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Letters

TWiV 126 Letters

Aaron writes:

Hi folks,

I'm a chemical engineer by background and I’ve done downstream process development in biopharma for years. Just lately, I've started working on a part-time bio Masters I’ve been taking all the standard cell/molecular bio classes I never had before. I'm about to start a course on "Biology of HIV/AIDS" and I've been using your back episodes to fortify my meager background in general virology. Thanks so much!

Okay, here’s my question, and stop if you’ve heard this one before:

One of the primary phenomena I work on is chemistry and physics in the freeze-concentrated state of frozen protein solutions. When you freeze the ice crystals out of an aqueous solution, the remaining excipients concentrate in interstitial space (like a slurpee). This gives you the opposing kinetics of high concentration at low temperature, which can lead to different chemistry than in the liquid state.

All this RNA talk raises a question I've thought about for awhile: I'm sure you guys are familiar with the Miller-Urey abiogenesis reflux experiments and some of the follow-up work showing that amino acids can be synthesized from H2O, CO2, NH3, CH4 and H2. Some follow-on experiments seem to show that the original frozen samples from this experiment formed even more amino acids when stored frozen for decades, possibly due to decomposition of some precursors formed in the original experiment. Additional work has shown that all 4 nucleotides can be synthesized from long term freezing of aqueous cyanide compounds (1).

I found some other articles that say that freeze-concentration is favorable for extra-cellular RNA polymerization (2), and for the spontaneous assembly of polynucleotides from precursors (3).

All of this points to the idea that the primordial cell-like environment in which life first evolved was the interstitial spaces of freeze concentrate in “dirty” ice. It makes sense to me because freeze-concentration is one of the few natural phenomena that dramatically reduce local entropy in a concentrated liquid. I’ve never heard of this idea before in my bio courses. Is “cryo-abiogenesis” a common part of the RNA-world hypothesis? Are there other major problems with this theory I am unaware of? Looking at these papers, it seems like primordial freeze concentration is the best explanation out there for the initial formation of organized bio-macromolecules. But, if this is so, I’m surprised I’ve never heard of it before. Any thoughts?

Thanks again for the wonderful podcast,

Aaron

1: The prebiotic synthesis of pyrimidines in frozen solution, Cleaves, Nelson, Miller

2: Ice as a protocellular medium for RNA replication, Attwater, et al, Nature Communications, September 2010 http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1076.html

3: Eutectic Phase Polymerization of Activated Ribonucleotide Mixtures Yields Quasi-Equimolar Incorporation of Purine and Pyrimidine Nucleobases, J.A.C.S., Monnard, et al., 2003

Lillian writes:

re: episode #125 and XMRV contamination

My question about contamination is: if it is so common via cell lines, reagents, etc., why are there so many XMRV studies that found no evidence of XMRV either in controls or cases? It would seem that if contamination were a recurrent/ common issue, many studies would find some positives, even if a low number, equally in cases and controls. Of course, this might get down to the nitty-gritty of the exact cell lines, reagents, PCR primers, what experiments the lab had performed in the past, and even what experiments the authors had done in the past (and thus what they were exposed to), etc. but these issues should be explored rather than just hand-waving explanations that with positive studies, the cases' blood samples were "handled" more than the controls or that these labs have been contaminated.

Thanks.

Bob Krug writes:

Hi Vince,

I enjoyed your podcast at the University of Washington. Several people here brought it to my attention. I just wanted to tell you one thing. I was NOT the second (nasty) reviewer of your paper.

I think that you would enjoy holding a podcast here at UT-Austin. People here would enjoy it. In particular, I think that you would enjoy meeting with two young virologists here, Sara Sawyer and Chris Sullivan.

Best regards, Bob

Robert M. Krug, Ph.D.

Professor and Chair

Molecular Genetics and Microbiology

University of Texas at Austin

Brian writes:

Dear Vince, Dick, Alan, Rich, et. al.

On a number of TWIV podcasts you've mentioned the quasi-species concept. In one podcast, Alan or Rich said something about having to look into that concept more closely. I assume this involves more than the elementary definition.

"Steps Toward Life" Manfred Eigen, Ruthild Winkler-Oswatitsch, Paul Woolley, provides among other things a rather concise "vignette" of the quasi-species concept for those of us who need the elementary approach. http://www.amazon.com/Steps-towards-Life-Perspective-Evolution/dp/0198547528

In addition, the authors provide scenarios for the beginnings of life from inorganic matter. (Less than perfect replication and compartments) And if that's not enough, there is a fascinating treatment of viral evolution positing that viruses replicate their genetic material with enough error and enough accuracy that they sit at the edge of thermodynamic dissolution while having the maximum flexibility for adaptation.

I have no formal background in microbiology other than a reading of the 3rd edition of "The Molecular Biology of the Cell" (Alberts et al.) Now it's time to buy the 5th edition to catch up with the last 20 years. That said, I have little trouble following the discussion.

I do have a question. I'm in my early 60's, have time and enough money so I don't have to work much. Is there any place in virology or parasitology for amateur participation?

Thank you so much for the podcasts, and for TWIP as well.

Best

Brian (The guy who sent Dick the Swiss vertical farm pics)

David writes:

Hi Vincent,

Was listening to your latest podcast (interesting and informative as always), and thought you might find a few additional items of interest.

First, you discussed in Ode to a Plaque the wonderful mechanisms that viruses use to move from cell to cell, and wondered if there were other examples. Here's a paper you might want to discus: http://www.ncbi.nlm.nih.gov/pubmed/20023636; "Biofilm-like extracellular viral assemblies mediate HTLV-1 cell-to-cell transmission at virological synapses." by Pais-Correia AM, Sachse M, Guadagnini S, Robbiati V, Lasserre R, Gessain A, Gout O, Alcover A, Thoulouze MI at the Pasteur Institute.

Another item: you discussed the PacBio sequencing system, a very clever nanotechnology method for ultra-high throughput sequencing. There's another technology that just came on the market that also uses very clever nano chemistry: the Ion Torrent system, now sold by Life Technology (www.iontorrent.com). It uses semiconductor technology to build tiny pH-sensitive chambers, each one containing a single synthesizing DNA molecule, and then detects the addition of each nucleotide by the change in pH caused by the release of a proton when the nucleotide triphosphate is hydrolyzed during incorporation. In that way, it doesn't require any special reagents, such as fluorescent-labeled nucleotides or fancy cameras, but just uses normal nucleotides and polymerase, which should result in reduced costs. Like the PacBio system, they are still trying to optimize read-length and accuracy, but it's a pretty clever idea.

Finally, you discussed the difficulties of conducting vaccine trials in humans. You may want to check out the work of John Treanor at Univ. of Rochester, who conducts influenza virus trials in volunteers, who are quarantined for 10 days following exposure to attenuated viruses, and provide daily nasal swabs to watch the replication and ultimate clearance of the viruses. See: http://www.urmc.rochester.edu/news/story/index.cfm?id=2899

"The investigational vaccine to be tested in this first isolation trial is similar to FluMist, the licensed nasal spray vaccine for seasonal flu, except that it contains two genes that help it mimic the H7N3 strain.

To participate, study volunteers must be between 18 and 49 years old and must not be pregnant, have an allergy to eggs, or have another medical condition that compromises their immune system and thereby would make live-virus vaccinations unsafe. If selected, study volunteers must stay a minimum of 12 days (two days before receiving vaccine, or “day -2” and “day -1;” the day of the vaccine, or “day 0;” and at least nine days following the vaccine, “day 1” through “day 9”). While on the unit, they will undergo daily physical examinations (e.g., vital signs) and nasal washes (to see how long the weakened virus remains in the nasal cavity, where vaccine is initially sprayed), and provide several blood samples. To be discharged, volunteers must go two consecutive days (after day 7) with no febrile or flu-like symptoms, including a negative nasal culture. Three separate outpatient follow-up visits, each requiring a nasal wash and blood sample, will be scheduled for one, two and six months after initially receiving vaccine."

It's popular amongst college students, who can make a couple of thousand dollars by participating.

Keep up the good work.

David
(the write is Professor of Pathology and Microbiology, New York University School of Medicine)

Jim writes:

Dick,

Your interest in information organization and display prompts me to send this link which is useful with the current public interest in the topic of radiation exposure:http://xkcd.com/radiation/

It's interesting to me as a retired nuclear power plant worker, too. We were just converting from rem to sieverts as I retired and this link helps in that regard. Five rem is the current federal standard maximum allowed exposure for a nuclear worker. You can see what that equates to in sieverts at this site.

Regards,

Jim

Smithfield, VA

 

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