Thursday's post described the hypothesis that bacteria might use gene transfer agent particles to inoculate other cells in the population with fragments of phage DNA, and outlined an experiment to test this.  Now I'm realizing that I need to know a lot more about the kind of immunity I should expect to see if this GTA-as-vaccine hypothesis is correct.Simplistic outline of the experiment:Infect GTA-producer strain of R. capsulatus with phage under conditions where the infection…

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Below is the line of reasoning showing that the genes responsible for producing GTA particles cannot maintain themselves or spread into new populations by GTA-mediated transfer of themselves into new cells.  I initially worked this out with a rigorous set of mathematical equations, but then realized that the problem was so glaringly obvious that math isn't needed.The main GTA gene cluster is too big to fit inside a single GTA particle, so GTA particles can't…

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Below is the line of reasoning showing that the genes responsible for producing GTA particles cannot maintain themselves or spread into new populations by GTA-mediated transfer of themselves into new cells.  I initially worked this out with a rigorous set of mathematical equations, but then realized that the problem was so glaringly obvious that math isn't needed.The main GTA gene cluster is too big to fit inside a single GTA particle, so GTA particles can't…

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My work at Dartmouth (to be described in upcoming posts) showed conclusively that genes encoding Gene Transfer Agents (such as the GTA system of Rhodobacter capsulatus) cannot be maintained by 'selfish' transfer of either whole GTA gene clusters or single GTA genes into GA- recipients.  Neither can the GTA genes be maintained by general recombination benefits that can arise when fragments of chromosomal DNA are transferred into new cells.  So, although 'gene transfer agent' does…

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I'm at Dartmouth for three months, working with Olga Zhaxybayeva's group to improve our evolutionary understanding of Gene Transfer Agent.  I'm writing an R-script simulation of the genetic exchange it causes (finally learning R), but my control runs with epistasis don't give the expected results.  So I'm writing this post and creating a Powerpoint deck to clarify my thinking.First, what's Gene Transfer Agent?  A number of different kinds of bacteria produce 'transducing particles' called Gene…

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Here's the description of my model addressing Explanation 1 for GTA persistence.  For now I've just pasted in the text of a Word file I prepared about 10 days ago.A constant-population-size model of large-head GTA transmission(Based on Xin Chen’s model, but with stepwise generations and without logistic growth.)Assumptions:The population:1.     Population size is constant.  Loss of GTA+ cells due to lysis during GTA production is made up by growth of all cells after the transduction step.2.    …

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The PhD student and I are trying to pin down the sources of variation in our sequencing coverage. It's critical that we understand this, because position-specific differences in coverage are how we are measuring differences in DNA uptake by competent bacteria.Tl;dr:  We see extensive and unexpected short-scale variation in coverage levels in both RNA-seq and DNA-based sequencing. Can anyone point us to resources that might explain this?I'm going to start not with our DNA-uptake data…

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The PhD student and I are trying to pin down the sources of variation in our sequencing coverage. It's critical that we understand this, because position-specific differences in coverage are how we are measuring differences in DNA uptake by competent bacteria.Tl;dr:  We see extensive and unexpected short-scale variation in coverage levels in both RNA-seq and DNA-based sequencing. Can anyone point us to resources that might explain this?I'm going to start not with our DNA-uptake data…

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I've been going over the RNA-seq data for our rpoD1 hypercompetence mutant, looking for changes in gene expression that might help us understand why the mutation causes induction of the competence genes in rich medium.Here's a graph showing the results of DESeq2 analysis of the expression differences between the wildtype strain KW20 and rpoD1 cells at timepoints B1 and B2.  B1 is true log phase growth in rich medium; OD = 0.02.  B2 is OD…

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Despite my sensible conclusion to the previous post, I've rushed in with a bit of analysis of the reasons for the differences between the NP and GG uptake-ratio peaks.I was able to do this because the PhD student just posted two new graphs, showing the uptake peaks in syntenic 20 kb segments of the NP and GG genomes. The peaks for the two genomes are in the same places because the underlying DNA sequences are…

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