These are shortened abstracts sent in by the participants of the www.crispr.kitchen. They are the participants personal thoughts, concepts and ideas. Please consider them as fiction-in-science.

GenoMix, a Unified Language for Defining CRISPR Genome Edits

Jacob Palumbo (palumbojacob@gmail.com)


Synthetic biology will never have the world-redefining impact that the personal computer has had unless it gains the two traits that made personal computing successful: a low entry barrier and the true potential for personalization. The former requires the mechanics of genetic circuits and genome engineering to be significantly abstracted to enable non-biologist users to participate in design. The latter requires the full sequence space of DNA to be available to all users, which can be accomplished with cheap in-home DNA printing. This project is intended to address the former with respect to CRISPR-based genome editing and related technologies. A comprehensive programming language that allows a user to abstractly define genome edits using a simple interface will allow even users without any understanding of CRISPR to fully utilize its potential for mass genomic edits. Mass democratization of CRISPR technologies is one of the surest ways to prevent inequality of relative power and enable all levels of society to create what is relevant to them. The name GenoMix is proposed, a combination of the words ‘genome’ and ‘mix’ pronounced to sound like “genomics.”

This language would primarily do two things: 1) allow a user to designate activities (cut, join, et cetera) to sites relative to annotations in a genome (beginning of an open reading frame (ORF), end of a promoter, et cetera) and 2) generate gRNA sequences based on the defined activity sites incorporating minimization of off-target activity. Usage would resemble a modern scripting language such as Python. This paradigm for design not only automates the tedious process of designing potentially hundreds of gRNA sequences that are error-free and have minimal off-target activity, but also totally abstracts the physical processes involved in CRISPR-based genome editing. This means a user can define their genome edits without extensive background knowledge in genetic engineering, thus extending the usefulness of the language from the few current practitioners of genetic engineering to virtually the entire population. Further, many extensions to this language and the Cas proteins used to actuate it are possible. Design of gene networks using orthogonal promoters with minimal cross-talk, selfish elements to ensure stability of the system in vivo, and the addition of transcription activator-like effectors (TALEs) could all be potential extensions to the language.

The creation of this language certainly would take a large amount of effort by a well-funded and dedicated group of researchers and experts in genomics, computer science, cell biology and adjacent fields. However, after the initial base of the language is created, it could and should be turned over to the larger community of biohackers open-source so that extensions and improvements to the language could be made based on what the community desires.

PhenoBuilder

Claus Weiland (monogatari99@gmail.com)


The vision of PhenoBuilder is to make synthetic biology accessible to interested parties ranging from researchers and industries to independent biohackers without requiring deep biological wet-lab experience. PhenoBuilder aims to provide a building tool with a graphical user interface (gui) of molecular building structures (bricks) and functions to design synthetic biology experiments. Furthermore, a novel forward genetic screen will be designed that will help to implement the molecular basis of the building bricks. This will be done by significantly narrowing down the search space for possible causal genes or pathways.

Existing standards and repositories mainly focus on describing the specific molecular structures and functions of genomic elements. They do not contain mechanisms and building blocks for high-level functions, which are essential for sharing, reuse and recombination of molecular building blocks to design genetic circuits. Consequently, new community projects and standards arise like BioBricks (http://biobricks.org), the Registry of Standard Biological Parts (http://parts.igem.org), and the Synthetic Biology Open Language (http://sbolstandard.org), which facilitate reuse of parts and molecular mechanisms across different bioengineering projects.

Intensifying an award winning approach from the 1st UK Biohackathon (http://labiotech.eu/cutec-biohackin-startup-synbio) PhenoBuilder aims to decompose existent synbio protocols and data into mechanisms and building blocks to provide (analytical) high- level functions (cellular pathways) and objects (phenotypes). Using these functions, operators will be designed, by which these 'molecular bricks' can be handled by a graphical interface, combined into new high-order blocks and streamed into a wetlab workflow, e.g. using a cloud-lab api like autoprotocol (http://autoprotocol.org) or a high-level language linking to laboratory hardware like antha (http://www.antha-lang.org). PhenoBuilder objects have annotations based domain ontologies (e.g. NCBI taxonomy) to make automatic reasoning on regarded procedures and entities possible and to enable combination of analytic results with information available in knowledge bases on model species like corn (http://www.maizegdb.org), rice (http://rapdb.dna.affrc.go.jp) and other crops (http://www.gramene.org).

PhenoBuilder will provide the framework to transfer determined molecular mechanisms and analyzed pathways to other organisms, for example from model species to underutilized wildtypes using gene-editing technologies like CRISPR-Cas

Emergency: Gene Drive and CRISPR techniques in the context of the environmental crisis

Emmanuel Ferrand (emmanuel.ferrand@upmc.fr)


The International Union for Conservation of Nature recently updated the Red List of Threatened Species, revealing, for example, “a devastating decline for the Giraffe”. At the same time, new techniques in gene editing open the way for dramatic improvements of the cognitive abilities of mammals (see, for example, https://mgm.duke.edu/wp-content/uploads/2015/02/Science-2015-Pennisi-21-3.pdf), and hence, of their fitness in a new, quickly changing environment. Gene Drive and CRISPR techniques would greatly facilitate such manipulations.

The above example is just one among an incredible diversity of actions based on bioengineering techniques that are now at hand to counterbalance the negative effects of the development of modern societies and the harsh challenges caused by the exponential growth of human population on earth (energy and food supply, health care issues). Of course such techniques are, to an extent, a leap into the unknown. In particular the long term effects of the dissemination of genetic modifications in ecosystems is difficult to evaluate.

Climate change and other environmental threats require a quick answer, and doing nothing is also a leap into the unknown. In other words, the main question is not whether biotechs are innocuous per se, but rather to find tools to make an optimal choice in a context of uncertainty and emergency.

Such an important debate should not be kept in the closed communities of scientists and politicians. It is important to provide an open framework of reflection, accessible to any citizen in any country. In this perspective, my contribution, as a mathematician trained in biology and involved in several citizen science initiatives, could be to shed some light on the dynamical aspects (evolutionary, population genetics) aspects of Gene Drive (see, for example, Burt and Trivers: Genes in Conflict : the biology of selfish genetic elements), and to initiate open source simulation and data visualization tools based on those ideas.

Biopresence, CRISPR-Forkbomb & HGP-Execute

Georg Tremmel georg@bcl.io


Biopresence

This is a project started with my partner Shiho Fukuhara in 2001. The basic idea is to encode an entire human genome within the DNA of tree, therefore creating 'living memorials' or - as they were dubbed by the Sunday Times - 'transgenic tombstones. While this idea was pre-speculative in 2001, advances in biotechnology in recent years - relatively affordable genome sequencing and genome editing - pushed into the realm of the possible. While we still focus to the technical challenges of realising this project, we were - and are - always concerned about the ethical and moral consequences, which get more pressing the closer we come to finishing the project.

CRISPR Forkbomb

Mixed metaphors are a common sight in the intersection of Biology and Informatics, examples are: Computational Biology, Biological Computation, Genetic Programming, Genetic Programmes, Virus, Infection, etc. Biology and Informatics will probably at some point become a unified information science, but until then we still have opportunities for intentional short-circuits fruitful misunderstandings. One of them could be a CRISPR Forkbomb. Here is a common and popular implementation in the bash shell :(){ :|:& };:

Can there be a biological mechanism that works analogous to a forkbomb? By making additional copies of itself, re-inserting it into the host operation system's genome, until the available space is exhausted the host OS freezes?

HGP-Execute

In early 2016 the original Human Genome Project was re-christened HGP-Read in order to differentiate it from the upcoming HGP-Write, where the human genome is planned to be synthesised, reformatted, defragmented re-inserted into a human cell, in a similar vain of Greg Venter's Synthia.

HGP-Read, HGP-Write... if we follow the sequence, the next logical step in this series must be: HGP-Execute. What exactly this is, what exactly it could be is up for discussion.

Potential application of decentralised information technology architecture such as blockchain in genome editing

Ksenia Bellman (k@diskordia.org)


Stateful databases provide integrity of data and code, which might be useful in bio commons context. Some other technologies I mention further also provide a secure and cryptographically signed, and therefore consistent way for transferring data. Decentralisation of the information technology level is important for citizen science. It may become a secure and reliable communication layer for smaller research facilities, so that they do not have to rely on traditional storage and communication.

I identified a number of potential applications which can be useful in the context of genome editing, storing and sharing results:

•           Using DAT to sync results obtained in a smaller research facilities in a secure way.

•           Using zcash memo field https://z.cash/blog/encrypted-memo-field.html?page... to send sensitive data in a way that it stays immutable, but can only be seen by people it is sent to.

•           Using secure scuttlebutt as communication layer in citizen science context. Secure-scuttlebutt provides tools for dealing with unforgeable append-only message feeds

One of the reasons I mentioned these three projects, is that I communicate closely with their core teams and can ask them to advice on implementation application layer for these protocols. I’m also closely communicating with the core teams of other projects: Raiden, Ethcore, Bigchain DB, IOTA, Golem, in the context of the podcast I’m doing and the events I am organising, which helps me to obtain information about which parts of those technologies are ready for building stable prototypes, and when they will be ready to move to industrial scale.

kitchen.bio: an educational prototyping tool for synthetic biology

Lars Kaltenbach (hello@larskaltenbach.de)


New technologies for synthetic biology will change our environment and even ourselves in the coming years. kitchen.bio aims to open up the tools and the knowledge about genetic modification to a wider public, so that we can have a more objective discussion about opportunities and risks.

The main research objective was to figure out what problems non-scientists have when they try to get involved in synthetic biology. More than eight different interviews with experts and potential users led to three opportunity areas:

1. Accessible tools for synthetic biology are missing

2. The knowledge, which is often hidden in scientific texts, is hard to come by

3. The legal situation is often not clear

During an intense brainstorming session, it was discovered that the process of planning genetically modified organisms is similar to CAD software and programming. Furthermore, focusing on hands-on tools for synthetic biology seemed to be a good way to deepen the knowledge of the users.

Many user tests and interviews helped to refine the final prototype from a broad concept to small interface details. The final prototype consists of three parts:

Software

The software helps to design the functionality of an organism. Different inputs and outputs can be connected in a LEGO-like manner. When the desired functionality was tested in the build-in simulator and thus works, the outcome can be exported to the app.

App

The app displays a walk-through of the steps involved in engineering an organism in the actual lab. Simple recipes tell the user what fluids to order and what preparations to take.

Hardware

A thermocycler is used to keep organisms growing at a constant temperature. But it is also used to heat shock bacteria – a process which makes the cell wall take in foreign DNA. The thermocycler can be connected to the app to find the right setting for the current step in the process.