osn-scott.bsky.social

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.

A reminder you/your lab can support FlyBase at Cambridge through the following link. Every bit helps. Please share if you yourself can't donate.

www.philanthropy.cam.ac.uk/give-to-camb...

This tool is great. I’d love it even more if I can compare the long read assembly that I have with an NCBI reference genome! Seems to only take NCBI genomes for comparisons.

Very sad news. I was building HMMER profiles to mine the nascent Celera mouse and human genomes. Such a powerful tool.

BEFORE THE BATHROOM SCALE WAS INVENTED, THE ONLY WAY TO WEIGH PEOPLE WAS MASS SPECTROMETRY.

Love today’s #xkcd comic on
#MassSpec
🤣

We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM

🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩‍💻

📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!

#bioinformatics #opensource #STEMeducation

"As with software, open DNA & strains promotes innovation around the world. I wish to extend Open Yeast & Yeast Protein Expression Toolkits, now in 50 countries, to permit engineering of Yarrowia lipolytica & creating truly open chassis to support boots on the ground innovators."

Here's another #MegabaseSpark submission, from
@osn-scott.bsky.social: "The Open Yarrowia Collection" (detail in reply) Like and repost if you like this idea! #SynBio #RootPath

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

chinnadevarapu.bsky.social has updated his tiny, low cost Pocket Spectrometer design that uses an M5StickC microcontroller and AS7341 spectral sensor - simplified hardware connections and software improvements. Nice job! Details at: github.com/scientistnob...

🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...

Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important

Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing Nature Biotechnology - Metabolites can be quantified using a combination of aptamers and DNA barcodes.

Delighted to share our latest paper describing a method to read the levels of hundreds of metabolites or drugs in parallel using DNA sequencing. This method, which we call ‘smol-seq’ (Small MOLecule sequencing), harnesses the power of DNA sequencing for metabolite detection:
rdcu.be/d8xLv (1/6)

What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...

New Journal Article: “Trust in #Scientists and Their Role in Society Across 68 Countries” www.infodocket.com/2025/01/20/j... #science #trustinscience

Two new studies provide some insights on red meat intake, with respect to both potential risks and how they can be mitigated.
erictopol.substack.com/p/the-update...

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...

Open Source Alternatives To Proprietary Software The world's largest directory for open source software. Discover 500+ popular open source alternatives to proprietary software products. 100% free.

For y’all’s consideration:

Use this site to find open source alternatives to whatever app you want to ditch.

www.opensourcealternative.to?searchTerm=I...

Here it is... it is exclusive, it is arbitrary, and membership will be determined solely by me. You should be upset if you are included, and also upset if you are not included

go.bsky.app/JZc9HXe

PDB101: Molecule of the Month: Assembly Line Polyketide Synthases Large multienzyme complexes that synthesize diverse small molecules in a stepwise manner.

I'm happy and humbled to take on a new role with @rcsbpdb.bsky.social. I'll be continuing David Goodsell's work on the Molecule of the Month, starting with my first article on Assembly Line Polyketide Synthases! Check it out (animation included!)
pdb101.rcsb.org/motm/301

Build instructions for DIYNAFLUOR, a $40 fluorimeter for DNA quantification - uses 3D printed filter cube, LED source, TSL2591 sensor, cheap 10mm square bandpass filters - with full protocols for SYBR Safe dye measurements
github.com/traulab/DIYN... and www.biorxiv.org/content/10.1...