RRResearch

Not your typical science blog, but an 'open science' research blog. Watch me fumbling my way towards understanding how and why bacteria take up DNA, and getting distracted by other cool questions.

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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...

Response to Ambur et al.

 The points in purple are objections raised by Ambur et 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...

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.    ...

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...

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...

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 the surprising 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...

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 reading Marc Solioz's PhD thesis (The Gene Transfer Agent of Rhodopseudomonas 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...

Summary of R. capsulatus Bioscreen growth curves

The previous post (GTA competition experiments) described the results of the follow-up set of R. capsulatus growth curves that I planned at the end of the previous experiment (R. capsulatus growth curves in RCV medium).  But it didn't pull together the results of all the Bioscreen growth curves, nor integrate them with what was previously known/thought). ...

GTA competition experiments

I'm in St. John's for the 'summer'*, doing GTA-related experiments in Andrew Lang's lab at Memorial University of Newfoundland ('MUN').The first experiments I'm going to do are growth competitions between GTA-producing strains and otherwise-identical non-producer strains created by deleting the GTA genes.  Because GTA production requires cell lysis,...

Wait, there's a much simpler explanation! (For CRISPR-Cas, not for GTA)

I'm in Halifax for a couple of weeks, visiting Ford Doolittle and his philosophical colleagues,  We've spent much of the time considering the extent to which CRISPR-Cas systems can or should be considered 'Lamarckian'.  I started with the simplistic perspective that of course it is, because an acquired character (immunity to future phage or plasmid...

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