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Ivana Cvijovic
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Benjamin Good 23. pro
Excited to announce a new preprint w/ on the ecological and evolutionary responses of the human gut microbiome during antibiotic treatment. . A lot of surprises in here for me -- will post a longer summary after the holidays.
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Eric Kelsic 30. stu
Odgovor korisniku/ci @ekelsic
Our approach generates high-resolution maps of 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!)
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Nature 20. stu
This week on the Nature cover: Waves of mutation. Barcode system images evolutionary dynamics of laboratory yeast. Browse the issue here:
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Ivana Cvijovic 18. stu
Odgovor korisniku/ci @PHumphreyT
Thanks, Parris!
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Ivana Cvijovic proslijedio/la je tweet
Nature 15. stu
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.
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Ivana Cvijovic 16. stu
Odgovor korisniku/ci @darachm @alex_nguyen_ba i 2 ostali
Thanks! Glad you found it helpful!
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José Ignacio Rojas Echenique 14. stu
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 and in 's lab. Read the paper here:
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Richard E. Lenski 14. stu
Odgovor korisniku/ci @ivana_cvijovic
Wonderful stuff! For those wondering about leapfrog, here's where Phil Gerrish & I introduced the idea: 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 13. stu
Odgovor korisniku/ci @skryazhi @alex_nguyen_ba i 2 ostali
Thanks, Sergey!
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Ivana Cvijovic 13. stu
Odgovor korisniku/ci @ivana_cvijovic
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 13. stu
Odgovor korisniku/ci @ivana_cvijovic
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 13. stu
Odgovor korisniku/ci @ivana_cvijovic
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 13. stu
Odgovor korisniku/ci @ivana_cvijovic
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 13. stu
Odgovor korisniku/ci @alex_nguyen_ba @jireva
and 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 13. stu
Odgovor korisniku/ci @ivana_cvijovic
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 13. stu
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 13. stu
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 , , in 's lab
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Richard Neher 25. lis
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!
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Sergey Kryazhimskiy 24. lis
Our Tn-Seq paper with , Alena Martsul and is out in . Accompanied by a nice perspective by Craig Miller with a cool fitness landscape: Here is my original summary:
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Sriram Srikant 8. lis
Our work is out on ! Check out how we altered substrate selectivity of an ABC transporter. Collaboration of and .
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