TWiV 287 letters

Wink writes:

It just occurred to me while listening to you jogging, that the disposition of human stool is changed when you are paralyzed. LOVE TWIX!

Wink

Mark writes:

Hello Vincent and this week’s hosts-in-attendance,

Late afternoon this past Memorial Day, in an unusually warm afternoon while visiting California’s Central Coast, I was engaging in a new pleasant activity: listening to TWiV while tending a bar-b-que. The new part was listening while cooking food on the grill. This joins “listening while driving” and “listening while dog walking” as favorite, enjoyable listening venues.

My iPhone was playing TWiV 286 recorded at ASM/Boston. While listening I was enjoying the waste product of Saccharomyces cerevisiae and grape juice aged in a French oak barrel – in other words, a fine California Cabernet.

From ear buds flowed conversation with the 2nd guest of the episode, a discussion with Dr. Julie Pfeiffer about her research on polio virus. An interesting, recurring theme developed – she invites colleagues for drinks on her patio to talk science. Different aspects of her work and the podcast conversation referred to conversations on that patio.

This triggered an idea: how about a TWiX drinking game.?!  It is modeled after Bingo, and the board is constructed of catch phrases commonly uttered by different hosts on TWiV, TWiP, and TWiM. How many times have TWiV listeners heard “ferrets are not humans” or TWiM listeners heard “Chamber of Commerce weather”? These and other phrases are familiar friends to listeners. Now they can be part of a game.

Attached is a PDF file with Bingo card with 25 common phrases I’ve heard in all the shows. To play, get a glass, an adult beverage, and start listening. Every time a phrase is used, take a drink and mark the card. Listeners can personalize the game by substituting some of their favorite phrases in lieu of mine. Also attached is a smaller image of the board suitable for embedding in a blog post.

Please keep recording shows from conferences and visits to other researcher’s labs. Hearing researchers talk about their work adds a dimension that interpretation and discussion of published papers can’t match.

All the best.

Joe writes:

Hi all,
Maybe I’m just totally downplaying the risks involved but I can’t understand why people don’t want these gain of function influenza experiments to be done. After all, nature does them all of the time! Though, this is mostly forgotten by the time these opinion articles reach the 6:00 news.

Thoughts?

I should probably add that I don’t think that these experiments are without risk. Any work with pathogenic viruses are always with risk. And I also don’t think that the proposed alternatives shouldn’t be done or are not worth pursuing. I think all of these experiments should be done, though as the authors surprisingly say (at least to me) in the opinion:

“Ultimately, studies with intact viruses will be necessary for a full understanding of human transmissibility, a phenotype of a whole virus.”

– Joe

Joseph Comber Ph.D.
Postdoctoral Fellow
Immunotope Inc
Doylestown PA

Rich writes:

Esteemed TWiV hosts

Follow up (Robin style):

Why a single stranded genome?  Single stranded DNA takes up less room than double stranded DNA, therefore packaging a single stranded DNA genome rather than a double stranded DNA genome permits propagating more genetic information in a limited size capsid.  (The packaging size is a fact, the extrapolation from that fact is my fantasy.)

I wonder if the higher mutation rate in ssDNA viruses doesn’t have to do with the absence of a spare copy of the correct information encoded on the complementary strand.  If a double stranded DNA containing virion sustains environmental damage, there is a chance that only one strand will be damaged and the correct information can be recovered via the complementary strand.  If a ssDNA containing virion sustains the same damage, there is no backup.

Richard Condit

Professor

Department of Molecular Genetics & Microbiology

University of Florida

Gainesville, FL 32610

Auntie Meeba Histolytica writes:

Nature ran a contest for the science fiction stories written in 200 characters or less.  I thought you guys would get a kick out of the biology related ones:

RUNNERS UP

Cynthia was learning faster than anyone had predicted. The apparently totipotent cells continued to proliferate at an exponential rate. Today would be the last time they would refer to her as a mouse.

As robots perform the laboratory work, it is cheaper just to electronically stimulate areas of the student’s brain associated with frustration and failure and then, after 3 years, call them doctor.

The Prof smiled. “I’ve isolated the plague vector! Now we can kill it.” I sighed with relief, “I’ll tell the others.” He held my arm as I turned away. “Hang on, old chap. Amy, pass me the syringe.”

Despite her growing love for him the mission demanded it happen now. He sat on the bed and placed his hand on her leg, she turned inside out enveloping the president. Endocytosis won the ten-day war.

It was a novel trial, the first of its kind, the charge was illegal human cloning, creating a sentient human in laboratory, the verdict was guilty, ironically the sentence was: life.

Years of cheap computer time allowed the TKLabs GeneCoin project to decode all the ‘junk’ DNA in the human genome. Now a lone tech sees the output flashing on the screen: “Intentionally left blank” …

I lost my arms at work. New arms made from tissue scaffolds take too long to grow. No work, no money. So, my boss fused a used pair of robotic arms onto me. My robot overlords finally promoted me!

http://www.nature.com/nature/journal/v508/n7494/full/508144a.html

Wael writes:

Dear esteemed professors;

I have developed an intimate relationship with your podcasts -TWIV/M/P.

I am certain great benefits are reaped from your podcasts, specifically in poor resource settings, and I have recommended it to a couple of friends in Sudan, who have now started listening. Your podcast is certainly a valuable (and FREE) educational resource for a country with a lot of the infectious agents that you have discussed in your various episodes.

Despite having a high burden of infectious diseases; we unfortunately remain lagging in our knowledge about them (whether human or zoonotic) – heck we even have our own virus -Sudan Virus (http://en.wikipedia.org/wiki/Sudan_virus)!

Not only that, but the Wellcome tropical labs were also based in our country (http://www.wellcome.ac.uk/About-us/History/WTX052449.htm). Civil war unfortunately left us where Henry Wellcome has found us nearly a century ago.

On a different note, I am amazed at the encyclopedic knowledge of both Prof. Despommier and Prof. Schaechter! Is there anything they don’t know; and how are they able to retain so much knowledge (serious question)?

Again many thanks for your kindness and I am certain you all have a good nights sleep as your conscience has to be clear for sharing this beauty with us.

Robin writes:

HERVs & stem cells

To what extent have these HERVs helped or hindered the repair and regeneration of body parts?

Salamanders regenerate amputated limbs, geckoes shed their tails when grabbed by the tail and flee, later regenerating them.  I have done it myself (i.e., grabbed household geckoes’ tails, not shed one of my own – except in the phylogenetic sense from primates to apes) and noted later the regrowth of that appendage. That should be at least as complex as the regeneration of a limb, with the regeneration of sclerotome, myotome and dermatome.

Even newborn humans will regenerate a distal phalanx including the nail if lost within the first week of life. Could the progressive loss of regenerative capacity from amphibian through reptile to mammal be related to genomic alterations induced by yet-unrecognised or now-unrecognisable viruses?

Herpesvirus saimiri and idiopathic pulmonary fibrosis.

Since Herpesvirus saimiri is found in squirrel monkeys, and squirrel monkeys are native to the tropical forests of Central and South America, the next step would be to get a travel history from idiopathic pulmonary fibrosis patients, in particular travel to or residence in Central and South America for patients and their close contacts. Exposure to squirrel monkeys outside their native geographic distribution might also be significant, such as in zoos, labs and pet shops.

[review Gammaherpesviruses and pulmonary fibrosis: evidence from humans, horses, and rodents and interview http://www.news-medical.net/news/20140114/Idiopathic-pulmonary-fibrosis-(IPF)-and-herpesvirus-saimiri-an-interview-with-Elazar-Rabbani-Chief-Executive-Officer-of-Enzo.aspx

EBV & freshmen

From your podcast It would seem that it has a predilection for freshmen that get fresh, an association that has been well-known for a long time.

____

“Gut microbiome educates the immune response that is not only local but also distal to the gut”

The word “distal” has a connotation of “further downstream” or “further away from the center”. It implies directionality, unlike the word “distant” which just refers to a spatial dimension. The former is in a sense vector while the latter is scalar. “Distal to the gut” (in the old days) would be the outhouse.

Jacob writes:

Hi all,

I response to Robyn’s email about helicopters (TWiV 272) Vincent said that it’s a pity that so much money is wasted on these that could be spent on science.

As a response I’d show you this link showing how sky cranes are very very useful for us Australians in bushfire season

http://fireaviation.com/tag/australia/

Weather is 17°C and alternating between overcast, drizzle and rain here in Sydney, pretty much the same as every day for the last 3 weeks, so we’re unlikely to need them right now.

While I’m here, I thought I’d wade into the discussion about the terms we avoid in science. I always have a problem with saying something is “designed” to carry out a function, rather than “has evolved to”, as designed implies there a designer. Just my AUS$0.02.

(Carl Zimmer keeps a list of Banned Words For Science Journalists at Banned Words)

Thanks,

Jacob

Melissa writes:

The debates about vaccinations continues. My friends who are health professionals post frequently articles such as this one. I wonder what the scientists at TWIV have to say about it. And do they know scientists or family members who don’t vaccinate? My dad got polio the year before they came out with the vaccine. In addition to almost dying back then, struggling through life as disabled, he now is suffering from post-polio and will probably die because of it. I don’t want my (future) child to suffer the same fate.

http://www.donotlink.com/j00

Thank you,

Melissa