Thinking about a post-pandemic world
I've been trying to think carefully about what our world will be like once the current pandemic is over. Most people are rightly focused on the current situation and on short term measures to limit the spread of the virus and the harm it causes, but we should also be thinking about, and planning for, what the world is likely to be like once populations reach some sort of equilibrium. How many people will the virus be infecting or killing every year? How much difference will a vaccine really make? Will we still need to wear masks? What follows is my non-rigorous back-of-the-envelope analysis.&nb...
Source: RRResearch - July 19, 2020 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Response to Ambur et al.
The points in purple are objections raised byAmburet al. to the hypothesis that the main function of DNA uptake by competent bacteria is acquisition of DNA as a nutrient:These points are typical of those raised when the goal is to dismiss the nutrient hypothesis rather than to carefully consider all the issues. (i) As yet, there is no clear evidence that the integration of nucleotides taken up by transformation become routed into DNA metabolism.Yes. Competence has mainly been studied in mucosal commensals, where investigations of metabolism are difficult. In these organisms absence of evidence is not eviden...
Source: RRResearch - May 26, 2020 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Designing better masks
Optimizing design of masks to prevent spread of COVID-19:(Originally a series of tweets that came out in the wrong order)1. COVID-19 is transmitted mainly by droplets and particles in the air we breathe, not by contact with contaminated surfaces.2. Surgical and cloth masks only poorly protect an uninfected wearer from becoming infected. 3. But these masks CAN reduce virus release by an infectious person, because exhalation produces large wet droplets that are relatively easy to trap on their way out but that rapidly evaporate to smaller dry particles...
Source: RRResearch - May 24, 2020 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
A semi-quantitative framework for long-term thinking about the COVID-19 pandemic
I think the current rush to invoke extreme flatten-the-curve measures needs to be accompanied by careful thought about what we'll do once the measures have had the desired effect. In particular, how long would restrictive measures need to remain in force, and how will we decide when they can be lifted? And how can we mitigate the personal, social and economic harms of the measures while they remain in place?So I've created a series of semi-quantitative graphs to help. ('Semi-quantitative means that there are numbers on the axes and specific doubling times for periods of exponential growth, but the finer d...
Source: RRResearch - March 16, 2020 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Planning the GTA work
My goal for the rest of my time in Andrew Lang's GTA lab is to gather data that constrains estimates of the efficiency of GTA transduction. I have lots of ideas but they're not very well organized, and I keep getting distracted by the minutiae of GTA biology (and our general ignorance of same). So this post is an attempt to get a sensible plan written out.The bottom line for efficiency is how many transductants are generated for each cell that produces GTA and then dies. This depends on many factors, so I'm going to try to break down the steps and evaluate their limitations.Here are some of the questions ...
Source: RRResearch - June 23, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Why doesn't all the GTA get taken up?
I ' ve been modelling the production and uptake of GTA particles in a culture, hoping to understand the cause of thesurprising GTA-accumulation curve I described in the previous post. But this has led me to a more fundamental surprise.Only a very small fraction of the cells in a GTA+ culture produce GTA particles and lyse, and all the other cells are able to bind GTA particles and take up their DNA. So why doesn ' t all the new GTA quickly get taken up by all the surviving cells?Here are the basic principles I ' ve been assuming, based on what ' s in the literature: GTA production: Cells in exponenti...
Source: RRResearch - June 15, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Why doesn't all the GTA get taken up?
I've been modelling the production and uptake of GTA particles in a culture, hoping to understand the cause of thesurprising GTA-accumulation curve I described in the previous post. But this has led me to a more fundamental surprise.Only a very small fraction of the cells in a GTA+ culture produce GTA particles and lyse, and all the other cells are able to bind GTA particles and take up their DNA. So why doesn't all the new GTA quickly get taken up by all the surviving cells?Here are the basic principles I've been assuming, based on what's in the literature: GTA production: Cells in exponential growt...
Source: RRResearch - June 15, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Marc Solioz's 1975 PhD thesis on GTA
PhD students, don ' t assume that your thesis will moulder unread in the library. More than 40 years after he submitted it, I ' m readingMarc Solioz' s PhD thesis (The Gene Transfer Agent ofRhodopseudomonas capsulata). I want to understand the kinetics of GTA production, and his is the only good data I can find.Here ' s what he reported:A. Stability of and transduction by GTA in various solutions: He tested a wide range of solutions. In these studies he didn ' t try to distinguish between conditions that stabilize GTA for storage and conditions that maximize its ability to attach to cells and inject...
Source: RRResearch - June 6, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Marc Solioz's 1975 PhD thesis on GTA
PhD students, don't assume that your thesis will moulder unread in the library. More than 40 years after he submitted it, I'm readingMarc Solioz's PhD thesis (The Gene Transfer Agent ofRhodopseudomonas capsulata). I want to understand the kinetics of GTA production, and his is the only good data I can find.Here's what he reported:A. Stability of and transduction by GTA in various solutions: He tested a wide range of solutions. In these studies he didn't try to distinguish between conditions that stabilize GTA for storage and conditions that maximize its ability to attach to cells and inject its DNA....
Source: RRResearch - June 6, 2018 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
