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Benjamin Good
@benjaminhgood
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23. pro |
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Excited to announce a new preprint w/ @MortezaRoodgar on the ecological and evolutionary responses of the human gut microbiome during antibiotic treatment. biorxiv.org/content/10.110…. A lot of surprises in here for me -- will post a longer summary after the holidays.
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Eric Kelsic
@ekelsic
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30. stu |
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Our approach generates high-resolution maps of #AAV capsid sequence space, illuminating how capsids work and how to make them better. Here’s a visualization showing tolerance to substitutions (red:beneficial, white:neutral, blue:deleterious, this view isn't even in the paper!) pic.twitter.com/nWUekmzoKP
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Nature
@nature
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20. stu |
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This week on the Nature cover: Waves of mutation. Barcode system images evolutionary dynamics of laboratory yeast. Browse the issue here: go.nature.com/336w2ip pic.twitter.com/pe16RxYmiG
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Ivana Cvijovic
@ivana_cvijovic
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18. stu |
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Thanks, Parris!
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Nature
@nature
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15. stu |
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A renewable barcoding system reveals the evolutionary dynamics of laboratory budding yeast, showing that fitness changes over time in a travelling wave of adaptation that can fluctuate owing to leapfrogging events, according to a Nature paper. go.nature.com/32NssJG pic.twitter.com/KH1aRQ68yS
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Ivana Cvijovic
@ivana_cvijovic
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16. stu |
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Thanks! Glad you found it helpful!
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José Ignacio Rojas Echenique
@jireva
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14. stu |
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Here's a thread telling the story of our new technique for genetic recording of lineage history during long term evolution experiments.
The work was co-led with @alex_nguyen_ba and @ivana_cvijovic in @MichaelMDesai's lab.
Read the paper here:
nature.com/articles/s4158…
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Richard E. Lenski
@RELenski
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14. stu |
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Wonderful stuff! For those wondering about leapfrog, here's where Phil Gerrish & I introduced the idea:
citeseerx.ist.psu.edu/viewdoc/downlo…
See Fig 7 for simple illustration, in which successively dominant genotypes may -- or not, in case of leapfrog -- represent sequential substitutions.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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Thanks, Sergey!
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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But it also exists in a limit that we don't currently have a good quantitative description for. Instead of proceeding smoothly, the wave exhibits large fluctuations as mutations cause clones to continuously leapfrog over each other!
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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We see that the population carries dozens of competing beneficial mutations, and that it forms a sort of 'traveling wave' if you look at its distribution of fitness. This agrees with theoretical predictions.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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I then developed an approach to use this lineage frequency data to reconstruct the clonal structure of the population and to detect individual beneficial mutations.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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By sequencing this genetic locus over time, we can measure the fractions of the population in different barcoded lineages.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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@alex_nguyen_ba and @jireva developed a remarkable new approach to continuously re-introduce enormous numbers of DNA barcodes into an evolving yeast population, one right next to the other in the genome.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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But it has been difficult to observe the majority of those mutations: theory had predicted that most would be lost before reaching fractions of the population detectable by available methods.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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We've known for the past couple of decades that many microbial populations adapt in an incredibly dynamic way, with large numbers of beneficial mutations continuously arising and competing.
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Ivana Cvijovic
@ivana_cvijovic
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13. stu |
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What do you expect evolution to look like in a microbial population? Check out our new study offering a view of that over 1000 generations in yeast in the lab.
co-led by @alex_nguyen_ba, @jireva, in @MichaelMDesai 's lab nature.com/articles/s4158…
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Richard Neher
@richardneher
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25. lis |
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We have an open post-doc position in the lab! Core current interests are recombination/reassortment/HGT in microbial evolution, but we can get excited about other questions as well. Please share!
neherlab.org/201910_BZ_post… pic.twitter.com/tHqeE0Xt72
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Sergey Kryazhimskiy
@skryazhi
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24. lis |
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Our Tn-Seq paper with @_miloj, Alena Martsul and @MichaelMDesai is out in @sciencemagazine.
science.sciencemag.org/content/366/64…
Accompanied by a nice perspective by Craig Miller with a cool fitness landscape:
science.sciencemag.org/content/366/64…
Here is my original summary:
twitter.com/skryazhi/statu… pic.twitter.com/Lu00tyqYUR
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Sriram Srikant
@sriram_srikant
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8. lis |
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Our work is out on #bioRxiv! Check out how we altered substrate selectivity of an ABC transporter. Collaboration of @RachelleGaudet and @EvolvingMurray. biorxiv.org/content/10.110…
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