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Friday, 05 October 2018 13:58

TWiM 186 Letters

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Published in Letters

Tom writes:

A rant:

I urge everyone listening to this podcast who hasn't yet done so, immediately set up a monthly donation to TWiV.

You probably don't think twice about adding a $1.00 candy bar or $1.50 soft drink to your weekly or bi-weekly grocery shopping cart.

Do the world (and your health) a favor and set up an automatic Patreon contribution of that money.

And when you're standing in the checkout line, remind yourself that you have already used that money to do something good for many, and not do something bad for yourself.

[Vincent: Feel free to read this rant on all the other podcasts.]

Looking forward to future TWiVs.

-- Tom in Austin

 

Adam writes:

Hi everyone,

In twim 182 it was stated that Maldi-tof id requires an isolated colony.

This is not technically true,  there are special techniques that can id from blood culture without a colony, and databases are being developed to id multiple organisms if present.

Also interesting to note that there are antibiotic resistance assays being introduced that use maldi-tof. Some measure decrease of antibiotic overtime in the case of the presence of beta lactamases.

Thank you for the great show.

 

Nicholas writes:

Hello TWiM team! How is everyone?

My name is Nicholas Gerbino and I'm reaching out to you from Rochester, New York, where I work at the University of Rochester Medical Center. I am currently a student in the Master of Public Health program at the London School of Hygiene and Tropical Medicine. I have only recently discovered TWiM but want to thank you all for the work you are doing.

My passion, above all else, has to do with poverty alleviation and securing health equity through the prevention of infectious diseases.

That being said, I was quite pleased to see a paper published in The CDC's Journal of Emerging Infectious Diseases, for no other reason than the fact that it focused on the disease burden faced by some of the poorest among us. The title is "Poverty and Community-Acquired Antimicrobial Resistance with Extended-Spectrum -Lactamase-Producing Organisms, Hyderabad, India."

https://wwwnc.cdc.gov/eid/article/24/8/17-1030_article

This article serves as a reminder to all, that we either succeed together or fail together and must commit to serving the most vulnerable among us.

Thank you all again!

Nicholas

 

Dallas writes:

Dear Twim team,

As usual an excellent podcast with the snippet being highly relevant to the future.  You could use these rapid methods to obtain fast and low cost results for things other than antibiotics that impact growth rates like nutrition, nutritional history, phage resistance, etc. etc.

On the diatom paper, finding out how Fe is taken up by the diatom and the use of CO3 ion along with Fe was excellent (always wondered about that).  Apparently most of the Fe in the oceans exist as particulate material such as Fe3O4 or Fe(OH)3 with a huge solubility difference between ferrous Fe++ and Ferric Fe+++ ions.  Under aerobic conditions like the ocean surface or the water in your toilet bowl, the soluble ferrous is oxidized into insoluble Ferric materials, staining your toilet bowl in areas with anaerobic groundwater where ferrous ions are soluble (also driven by microbiology).  

However, a statement was made that the increasing CO2 in the atmosphere will decrease the pH (true at constant alkalinity) and implied the pH determines the carbonate/bicarbonate ratio and decreases the carbonate concentration ( true ) even as to total of all carbonate species (free CO2, carbonic acid, bicarbonate and carbonate) increases (true).  However the implication that this pH decrease would impact the Fe transport system may be wrong. The highly insoluble particulate ferric hydroxide Fe(OH)3 in seawater would increase in solubility with decreasing pH to the cube of the hydroxyl ion concentration effectively increasing the solubility much faster than the carbonate concentration decrease with increasing CO2.  With iron concentration increasing and carbonate concentration decreasing, the lower concentrations of iron relative to carbonate combined with the iron solubility increasing much faster with increasing CO2 would say the Fe complexing system would preform better at high CO2. Back to the physical chemistry, mass transport theory I loved.

Another related part of the discussion regarding O2 production and O2 in the atmosphere seemed to be following the lines of Paul Ehrlich’s faulty thinking back in the late 60’s and continuing on.  I keep hearing this thinking so that is why I am bring it up.

Back in the 60's, when I was a Ph.D. student in Edward Teller's Department of Applied Science at UC Davis, I encountered Ehrlich's intellectual impenetrability first hand. Ehrlich had been going on about how chemical X impacted algae growth in the oceans (true) and that the oceans produce about 2/3 of the world's oxygen production (approximately true). However, Ehrlich had then extrapolated to claim that continued pollution of the ocean will impact the O2 on the planet and jeopardize our survival. This was where we parted company.

Years later, trying to stimulate the thinking of graduate level Environmental Engineers in a class I taught at USC, I turned Ehrlich's statement into an exam question. Ehrlich had continued to spout the same statement about which I had confronted him. He had ignored me then and continued to ignore the basic mass balance science of the situation. I had been a mere grad student, so what did I know.

The premises of Ehrlich's statement are true, but his conclusion is not. In the exam question my students were challenged to examine the case and then determine the actual impact of killing all the algae in the ocean with a permanent toxin.

Proving the conclusion is wrong was the easy part, because the premises' implicit assumption confused gross and net production of oxygen. Oxygen in the ocean undeniably produced by photosynthesis does not make a permanent contribution to the oxygen supply in the world, because it is mainly consumed by the metabolism of the organisms that eat the algae and the organisms that eat them, all the way down the food chain. This results in very little net O2 production. The actual inventory of oxygen in the ocean is small relative to the atmosphere.

The more difficult challenge is to estimate the amount of net production of O2 by the oceans when you know the gross photosynthesis. Many students tried working down the food chain, which is nearly impossible with available knowledge. However, a few thought outside the box, noting that net O2 from the ocean to the atmosphere is only created when carbon is buried in the sediments. One can look up the sedimentation rates and their carbon contents and calculate one mole of net O2 for every mole of buried carbon.  Remember there are 2.1 tons of O2 in the atmosphere for every square meter of the earth’s surface and few 10’s of kg of O2/M2 of the open ocean (surface to bottom) and the open ocean sedimentation rates are very very slow.   

If we used photosynthesis to remove and bury (sequester) all the CO2 in the atmosphere at 400 µ atm we would only add 400 µatm of O2 to an atmosphere containing 200,000 µ atm which would be near unmeasurable. 

The world of science has expanded in all areas to the point where it is impossible to even know the boundaries of human knowledge making us even more interdependent on each other to achieve a realistic view of the real world and how it works.  These podcasts help pass information to those of us who know little of biology, but know that it is important.

Dallas

Dallas E. Weaver, Ph.D. , P.E.       

Scientific Hatcheries

Huntington Beach

 

Reply from Dr. Jeff McQuaid:

Hello TWiM and Dallas-

This is a great question which really cuts to the heart of the iron cycle in the marine environment.  In the ocean, dissolved iron concentrations are are far higher than predicted, and this is due to the fact that in the marine environment, most iron is complexed to an array of diverse (and largely uncharacterized) organic ligands - these can be anything from saccharides and hemes to humic-like molecules and siderophores.  Ultimately, it is the kinetics between this soup of organic ligands and the dissociation constant of iron which determines the concentration of labile iron, and these 'gemisch kinetics' tend to dominate over inorganic Fe solubility. Understanding how changes in sea surface temperature and pH will affect the pool of naturally complexed iron is an active, and highly relevant, area of research  --- if this is interesting, please check out an excellent review which was published on iron in ocean biogeochemsitry in Nature in March of 2017.

In our work, we avoided the uncertainties of the ligand soup by buffered our concentration of labile iron with a large excess of the synthetic chelator EDTA.  This allowed us to precisely calculate labile iron as the pH changed -- we were extremely lucky in that much of this iron-EDTA chemistry in seawater was worked out by Susan Hunstman and Bill Sunda through a decade's worth of highly detailed experimentation.  If you dig through our published datasets, you can see how it is these changes in the favorability of Fe-EDTA dissociation which drove the concentration of labile iron, swamping out changes in inorganic iron solubility.

Some of our next steps will include verifying this effect in other phytoplankton, and equal in importance will be moving away from simplified systems and synthetic chelators like EDTA to study how acidification-induced changes to iron and iron complexes will alter phytoplankton uptake rates, thus embracing the 'gemisch'.

Thanks again    ---- Jeff

Vincent Racaniello

Vincent Racaniello, Ph.D. is Professor of Microbiology at Columbia University Medical Center. As principal investigator of his laboratory, he oversees the research that is carried out by Ph.D. students and postdoctoral fellows. He also teaches virology to graduate students, as well as medical, dental, and nursing students.

Vincent entered the world of social media in 2004 with virology blog, followed by This Week in Virology. Videocasts of lectures from his undergraduate virology course are on iTunes University and virology blog. You can find him on WikipediaTwitter, Facebook, and Instagram. His goal is to be Earth’s virology professor. In recognition of his contribution to microbiology education, he was awarded the Peter Wildy Prize for Microbiology Education by the Society for General Microbiology. His Wildy Lecture provides an overview of how he uses social media for science communication.

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