Gilberto Alvarez

One of my favorite transposon facts. Think LTR retrotransposons are a homogeneous group? The two main kinds -- Ty1 and Ty3 -- are as evolutionary diverged as GIANT SQUID and PINE TREES.

It is good news, but the fact that a headline like this is even possible is very grim news indeed.

😍

🔗 to paper: journals.biologists.com/dev/article/...

Are you a developmental biology researcher working with complicated volumetric data?

Discover LimbLab, an open-source tool that can help you to visualise and analyse 3D data for developmental processes.

www.embl.org/news/science...

It was always clear this was an injustice - but now we know by how much. Absolutely shameful, and as bad as the Nobel neglect of Lise Meitner, if not worse.

So there you have it: AlphaGenome is a great start, and will surely be a valuable tool. Whether it will lead to clinical advances remains to be seen. Its applicability will be limited by its very nature. And we still need to do the basic science. 32/32

… as the researchers say, because they involve “broader biological processes… beyond the direct sequence-to-function scope of the model”. Let me say that more plainly: they are not predictable from genomic sequence, because that is not where the predominant causes lie. /31

Great book! I am enjoying the dynamics of regulation and TAD section a lot! 🙌 😊

(If only someone had written a book explaining all this stuff about the complexities of gene regulation, regulatory sequences, noncoding genes etc… A book about "how life works" 😉). /18

But not only is more of our genome functional than we once thought; also the distinction between what is functional and what isn’t is rather blurry, and there’s no cut-and-dry technique for distinguishing them. /15

This was never really the case. We have known since the 1960s that some of our non-coding DNA has a crucial role in gene regulation: turning the expression of coding genes on & off. It’s been clear for decades that the regulatory DNA is at least comparable in proportion to the protein-coding DNA. /5

I recommend this as a great summary of the debates and the state of play in eukaryotic regulation. I particularly commend the discussion of causation.

The call for Health + Life Science Alliance post doctoral fellowships has just opened: lnkd.in/dw9zxKSN.

Joint with my group @embl.org , Victoria Ingham Uni. Heidelberg, and Felix Hol at Radboud Univ., we are exploring how climate and chemistry shape mosquito behaviour for next-gen. vector control

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General. 

We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/

interesting case of human creativity

Lise Meitner – the forgotten woman of nuclear physics who deserved a Nobel Prize Left off publications due to Nazi prejudice, this Jewish woman lost her rightful place in the scientific pantheon as the discoverer of nuclear fission.

Great photo. Her omission from the 1944 Nobel Prize for the discovery of nuclear fission is said to represent "one of the worst examples of blatant racism and sexism by the Nobel committee."

theconversation.com/lise-meitner...

A photo of the physicist Lise Meitner.

Always loved this picture of Lise Meitner looking like she doesn't take any shit from anyone.

Biologist Elias Barriga studies how frog embryos generate electrical fields to guide cell migration. The study of bioelectricity, formerly stranded in biology’s backwaters, is “coming back like crazy,” he said. www.quantamagazine.org/cells-use-bi...

Advertisement for the book "Quantum Mechanics: A Physical Approach" by Ana Maria Cetto and Luis de la Peña, available as open access on Cambridge Core. The image shows a graphic of the book cover with bold, abstract lines on a blue and green background.

"Quantum Mechanics: A Physical Approach" by Ana Maria Cetto and Luis de la Peña.
This quantum mechanics textbook, suitable for undergraduate and graduate courses, emphasizes conceptual understanding of the subject.
Available #openaccess on Cambridge Core https://cup.org/4alHPzC

For decades, it was thought animals arose via a rapid burst of genetic innovation. But by sequencing their closest unicellular relatives (our beloved protists), we now know most of those genes originated before animals evolved. We have tons of data on that! 😀

The visual system of the longest-living vertebrate, the Greenland shark - Nature Communications The Greenland shark, the longest-living vertebrate, inhabits the dim, frigid depths of the Arctic Ocean. Despite its extreme lifespan, this study finds that its vision remains intact and well-adapted for life in dim light, revealing remarkable preservation of sensory function across centuries.

The Greenland shark, the longest-living vertebrate, inhabits the dim, frigid depths of the Arctic Ocean. A study in Nature Communications finds that its vision remains intact and well-adapted for life in dim light, revealing remarkable preservation of sensory function across centuries. 🧪

🤩

Short linear motifs - Unexplored players driving Toxoplasma gondii infection Pathogens infect hosts by interacting with host proteins and exploiting their functions to their advantage. Short linear motifs, small functional regions within intrinsically disordered protein regions, are common mediators of host-pathogen protein interactions. While motifs have been more extensively studied in viruses and bacteria, the extent to which eukaryotic unicellular parasites use motifs during infection remains unexplored. Toxoplasma gondii is a widespread intracellular Apicomplexan parasite capable of infecting all warm-blooded animals and invading any of their nucleated cells. Toxoplasma's secreted proteins are key in interacting with host proteins during infection, making them potential sources for motifs. To highlight the role of motifs in Toxoplasma gondii infection, we curated 20 known motif instances in Toxoplasma proteins from the scientific literature. To identify more motifs in Toxoplasma secreted proteins, we developed a computational pipeline that annotates putative motif matches with structural and functional features. Through this approach, we identified a set of 27,832 motif matches in 296 secreted proteins. We highlight strategies for further prioritisation of likely functional motif matches by focusing on integrin motifs, degrons and TRAF6-binding motifs. We subjected four predicted TRAF6-binding motifs to experimental validation, supporting the predicted motifs in the Toxoplasma proteins RON10 and GRA15. Our motif predictions provide a valuable resource for generating hypotheses and designing experiments to study infection mechanisms. The characterisation of motifs in Toxoplasma will be key to understanding the molecular principles underlying its broad host range and more comprehensive Apicomplexan infection strategies. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, 449991970

New preprint! Here, we highlight the role of motifs during the Toxoplasma host cell invasion, predict thousands of motifs in its effector proteins, and validate the binding of TRAF6 motifs. Our results are intended to catalyse further research on motifs and parasites.
www.biorxiv.org/content/10.6...

First hours of embryonic zebrafish development. Credit to Mona Wellhäusser, Timo Schreiber, & @lennarthilbert.bsky.social. #ZebrafishZunday 🧪

Fundamental logic of life paper receives Outstanding Publication award In October, the International Society for Artificial Life recognized several SFI researchers and co-authors with the ISAL Award for Outstanding Publication of 2024. The award celebrates the paper “Fun...

In October, the International Society for Artificial Life recognized several SFI researchers and co-authors with the ISAL Award for Outstanding Publication of 2024.

The award celebrates the paper “Fundamental constraints to the logic of living systems," which was published last fall.

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...

Well well. The standard model for how frequencies of recessive disease genes are established doesn't work. And that seems to be because recessive variants are visible to selection due to pleiotropy. (But still we teach Mendelian genetics...)
www.biorxiv.org/content/10.6...

Read more here www.dpag.ox.ac.uk/named-lectur...

Generative epigenetic landscapes map the topology and topography of cell fates | PNAS Epigenetic landscapes were proposed by Waddington as the central concept to describe cell fate dynamics in a locally low-dimensional space. In mode...

Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection - Nature Microbiology The Toxoplasma gondii effector TgROP1 mimics host factors to bind VAPA/B, thereby establishing parasite–host ER contact sites.

During host cell invasion, Toxoplasma mimics the FFAT motif and repurposes it to associate its parasitophorous vacuole to the endoplasmic reticulum!

I'm happy to have been part of this work! Congratulations to Chahat Mehra and Lena Pernas for all the hard work!
www.nature.com/articles/s41...