Philipp Niethammer
@niethammerlab.bsky.social
Cell biologist interested in how tissues sense and adapt to physical and chemical stress. Wound healing and regeneration. Quantitative imaging approaches. Nuclear mechanotransduction, ROS signaling & metabolism. All opinions are my own.
A 15-year history of my lab in signed champagne bottles. We always find some reason to celebrate: papers, fellowships, prizes - 🙏 to all the good people in the lab. Yet we have never opened the BIG bottle - now it's time 😅. Hope it fits on the shelf.
Very interesting work! www.nature.com/articles/s41...
Screening of amphipathic helices identifies features linked to inner nuclear membrane properties - Nature Communications
The properties of the nuclear envelope and mechanisms of peripheral protein association are poorly understood. Here, authors show sensing lipid packing defects and a minor electrostatic contribution g...
nature.com
I just updated LCS turbo adding a compatible Connector app at Zenodo. The Connector connects logical or marker/scRNAseq clusters across different experiments/data sources into Cytoscape compatible enrichment networks. Hope it is useful - I count downloads as ❤️. zenodo.org/records/2064...
Philipp Niethammer@niethammerlab.bsky.social · 2mo agoNow live: LCS 3.0 engine rebuild with C++ with command line our GUI interface. Optional bioconductor edgeR filters and stats (slow), and fast internal stats (correlationdistance & welch test). Can be integrated into any bioinformatics pipline as executable. (1/5)🧵 zenodo.org/records/2063...
Independent thinkers are rare, technically adept followers are plenty. Understanding/questioning what is closest to us -current concepts, life, reality, ourselves, etc- is the most difficult thing. It has never been different. No wonder that many people prefer to 👉 „shut up and calculate“ 😉
Thiago Carvalho@cyrilpedia.bsky.social · 2w ago"For me, the ending of the talk was the most relevant part. Chalfie asked how we can become better at making new discoveries. His answer was surprisingly simple: we need to 'question what is right in front of us' and 'question our assumptions'." network.febs.org/posts/thinki...
www.nature.com/articles/s41...
CD44 restricts EGFR mobility to polarize cytoskeletal signalling modules driving bleb-based migration - Nature Cell Biology
Jha et al. show that the transmembrane protein CD44 restricts EGFR mobility to maintain an EGFR–PI3K–Rac gradient during bleb-based cell migration.
nature.com
So proud of @sydsat.bsky.social, the lab’s first graduate student, for leading this work! Special thanks to the Searle Scholars Program and the Royalty Research Fund for making it possible. Check out the preprint here: www.biorxiv.org/content/10.6...
Early immune cell development precedes gastrulation in annual killifish
During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...
biorxiv.org
Our Special Issue: Cell Biology of the Nucleus is complete Explore our Toc: journals.biologists.com/jcs/issue/13... Our cover image shows the posteriorly positioned nuclei (Nup50-mCherry - pink) of notochord cells in Ciona embryos. See article by Peng et al. journals.biologists.com/jcs/article/...
Can somebody implement a bot-safe preprint server pls? I'd love to submit our preprints somewhere safe from gold-digging AI venture capitalists that, while pretending to do us a service, end up milking the scientifc community as usual.
"Humanity is put to the test, claimed, and challenged by a power that becomes manifest in the essence of technology and which humanity itself no longer controls." nissenbaum.tech.cornell.edu/papers/heide...
nissenbaum.tech.cornell.edu
Now live: LCS 3.0 engine rebuild with C++ with command line our GUI interface. Optional bioconductor edgeR filters and stats (slow), and fast internal stats (correlationdistance & welch test). Can be integrated into any bioinformatics pipline as executable. (1/5)🧵 zenodo.org/records/2063...
www.nature.com/articles/s41...
Long-range mutual activation establishes Rho and Rac polarity during cell migration - Nature Cell Biology
De Belly et al. show Rac induces membrane-tension-mediated mTORC2 activation to stimulate long-range Rho activation. Meanwhile, Rho-mediated contractility and blebbing at the opposite side of the cell...
nature.com
I am (well...AI is) currently porting LCS 3.0 from MATLAB to C++ to compile it into binaries that can be used by standard bio-info pipelines. Stick around...
Philipp Niethammer@niethammerlab.bsky.social · 7mo ago
Fintastic lay summary by @unevadareno.bsky.social on recent #cavefish work from the Riddle Lab 🐟 🔗 to original research published in @currentbiology.bsky.social: www.cell.com/current-biol...
Disruption of carotenoid metabolism in cavefish via loss of beta-carotene oxygenase 2a
Guerra et al. show that carotenoid-accumulating cavefish harbor loss-of-function mutations in beta-carotene oxygenase 2a. The locus shows signatures of selection, consistent with an adaptive role for ...
cell.com
The University of Nevada, Reno@unevadareno.bsky.social · 2mo agoWhat can eyeless cavefish teach us about nutrition and evolution? College of Science researchers are uncovering how these fish process carotenoids in surprising ways, offering new insights into how organisms adapt to extreme conditions. https://bit.ly/4uEd28m
Smile like Megalochelys atlas because it’s #FossilFriday! This species was one of the largest known land turtles & lived during the Late Pliocene ~2 million years ago. This specimen’s shell measures some 7.4 ft (2.3 m) long and in life, it may have weighed more than 2,000 lbs (907 kg)!
Bumble bees - the dolphins of the insect clade. Their short little lives are very well lived. Bumble bees are smart... www.science.org/doi/10.1126/... ...and groove! www.science.org/doi/10.1126/...
Spontaneous problem-solving in bumble bees
Problem-solving using novel solutions without explicit training is often considered a hallmark of cognitive flexibility. We investigated whether bumble bees (Bombus terrestris) could solve a novel obj...
science.org
A membrane-permeable small molecule biosensor accesses intractable cells and animals without genetic manipulation www.biorxiv.org/content/10.6...
biorxiv.org
www.nature.com/articles/s42...
Overlapping expression and co-operative function of the zebrafish pcdh15 paralogs - Communications Biology
Contrary to previous reports, zebrafish paralogs pcdh15a /15b both contribute to ear and eye development but display isoform expression bias. Double mutants have the most severe phenotypes, including ...
nature.com
If the technicalities of writing and convincing become cheap „word math“, will this help us to finally embrace depth of thought over form and persuasion? Less word-pushing , more scientific creativity? Or just more slop? www.nature.com/articles/s44...
Thinking is not only writing - Nature Reviews Bioengineering
Generative artificial intelligence (AI) raises valid concerns about the loss of cognitive work embedded in scholarly writing. However, universally dismissing AI-assisted drafting mistakenly conflates ...
nature.com
New preprint from the lab, led by Bradley Cutler. With the @james-gagnon.bsky.social lab we use zebrafish to show that fever is not a reduction in the perception of warmth. Immune signals instead increase the valence of warming stimuli while cooling turns aversive. www.biorxiv.org/content/10.6...
so maybe this protein is acting as a calcium sensor to let the cell keep track of its current stimulation state or past stimulus history. right now, almost any hypothesis can be on the table. in case you missed the paper you can read it here: www.cell.com/current-biol...
Molecular pathways for learning in the single-cell Stentor coeruleus
Rajan et al. explore the molecular basis of habituation in the unicellular organism Stentor coeruleus using a combination of pharmacological methods, proteomics, transcriptomics, and RNAi. These exper...
cell.com
My PhD work showed that resting neutrophil -> activated/prime neutrophil is a pretty big volume change needed for motility :) Super fast, only a couple minutes to swell so not like other slower changes elifesciences.org/articles/90551
Neutrophils actively swell to potentiate rapid migration
Actin-independent water influx complements actin-driven cytoskeletal forces to potentiate chemoattractant-induced migration in primary human neutrophils.
elifesciences.org
