Chris writes:

This podcast had a few mentions of Archaea, but neglected to credit them for the color of the “non-GMO salt.” There are actual prehistoric DNA in that salt:

http://microbialfoods.org/scie…

From Seattle, where I will tell you that it is cold, dark, cloudy and drippy even when it is not. We want to move to a smaller house and even those are horribly expensive because too many people are moving into my neighborhood. ūüėČ

Chaim writes:

Saying salt is kosher is in exactly the same category as saying it is gluten free –it can’t not be! (Though, to be fair, there are certainly people who won’t eat anything that’s not explicitly certified as kosher, regardless. The same is probably true for GF.)

What is called “kosher” salt is more accurately “koshering” salt, ie coarse salt that is used to help extract the blood from meat, a necessary (though not sufficient) step for it to be permitted for eating in accordance with kosher rules.

Best,

Chaim

Kevin writes:

Hi Twiverinoes,

A quick follow-up comment regarding Rich Condit’s pick from last week’s episode: the so-called “missing link” between Archaea and Eukaryotes. The conversation seemed to perpetuate a common misconception about evolution that I wanted to quickly set right. Rich said that the current view is that Eukaryotes “evolved from” Archaea, when in fact Eukarya and Archaea share a common ancestor more recently than with Eubacteria.

I know you guys know this, but this idea that any modern organism “evolved from” any other modern organism (like “humans evolved from apes”) is a concept often misunderstood by biologists and non-biologists alike.

Incidentally, I’m also a bit perplexed by the fact that Carl Zimmer’s article contained the phrase “missing link,” since he’s written about the absurdity of that phrase in the past (http://www.slate.com/articles/health_and_science/science/2010/04/yet_another_missing_link.html). It’s even more absurd to use this phrase for a modern organism. This makes the tree of life a bit more bushy in a place that it was bare. Maybe it’s a link, but it’s not the link between our branch and Archaea.

Cheers!

Kevin (from audiommunity)

Dirk writes:

Dear Virophils,

Just to let you know there is a company in Estonia (Protobios.com) that uses a similar approach (serum, phage library, NGS, ‚Ķ) to characterize the ‚Äúimmunoprofile‚ÄĚ of a person. Interestingly they use a ‚Äúrandom‚ÄĚ library of peptides on their phages with the idea of finding biomarkers for all types of diseases. It‚Äôs a bit of a black-box approach, but I can imagine that with a strong signal one can work its way up to finding the antibody, finding the antigen and perhaps the cause of the disease. They refer to it as MVA (Mimotope Variation Analysis).

Greets from sunny Belgium (with rain in the forecast obviously, otherwise it would not be Belgium J),

Dirk

Dirk Jochmans, PhDResearch Manager

Laboratory of Virology and Chemotherapy

Rega Institute for Medical Research | University of Leuven

Piet writes:

Hi Team,

From Stellenbosch, South Africa, where it is currently cold; 17 C Fair, slightly overcast, wind speed roughly 14km/h.

Really enjoy the podcast and appreciate all the effort you guys have put into it. It is a brilliant mix of humour and fun science. I am currently working in bioinformatics (coming from a finance and statistics background). I have therefore learnt a lot from the show and I am continuously amazed at the intricate, eloquent dynamics of molecular interactions. The show has also given me a new-found appreciation for traffic.

Found this interesting paper on flu, which highlights some interesting aspects of the epidemiology of flu as well as the stratification of infected individuals based on age of the host and the rate of mutation of the virus.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14460.html

Kind Regards,

Piet

Steen writes:

Dear twiviridae,

Plant RNA silencing is going through a bit of a rough patch. We could really use a TWiV bump for a new paper from our lab published in PLOS Pathogens. I hope our overview and summary figure provide an accessible overview.

As you and your listeners may know, small RNAs were discovered in the context of plant virus infection and transgene silencing. Less often appreciated is that plant virologists predicted an RNA-based immune system as early as 1993 (see Lindbo et al. Figure 4). In 1998, three groups demonstrated that potyviral helper component protease (HC-Pro) suppresses RNA silencing, providing a clear demonstration that RNAi functions in defense. As previously noted, these discoveries demonstrate the importance of fundamental research, including in plants, fungi, etc.

Our work sheds new light on HC-Pro function, suggesting that it might interfere directly with Argonaute proteins, which are the workhorses of small RNA action. Argonautes are quite diverse in plants: rice has nineteen. We used the proverbial “awesome power” of reverse genetics to dissect AGO function in Arabidopsis thaliana, the species in which they were first described. Many plant microRNAs target developmentally important transcription factors, so when the main Argonaute (AGO1) is nonfunctional you get messed up plants‚ÄĒthe original mutants were named because they look like argonaute squids. Interference with microRNA regulation is a likely explanation for why many viruses stunt plant development. We showed that at least three Argonautes bind small RNAs derived from the Turnip mosaic virus genome, but only in the absence of functional HC-Pro.

Lead author Hernan Garcia-Ruiz recently started a new research program at the University of Nebraska.

References (most linked above)

Fun fact: your guest Jack Morris was Jim’s PhD supervisor, and Hernan has moved into his old lab space at UNL.
The Voinnet story has developed further, but no investigation results have been released yet. RetractionWatch picked up the story (1, 2), as did German and Francophone outlets, and Leonid Schneider wrote a second Lab Journal piece, which is probably still the best summary. Since then, several figure mixups have been corrected (1, 2, 3, 4, 5, 6, 7) and the most heavily criticized paper was retracted.

Mauricio writes:

Dear Vincent et al.,

I have been catching up with the latest TWiVs and I have a follow up about TWiV 321. I can understand that a handful of scientist might be against research that could potentially “create” a pandemic virus; having a Ph.D. or M.D. does not imply that a person can see beyond their fears or personal obsessions. However, I think that the way this moratorium on “gain-of-function” research was done indicates that NIH, the American Academy of Sciences, ASM, FASEB and other scientific organizations have failed. I can’t understand how this moratorium was imposed without any debate organized by any of these organizations. These professional associations should have a presence within the political circles so whenever there are problems like these, politicians could have a more informed position.

The question of whether a particular branch of research is dangerous or not  should first be discussed by a widely arranged scientific panel, so the conclusions of such forum could be used as guidelines for the White House. This problem raises a very important questions; What is the function of the National Academy of Sciences? Is this very selective group of scientists only good for having a high profile journal? Is creating a very selective group of remarkable scientists the only goal of this organization? I think that the fact that the White House did not ask the National Academy of Science for an opinion on this matter shows that it might be a worthless institution.

Sorry for such a negative e-mail but I can’t believe that this decision was taken before any discussion happened. As you mentioned in this twiv episode there are two completely opposite groups, and I think most likely the truth is in between, hence debate should take place; science is not a place to impose a view or a theory. However I think that imposing moratoriums in science is an action from the Medieval times, like the Holy Inquisition did it for hundreds of years.

In a more positive matters I should say that your episode with John Coffin was just amazing. I think you should invite Jack (John) Johnson from Scripps. I am sure that your listeners would have a blast, he is just wonderful.

Oh, one more thing. I have been trying to get to the episode where you explain why “reverse genetics” is the wrong term. Could you elaborate on why this is the wrong term?

Thanks for everything

Mauricio

Mauricio Comas-García, Ph.D.

————————————————————-

————————————————————-

HIV Drug Resistance Program

National Cancer Institute

Frederick National Laboratory for Cancer

Research

Anthony writes:

For the TWIV episode of June 14 before this year’s Bloomsday (June¬†16), perhaps it might be interesting to mention literature’s most¬†important virus, the FMD picornavirus.

Joyce shows us that nonsense in newspapers about viruses is nothing new.  Thank you for TWIV, that inoculation against ignorance and disinformation.

Anthony

# # #

Ulysses

by James Joyce

“…

–I have put the matter into a nutshell, Mr Deasy said. It’s about the¬†foot and mouth disease. Just look through it. There can be no two opinions

on the matter.

May I trespass on your valuable space. That doctrine of LAISSEZ FAIRE which so often in our history. Our cattle trade. The way of all our old

industries. Liverpool ring which jockeyed the Galway harbour scheme. European conflagration. Grain supplies through the narrow waters of the

channel. The pluterperfect imperturbability of the department of agriculture. Pardoned a classical allusion. Cassandra. By a woman who

was no better than she should be. To come to the point at issue.

–I don’t mince words, do I? Mr Deasy asked as Stephen read on.

Foot and mouth disease. Known as Koch’s preparation. Serum and¬†virus. Percentage of salted horses. Rinderpest. Emperor’s horses at

Murzsteg, lower Austria. Veterinary surgeons. Mr Henry Blackwood Price. Courteous offer a fair trial. Dictates of common sense. All important

question. In every sense of the word take the bull by the horns. Thanking you for the hospitality of your columns.

 

–I want that to be printed and read, Mr Deasy said. You will see at the¬†next outbreak they will put an embargo on Irish cattle. And it can be

cured. It is cured. My cousin, Blackwood Price, writes to me it is regularly treated and cured in Austria by cattle doctors there. They offer

to come over here. I am trying to work up influence with the department.¬†Now I’m going to try publicity. I am surrounded by difficulties,

by … intrigues by … backstairs influence by …

…”

https://archive.org/stream/ulysses04300gut/ulyss12.txt

Sean writes:

Hello fabulous TWIV team!

Greetings and salutations from UCLA. I found this cool article on Facebook and was wondering what you all thought about it:

http://neurosciencenews.com/lymphatic-system-brain-neurobiology-2080/

It’s been a beautifully sunny and temperate 23C/73F here in Los Angeles, but incredibly dry. Next winter, please Fed Ex some snow to us since we are running out of water.

Alan and Vincent, it was lovely meeting you both at ASM last year!

Warm regards,

Sean

Andrea writes:

Nature Article – http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14432.html

Hi TWIV! By the time you all have a chance to read this, the news will probably be a few weeks ago, but I can’t help but send in this article as soon as I read it this beautiful dark 72 degree Fahrenheit night in Naples, Florida, at 2:30 in the morning (I wasn’t kidding about not being able to wait).

According to what I was able to understand, we’ve discovered a completely new part of the immune system! I can’t wait to see how such an exciting new discovery will affect both science and medicine, especially in the field of Virology.

As an unrelated note, thank you so much for the podcast. I listen to it all the time while I work in my retail job. I’m 21 and you all help motivate my dream to save and get back into school as fast as possible to major in microbiology. Maybe someday specialize in Virology! I can dream, can’t I?

Dakoda writes:

Hello Vincent and cohorts! I am an undergraduate Biology student recently turned on to your pod-cast by my cell bio professor after expressing interest in the field. I’ve spent much of my free time early into this summer listening to TWiV and with each episode find myself wishing more and more that the break would hurry up and end so I can get back into the classroom and labs.

I am sitting in a library in Kalamazoo, Michigan. The sites and sounds of Bronson Park, just across the street, are bursting with life as people enjoy the Kalamazoo Institute of Arts Fair. It is an ideal June Day. Clear blue skies, 18 degrees C, 13 km/h wind, 51% humidity and no notable seismic activity in the last month (http://www.mlive.com/news/kalamazoo/index.ssf/2015/05/feds_on_michigan_earthquake_un.html).

After that not so brief introduction, I have a question. I just listened to TWiV 333 and really enjoyed the discussion with Megan, Meredith, Boback and Ben from Vanderbilt University. I was wondering if there are any other episodes that you interview PhD students? Currently I’m in a transfer program from a community college to a four year university and while I feel that I’m being well prepared to finish my undergrad, there isn’t much information on what to expect/prepare for after that. Any relevant links would also be appreciated!

Cheers!

Mary writes:

Hi Guys,

I love your shows!  I am an MPH student in Environmental Systems and Human Health and I have been enjoying your TWIP, TWIV, and TWIM shows immensely.  I recently discovered the podcasts and am still making my way through all the episodes.  I do have a question I was hoping you could answer for me.  I heard a story in May about a doctor who had been infected with Ebola and several months after the virus had been cleared from his bloodstream, they found it still living in his eye.  My question is, how was the virus able to survive in the eye without being detected in the bloodstream.  Does this have implications about latent Ebola infections that could potentially be reactivated?  Any information you can provide would be appreciated.

Thank you so much and keep up the great work!

Cheers,

Mary

May writes:

Hi Vincent and Twiv-masters,

I just finished listening to audiobook “p53: The Gene that Cracked the Cancer Code” by Sue Armstrong. Sue is a science writer, same line of work as Alan Dove.

The book is entertaining and an easy read, with very little science jargon, but plenty of stories and vivid characters. It traced  the history of p53, from its discovery as a band of 53 kDa with no known function, to p53-based gene therapy approved in China.

The story of p53 has many twists and turns. p53 is involved in DNA damage repair, as such it’s described as “guardian of the genome”. But in the beginning, people thought it was an oncogene. There were papers published implicating p53 as an oncogene, only one guy could not get the same result. (I can’t remember his name, you will have to read the book. That’s the problem with audiobook, it’s hard to flip back to get the details.) Turns out only this guy had wild-type p53 protein, while all others did their experiments with mutant p53. This somehow reminded me of the XMRV story.

Then Vogelstein found mutant p53 in colorectal cancer patients and declared p53 as a tumor suppressor gene. p53 mutation was found in smokers and this finding helped to bring down the tobacco industry.

What I enjoyed most are the stories about how discoveries were made, as the author quotes Isaac Asimov, “The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ but ‘That’s funny…'”

It’s a nice beach read. I highly recommend it.

Regards,

May

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