TWiV 212
Richard Virgen-Slane writes:
Awesome, you guys reviewed my paper! The hunt for VPg unlinkase sure taught me a thing or two about protein biochemistry.
Robin writes:
An LPN – licensed practical nurse – (sometimes interpreted as a low-paid nurse) is also known as an LVN – licensed vocational nurse. They do not have the same level of training as a Registered Nurse (RN). A certified registered nurse practitioner (CRNA) has substantial additional training past the RN.
Chris writes:
Hello TWiV hosts and audience–
Just wanted to share an interesting article with you:
http://dcist.com/2012/10/national_park_service_to_start_kill.php
Reminds me of Dickson’s old diatribe on the problems of deer overpopulations and the expanding Trichinella infestation in the early days of TWiV. Anyway, maybe some TWiV listener out there could arrange to get some samples from this? Seems like it could be a useful resource….
Thanks for all the awesome podcasts and thanks to the other listeners for the great and challenging questions–totally makes my science life (and maybe my personal one, too…).
Cheers,
Chris
Department of Microbiology & Immunology
Georgetown University Medical Center
Jacqueline writes:
I wanted to e-mail you about a program I found some time ago called Evernote (I apologize if this has already been recommended, still trying to get caught up). I just listened to episode 45 where Dr. Dove recommended MediaWiki. This sounded complicated for those of us who are not tech savvy. Evernote on the other hand is a very simple program. You can create notes of any length, attach files, create tags, and sort things in notebooks. In addition there is a very nice search feature that will find particular words within notes. I have been using this since I started grad school last year and have found it invaluable. The one caveat to the program is that there is a maximum you can add to it per month (for the casual user this will not likely be reached), however for a nominal fee per year that maximum is drastically increased. And there does not seem to be a lifetime limit. You can either download the program on your computer or interface with the program on the internet. In addition, you can sync your notes between multiple computers and access them anywhere there is internet. I use this program on my I-Pad, I phone and my PC at home so the program works on multiple platforms.
Thank you again for the great podcast as it kept me busy during my 20+ hours of travel this previous holiday weekend!
Edward writes:
Hello Twiverers,
thank you for the entire stable of TWi podcasts, which have turned the ‘cookery’ parts of benchwork into a chance for wider reading.
In TWIV 210 Mike wrote asking whether GM chickens and pigs lacking sialic acid receptors could be introduced, reducing the number of domestic animals able to harbour influenza. As you may have seen, something similar has already been demonstrated in priniciple. GM poultry and pigs have been around in labs for a long time (many of them using GFP as a marker, which leads to an amazing selection of glow-in-the-dark animals; surely a missed commercial opportunity in itself). In 2011 Laurence Tiley and colleagues showed that the same technology could be used to introduce shRNA with anti-influenza activity:
Lyall et al. (2011) Suppression of avian influenza transmission in genetically modified chickens. Science 331 (6014) 223-6.
http://www.sciencemag.org/content/331/6014/223.long
Although it’s not really discussed in the paper, I gather that the small number of progenitors used to rear the world’s current massive numbers of broiler chickens means that a transgene of this sort could be introduced very quickly – if there was the will to do so. However, as you commented, just because you can do something doesn’t mean that there is any desire to do it, and at the moment the public’s concerns about GMO (both considered and reflexive) clearly outweigh the fear of globally disseminated avian flu reservoir. Let’s hope this possibility doesn’t become more alarming in years to come, but if it does it’s good to think that we may have the technology to intervene.
Thanks again for the podcasts, and best wishes,
Ed
Junior Research Fellow
Worcester College
University of Oxford
Ricardo writes:
Hello Twiv fellows.
Just a word of friendship. Hope everything is ok with all of you, after “Sandy”.
My best regards.
Ricardo Magalhães
UFP
Portugal
Lance writes:
Just looking at all the pictures of Sandy on the web. Hope you are all OK.
Lance
Peter writes:
Hi Twivvers,
There was an interesting article in our local media today about a Hendra virus vaccine for horses. I thought it was unusual in the level of technical detail it included. Thanks to listening to TWIV I understood a little more of the background to the technicalities than I would otherwise.
One interesting point the article makes is the use of a cross-disciplinary team to develop the vaccine. That made me consider that your coverage is centred on straight Virology papers, and I have not heard a lot of discussion about such teams. Do the presenters have much experience with such teams? Are there interesting stories about how the different specialities bring different pieces to a solution? Just thought it might generate a bit of a different discussion.
Plus, I am sure there are some interesting finer details about bats, horses, humans and Hendra.
Thanks for the podcasts,
Pete
Sydney, Australia
Adrian writes:
Dear Professor Racaniello,
Hi! This is Adrian from Singapore where the temperature is 25 degrees Celsius with 94% Humidity.
I’ve heard about Hurricane Sandy and was following your twitter and hope that you and your family are fine!
I’m a recent Phd graduate from the National University of Singapore from A/Prof Paul MacAry’s lab working on antigen processing of Epstein-Barr Virus but used to work on dengue and Enterovirus 71 before that but now am looking for a postdoc somewhere.
My wife introduced me to TWIV and am a recent convert of TWIV and have been trying to catch up with the past podcast.
You guys are GREAT!!! I really enjoy the discussions about great papers and the virology 101. Please keep up this great service!
We’ve visited your TWIV Facebook page and we saw Rea’s fort! And we thought “Finally!!! someone else out there understands us!!”, as we also have our own collection of plaque plates as we did our fair share of plaque assays with both dengue and enterovirus 71.
Best regards,
Adrian Sim, PhD
Immunology Programme,
Lab of A/P Paul A. MacAry
National University of Singapore
Steve writes:
So, if and when it seemed appropriate, it would be nice to hear what TWiV thinks about what disruption the new online education model may have on the operation of universities. By the initial quality offerings by Coursera (and others), it seems that online models could eventually displace some, even much of on-site non-hands-on courses delivered at most academic institutions.
Do you think the growth of quality online information and training will change the role of universities?
If the ability to take good quality academic training at reasonable costs online challenges and begins to displace significant portions of the current mass under-graduate training model, how will, could, and should institutions response? How should they re-define themselves? What could be the benefits and the dangers in shifting to more accredited academics online?
More importantly, if shift and disruption happens, how should basic-research science view this disruption and position itself to grow and prosper during this time? How can the academic science system adapt to embrace the change and feed more minds and create more social and political awareness of the deep benefits and fascinations in science?
If the model changes, how might this change effect how basic academic science is done and/or funded?
There’s a lot of questions that could be asked — from will it change; to if it changes, what will change; to what are the core services and functions the current university model gives to basic research that it might lose with change; to are there good alternative models to the current system, and what elements of any alternative should the academic science system try to adopt now and under conditions of change?
Taylor writes:
Vincent & Friends,
I work at Children’s Medical Center in Dallas. I’m a huge fan of your podcast and so are all the students working here in credentialing. I follow a number of podcasts and I recently listened to one called Science Sort of. I think it would be interesting if you and your co-hosts listened in and critiqued the information here and generally made fun of it whenever possible. Just an idea. I think that it would be ridiculously entertaining to hear you guys add your two cents, shoot down falsities, and show your own listeners the broad spectrum of questions that can be answered by looking at things under the microscope. So often, podcasts regarding science and technology can be pandering to the novice or only covering general information. You guys are keeping things real on TWIM and you’re seriously doing the lord’s work. Keep it up!
Daryn writes:
Hi everyone,
I just want to say thanks for your podcast. Over the last few days I’ve been listening to the episodes at work and I’ve really enjoyed them. The show is awesome. I really appreciate it.
-Again, just saying thanks and keep up the good work,
daryn
Quantitative Analyst, QuaRC
Manuel writes:
Dear TWiV,
http://online.wsj.com/article/SB10001424052970204349404578100942150867894.html?mod=e2fb
“A cure for colorblindness might even be in the offing. Vision scientist Jay Neitz and his colleagues at the University of Washington are building on their 2009 breakthrough in which they restored red-green vision in two colorblind squirrel monkeys by inserting the missing gene into a virus and injecting it into their retinas. Four years later, the monkeys, Sam and Dalton, still pass daily vision tests, identifying colors on a computer screen correctly. They also have a newfound liking for green M&M’s, Dr. Neitz says.”
Have a nice day.
Paul writes:
I saw your Penn & Teller video on vaccination (on the twiv page [listener pick on TWiV 202]), apparently advocating the acceptability of a 1% autism rate. They failed to mention that a 1% fatality rate from variolation was considered highly risky, even in the 17th century:
http://www.nlm.nih.gov/exhibition/smallpox/sp_variolation.html
spurring the zeal for, and popularity of, a truer prophylactic (cowpox). So the clarity of their point defeats me a little.
Other than the above, I have no opinion on the acceptability or otherwise, of vaccination.
Sara writes:
Dear Team TWIV,
Sorry if this question has already been posted to TWIV as I’m just catching up in the last few months. I remember a while back hearing a story that FDR may not have actually contracted poliomyelitis but rather Guillain-Barre syndrome. I haven’t heard much mention of this since and was wondering, what with your collective knowledge about poliovirus, you might have a good insight to this. Love your show, it makes the hours spent on plaque assays fly by. Keep up the good work!
Sara
PhD Candidate in the laboratory of Karla Kirkegaard
Stanford University
Jim writes:
Vincent,
I just read about LearnStreet in an Uncollege newsletter, went there and started using it. I don’t code, hear it’s an important skill, made furtive starts at Code Academy, and am impressed enough with the introduction and beginning steps at LearnStreet to pass on the info. Your students and perhaps some of your listeners might have a need.
FYI in case you haven’t seen it already this Quora topic on skills researchers should have to communicate caught my eye.
Hope you and your workplace have made it through the storms ok.
Regards,
Jim
Smithfield, VA
Faruku writes:
Dear Sir,
I am just curious to ask what link the Th1 and Th2 responses?
Regards
Faruk
Tony writes:
Dear twiv,
I am an aspiring molecular virologist. I listened to the the interview Prof Vincent had with Prof Phillip Marcus about cloning HeLa cells [TWiV 197]. I couldn’t understand though the part where Prof Marcus refers to the situation where his supervisors thought they thought they were converting a Gram positive to a gram negative and he advised them otherwise which led to him losing his place. Could you please elaborate on what happened in this situation as I couldn’t get my head around it.
Regards
Anthony
King’s College London
David writes:
Hi,
Sorry for the shameless self promotion but I thought our latest paper might be of interest to TWiV. We show how to combine deep sequencing and high throughput proteomics to study adenovirus infection of human cells.
Why? Well two things seemed useful to us, firstly we demonstrate that this approach correctly collates and identifies all the detectable proteins and transcripts present in this well understood system – this means it will work even if you did not know that we were working on human cells infected with human adenovirus. In principle you could look at any new virus in any eukaryotic host (mammalian, plant or insect) and gain insight into changes in gene and protein changes on a very large scale and instantly identify pretty much all of the proteins detectable by mass spectrometry and connect them to their transcripts (both viral and host cell). So you can use this approach with any virus in any cell type even if the host organism or the virus has not had their genomes sequenced or properly annotated.
Secondly, we showed that by monitoring changes in gene expression and correlating that with protein levels you can focus in on proteins that are targeted for degradation by virally induced mechanisms (i.e. the virus deliberately has the protein destroyed because it gets in the way of viral replication or spread). We searched for proteins that had been degraded during viral infection that still had healthy (or even rising) levels of gene expression in the host cell – i.e. the gene is not switched off but the protein is being destroyed instead. This analysis correctly identified all the ones we know about in adenovirus (and are known to be functionally important) and identified some new ones, one of which we were able to verify as an exciting new target.
We think this will be useful to study well understood viruses in order to see if they are targeting host proteins for destruction and for the study of animal/plant/insect viruses in their normal non-human host especially if you want to examine zoonotic viruses such as the ones that recently jumped from bats to humans in the middle east.
Anyway, hope you find it interesting!
Best Wishes,
David.
Paper attached and can be found at:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2227.html
Dr David A. Matthews
Senior Lecturer in Virology
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Mary writes:
Hi i had a question i was listening to Bats, elephants, and AIDS Twiv 10.
I got everything about the elephants but i didn’t really get about the bats and the AIDS. What were the main points of that and why are we so concerned about it? What were the over views of those topics? thank you.
Blaine writes:
Hello there Vincent and Dickson and colleagues,
I am a biology instructor at a college in Northern Alberta and I have absolutely loved your podcasts (This Week in Parasitism and This Week in Virology) as they have helped me learn new and wonderful things. Now that I have given you some glowing praise, will you please read my questions in your next podcast?
My first question is relevant to both TWIP and TWIV, so I sent it to both podcast emails in hopes that there is someone out there that may have an answer or two.
1. I have been thinking a lot about phage therapy. So my question is this, can we use these viruses in some sort of therapy analogous to phage therapy?
(I have recently learned that the protist Trichomonas can sometimes harbour a virus that can make the disease more severe, clearly we don’t want to encourage these viruses…)
2. I have been learning about Herpes viruses and had a basic question about herpes virus lifecycles that I am unable to find a sufficient answer to. How do these viruses go latent? Do they incorporate themselves into host genomic DNA like retroviruses, or is it by some other mechanism?
Thanks a bunch for all the work you put into these podcasts,
Blaine
Steve writes:
Hi,
Attached is the transcript for TWiV #206, Viral turducken, in both WORD and PDF formats. I did something a little different this time. Because of its length I did not transcribe the introduction (first 9+ minutes) and the email and picks at the end. I did transcribe the 50 minutes of discussion about the two articles covered in this episode.
If you’d really prefer to have the entire podcast transcribed, just let me know and when the new sledge-hammer head arrives I’ll get back to the rock pile on this one.
Steve
My sympathies to Kathy… sometimes the long-in-the-tooth dogs can talk and talk and talk. Actually, really informative for me. Thanks.
Andreas writes:
Dear Vincent, I am an avid reader of TWIV since some time and I believe the following story would be in your “scope”: I worked for some time on “host factor targeting” (broad range) antivirals: Bottom line: we identified a physico-chemical (!) mode of action applying a FDA approved compound acting antiviral against a broad range of pathogens. Understanding this mode of action enables now to develop better, more targeted compounds opening a completely new field of antiviral development. It`s pretty much the first time, a host-mechanism is targeted which has the significant benefit of not being “virus-specific” (shared pathways). There are also other nice aspects like synergy with compounds that could not be applied till now since they are too toxic in their effective range but combining two different modes of action with the same target significantly limits tox.
I hope the readership of your blog would be interested in such a finding. The paper was published very recently in PLOS Pathogens:
Niclosamide Is a Proton Carrier and Targets Acidic Endosomes with Broad Antiviral Effects
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002976
I hope you find the paper interesting and worth to be “spread” – please contact me any time if you have questions.
thanks a lot & all the best!
andreas
PS.: I am not active in academia any more and thereby do not wanna “hijack” your blog for my career – I however truly believe that our work will enable completely new ways of developing antivirals, something we desperately need. The more people in the field are aware of it, the better.
Jim writes:
Vincent,
I saw this NEJM article about the response after Sandy. At the article’s end is a reference to the National Center for Disaster Preparedness, Mailman School of Public Health, Columbia University, New York, which I’ve not noticed anywhere before. I emailed one of the article’s authors, Dr Redlener, and the Center to see if they had heard about programs like Sahana Eden and got this interesting response from the Center that includes a webinar tomorrow, the 27th:
Hi Jim,
Thanks for touching base with us about online central data collection systems. Yes, we’re interested in this as well, and have been looking into best practices. Sahana Eden and Ushahidi (http://www.ushahidi.com) seem to be the most widely used, but there are always new developments. At the current time, the Columbia Regional Learning Center does not provide actual software systems for this purpose. That said, we do have some online courses pertaining to usage of social media during disasters, which can be found here: http://ncdp.crlctraining.org/catalog/?id=3 In particular, “COM 2302 Risk Communication for High Risk and At-Risk Populations,” should be of interest.
There is also an upcoming free webinar re usage of social networks during disasters, that will cover these trends. You can register below.
Please plan to attend the NYDLA webinar on Social Media in Disasters
Reserve your seat for this FREE webinar @ http://www.nydla.org/. Experts from the Social Media world as well as from FEMA and DHS will share valuable information.
Social media has changed the way that we work and play. Social media is now changing the way that we deal with disasters such as Superstorm Sandy.
Register today so that you can ask questions live from the panel!
– Columbia Regional Learning Center
=====================================================
I see that there is a NY Distance Learning Association, which is news. Also through that site this list of PDF’s dealing with such health-related topics as vaccines and dengue. You probably deal with these places and sources because they are local, but they might be of interest to your listeners, too. I was particularly pleased to get information about Usahahidi, another means of dealing with disasters. The COM 2302 class didn’t look too useful.
Jim
Smithfield, VA
Marion writes:
1. Regarding the extended discussion of the usefulness of the (SARS)-CoV ExoN mutation for attenuation of SARS virus in hopes of future vaccines:
Just an opinion, but the success and extremely high safety of the subunit HBV and HPV vaccines suggest that most future vaccines will be engineered– Especially considering the climate caused by the anti-vaccine wack-a-loons. Finding correlates of protection will be more important than correlates of attenuation.
2. Regarding Matt’s pick Virus-associated pyramids (slide #11): Having been educated at Rockefeller University, one of the founding places of cell biology and being taught by several Nobel Laureates who DISCOVERED organelles, it was drilled into me that EM is highly prone to artifacts. You could look at NaCl and see “7-faced pyramidal structure” . EM data alone are meaningless. It must be corroborated with data from other methods. Moreover, it was a color-enhanced EM—Electrons are not in color. Many people do not understand that. While I understand that his pick was aesthetic, it should have been accompanied by such warnings.
Winkler writes:
Is there any way to compare the productivity of the NIH research model with the university research model?
Winkler, MD
from Jon Yewdell:
Two thoughts
1. Yes, in principle. Can take some objective measure (# citations) and divide by $$ funding. But both are problematical. We all know difficulties of measuring true impact, so citation # is an indirect proxy. $$ funding is surprisingly difficult to nail down , since universities have byzantine financing and with many subsidies for supporting research, and typically can’t provide real costs. On the other hand, devoted research institutes (limited in number), particularly small ones, exactly know their costs.
2. As members and stewards of a profession, we would be completely stupid not to factor in some level of investigator happiness in improving the current system or trying to rationally design an optimal system. If system A is demonstrably more efficient, but the investigators are miserable, is this really preferable? System A will also over time, drive out/repel more talented/creative individuals, and the lost productivity is incalculable.
Jon
Steve writes:
Hi,
I only have listened to about 25 TWiV podcasts, if it is not a regular recurring segment, I encourage you to have a host periodically focus on the statistical methods and analysis in various studies. Statistics is an important broadly-applied, and sometimes misapplied, general science tool that could benefit from more in-depth critical discussion.
Also, in doing various topic searches in the TWiV archives, I find it difficult to get good search results. In addition to listing the podcast number and title fields, it would be nice if the description field was also shown—these more clearly express the content covered in each podcast.
Josh writes:
Vincent,
It looks like the powers that be did a pretty good job in choosing the flu strains for this year’s seasonal 2012-2013 vaccine (see Antigenic Characterization of CDC link)
http://www.cdc.gov/flu/weekly/index.htm#whomap
Outpatient visits are up compared to the pandemic season…but it seems too early to tell as of yet.
Keep up the great work.
Josh in Georgia
Ivva writes:
Dear Vincent,
I really enjoy your podcasts.
In the last episode of TWIM about the spores you mentioned that you have had an argument about whether the viruses are living or not. It seems a very interesting topic to me and it will be great if you could sent me a link to that podcast.
Thank you in advance.
Doug writes:
TWiV folks (especially Vincent, I mean, Dr. Racaniello):
I have been listening off & on for the better part of a year, & with the successful acquisition of a functioning iPod, you guys have filled my lonely hours on the bus as I transit through the Appalachians to & from graduate school. Anyhow, being a bit Obsessive-Compulsive, I wanted to start TWiV from the beginning, &, after being heartily entertained by a rant from Dr. Racaniello & Dr. Dove (Alan) about stomach viruses being blamed for all GI ailments, this headline immediately made me think of you guys.
Clinton cancels Middle East trip over illness
http://news.msn.com/politics/clinton-cancels-middle-east-trip-over-illness?ocid=ansnews11
So my questions- in accordance with the VincentAlanian Standards of Proof for Virus-Caused GI Distress (similar to Koch’s postulates, but tougher):
1. Is there a reasonable expectation for a Secretary of State to perhaps have not a PCR machine in her bedroom (for virus ID, as you’ve suggested), but at least some lackey in the Department of State who can run a sample of some body fluid/ tissue to a person capable of confirming the presence/ absence of a Norwalk… er, Norovirus/ Rotavirus?
2. If yes to the above, when did this capability become available to cabinet officials?
3. Are there any historical precedents for virus-induced illnesses cancelling high level, if futile, summits?
Thanks for giving me an excuse to blow ten minutes off from studying for finals/ oral candidacy. You guys rock!
The BigWhale
