the number of times a RNA polymerase passes by a certain DNA point per second; and RiPS or Ribosomal initiations per second, the number of times a ribosome passes a certain point on mRNA each second.[7]
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The original BioBricks only use two of the compatible restriction enzymes XbaI and SpeI. Recently, Xu et al [8] have expanded this concept and used four of the compatible restriction enzymes AvrII, XbaI, SpeI and NheI. The engineered ePathBrick vectors comprise four compatible restriction enzyme sites allocated on strategic positions so that different regulatory control signals can be reused and manipulation of expression cassette can be streamlined. Specifically, these vectors allow for fine-tuning gene expression by integrating multiple transcriptional activation or repression signals into the operator region. At the same time, ePathBrick vectors support the modular assembly of multi-gene metabolic pathways and combinatorial generation of pathway diversities with three distinct configurations.
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<td>&#9733;</td>
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_B0034">BBa_B0034</a></td>
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<td>RBS</td>
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<td>RBS (Elowitz 1999) defines RBS efficiency</td>
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<td>Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.</td>
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<td>12</td>
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DNA
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_K314100">BBa_K314100</a></td>
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<td>Composite</td>
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<td>f1 phage origin, J23100 promoter and B0034 RBS - High constitutive expression cassette</td>
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Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Along with RNA and proteins, DNA is one of the three major macromolecules essential for all known forms of life. Genetic information is encoded as a sequence of nucleotides (guanine, adenine, thymine, and cytosine) recorded using the letters G, A, T, and C. Most DNA molecules are double-stranded helices, consisting of two long polymers of simple units called nucleotides, molecules with backbones made of alternating sugars (deoxyribose) and phosphate groups (related to phosphoric acid), with the nucleobases (G, A, T, C) attached to the sugars. DNA is well-suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a built-in duplicate of the encoded information.
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<td>Thomas Huber, Justin Siegel</td>
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<td>518</td>
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These two strands run in opposite directions to each other and are therefore anti-parallel, one backbone being 3' (three prime) and the other 5' (five prime). This refers to the direction the 3rd and 5th carbon on the sugar molecule is facing. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription.
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Within cells, DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts.[1] In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
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<td>W</td>
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<td><a class="part" href="http://partsregistry.org/Part:pSB1C3">pSB1C3</a></td>
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<td>Plasmid_Backbone</td>
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<td>High copy BioBrick assembly plasmid</td>
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<td>Austin Che</td>
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<td>2070</td>
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<td>Oxytocin-Neurophysin I_pUC57</td>
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<td>Coding</td>
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<td>Oxytocin hormone and carrier protein Neurophysin I genes in pUC57 plasmid</td>
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<td>Lethbridge High School iGEM</td>
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<td>406</td>
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<td> </td>
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<td>NECI_pUC57</td>
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<td>Coding</td>
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<td>Cleavage enzyme NECI gene in pUC57 plasmid</td>
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<td>Lethbridge High School iGEM</td>
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<td>2277</td>
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<td>&#9733;</td>
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<td> </td>
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<td><a class="part" href="http://partsregistry.org/Part:BBa_J06702">BBa_J06702</a></td>
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<td>Reporter</td>
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<td>mCherry, bacterial with RBS and forward terminator </td>
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<td>Yves Wang</td>
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<td>869</td>
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<img class="parts_banner_image" src="https://static.igem.org/mediawiki/2013hs/a/a6/Lethbridge_hs_igem_2013_banner_finalcontructs.png">
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    <th>Name</th>
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    <th>Description</th>
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    <th>Expanded Length</th>
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    <th>Total Length</th>
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  </tr>
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<td><a href="http://parts.igem.org/Part:BBa_K988003">K314100+oxytocin-neurophysin I in pSB1C3</a></td>
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<td>BBa_K314100 (f1 phage origin, J23100 promoter and B0034 RBS) and oxytocin-neurophysin I gene in pSB1C3 plasmid</td>
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<td>518 + 406 + 2070</td>
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<td>2994</td>
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</tr>
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  <tr>
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<td><a href="http://parts.igem.org/Part:BBa_K988002">Oxytocin-neurophysin I</a></td>
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<td>Oxytocin-neurophysin I gene in pSB1C3</td>
 +
<td>406</td>
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<td>406</td>
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</tr>
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<tr>
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    <td>K314100+NEC1 in pSB1C3</td>
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    <td>BBa_K314100 (f1 phage origin, J23100 promoter and B0034 RBS) and NEC1 enzyme in pSB1C3 plasmid (in progress)</td>
 +
    <td>518 + 2277 + 2070</td>
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    <td>4865</td>
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    </tr>
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    <tr>
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  <td>J23100+J06702 in pSB1C3</td>
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  <td>BBa_J23100 (high constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress)</td>
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  <td>35 + 869 + 2070</td>
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  <td>2974</td>
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</tr>
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<tr>
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    <td>J23108+J06702 in pSB1C3</td>
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    <td>BBa_J23108 (medium-high constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress)</td>
 +
    <td>35 + 869 + 2070</td>
 +
    <td>2974</td>
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    </tr>
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    <tr>
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    <td>J23113+J06702 in pSB1C3</td>
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    <td>BBa_J23113 (medium-low constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress)</td>
 +
    <td>35 + 869 + 2070</td>
 +
    <td>2974</td>
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    </tr>
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 +
    <tr>
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    <td>J23114+J06702 in pSB1C3</td>
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    <td>BBa_J23114 (low constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress)</td>
 +
    <td>35 + 869 + 2070</td>
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    <td>2974</td>
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    </tr>
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Latest revision as of 03:54, 22 June 2013

Parts

Name Type Description Designer(s) Length
♥ ★ W BBa_J23100 Regulatory High constitutive promoter John Anderson 35
♥ ★ W BBa_J23108 Regulatory Medium-high constitutive promoter John Anderson 35
♥ ★ W BBa_J23113 Regulatory Medium-low constitutive promoter John Anderson 35
♥ ★ W BBa_J23114 Regulatory Low constitutive promoter John Anderson 35
♥ ★ W BBa_J61002 Plasmid_Backbone EX-Ptet-S-rbs-RFP-P “RFP reporter” John Anderson 2948
★ W BBa_B0034 RBS RBS (Elowitz 1999) defines RBS efficiency Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003. 12
♥ W BBa_K314100 Composite f1 phage origin, J23100 promoter and B0034 RBS - High constitutive expression cassette Thomas Huber, Justin Siegel 518
★ W pSB1C3 Plasmid_Backbone High copy BioBrick assembly plasmid Austin Che 2070
Oxytocin-Neurophysin I_pUC57 Coding Oxytocin hormone and carrier protein Neurophysin I genes in pUC57 plasmid Lethbridge High School iGEM 406
NECI_pUC57 Coding Cleavage enzyme NECI gene in pUC57 plasmid Lethbridge High School iGEM 2277
★ BBa_J06702 Reporter mCherry, bacterial with RBS and forward terminator Yves Wang 869
Name Description Expanded Length Total Length
K314100+oxytocin-neurophysin I in pSB1C3 BBa_K314100 (f1 phage origin, J23100 promoter and B0034 RBS) and oxytocin-neurophysin I gene in pSB1C3 plasmid 518 + 406 + 2070 2994
Oxytocin-neurophysin I Oxytocin-neurophysin I gene in pSB1C3 406 406
K314100+NEC1 in pSB1C3 BBa_K314100 (f1 phage origin, J23100 promoter and B0034 RBS) and NEC1 enzyme in pSB1C3 plasmid (in progress) 518 + 2277 + 2070 4865
J23100+J06702 in pSB1C3 BBa_J23100 (high constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress) 35 + 869 + 2070 2974
J23108+J06702 in pSB1C3 BBa_J23108 (medium-high constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress) 35 + 869 + 2070 2974
J23113+J06702 in pSB1C3 BBa_J23113 (medium-low constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress) 35 + 869 + 2070 2974
J23114+J06702 in pSB1C3 BBa_J23114 (low constitutive promoter) and BBa_J06702 (mCherry) in pSB1C3 plasmid (in progress) 35 + 869 + 2070 2974

Retrieved from "http://2013hs.igem.org/Team:Lethbridge_Canada/parts"