TWiV 266 letters

Ken Stedman writes:

Vincent et al.,

Wonderful end of year podcast. Based on your discussions of the Giant Viruses Live TWIV (261), I wanted to share my recent attempt at broader communication about viruses in the universe from the New Scientist Holiday Edition. Moreover, I think that Eugene Koonin at the NCBI would be a GREAT TWiV guest, he has very interesting theories about virus origins, some of which I agree with. Another great potential guest would be Patrick Forterre, who has some other ideas about virus origins.

As the Germans say “Have a nice slide (Guten Rutsch) into the new year”.

Cheers,

-Ken

Michael writes:

Hi Vincent et al.,

Long time listener, first time emailer.

Just came across this article and recall that this topic has been discussed recently on TWIV recently. A journalist wrote about her experience with three personal genome sequencing companies and they each came back with differing interpretations: everything from the semantics of how the results were described to which SNPs were used as predictors by each company.

http://www.nytimes.com/2013/12/31/science/i-had-my-dna-picture-taken-with-varying-results.html?nl=health&emc=edit_hh_20131231

Thoughts?

Regards and a sincere thank you for all of your time and efforts,

Mike from the University of Washington in Seattle

weather: 46F and foggy

Matt writes:

Hello TWiV team,

My name is Matt and I am a Veterinary student at Washington State University. I just got done listening to the latest TWiV episode while walking home from school. I’m pleased to report that it is currently -17C, with no wind, and clear sky.

Fascinating and informative episode. I remember reading the abstract of the Pandoravirus paper while working during the summer and getting that excited feeling when something novel is brought to one’s attention.

There are many questions, but I think this one has the most potentially exciting answer:

Considering that these viruses (and presumably others like the two described in the Science paper) had so little in common with currently available databases, it is possible that they, or at least fragments of their genomes, have been identified before but simply discarded. For example, if you are taking a sediment, water, or other sample and doing some brute force sequencing on any recoverable DNA, one of the first sensible things to do after getting the sequence off the machine is to BLAST or otherwise compare to known databases. The stuff that doesn’t match up at all would be discarded as junk/sequencing error.

I wonder if one were to go back through old data from many different studies and get their raw sequencing data if you would see similar sequences? (if the researchers, however, were doing targeted sequencing, e.g. 16s genes, this would likely not recover any of these viruses DNA and would be a bust).

Perhaps Chantal or Jean-Michel are interested in a new student to help figure this out? Either way I will certainly have many exciting papers to read this weekend to catch myself up.

Thoughtfully submitted,
Matt
Washington State University

Andy writes:

Saw this hypothetical vaccine ad that markets them the same way pharmaceutical companies market drugs and thought the TWIV crew might enjoy it.

http://www.upworthy.com/how-would-it-look-if-vaccines-were-advertised-just-like-prescription-drugs?g=2

Geoffrey writes:

Doctors:

The electronic data age bring banes and boons. It allows for a proliferation of on-line publications (boon, bane, or both – take your pick!) but it may offer some innovative advances in science review / authentication as well. In listening to your discussion in episode 257, I had some intriguing thoughts on the process.

Publications that wish to retain peer-reviewing should do so. I think that it has a place. They will, however, be responsible for improving the process. Those who retain the current methodologies will be left behind in reputation.

On the other hand, there is a lot to be said for publications like PLoS that will publish any article that meets their minimum guidelines (and publication fees). However, such publications should have, in my opinion, an absolute obligation to publish dis/confirming papers as well. The journals could provide well-organized comment sections in which peers (probably not the general public – somehow) could attach comments and analyses of the paper (including proof of fraud. Even discredited papers could remain on-line with the history of their discreditation). The journals would also provide well-organized follow-up sections in which other groups could publish attempted duplications of the original work. I feel that such a core structure would provide a very robust distributed peer-reviewing. It would provide a history of attempts to duplicate works as well as provide a place to record the effects of lab-to-lab variations in techniques – resources that, to my knowledge, is sorely lacking in today’s research environment.

Such an approach could also open up avenues for publishing negative data – also a resource sorely lacking in today’s research environment.

Well, thanks for all your hard work with the podcast and providing me a chance to think a little deeper on possible way to use the internet to improve science authentication.

Geoffrey

Varun writes:

Greetings

Thank you for reading my last letter “Queries on HIV”. I apologize for not sending u the link regarding for my question. So here i have re- posted the questions, with the links you requested.

1. I recently came to know that individuals producing response against HIV- Env are more likely to have higher viral titers, compared to people with Gag response with opposite effect. Is there any mechanism that is being known or studied? Insights please. I couldn’t trace back the literature where i read it, but the research channel video should be of help.

Vaccines and HIV Evolution: http://www.youtube.com/watch?v=xqrJisnQWzA
Time: 40.00- 43.00.

2. HIV ELITE carriers have elevated 2-LTR circles in nucleus that cripple HIV integration. Noting from other literature. I concluded that there is not much difference in HIV replication steps in cytoplasmic events (ELITES vs Non ELITES). So is it reasonable to believe that there is some difference in nuclear machinery (probably an enzyme or micro-RNA etc), that is variant enough to be involved in this difference? Are there any studies enlightening the same?

Link 1: Elite Suppressors Harbor Low Levels of Integrated HIV DNA and High Levels of 2-LTR Circular HIV DNA Compared to HIV+ Patients On and Off HAART. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1001300

Link 2: Inhibition of HIV-1 Integration in Ex Vivo-Infected CD4 T Cells from Elite Controllers. http://jvi.asm.org/content/85/18/9646.long

Thank you TWiV team

Larry writes:

How might these megaviruses relate to Margulis’s conception of symbiogenesis? Could large viruses have become a part of the cell, or play a role in the gene transfer on an evolutionary scale, and how could one know?

Larry

Shane writes:

Hi Guys,

I recently read an article in UW Today, which is making the social networking rounds for its seemingly far reaching consequences.

http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/

My first thought on reading this article was that a lot of work is done on comparing the ratio of synonymous to non-synonymous mutations. Well if it turns out that a lot of our previously thought synonymous changes are not actually synonymous, would this work be invalidated?

I also had a thought that evolution of prions could possibly explained by this?

I could be completely overblowing this or be completely wrong in my interpretation, I am just an IT Guy after all.

Thanks for the awesome podcasts, keep up the great work.

It’s a warm 29 degrees C with scattered clouds.

Kind Regards,

Shane From Australia

Joe writes:

An example where Mosquitos respect national borders. Perhaps there’s a language barrier: on the affected side of the Island French is spoken while Dutch is spoken on the unaffected side of the Island. Of course, there may be other explanations.

http://www.caribbeannewsnow.com/headline-Mosquito-borne-chikungunya-virus-confirmed-in-the-Caribbean-island-of-St-Martin-19069.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+CaribbeanNewsNowDailyHeadlines+%28Caribbean+News+Now%21+Daily+Headlines%29

Another regular listener to TWIV
Joe

Emily writes:

Twiv Hosts,

I love the show, and finally have a reason to write in, for my listener pick.

This fall I began my PhD program in Microbiology and Immunology (although I’m focusing on virology) and just finished my first rotation in a dengue lab. After a few months of staring at the virus crystal structure and countless hours playing around with PyMOL, I realized the virus was something I could easily build. All I needed to do was knit 30 envelope protein rafts (made up of three E protein dimers of course) and connect them together following the 3-fold and 5-fold symmetries of the dengue virus, then fill the virus (I opted for pillow stuffing, instead of RNA and capsid proteins) and knit it shut.

The dengue pillow was a gift to the lab, and now lives there.

It was a fun project to work on, and through making it, I have a much better appreciation for the beautiful virus structure (seemingly complicated, but in fact quite simple).

I know this will be the first of many projects, combining my loves of art and science.

Pictures here (and the oats, rhymes with the correct pronunciation of my surname):
http://emilyandtheoats.tumblr.com/post/68633348809/structurally-accurate-dengue-virion-pillow-is-now

Thank you for the great podcast, I eagerly await the new episode each week!

-Emily

p.s. the weather where I currently am (Paraty, Rio de Janeiro, Brazil) is a brutal 38* Celcius (100.4* Farenheit)!