Is age really just a number? Hundreds of “aging clocks” developed over the last 10–15 years suggest that it is. These clocks aim to measure biological age rather than chronological age—initially using DNA methylation, more recent examples use, e.g., blood proteins. A recent preprint goes a step further by developing “tissue clocks” that predict the biological age of different human tissues from images or even blood samples. The authors reason that tissue structure, with its direct links to physiological fitness, is a better indicator of aging than molecular and cellular changes. For example, dwindling blood vessel numbers and accumulating fibrosis (scarring) are tell-tale signs of tissue aging—wrinkles are not just skin-deep… Perhaps we will soon be able to test which of our organs are aging faster than others, taking personalized medicine to a new level.

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Tissue clocks derived from histological signatures of biological aging enable tissue-specific aging predictions from blood
bioRxiv, November 2024
From the lab of André F. Rendeiro.

Snippet by Katrina Woolcock.

Consider whether you would read an article that reached a conclusion like this: “Our results thus reveal a range of strategies for investing resources in the most expensive machines at the heart of this process.” I probably wouldn’t, since words like “invest” and “expensive” are—shall we say—unattractive to me. But what if the sentence is actually this: “Our results thus reveal a range of strategies for investing resources in the molecular machines at the heart of cellular self-replication.” That’s a sentence from the abstract of this interesting paper in Nature Communications, “Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population.” The authors looked at ribosome numbers and synthesis in individual bacterial cells and found surprising diversity in ribosomal mass and in the timing of responses of individual cells to challenges. Populations are known to respond to metabolic challenges with corresponding shifts in allocation of resources to ribosomal synthesis, but the new paper shows that individual cells vary dramatically in how they do this.

The authors end their paper with this clear and compelling overview, brimming with great metaphors:

…we thus quantified, using a combination of reporter genes and statistical inference algorithms, dynamic investment in ribosomes on the single-cell level. The results reveal a surprising variability in the allocation of resources to ribosomes, the most costly molecular machine in bacterial cells, during both balanced and unbalanced growth. This raises fundamental questions on the role of the variability of ribosome concentrations in shaping the growth of a bacterial population and its adaptation to changing environments. Given the importance of growth and adaptation in biomedical and biotechnological applications, we expect our findings to have practical implications as well.

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Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population
Nature Communications 2 Jan 2025
From the labs of Johannes Geiselmann and Hidde de Jong.

Snippet by Stephen Matheson

Bats are wonders. These are mammals with powered flight, a group of species with a diverse array of senses (sonar!) and lifestyles, that dart around the Sonoran desert where I live, eating flying insects and pollinating native plants. Okay, so they’re also vast reservoirs of coronaviruses, but even that is wildly interesting. Consider a new paper in Nature that just added ten new bat genomes to the genomeosphere (it’s part of an effort called Bat1K; what a time to be alive). They describe scores of immune-related adaptations in bats, many of them clearly positively selected during bat evolution. That alone is interesting, but the work adds to our answers to some big questions: why are bats so tolerant of coronaviruses (they harbor zillions of them but don’t get sick), and how did that come to be in bat lineages? The possible answers are related: bats don’t respond to viral infections (of all kinds) with inflammatory outbursts, and one postulated reason for that is the need for flying mammals, with huge metabolic rates, to avoid triggering inflammation just by being intense. The new paper strengthens this hypothesis by describing significant evolution of immune-related genes in bat lineages, beginning in the ancestral lineage.

Here is some nice science writing from the Results section (lightly edited to remove figure references):

…the ancestral chiropteran branch has almost twice as many immune genes under selection than expected […], thus exhibiting a higher excess of immune gene selection than ancestral branches of all other orders (for example, 42 versus 25 for Afrotheria and 20 versus 21 for Rodentia). A similar pattern is observed for GO ‘immune response’ and SARS-CoV-2 relevant immune pathways. By contrast, genes that are potentially relevant for other bat adaptations (such as longevity and echolocation) show no excess of selection. Together, these data indicate that chiropteran immune system changes are distinctive adaptations that originated early in the chiropteran lineage at the branch in which powered flight also evolved.

 

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Bat genomes illuminate adaptations to viral tolerance and disease resistance
Nature 29 Jan 2025
From the labs of Michael Hiller and Aaron Irving

Snippet by Stephen Matheson