osn-scott.bsky.social

Plant assembly in OpenCloning soooooon!

I am very much looking forward to SynBio 8.0 in June. I will be speaking on a panel regarding open lab resources and IP -details to follow. It will also be awesome to connect in person with friends back east. This is Canada’s premiere synthetic biology meeting, hosted by U of Waterloo. Go Register!

I've been working with the OpenCloning Assembler with the syntax of my Open Yeast System - both the Open Yeast Collection and Yeast Protein Expression Toolkit. It is a very powerful open approach for rapidly assembling constructs when you have a library of parts. Try it with your Golden Gate system.

Registration now open for SynBio 8.0, June 15-17 at the University of Waterloo. www.synbiocanada.org/synbio8

Join us at Canada’s premier synthetic biology conference, bringing the community together to showcase advances from across the country and across the full breadth of the field! #synbio8 🍁🧬

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

Alliance version 8.3.0 is now live at alliancegenome.org. Release notes are here www.alliancegenome.org/release-notes

Revised estimates of CO2 sources and sinks improve global carbon accounting Updated estimates of the worldwide sources and sinks of anthropogenic carbon dioxide provide a firmer basis for monitoring climate action.

I am happy to share my @nature.com News & Views summarizing the recent adjustments to the Global Carbon Budget www.nature.com/articles/d41...

LLM use in scholarly writing poses a provenance problem Nature Machine Intelligence - LLM use in scholarly writing poses a provenance problem

It’s good to see papers start to address LLMs as structural plagiarism — provenance, more hidden than the original words or training data. www.nature.com/articles/s42...

That is a very short statement!

🚀 A long-requested feature just landed in #OpenCloning

🔬🧬 You can now manually annotate sequences and create primers right from the editor

✨ Hope it makes your workflow a bit smoother!

📨 If you want to stay updated with upcoming features, subscribe to the mailing list (link in the comments)

@atinygreencell.bsky.social

Here is another paper that gives a lot of background on the IS10 transposon integration and what regulates it. pmc.ncbi.nlm.nih.gov/articles/PMC... What is the e coli strain that you used?

I see. Is the transposon jumping into the same sequence in your two plasmid examples? There might be clues to help you in PMID: 11683262 and PMID: 8863735 (who's plasmid SCU46780 is in Genbank).

You don't say which tool(s) you are using to create/annotate the plasmid map. Looks like it could be an annotation from pLannotate. If you have your file in the Genbank format, rather than a proprietary one, you can open it and delete any annotation that bugs you.

Estimation and mapping of the missing heritability of human phenotypes - Nature WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...

First time on Bsky and first big announcement!

I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.

Our manuscript is here: www.nature.com/articles/s41....

Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.

(Please repost to reach a broad audience.)

Better than making Marmite. 😝

Origins of the Lab Mouse How the mouse found its way from Victorian novelty to a biomedical mainstay.

'When Mendel began his investigation, his first inclination was to try breeding mice of different colors. However, before his mice experiment really got going, Mendel was forced to switch the subject of his experiments to peas by a prudish bishop uncomfortable with animals having sex in the abbey.'

Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats sheds new light on bat-borne coronaviruses evolution Understanding the viral diversity harboured by wildlife is essential for effective prediction and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for...

Helpful to read the preprint in this discussion (for those who care to). www.biorxiv.org/content/10.1...

Remembering Hamilton O. Smith Hamilton O. Smith August 31, 1931 – October 25, 2025 It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...

My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...

R.I.P Hamilton Smith, 1978 Nobel Laureate for the discovery of type II restriction-modification systems (HindII).

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity A prokaryotic RNA–directed targeting system can be designed to cleave any DNA sequence.

13 years ago, the revolutionary genetic tool #CRISPR/Cas9 was published in Science, work that Emmanuelle Charpentier and Jennifer Doudna won a #NobelPrize for in 2020.

On #WorldCRISPRDay, read the landmark paper that describes the discovery: https://scim.ag/42JHuSN

As a member of the @igemcommunity.bsky.social Engineering Committee I received additional small grants to extend these toolkits both of which are now in over 50 countries around the world. Congratulations to the four other recipients. |5/5|

More recently, @jenny-molloy.bsky.social, through a grant from the University of Cambridge Impact EPSRC Impact Acceleration Account, funded the synthesis of the first round of the Yeast Protein Expression Toolkit. ...4/5

The original OYC is a foundational and enabling framework for contributing to the creation of an open, sustainable and equitable bioeconomy. Synthesis of the original Open Yeast Collection was funded and distributed by @drewendy.bsky.social's BioBricks Foundations FreeGenes program. ...3/5

The Yeast Protein Expression Toolkit extend the Open Yeast Collection by offering a library of DNA parts for adding protein fusion tags, including secretion signals, purification tags, linkers, fluorescent proteins and protease cleavages sites.

Yeast Protein Expression Toolkit to permit engineering of the “non-conventional” oleaginous yeast species Yarrowia lipolytica. Imagine one universal toolkit for all of the common industrial and research yeast species. ...2/5

The Open Yeast Collection (OYC) is an open DNA toolkit released under the OpenMTA for engineering yeast. It is a library of DNA parts that can be assembled into constructs to produce proteins or develop metabolic pathways in yeast.

A big thank you to RootPath and its reviewers on selecting my project for the inaugural #MegabaseSpark competition. 100kbp of free rBlock DNA synthesis is very significant. I am very excited to put this win to good use in extending Open Yeast Collection (OYC) and the ...1/5

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

Related but cool combo of cytogenetics and phenotype. Know when the first QTL was mapped?

Sax, K. 1923. The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552-560.