31:T529,md`In 1986, Capecchi & al publish (*10.1016/0092-8674(86)90463-0*) an article in which they show how they "corrected a defective gene residing in the chromosome of a mammalian cell". To do that, they need to select the cells that repaired a break at the right location using **HDR**. They use a selection & antiselection procedure that they dub "gene targeting": - First you generate a DNA piece with a gene of interest + **selectible marker** compound, and flank both extremities with sequences similar to the region you want this piece to be integrated in (homology arms). - **Then you have a problem**: how do you know it's in the *right place*? How do you know it was integrated through HDR rather than by random insertion? How do you know a broken chromosome didn't just swallow your sequence that happened to be there? The solution found by Capecchi & al is to add an **anti-selection marker** after the second homology arm to be able to distinguish the two possibilities: random insertions will still have the TK, while HDR will stop before the homology arm begins, and hence will not include the TK. ✅ It is *theoretically* possible to modify or "correct" a gene in a mammalian cell using gene targeting. ❌ It is *de facto* so hard to obtain that it could not really be used for any real-life purpose. `32:T61a,md`What remained unclear before the 1994-1995 papers by Jasin & al on the one side, and Nicolas & al on the other, is whether this could be used in *somatic mammalian cells using an available delivery strategy*. Can you use the HDR pathway **to change the content of a gene** with a template that you artificially provide? And if you do, at what rate? To determine that, you need to cleave DNA at a precise locus. That's when nucleases get involved. In order to see to what extent sites that have been cleaved are recombined with HDR (compared with other repair pathways, i.e. NHEJ), what you can do is: - integrate a resistance gene (neo for neomycin) in a cell line - interrupt that resistance gene with a sequence that is a target to a homing endonuclease (I-Sce1) - if you transfect the nuclease to the cell and then add neomycin, only those that have been restored after the cut (supposedly through HDR) can survive. The data shows that the indels provoked by NEHJ can also provide resistance. Both studies are more elaborate than that, but the general idea is to show that following a double-strand break, different repair pathways occur in mitotic mammalian cells. ✅ That's where you could start the history of **"genome editing": an endonuclease able to target a specific site, cleave that site and hope to get an outcome that is favorable to your own purpose.** ❌ Yet this isn't really useful either, since the homing endonuclease is only able to target one site, and that site is usually not present in mammalian genomes (18bp length). `33:T914,md`The concerns raised by a capacity to alter genes in living organisms are now **more than a century old**. Sheila Jasanoff summed up their political component in the early XXIst century with a two-fold question : “[…] will continued advances in the life sciences produce a new genetic underclass, and will they simultaneously increase the state’s already immense power to define, classify, and regulate life itself?”. Genome “edited” babies have been born, oils from extracted from TALEN-modified soybeans are on the market, and hornless cattle have been both brought to life and exterminated (following an FDA injunction). Cosmo, first in the second-generation of genome-edited calves, has had a seven-fold inclusion of the variant included in its 17th chromosome. Continued advances in life sciences have produced biological organisms whom, by their sheer existence, question the existing categories among these groups of organisms. **The biosphere is now home to both the edited and the non-edited**. States' “power to define, classify, and regulate life itself”, commonly referred to as biopolitics (or **biopouvoir** in French), has been theorised in a number of ways. The profusion of biopolitical theories, their complexity, and the dominance of bioethics in some parts of the debates on what should or should not be done with CRISPR might have diluted discussions on what genome editing meant for such powers on life. The inclusion of genome editing’s anticipated products in prior controversies, the bioethical debate on its potential and already-existing uses on human germline cells, the framing of life sciences as a risk to be mitigated by state policies have all occurred. But the absence of both a comprehensive institutional framework to make sense of CRISPR on a policy level (in any country) and the stifling the debate of what it meant to States, not as a challenge to their risk-management abilities but as a tool to exert influence over biological lives, is surprising. This is the open question that you might want to think about: not what individuals should or shouldn't be able to do with genome editing, but rather **how can societies decide what States should do with CRISPR?** If you want to learn more, you can watch [this](https://www.youtube.com/watch?v=AxH_MwcO4Y8). `34:[{"id":"0c7dbdb5351f57e141558f3a8dd1c09aa06a4b8fed2e2aadca87dd3ad2fa2b878fd9a5e9cec138cba3ad067fc402f53c3569efc06c7d316836615ebd158ca45f","href":"https://static.observableusercontent.com/files/0c7dbdb5351f57e141558f3a8dd1c09aa06a4b8fed2e2aadca87dd3ad2fa2b878fd9a5e9cec138cba3ad067fc402f53c3569efc06c7d316836615ebd158ca45f","name":"Capture.PNG","type":"image/png","lastModified":1599296981675.549,"size":71751},{"id":"63b3966d1740ddb99ef7958838b9132bdaa9f4a1bf4917571d90f06ace48e99c4c68314a4112a3571f7834f368be52fa791b39dbb602f4c5777589f6a519e618","href":"https://static.observableusercontent.com/files/63b3966d1740ddb99ef7958838b9132bdaa9f4a1bf4917571d90f06ace48e99c4c68314a4112a3571f7834f368be52fa791b39dbb602f4c5777589f6a519e618","name":"Regalado - Gene editing and journalism- What story Whose story And why_1.mp4","type":"video/mp4","lastModified":1599294755352.237,"size":14942012},{"id":"0851f4c94e228733e907011a638ac599f4f1db4b3a7347375329061d8c3744c50cf87704918fd3fb0b5bf297291ec293fa57dbe21c26bd6a7c6447bddf664491","href":"https://static.observableusercontent.com/files/0851f4c94e228733e907011a638ac599f4f1db4b3a7347375329061d8c3744c50cf87704918fd3fb0b5bf297291ec293fa57dbe21c26bd6a7c6447bddf664491","name":"human_practices.png","type":"image/png","lastModified":1599294296087.947,"size":349578}] 2f:{"title":"Biopolitics in the nuclease age: from early genome editing to CRISPR","cells":[{"id":0,"value":"md`# Biopolitics in the nuclease age: from early genome editing to CRISPR\n## iGEM Worldwide Virtual Meetup - Paris 2020 \n\n_CRISPR_ are relatively recent syntagma, but the idea of being able to induce DNA cleavages at precise sites and to ride on a favored repair pathway to achieve an outcome of interest has been present for decades. This short presentation will trace the history of genome editing back from “gene targeting” to the challenges raised by genome editing today.\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":71,"value":"md`\n_This presentation is an interactive [Observable notebook](https://observablehq.com/@observablehq/five-minute-introduction?collection=@observablehq/introduction). Feel free to inspect its code, fork it and explore its dependencies._\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":83,"value":"md` ### Avant-propos: What is left from the SynBERC's parts, devices, chassis, practices and testbeds?`","pinned":false,"hidden":false,"mode":"ojs"},{"id":41,"value":"FileAttachment(\"human_practices.png\").image()","pinned":false,"hidden":false,"mode":"ojs"},{"id":88,"value":"md`\nFrom the project's self-description:\n>Synberc’s research programs focused on projects that developed the foundational understanding and technologies needed to routinely build large numbers of **useful biological systems from standard interchangeable parts**. Synberc also developed a set of collaborative, cross-cutting testbed projects that drove the development of tools and technologies, and provided proof of principle in **building complex applications for real-world problems**.\n\nAmong the five elements that were constituting its core, one stood out:\n> **PRACTICES** – Policies, procedures and ways of thinking about ethical, legal and social issues, as well as safety and security.\n\nThe fact that iGEM exists under its current form, and that this event took place at all, is a clear sign that the _Practices_ element is among those which ended up producing a tangible result. \n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":99,"value":"md`### From gene targeting to genome editing`","pinned":false,"hidden":false,"mode":"ojs"},{"id":115,"value":"html`

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":127,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":68,"value":"neoGene","pinned":false,"hidden":false,"mode":"ojs"},{"id":145,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":102,"value":"md`### Programmable nucleases: the CRISPR acceleration\nBefore CRISPR came Zinc Fingers and TALENs, which are also programmable nucleases. You might learn more about them if you need to achieve outcomes that are hard to get with Cas proteins, but the vast majority of life scientists trained today will most likely start with CRISPR.\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":12,"value":"Fig1","pinned":false,"hidden":false,"mode":"ojs"},{"id":14,"value":"legDiv1","pinned":false,"hidden":false,"mode":"ojs"},{"id":105,"value":"md`### Repair pathways: the example of NHEJ`","pinned":false,"hidden":false,"mode":"ojs"},{"id":21,"value":"Fig2","pinned":false,"hidden":false,"mode":"ojs"},{"id":18,"value":"legDiv2","pinned":false,"hidden":false,"mode":"ojs"},{"id":111,"value":"md `### CRISPR in our biopolitical times`","pinned":false,"hidden":false,"mode":"ojs"},{"id":154,"value":"html`

"This is a restraining order for all genome editors to stay the living daylights away from embryo editing.”

U.K. scientists found that CRISPR caused major unintended edits in human embryos. New from me: https://t.co/DiIBUHuTX8
— Emily Mullin (@emilylmullin) June 16, 2020

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":46,"value":"html`