Lightnews — Scholar-powered news

Reposted by Gavin Woodruff

Wellcome Sanger Institute @sangerinstitute.bsky.social · 3h

Read ‘Sperm sequencing reveals extensive positive selection in the male germline’ from @sangerinstitute.bsky.social and collaborators in @nature.com below:

nature.com/articles/s41...

Sperm sequencing reveals extensive positive selection in the male germline - Nature

A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.

nature.com

6 9

Reposted by Gavin Woodruff

James Briscoe @jamesbriscoe.bsky.social · 1d

Very sad news, John Gurdon has died.

A developmental biologist's developmental biologist, Nobel prize winner

His work is the foundation of much of today's dev & stem cell bio.

An inspiration to many, including me. Always asking questions & wanting the answers

www.magd.cam.ac.uk/news/profess...

Professor Sir John Gurdon FRS (1933-2025) | Magdalene College

Magdalene College is deeply saddened to announce the death of Professor Sir John Gurdon FRS, who served as Master of the College from 1995 to 2002.

www.magd.cam.ac.uk

7 100 180

Reposted by Gavin Woodruff

Matthew Hahn @3rdreviewer.bsky.social · 2d

The most important paper in evolutionary biology I'd never heard of:

1/

www.sciencedirect.com/science/arti...

2 20 45

Reposted by Gavin Woodruff

Cameron Thrash @jcamthrash.bsky.social · 5d

Bifurcations and phase transitions in the origins of life royalsocietypublishing.org/doi/10.1098/... #jcampubs

2 4

Reposted by Gavin Woodruff

Priti Agarwal @pritiagarwal.bsky.social · 5d

🚨 New preprint!
We profile the transcriptome of the C. elegans distal tip cell: a persistent leader cell that invades basement membrane to shape the gonad.

Our dataset defines the molecular signature of invasive leader cells & uncovers new regulators of collective cell invasion.

Stage-specific transcriptomics of a leader cell reveals cell machineries driving collective invasion

Collective cell invasion underlies organ development, epithelial repair, and cancer metastasis. Leader cells remodel extracellular matrix, sense guidance cues, reorganize their cytoskeleton, and coord...

www.biorxiv.org

1 6 11

Reposted by Gavin Woodruff

Brian J. Enquist @bjenquist.bsky.social · 11d

Genomic divergence across the tree of life 🧪🌐https://www.pnas.org/doi/10.1073/pnas.2319389122

Genomic divergence across the tree of life | PNAS

Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed. Bu...

www.pnas.org

1 24 77

Reposted by Gavin Woodruff

Matt Rockman @wormsrock.bsky.social · 13d

That is, Oceania looks like a source for Asian species, not the reverse! Here’s the preprint.

Caenorhabditis diversity on Pohnpei, Micronesia, provides evidence that the Elegans Supergroup has its roots in the Americas and diversified in the Pacific en route to Asia

The microscopic nematode Caenorhabditis elegans stands unrivaled as a model for developmental biology, neurobiology, and genetics, but fundamental aspects of its ecology, biogeography, and natural his...

www.biorxiv.org

1 5 28

Reposted by Gavin Woodruff

Jennifer Mach (she/they) @jennifermach.bsky.social · 15d

#PlantScience and #TESky!

Hugues Renault @huguesrenault.bsky.social · 15d

Transposable elements are vectors of recurrent transgenerational epigenetic inheritance | Science www.science.org/doi/10.1126/...

Transposable elements are vectors of recurrent transgenerational epigenetic inheritance

DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...

www.science.org

4 10

Gavin Woodruff @weirdworms.bsky.social · 17d

Aging by the clock and yet without a program

www.nature.com/articles/s43...

Aging by the clock and yet without a program - Nature Aging

Meyer and colleagues refute the idea that, as aging can be tracked precisely by clocks, it must be driven by a biological program. They propose that imperfect maintenance and repair processes resultin...

www.nature.com

1 2

Reposted by Gavin Woodruff

mathiaseder.bsky.social @mathiaseder.bsky.social · 19d

✨Exciting news: the main story of my PhD is out in Science!

Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.

📖 Read the full story here: www.science.org/doi/10.1126/...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

www.science.org

3 37 93

Reposted by Gavin Woodruff

Nature Methods @natmethods.nature.com · 19d

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

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

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

21 81

Reposted by Gavin Woodruff

Alex Crits-Christoph @acritschristoph.bsky.social · 20d

Great and nuanced thread. But I think we can expand further. As noted, phage selected for synthesis, and that worked, were significantly less novel.

In Fig 4D, there's a very strong correlation between novelty and not working. The phage that worked were much less novel. This is nucleotide ID!

1 4 14

Reposted by Gavin Woodruff

Jase Gehring @skyjase.bsky.social · 20d

very cool work and a milestone in synthetic biology. how impressive are the new phage genomes?

with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look

Samuel King @samuelhking.bsky.social · 21d

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

2 9 12

Reposted by Gavin Woodruff

Julius Brennecke @juliusbrennecke.bsky.social · 21d

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...

2 41 89

Reposted by Gavin Woodruff

Ákos T Kovács @evolvedbiofilm.bsky.social · 24d

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation

Penicillium solitum over 8 years in a cheese cave => green-to-white shift

@currentbiology.bsky.social from @benwolfe.bsky.social with @kellerlab.bsky.social

www.cell.com/current-biol...

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation

Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated Penicillium population has adapted in an artisan cheese production facility in Vermont, USA. Adaptation i...

www.cell.com

13 33

Reposted by Gavin Woodruff

Charlotte Wright @charlottewright.bsky.social · 27d

How many chromosomes can an animal have?

In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...

Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly

The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...

tinyurl.com

4 99 210

Reposted by Gavin Woodruff

Maria Paz Fernandez @mariadelapax.bsky.social · 29d

New publication from our lab, in Science Advances:

Synaptic targets of circadian clock neurons influence core clock parameters

www.science.org/doi/10.1126/...

Synaptic targets of circadian clock neurons influence core clock parameters

A neuron type downstream of circadian pacemakers regulates daily sleep and activity timing in Drosophila.

www.science.org

3 14 57

Reposted by Gavin Woodruff

David Schoppik @schoppik.com · Sep 8

There’s a ton of work by e.g. @bassemh.bsky.social and co exploring this interesting question. www.science.org/doi/10.1126/...

A neurodevelopmental origin of behavioral individuality in the Drosophila visual system

Individual variation in how neural circuits develop in fruit flies underlies variations in individuals’ behavior.

www.science.org

1 5 17

Reposted by Gavin Woodruff

Maren Wellenreuther @marenwellenreuther.bsky.social · Sep 5

Size matters—but maybe not how we thought. Most chromosomal inversions are just a few hundred bp. Ignoring these “small players” could mean we’ve misunderstood how genomes evolve -out in TREE authors.elsevier.com/a/1ljL1cZ3X3...

10 24

Reposted by Gavin Woodruff

Emily Josephs @emjo.bsky.social · Sep 4

A student in my undergrad genetics class asked me about my favorite example of epistasis and I totally blanked. Does anyone have any favorites to share?

15 11 28

Reposted by Gavin Woodruff

Luisa Cochella @lcochella.bsky.social · Sep 3

Our work on the function of miR-51/miR-100 is out! miR-100 is widely conserved across eumetazoans but its function has been mysterious. Emilio Santillán found in worms it regulates signaling and extracellular matrix genes, some of which seem to be conserved targets! www.science.org/doi/10.1126/...

An ancient and essential miRNA family controls cellular interaction pathways in C. elegans

A microRNA that arose at the origin of eumetazoans regulates cell adhesion and signaling in C. elegans through conserved targets.

www.science.org

5 35 92

Reposted by Gavin Woodruff

Craig Kaplan @triggerloop.bsky.social · Sep 3

Look at this crazy thing!
www.nature.com/articles/s41...

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

www.nature.com

4 65 150

Reposted by Gavin Woodruff

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · Sep 1

What's the difference between dominance and epistasis? Two physically distinct mutations in a gene interact such that the het is identical to one of the homozygotes. If I define the gene as a locus, we call this dominance. If I define each bp as a locus, we call this epistasis.

16 23 84

Reposted by Gavin Woodruff

Emily Troyer @fishfetisher.bsky.social · Sep 1

Excited to announce that the 1st paper from my postdoc is now out in @currentbiology.bsky.social ! Using a large dataset of 3D preserved fossils, we explore the diversification of jaws in early bony fishes. 1/15
www.cell.com/current-biol...

Macroevolutionary role reversals in the earliest radiation of bony fishes

Troyer et al. examine lower jaw evolution in Silurian-Devonian bony fishes and find substantial differences in patterns of morphological disparity, rates of shape evolution, and functional diversity b...

www.cell.com

8 67 180

Reposted by Gavin Woodruff

Current Biology @currentbiology.bsky.social · Aug 28

Feeling mitochondrially challenged lately?

Here are two classic reviews on #mitochondria that should help.

www.cell.com/current-biol...

www.cell.com/current-biol...

The Origin and Diversification of Mitochondria

Moving beyond the simplistic view of mitochondria as the power house of the cell, Roger et al. present the immense diversity of mitochondria and mitochondrial functions across eukaryotes, and bring th...

www.cell.com

3 44 120