This is the release of v0.1.1, which includes stable Nucleus content (i.e., passing our internal testing and generally working). Parts of Nucleus that we’re still working on are also available, and are flagged as “in development”.
New to v0.1.1
- Introduces
Developer Notes, describing intermediate results and data in support of content development for Nucleus
Introducing 
Container Documentation, a landing page containing background information, links, and guides in support of making Containers:
- Getting started - introduction to Containers
- Guides - discursive introductions to techniques used to making and measuring Containers
Container Protocols updated with the following:
- updated
Inner and Outer Solutions protocol for clarity
PURE Protocols now includes the following:
Make Energy Mix: a protocol that describes how to make Energy Mix, the non protein components of PURE
Cytosol Documentation now includes the following:
PURE protein expression in pOpen vs pET28a : a developer note describing our experience expressing PURE proteins in pOpen and pET28a
Modules now includes the following:
- Alpha hemolysin module: enables passive small molecule transport across the the cell membrane
- LacI Inducible Module: enables lactose inducible transcription using the
lacOoperator - TetR Inducible Module: enables tetracycline inducible transcription using the
tetOoperator - two (2) inducible T7RNAP promoters (pT7)
- one pT7 with a lactose responsive regulatory element (pT7-lacO)
- one pT7 with a tetracycline responsive regulatory element (pT7-tetO)
Modular sensing and response describes our goals to build three (3) classes of synthetic cells:- Detector cells: use sensor modules to detect target molecules.
- Emitter cells: use enzymatic modules to emit extracellular signals.
- Responder cells: integrated detector and emitter modules to enable cell-cell communication.
In Development
We are actively developing the following features. They are intended to be fully released in a future release. Keep up to date on the current status of these features by joining our mailing list at bnext.bio/build.
We are developing the following 
Detector cells:
- lactose responsive cells: detects the presence of IPTG and other lactose derivatives
- tetracycline responsive cells: detects the presence of aTc and other tetracycline derivatives
- lac AND tet responsive cells: implements an AND gate; turns on expression in the presence of IPTG AND aTc
Container Protocols will include protocols for the following:
- Brightfield / fluorescence microscopy for observing liposomes
- Liposome Analysis Toolkit: Jupyter Notebook to help analyze microscopy data
PURE Protocols will include protocols for the following:
- Multiplexed protein purification on microwell plates
DNA Distribution includes digital and physical DNA sequences encoding the following, although we are currently testing their biological function:
- two (2) inducible T7RNAP promoters (pT7), each implementing an AND gate
- pT7-lacO-tetO
- pT7-tetO-lacO
- two repressor proteins that regulate the transcription of the above inducible pT7s:
- lacI
- tetR
- a constitutively expressed plamGFP (green fluorescent protein) reporter; compatible with E. coli cell lysates (e.g., S30 extract, myTXTL)
- four fluorescent reporters under lactose induction (pT7-lacO)
- two variants of cjBlue (blue chromoprotein) under pT7-lacO; one is His tagged, one is not
- two variants of eforRed (red chromoprotein) under pT7-lacO; one is His tagged, one is not
Known Issues
- DNA Distribution uses pOpen as an expression backbone. We are noticing lower than expected protein yields from pOpen expression plasmids. See PURE protein expression in pOpen vs pET28a for details.
- Three of the PURE genes (ArgRS, LeuRS, and T7RNAP) were unable to be resynthesized in the Nucleus DNA Architecture for the v0.1.0 release. They are included as OpenMTA parts in the pET28a backbone. As a result they may have different expression levels relative to the other parts, and are not compatible with all the Nucleus DNA Architecture assembly standards.
- Several reporters (particularly cjBlue) have a long maturation time, which makes them less useful for expression in PURE.
More Information
- Code and DNA designs are available on Github
- To ask questions or participate in the development of Nucleus, join our nucleus-discuss mailing list