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Requests for Comments (RFCs)

Mostrando recursos 1 - 20 de 74

  1. BBF RFC #111: Inducible expression vector with His tag fusion for purification of RFC25 parts

    Husser, Mathieu; Narcross, Lauren; Sundarakrishnan, Adithi
    This Request For Comments (RFC) describes a new expression vector based on the pET expression system and designed for BioBrick RFC25 parts. This design includes all the features of pET expression vectors with a new origin of replication, resistance marker and Multiple Cloning Site (MCS). This MCS contains new restriction sites and a 5’ poly- histidine tag that allows the purification of expressed RFC25 parts. Previous attempts have been prevented by restriction site incompatibility, but using RFC25 parts and their restriction sites enables 5’ fusion to these parts. This new expression vector enables the cloning of RFC25 parts with a...

  2. BBF RFC 112: Synthetic Biology Open Language (SBOL) Version 2.1.0

    Beal, Jacob; Cox, Robert Sidney; Grünberg, Raik; McLaughlin, James; Nguyen, Tramy; Macklin, Chris; Bissell, Michael; Madsen, Curtis; Roehner, Nicholas; Oberortner, Ernst; Misirli, Goksel; Clancy, Kevin; Pocock, Matthew; Zhang, Zhen; Myers, Chris; Zhang, Michael; Samineni, Meher; Zundel, Zach; Bartley, Bryan; Choi, Kiri; Gennari, John H.; Sauro, Herbert
    The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information.

  3. BBF RFC 108: Synthetic Biology Open Language (SBOL) Version 2.0.0

    Bartley, Bryan; Beal, Jacob; Clancy, Kevin; Misirli, Goksel; Roehner, Nicholas; Sauro, Herbert; Oberortner, Ernst; Madsen, Curtis; Pocock, Matthew; Wipat, Anil; Nguyen, Tramy; Zhang, Zhen; Myers, Chris; Gennari, John H.; Bissell, Michael
    The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards.

  4. BBF RFC 94: Type IIS Assembly for Bacterial Transcriptional Units: A Standardized Assembly Method for Building Bacterial Transcriptional Units Using the Type IIS Restriction Enzymes BsaI and BbsI

    Haddock, Traci L.; Densmore, Douglas M.; Appleton, Evan; Carr, Swati; Iverson, Sonya; De Freitas, Monique; Jin, Shawn; Awtry, Jake; Desai, Devina; Lozanoski, Thomas; Shah, Pooja; Agarwal, Yash; Lewis, Kathleen; Pacheco, Alan
    This RFC94 describes an assembly standard based on the Type IIS restriction enzymes BsaI and BbsI (also called BpiI). This assembly standard is based upon the Modular Cloning (MoClo) assembly strategy, which was introduced in 2011 by Weber et al. [1] and is based upon Golden Gate cloning [2]. In this RFC, we describe our proposed MoClo standard for generating a library of bacterial DNA parts for generating four-part transcriptional units (promoter : 5’UTR : CDS : 3’UTR). In this work, we define 5’UTRs as including ribosomal binding sites (RBS) and bi-cistronic design elements (BCDs) [3], and 3’UTRs as transcriptional terminators....

  5. BBF RFC 107: Copyright and Licensing of BBF RFCs

    Beal, Jacob; Endy, Drew; Grewal, David; Johnson, Richard; Kahl, Linda
    In this BioBricks Foundation Request for Comments (BBF RFC), we update and clarify the copyright and licensing notice of BBF RFC documents.

  6. BBF RFC 105: The Intein standard - a universal way to modify proteins after translation

    Ahlmann-Eltze, Constantin; Bunne, Charlotte; Büscher, Magdalena; Gleixner, Jan; Horn, Max; Huhn, Anna; Klughammer, Nils; Kreft, Jakob; Schäfer, Elisabeth; Schmelas, Carolin; Schmitz, Silvan; Waldhauer, Max; Bayer, Philipp; Krämer, Stephen; Neugebauer, Julia; Wehler, Pierre; Beaudouin, Joel; Di Ventura, Barbara; Eils, Roland
    This Request for Comments (RFC) proposes a new standard that allows for easy and flexible cloning of intein constructs and thus makes this technology accessible to the synthetic biology community.

  7. BBF RFC 104: BrickClip – rapid assembly of multiple RFC10 BioBricks

    Trubitsyna, Maryia; Chan, Karen; Cai, Yizhi; Elfick, Alistair; French, Chris
    This BioBrick Foundation Request for Comments (BBF RFC 104) describes a new approach to multiple part DNA assembly – BrickClip, which does not require use of any restriction enzymes, nor cloning of the parts to specific donor and acceptor vectors. BrickClip allows assembly of up to six parts from existing parts collections, including the Registry of Standard Biological Parts, in a single reaction, in any desired order. The resulting product is exactly the same as would be obtained from normal RFC10 BioBrick assembly. In contrast to other commonly used methods such as Gibson assembly, BrickClip does not require ordering new...

  8. BBF RFC 106: A Standard Type IIS Syntax for Plants

    Rutten, Virginia; Munabi, Angelina; Riche, Fergus; Lewy, Guy; Wilson, Hugh; Pipan, Miha; Bhate, Salil; Nghiem, Trang-Anh; Kaufhold, Will; Haseloff, Jim; Rubert, Alba; González, Alejandra; Quijano, Alfredo; Llopis, Ivan; Gavaldá, Jose; Estellés, Lucía; Vásquez, Marta; Orzáez, Diego; Deal, Cara; Gray, Jessica; Spiegel, Mischa; Monsey, Steven; Middlemiss, Alistair; Day, Jack; Patron, Nicola
    Here we define a standard syntax for assembling standard parts for expression in plant cells, extensible to all other eukaryotes. Variations of the Type IIS mediated cloning method known as Golden Gate Cloning, most notably Golden Braid (GB2.0) and Golden Gate Modular Cloning (MoClo) are in common use, particularly for the assembly of plasmids for delivery to plant cells. Many characterised plant parts compatible with Type IIS mediated assembly are available outside of the Registry of Standard Parts, as well as plasmids with the features necessary for delivery of DNA to plants cells via the shuttle chassis, Agrobacterium tumefaciens. This...

  9. BBF RFC 101: Logic Gene Module Standard

    Wang, Lingjue; Tong, Yin; Zhou, Liqun; Ni, Zhuangdian; Zhu, Xiaodan; Li, Hanrun
    This Request for Comments (RFC) describes a new framework for standardize logic gene relations among gene circuits. Each type of logic module in gene circuit can be summarized in a standard device in electronics. In this paper, we collect several frequently-used logic modules and the corresponding classic gene structure.

  10. BBF RFC97: Genetic Circuit Standard 1.0

    Wang, Lingjue; Zhu, Xiaodan; Li, Hanrun; He, Huiyu; Ni, Zhuangdian; Zhou, Liqun
    Current, there is well adopted documentation of biobricks. The Registry of Standard Biology Part set the standard documentation for biobrick. However, there is no standard way to document a genetic circuit, what information should be included in a description of a genetic circuit. We have therefore develop the technique standard for recording a genetic circuits. This standard will help the sharing of genetic circuits’ information among synthetic biology community.

  11. Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques

    Hammerling, Michael J.; Gottel, Neil R.; Alnahas, Razan N.; Slater, Ben; Huang, Yunle; Okasheh, Yousef; Howard, Marco; Mortensen, Catherine; Monk, Jordan; Detelich, Madeline; Lannan, Ryan S.; Pitaktong, Areen; Weaver, Evan; Das, Siddharth; Barrick, Jeffrey E.
    The discipline of synthetic biology emphasizes the application of engineering principles such as standardization, abstraction, modularity, and rational design to complex biological systems. The archetypical example of such standardization is BioBrick RFC[10], introduced in 2003 by Tom Knight at MIT. BioBricks are stored on a standard plasmid, pSB1C3, which contains prefix and suffix sequences flanking the DNA sequence specifying a biological part. The prefix and suffix sequences contain two pairs of 6 base-pair (bp) restriction enzyme sites (EcoRI+XbaI and SpeI+PstI), which can be used for both part assembly and quality control. BioBricks are intended to be well- characterized biological parts,...

  12. Standard for Synthesis of Customized Peptides by Non-Ribosomal Peptide Synthetases

    Beer, Ralf; Christiansen, Tania; Herbst, Konrad; Ignatiadis, Nikos; Kats, Ilia; Kurzawa, Nils; Meichsner, Johanna; Rabe, Sophie; Riedel, Anja; Sachs, Joshua; Schessner, Julia; Schmidt, Florian; Walch, Philipp; Adlung, Lorenz; Genreith, Katharina; Georgi, Fanny; Heinemann, Tim; Meyer, Hannah; Niopek, Dominik; Di Ventura, Barbara; Eils, Roland
    The purpose of this RFC is to introduce a standardized framework for the engineering of customizable non-ribosomal peptide synthetases (NRPS) and their application for in vivo and in vitro synthesis of short non-ribosomal peptides (NRPs) of user-defined sequence and structure.

  13. HiCT: High Throughput Protocols For CPE Cloning And Transformation

    Beer, Ralf; Christiansen, Tania; Herbst, Konrad; Ignatiadis, Nikolaos; Kats, Ilia; Kurzawa, Nils; Meichsner, Johanna; Rabe, Sophie; Riedel, Anja; Sachs, Joshua; Schessner, Julia; Schmidt, Florian; Walch, Philipp; Adlung, Lorenz; Genereith, Katharina; Georgi, Fanny; Heinemann, Tim; Meyer, Hannah; Niopek, Dominik; Di Ventura, Barbara; Eils, Roland
    The purpose of this RFC is to provide instructions for a rapid and cost efficient cloning and transformation method which allows for the manufacturing of multi-fragment plasmid constructs in a parallelized manner: High Throughput Circular Extension Cloning and Transformation (HiCT). Description of construct libraries generated by the HiCT method can be found at This RFC also points out further optimization strategies with regard to construct stability, reduction of transformation background and the generation of competent cells.

  14. GenBrick – A Rapid Multi-Part Assembly Method for BioBricks

    Gasiūnaitė, Lina; Lewicka, Aleksandra; Pashkuleva, Hristiana; Villanueva, Hugo; Thornton, Harry; Trubitsyna, Maryia; French, Chris
    This BioBricks Foundation Request for Comments (BBF RFC) describes a novel approach, GenBrick, for the rapid assembly of multiple BioBrick RFC10-compatible parts in a single reaction, with completely flexible part order, without recloning or reamplification.

  15. The AutoAnnotator - Standardized annotation of protein-encoding BioBricks

    Wolf, Christopher; Albrecht, Florian; Brüggenthies, Johanna; Brunner, Andreas; Ciccone, Rosario; Fischer, Katrin; Froehlich, Fabian; Funke, Louise; Morath, Volker; Polte, Ingmar; Reichart, Leonie; Schneider, Philipp; Truong, Jeffery
    For protein-encoding BioBricks a large number of useful parameters, such as the amino acid sequence or the molecular weight, can easily be computed. Furthermore alignments against databases and predictions of various features, for instance transmembrane regions, are very interesting and informative when viewing a part. However, this information is not presented or very hard to find in most part descriptions and requires the user to use external websites to obtain it. To resolve this issue we propose a standardized table containing this information. For this purpose we developed a web tool, called the AutoAnnotator, in JavaScript gathering this information and...

  16. Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0

    Quinn, Jacqueline; Beal, Jacob; Bhatia, Swapnil; Cai, Patrick; Chen, Joanna; Clancy, Kevin; Hillson, Nathan; Galdzicki, Michal; Maheshwari, Akshay; P, Umesh; Pocock, Matthew; Rodriguez, Cesar; Stan, Guy-Bart; Endy, Drew
    In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language Visual standard (SBOL Visual) to enable consistent, human-readable depiction of genetic designs.

  17. The GoldenBricks assembly: A standardized one-shot cloning technique for complete cassette assembly

    Pauthenier, Cyrille; El-Sayyed, Hafez; Rostain, William; Cerisy, Tristan; Lopez, Carolina Gallo; Ferreira, Raphael; Moreira, Jorgelindo Da Veiga; Souterre, Tiffany; Eeckhout, Joachim; Nogue, Pierre Yves; Llamosi, Artemis; Parutto, Pierre; Nikolayeva, Iryna; Machat, Mohamed; Marquet, Clement; Młynarczyk, Anna; Thelie, Aurore; Landrain, Thomas; Tolonen, Andrew; Pollet, Nicolas; Faulon, Jean-Loup; Jaramilo, Alfonso
    BBF RFC 92 proposes a new standard assembly method for the Parts Registry. The method makes one-shot cloning of a complete eukaryotic or prokaryotic cassette possible in one day while keeping compatibility with the BBF RFC 10 BioBrick assembly standard.

  18. Yeast Golden Gate: Standardized Assembly of S. cerevisiae Transcriptional Units

    Boeke, Jef; Mitchell, Leslie; Cai, Yizhi; Stracquadanio, Giovanni; Chuang, James; Tan, Scott; Heston, Margo; Wang, Jiarui; Kim, Dong Won; Noronha, Anne Marie
    BBF RFC 88 describes a new standard for the assembly of basic Saccharomyces cerevisiae transcriptional units (TUs) consisting of a promoter/5’untranslated region (UTR), open reading frame (ORF), and 3’UTR/terminator. Note that we use the term “promoter” here to refer to both the promoter and the 5’ UTR, which we currently define as a single part. Future iterations of this standard will incorporate subdivision of currently defined parts e.g. into promoter and 5’ UTR. The standard makes use of the type IIS restriction enzyme BsaI to generate standardized and user­‐defined ‘signature overhangs’, thus enabling directional and seamless TU assembly. RFC88 is...

  19. The Measurement of rho‐independent Transcription Terminator Efficiency

    He, Jiankui; Jing, Shui; Zhang, Mengshi; Liu, Xianggeng; Chen, Yao; Qie, Boyu; Shen, Liuxing; Wu, Zishan
    The purpose of this RFC is to provide standard methodology for the measurement of the absolute strength of terminators in bacteria. Because we have characterized the performance of terminator in E. coli and used a simple equation model, it can be expressed in PoPS.

  20. The minimum information for a qualified BioBrick

    Zhou, Mubing; Zhang, Junqiu; He, Jiankui
    Since the information of many existing BioBricks is incomplete, thus the usage of the BioBricks will be affected. It is necessary to standardize the minimum information required for a qualified BioBrick. Furthermore this standardization will reduce the time to locate and find a BioBrick. So it is essential to create a default template of storing the information of BioBricks.

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