New paper from the lab on phage-assisted evolution of allosteric light-switches now out in Nature Comms. Congratulations to Nick and all co-authors! www.nature.com/articles/s41...

Job Summary: The FlyBase project is an international collaboration of ~35 people distributed at several sites. This position is located at Harvard University, Cambridge, MA. All FlyBase staff work as a part of a team, in which curators and software engineers collaborate extensively. Each site has its own set of responsibilities. The Harvard FlyBase curators focus on curation/annotation of literature and high-throughput data pertaining to the Drosophila genome, transcriptome and proteome. FlyBase is constantly evolving, seeking both to improve and to expand its role within the Drosophila and wider scientific communities. The ideal applicant will be enthusiastic about participating in this process, bringing to the FlyBase group expertise and ideas concerning emerging directions in Drosophila biology and genomic/proteomic analysis. FlyBase is increasingly integrating artificial intelligence and machine learning tools into its curation workflows. The ideal candidate will be open-minded and enthusiastic about exploring AI-assisted approaches to biological data curation, including the use of large language models and AI coding assistants to accelerate and enhance curation tasks.

Job-Specific Responsibilities: • Reading and abstracting of data from the current Drosophila literature, including its relationship to human disease, physical interactions, and gene expression • Evaluating and validating AI generated annotations and curation suggestions, ensuring accuracy and biological relevance before integration into the database • Using AI coding assistants (e.g. Claude Code, Codex, Gemini) to write scripts for data wrangling, format conversion, and routing curation tasks • Providing feedback on AI model outputs and refining prompts to help improve automated curation pipelines and annotation quality over time • Annotation and analysis of the Drosophila melanogaster genome, including gene models, mapped mutations, and regulatory features • Together with curators and developers at other sites, interact with broad research community by answering helpmail and giving presentations and tutorials at research conferences • Handling high-throughput datasets and associated metadata

FlyBase is seeking a new scientific curator at our Harvard University site.
More information here: wiki.flybase.org/wiki/FlyBase...

Result of yesterday's sourdough session.

France is switching from Microsoft to Linux

"We must become less reliant on American tools and regain control of our digital destiny. We can no longer accept that our data, our infrastructure, our strategic decisions depend on solutions whose rules, pricing, evolution, and risks we do not control."

Hey Hungary, thanks for this deeply unfamiliar emotion I just experienced while checking the news. If I remember correctly it's called 'optimism'. 🇭🇺

Prime Minister Sanchez:

“.. Spain will not applaud those who set the world on fire just because they show up with a bucket.” 🇪🇸

The variety of German bees before the Industrial Revolution (187, top) vs after the introduction of pesticides (43, bottom), DHM

You need to make AI guidelines for your lab Here's why you should, and how to start

I wrote about why every lab should have AI use guidelines, and how to do it.

open.substack.com/pub/blekhman...

Immune evasive DNA donors and recombinases license kilobase-scale writing - Nature INSTALL overcomes fundamental challenges for DNA delivery and integration methods by synergizing immune-stealth nucleic acids with recombinases to enable kilobase-scale integration strategies without ...

Today in @nature.com we introduce INSTALL, which bypasses mammalian DNA immune sensing to enable non-viral DNA integration with recombinases—a step toward safe, and mutation-agnostic genome editing. 🧬 🧵 (1/13)

www.nature.com/articles/s41...

@harvardmed.bsky.social @mgbresearch.bsky.social

Germ cells have their own versions of core transcription factors and fertility depends on them.
We're hiring a PhD student to figure out how! 📢
Fly genetics + proteomics + genomics. Fully funded.
Aarhus University 🇩🇰
Deadline May 1 👇

Please share with anyone who might be interested!

Obviously just self defense to avoid having his mentions clogged up with RHCP songs... 😆🎸

ERK inhibits Capicua repressor function via multisite phosphorylation Highlighted Article: Multisite phosphorylation is important in the regulation of the Capicua (Cic) repressor by ERK, in part because multiple phosphosites contribute to Cic protein degradation.

I am excited to share that our paper on ERK-mediated Capicua (Cic) phosphorylation was published in its final form at @jcellsci.bsky.social ! A short 🧵 1/5
journals.biologists.com/jcs/article/...

Details of all Heidelberg CFD CRISPR Library lines distributed by the VDRC (Cas9- and Cas12a-mediated mutagenesis and Base Editing): shop.vbc.ac.at/vdrc_store/h...
GRACE reporter stocks available: shop.vbc.ac.at/vdrc_store/3... and shop.vbc.ac.at/vdrc_store/3....

Figure showing the principle of the GRACE reporter: CRISPR mutagenesis inactivates an uORF that inhibits GFP translation. Below are several examples of Drosophila wing imaginal discs expressing GRACE and Cas12a+ under control of different Gal4 drivers.

Mapping #CRISPR activity patterns with GRACE. In vivo gene editing sometimes happens at unexpected places. Reporters, such as GRACE, light up the cells that have been mutated. Flies are at @vdrc-flies.bsky.social and plasmids @addgene.bsky.social

Described here:
www.nature.com/articles/s41...

graphical abstract for "Developmental determinants of male bias in medulloblastoma" preprint. We propose that boys are more likely to develop Group 3/4 medulloblastoma more vulnerable cells-of-origin are available for transformation. Specifically, GC_UBC progenitors in the developing cerebellum are more abundant in male murine embryos, as a result of testosterone exposure and the XY genotype.

New preprint alert! I'm excited to share our latest preprint where we investigate the underlying developmental causes of the male bias in the pediatric brain tumor Group 3/4 medulloblastoma. www.biorxiv.org/content/10.6...

A high-affinity split-HaloTag for live-cell protein labeling Nature Communications - Lin and colleagues present high-affinity split-HaloTag pairs for protein tagging and multiplexed labelling. This versatile system allows protein visualisation with diverse...

A high-affinity split-HaloTag for live-cell protein labeling. And much more.
www.nature.com/articles/s41...

This paper is super cool. Squeaky-clean genetic evidence that Wnt cis-regulatory alleles tune horn length in caterpillars.

Header image for the PhD position "Advanced genome engineering to investigate Wnt signaling in animals."

Join us in Heidelberg for your PhD! If you are excited about CRISPR genome engineering and would like to develop and apply new methods to investigate Wnt signaling in different model systems, than this project is for you. More info here:

my-hbigs.uni-heidelberg.de/site/index.p...

🧪🧬🔬

Header image for the PhD position "Advanced genome engineering to investigate Wnt signaling in animals."

Join us in Heidelberg for your PhD! If you are excited about CRISPR genome engineering and would like to develop and apply new methods to investigate Wnt signaling in different model systems, than this project is for you. More info here:

my-hbigs.uni-heidelberg.de/site/index.p...

🧪🧬🔬

For us it often looks like this:

Get a rough idea what's going on: >Sanger

then quantify and see what mutations are present with:

Miseq, when editing with single sgRNAs, prime- and base editing.

Nanopore, when editing with multile sgRNAs per locus.

All of these methods are typically run on PCR amplicons of the target locus, which comes with some problems (PCR bias, chimeras, etc.).

Depends on what you need. Sanger: Cheap and fast, but low sensitivity and bulk read-out. Short-read (e.g. Miseq): Sensitive and single molecule, but blind to large mutations. Expensive or cheap denpending on how many samples you multiplex. Nanopore: Fast and better for larger mutations deletions.

Proper organelle regulation during mitosis is a must, but how do membrane-less condensates like PML bodies behave during cell division? In work led by Eric Aird, we found the balance of speckled proteins SP110 & SP100 to be the key. doi.org/10.1038/s415...

Delighted to announce the posting of our latest preprint, which links stress-induced relocalisation of multiple organelles by dynein to adaptive changes in gene expression in the nucleus (1/n) 🧵

www.biorxiv.org/content/10.6...

Data Organization in Spreadsheets Karl W. Broman & Kara H. Woo Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018 1. Introduction 2. Be Consistent 3. Choose Good Names for Things 4. Write Dates as YYYY-MM-DD 5. No Empty Cells 6. Put Just One Thing in a Cell 7. Make it a Rectangle 8. Create a Data Dictionary 9. No Calculations in the Raw Data Files 10. Do Not Use Font Color or Highlighting as Data 11. Make Backups 12. Use Data Validation to Avoid Errors 13. Save the Data in Plain Text Files ABSTRACT Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.

Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice.

www.tandfonline.com/doi/full/10....

I started Awesome Life Science Resources: a curated list of resources on work culture, career, and communication for life scientists. Built for PhD students, postdocs, and PIs.

Check it out:
github.com/jjfroehlich/...

Germany does not lack talent, and it does not lack funding. But we are trapping 21st-century minds inside 19th-century academic hierarchies. We are asking brilliant young scientists to build the future of the German economy, but refusing to give them the lab space, the job security, or the scientific independence to actually do it. If we want to reclaim our place as an industrial superpower, we have to stop the rat race of trying to keep every technology and structure alive that made us successful in the 20th century. Instead, we must fix our system that pushes our most ambitious scientists away. The money is there. The talent can be there. Now, we also need the courage to fix what’s broken.

“we are trapping 21st-century minds inside 19th-century academic hierarchies.” This essay gets a lot right about problems with German science. I would add that the hierarchies and precarious contracts lead also to systemic abuse and scientific misconduct. open.substack.com/pub/realimag...

For the full 2005 vibe you should use Comic Sans for the yellow and blue sections... 😆

Very cool! 🤩

4D4 is 🏅. Thanks @dshb-antibodies.bsky.social for everything you do! #Dros26 #fluorescencefriday