17 May 2023

 


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3 Sep 2023

Back from travel and I had time to spot lots of interesting science to dump here, maybe too many this week. A lot of bacterial and phage microbial ecology this week, a dash of cancer, antibiotics, and covid. Lots of game theory! I like that the focus is changing week to week. We have:   Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein Another week, another Lauring Lab paper. They assay 84% of all substitutions in the AH1N1 flu polymerase catalytic subunit, since it’s commonly involved in host adaptations when jumping species barriers. They compare their experimental data of the fitness effects of individual mutations to observational data from flu genomic surveillance. A lot of interesting lessons here, but I’ll note real mutational landscapes are a lot more constrained than the experimental data shows, in good part determined by mutation accessibility. https://doi.org/10.1101/2023.08.27.554986 ...
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6 Aug 2023

Some papers and resources from the past couple of weeks! Big backlog here, something for everyone here: Genetic effects on molecular network states explain complex traits . Molecular Systems Biology papers are usually fun (imo). Here, the authors show how mutations result in system-level homeostatic adjustments that can actually be described in terms of PKA and TOR signaling. It’s an interesting exploration into how exactly genotype manifests into phenotype. https://www.embopress.org/doi/full/10.15252/msb.202211493 https://twitter.com/AndreasBeyer012/status/1683417817666732035   Evolutionary histories of breast cancer and related clones . A tour de force where the authors apply phylogenomics to reconstruct the evolution of breast cancer cell lineages over the lifetime (!) of human patients. What surprised and interested me (a non-cancer biologist) the most was that although all cancer cells descended from a common ancestor with cer...
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13 Aug 2023

There are lots of papers this week, buckle up Predicting evolutionary outcomes through the probability of accessing sequence variants . Thanks Sarah for sharing this one! This is such a simple but important idea. Essentially, evolution follows not only the contours of the fitness landscape but also the “genotype-accessibility landscape”, which is shaped by stuff like codon bias and biochemical mechanisms of mutation changing the likelihoods of some mutations. They look at some examples of this in fu. https://www.science.org/doi/full/10.1126/sciadv.ade2903   Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2 . These folks do some population genetics archaeology to try to put together what was happening with the genomes of SARS-CoV-1 and SARS-CoV-2 around the time they jumped into humans. They find most things are under purifying selection (which is generally the case with viruses as they “live on the (evolut...
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