TWiV 382 letters

Suzanne writes:

On So.

I hear every so in interviews on the radio and in podcasts. Some days they drive me nuts. But until you mentioned it, I didn’t notice that you use the word as often as you do. I think it’s because you’re using it properly. So has become the new um for a lot of people. They stick it on the beginning of a thought while they’re gathering their thoughts. You use it to connect a following thought to a previous one the way it’s meant to work. I suppose it’s still usually an unnecessary word and who am I to tell you what to change about yourself. But I wanted at least to say that you’re not abusing the word. Mostly you use it a lot when you seem to be excited about something which is cool!

Ricardo writes:

Hello TWIV Friends.

First of all let me thank you all for the enormous hours of FUN and specially, learning.

The weather here is beautiful for a “Primavera” (Spring) day. 13º Celsius with no clouds in the sky, and… 40% humidity, 3 UV, wind from the east at 22km/h with 0 dew point.

Now for science…

In volume 531, number 7593, Nature magazine raises an interesting question. This issue is about CRISPER and genome editing, but I notice, particularly, the term “citizen-science”. I think it has been an “arc” on TWIV . An interesting curiosity, (I remember a basement lab with wonderful microscopes) but a curiosity.  

So the question is, in a time when we can literally build a lab* in any one’s backyard, isn’t Crisper (or other similar) the technology that will bring the home lab out of the curiosity to the relevance world? Will that be a problem or an advancement?

http://www.nature.com/nature/journal/v531/n7593/index.html

* http://www.nature.com/news/open-hardware-pioneers-push-for-low-cost-lab-kit-1.19518

p.s. In my opinion it might be an advancement, as we have seen in software and electronics, but we really need better education.

Ricardo Magalhaes, Ph.D.

Associate Professor of Microbiology

********************************************************

Faculty of Health Sciences of Fernando Pessoa University

Portugal

Yegor writes:

Dear TWiV-casters,

The Visual Science company, which was mentioned (by me and others) in past episodes, just released a gorgeous 3D model of the Zika virus:

http://visual-science.com/projects/zika/illustrations/

Don’t miss the additional tabs that show the interactive model of the virus as well as the 3D animation.

Cheers,

Yegor

Yegor Voronin, PhD

Senior Science Officer

Global HIV Vaccine Enterprise

Mauricio writes:

Dear Twivers,

 I was extremely excited when I heard you were talking about a plant virus, but I got even more excited when I realized that you found interesting (or hopefully fascinating) that some plant viruses have multi-partite genomes and its implications with efficient cell infection. Some viruses are only bi-partite but some others like cowpea chlorotic mottle virus (CCMV) (or its “cousin” brome mosaic virus) have four RNAs; RNAs 1 and 2 are packaged individually in different capsids while RNAs 3 and the subgenomic RNA 4 are always co-packaged in (1:1 mole ratio) in a single virion. Furthermore, the subgenomic RNA 4 is not necessary for infection but is always co-packaged.  As a side note, when I become an independent researcher I wanted to really understand co-packaging of the sgRNA4. The fascinating thing is that in order to produce an infection, at least three virions containing the four RNAs have to localize within the same cell, or at least within neighboring cells. I find this fascinating!

My Ph.D. thesis focused on understanding the physical rules by which CCMV packages its genome; how small and how big can a ssRNA be in order to be packaged by CCMV capsid protein?; does in vitro packaging efficiency depend on the length of the packaged RNA? and how does the assembly mechanism depend on the length of the RNA? All this work was done with in vitro purified capsid proteins (from the virions) and in vitro transcribed RNAs. The main points are that packaging efficiency is maximum at the length of the RNA1 (3.2 kb) and that as you go shorter or longer the efficiency decreases; the short RNAs are preferentially co-packaged (and this assembly mechanism is different from that of the “long RNAs’ [~3.2 kb]); and when the RNAs are too long then they cannot fit within a capsid. I won’t tell you what happens when the RNA is too long, I will  be mean — hence you will need to read at least one of the papers to figure out what happens (hint: Cadena-Nava et al). I hope you enjoy them.

All the best

Mauricio

Mauricio Comas-García, Ph.D.

 

HIV Dynamics and Replication Program

National Cancer Institute

Marie writes:

Listening to a TWIV (TWIV 376, I believe), you mentioned an outbreak of anencephaly along the Texas/Mexico border and it not being linked to a known pathogen.  I thought about these papers showing it being linked to the mycotoxin, Fumonisin, that is produced by some species of Fusarium. I believe this might be the answer to the question that you were asking.

1. Marasas, W. F. O., Riley, R. T., Hendricks, K. A., Stevens, V. L., Sadler, T. W. , Gelineau-van Waes, J., Missmer, S. A., Cabrea, J., Torres, O., Gelderblom, W. C. A., Allegood, J., Martinez, C., Maddox, J., Miller, J. D., Starr, L., Sullards, M. C., Roman, A. V., Voss, K. A., Wang, E. and Merrill, A. H. 2003. Fumonisins disrupt sphingolipid metabolism, folate transport, and neural tube development in embryo culture and in vivo: A potential risk factor for human neural tube defects among populations consuming fumonisins-contaminated maize. Journal of Nutrition 134:711-716.
2. Missmer, S. A., Suarez, L., Felkner, M., Wang, E., Merrill, A. H., Rothman, K. J., and Hendricks, K. A. 2004.Exposure to fumonisins and the occurrence of neural tube defects along the Texas-Mexico border. Environmental Health Perspectives 114:237-241.

Always listening for you to include plant virus,

Marie A. C. Langham

Marie A. C. Langham, Ph.D.

Professor

South Dakota State University

Suzanne writes:

I was just following links from your show notes and realized I ought to thank you for them. All your podcasts have the most organized, useful, and easy to use show notes of any podcast I listen to, professionally or individually produced. And I think I’m up to about 50 now!

Thanks!

Suzanne

Anthony writes:

Blood sharing in vampire bats has been studied.  It’s been shown that this apparent altruism involves reciprocity, not selfish genes:

http://rspb.royalsocietypublishing.org/content/280/1753/20122573

I hadn’t heard about Rabies being spread by blood sharing and a quick Google search doesn’t seem to show it.  My understanding is that to infect, the Rabies virus needs to be transmitted by a bite; a trip through the GI winds up nowhere.  And even if Rabies was spread by blood sharing, it wouldn’t explain how North American bats — mostly insectivores — catch the disease.

And on the subject of bats, in the recent TWiEvo, the paper discussed states “All cell lines were maintained in a humidified 37°C.”  My understanding is that bats — with the exception of breeding females — go into a daytime torpor with much higher temperatures during flight.  Might similar temperature change in cell cultures be something to look at?

Also, there was a mention of not being able to bring specimens to the US.  Was this because of an oversight in obtaining the permits or because of some daunting aspect of the paperwork?  I believe that there also was something about a lab in Africa inadvertently destroying specimens.  In what country did this happen?  Was the error egregious or unavoidable?  Much work is going to be needed on African bats and it will be great if other researchers can avoid hurdles.

Thank you.

Robert writes:

Good afternoon TWIV folks –

Apropos the discussions of Kevin Folta  and Monsanto, this appeared this week from WBEZ (NPR affiliate) in Chicago:

https://www.wbez.org/shows/wbez-news/why-didnt-an-illinois-professor-have-to-disclose-gmo-funding/eb99bdd2-683d-4108-9528-de1375c3e9fb

> A WBEZ investigation has found that a University of Illinois professor was given more than $57,000 over less than two years from GMO maker Monsanto to travel, write and speak about genetically modified organisms–including lobbying federal officials to halt further regulation on GMO products.

I also note that Whole Foods is launching a big “GMO: Your Right to Know” campaign … I find it interesting that in their GMO FAQ page that missing among the list of questions is “Why should I avoid GMOs”.

—bob

Patrick writes:

Hi TWIV,

I’m presenting the Levasseur et al. MIMIVIRE paper in our lab’s journal club, and came across the original PLoS One paper describing the Zamilon virophage.  In the methods section they describe that it “…was named Zamilon (“the neighbor” in Arabic).”

While that’s all good, the real reason I’m writing in is to tell you about the weather, which is 75oF and sunny in Berkeley.

Thanks as always – and can’t wait for the Carl Zimmer episode.

Patrick

(formerly of the Malik Lab, and now working on innate responses to bacteria (oh no!) in the Vance Lab at UC Berkeley)

Asal writes:

Hi TWiV hosts,

I thought you might find this article about Mendel, the father of genetics, fascinating. It  briefly touches on different aspects of a scientist’s scientific life.

Did you know Mendel sent 40 reprints of his results, published in a low impact journal, to various botanists and biologists including Darwin? I did not know it!

I am sure Dickson, the father of vertical farms, will like the article.

Here is the link:

http://www.ascb.org/lost-paper-gregor-mendel-patron-saint-low-impact-scientific-publishing/

I am a long-time listener, blog, Facebook, Twitter follower, and a second-time writer.

Weather right now is not so Texan here in Dallas Fort Worth, Texas. And, by that I mean a mild temperature, a 70% humidity, a moderate wind speed, and isolated showers.

In fact, my light sweater with a TWiV logo on it sufficed throughout the day today!

Regards,

Asal

Dennis writes:

Hi Docs,

Thanks for another wonderful twiv #380.  At the end during the picks section I believe Rich Condit picked the youtube Physics Girl who does wonderful explanation videos.  Coincidentally there was a recent article about a different physics girl prodigy at Harvard who is researching gravity and related fundamental phenomena.  Her website is physicsgirl.com.  She is definitely one to watch as her work breaks new barriers as does she.  So my pick for today is physicsgirl.com for Sabrina Gonsalez Pasterski.

Separately, the TWIM on MAGE with Harris Wang was action and info packed and answered a lot of questions!

Best,

Dennis

Jacob writes:

Hi all,

Hearing you discussion about the second page of Google results reminded me of this XKCD comic: http://xkcd.com/1334/

My Listener Pick of the Week is an interview in ACI about some guy you might know http://aci.info/2016/03/15/aci-interview-with-professor-scholarly-blogger-dr-vincent-racaniello/

Thanks,

Jacob.

Molecular Biologist

Sydney, Australia (Scattered Thunderstorms, 21°C)