Field of Science

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 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 evidence of absence.

(ii) The presence of exogenous DNA does not appear to induce competence in any transformable species.

Yes, but I don’t see why this is more relevant for the nutrient hypothesis than for other hypotheses.  (Also, Vibrio does use chitin as a signal for competence; its presence indicates biofilms and abundant DNA.)

(iii) Competence in streptococci, like S. pneumoniae, is induced for only a short time period during exponential growth when other resources are highly abundant.

Because laboratory growth conditions for human commensals and pathogens are so different from natural growth conditions, lab cultures are very poor guides to what matters in the real world.  That’s why our work focused on understanding the regulatory machinery.

(iv) Transported DNA is heavily protected against nuclease digestion within the cell, potentially enabling transported fragments to remain intact as a substrate for recombination.

And yet most competent bacteria take up all DNAs they encounter, and DNA that cannot be recombined is efficiently degraded.  The proteins that protect the DNA are also common in non-competent species and so must function outside of transformation.

(v) The hypothesis does not explain why several competent species only take up DNA from close relatives due to conserved DNA uptake sequences (USS and DUS) despite the fact that non-homologous DNA could be used as a source of nucleotides for direct use or degradation.

On the flip side, almost all competent bacteria take up DNA indiscriminately, so DNA’s benefit can’t depend on its information content.  For these exceptions, we have hypothesized that sequence-dependent uptake constraints exist in these species, and have shown that these create molecular drive that causes uptake sequences to accumulate in genomes at frequencies and distributions corresponding to those seen in real genomes with DUS and USS.

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 that are hard to trap on their way in (see Wells Curve). 

4.     So the general public should wear masks not to protect themselves from infection but to protect other members of the community, in case the wearer is unknowingly infected. But design of surgical and cloth face masks has not been optimized for this function. 

5.     What properties should such a mask have?
a.     The fabric should block passage of most respiratory droplets.
b.     Most exhaled air should pass through the mask, not around it, even after a cough or sneeze.
c.      Any exhaled air that escapes should escape downward, not upward.
d.     Air and water molecules should pass easily through the mask fabric.
e.     For ease of breathing, exhaled and inhaled air should be filtered over a large area of mask. The mask should not be tightly pressed to the nostrils and mouth.
f.      To maximize air exchange, the mask should not normally enclose a large volume of air.
g.     The space inside the mask should expand in the event of a cough or sneeze, to trap the large volume of air and allow it to be gradually released through the mask (not around it). 

6.     These goals may best be met by long lightweight scarf-type masks that fit snugly around the nose, cheeks and ears, and settle loosely on the shoulders.