Why GTA genes can't be maintained by'selfish' transmission
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 transmit DNA that converts a GTA- cell into a GTA+ cell. Some genes outside the main cluster are also required for GTA production.But GTA particles can ...
Source: RRResearch - January 11, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Might GTA be a vaccination system for infecting phages?
My work at Dartmouth (to be described in upcoming posts) showed conclusively that genes encoding Gene Transfer Agents (such as the GTA system ofRhodobacter 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 accurately describe one activity of these genes, it cannot be the activity for which they are selected.The main obstacle to the maintenan...
Source: RRResearch - January 11, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Why GTA genes can't be maintained by 'selfish' transmission
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 transmit DNA that converts a GTA- cell into a GTA+ cell. Some genes outside the main cluster are also required for GTA production.But GTA particles can (and...
Source: RRResearch - January 11, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Might GTA be a vaccination system for infecting phages?
My work at Dartmouth (to be described in upcoming posts) showed conclusively that genes encoding Gene Transfer Agents (such as the GTA system ofRhodobacter 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 accurately describe one activity of these genes, it cannot be the activity for which they are selected.The main obstacle to the maintenan...
Source: RRResearch - January 11, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Why GTA genes can't be maintained by 'selfish' transmission
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 transmit DNA that converts a GTA- cell into a GTA+ cell. Some genes outside the main cluster are also required for GTA production.But GTA particles can (and...
Source: RRResearch - January 11, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Thinking about Gene Transfer Agent
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 Transfer Agents. These look line small phage capsids but they don't usually contain phage DNA; instead they co...
Source: RRResearch - October 16, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Model of GTA evolution by infectious transfer
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. Dense, well-mixed culture in liquid medium (so cells frequently encounter GTA pa...
Source: RRResearch - October 16, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Thinking about Gene Transfer Agent
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 Transfer Agents. These look line small phage capsids but they don't usually contain phage DNA; instead they co...
Source: RRResearch - October 16, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Model of GTA evolution by infectious transfer
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. Dense, well-mixed culture in liquid medium (so cells frequently encounter GTA pa...
Source: RRResearch - October 16, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
What's noise, what's Illumina bias, and what's signal?
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 but with someH. influenzae RNA-seq data. Each of the two graphs below shows the RNA-seq coverage and ordinary seq coverage of a 3...
Source: RRResearch - August 18, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
What's noise, what's Illumina bias, and what's signal?
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 but with someH. influenzae RNA-seq data. Each of the two graphs below shows the RNA-seq coverage and ordinary seq coverage of a 3 or ...
Source: RRResearch - August 18, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
What's noise, what's Illumina bias, and what's signal?
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 but with someH. influenzae RNA-seq data. Each of the two graphs below shows the RNA-seq coverage and ordinary seq coverage of a 3 or ...
Source: RRResearch - August 18, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Do the rpoD hypercompetence mutations eliminate the normal diauxic shift?
Conclusion: I was wrong. TherpoD mutants are just as likely to show a clear diauzic shift blip as KW20.Just to further complicate the picture, here's a Bioscreen run using a quite different strain, a clinical strain called 86-028NP, whose DNA sequences differ by 2-3% from the KW20 sequences: No sign of a diauxic shift. Maybe KW20's diauxic shift was selected for by many generations of growth in lab cultures! (Source: RRResearch)
Source: RRResearch - August 15, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Analysis of NP-GG differences (I can't help myself!)
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 very similar. Most of the peaks also have similar heights in the two genomes, with two obvious exceptions (labelled Discordant peak 1 and Discordant peak 2). Here are those peaks side-by-side, to the same s...
Source: RRResearch - August 12, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Unexpected differences in uptake of DNA from two closely related strains
The PhD student's long careful reanalysis of the DNA uptake data has finally produced uptake ratio plots. These confirm a surprising difference between the DNAs from two closely related strains, 86-028NP ('NP') and PittGG ('GG'). We also saw this difference in our preliminary analysis, but we thought it might be an artefact of how the analysis was done.In the experiment underlying this data, cells of a third strain, KW20, took up DNA that had been purified from NP or GG cells. We recovered the taken-up DNA and sequenced it, comparing how well each position in the ~1,800,000 bp genome was represented in the '...
Source: RRResearch - August 11, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
