TWiV 223 letters
James Chen writes:
Hi Rich, thank you so much for featuring our work on your podcast – it was a great honor. It is really gratifying for my postdocs and students to hear their work analyzed and praised by the experts. Quick answers to some of your questions:
1) cGAS can be activated by ssDNA, albeit more weakly than dsDNA. It’s not activated by RNA.
2) there is some cCAS in the nucleus, but the majority is in the cytoplasm, where it detects viral DNA, possibly on their passage through the cytoplasm (or release from the phagosome)
3) in our vaccinia virus experiments, we used heat inactivated virus, which can be taken up by cells and deliver DNA, but probably lost the ability to make new viral proteins that might antagonize the DNA sensing pathway.
4) malaria most likely engage this pathway.
I’ll just add that for the purification of cGAS, we used more than 2000 15-cm plates of L929 cells, performed mass spec of >100 bands (by my student Jiaxi Wu), which generated >100 Giga bytes of data that were analyzed by ‘label-free quantification’ to identify a set of proteins that co-purify with the activity throughout the purification steps. We had to do all of these because of the very low abundance of the protein – we estimated that we needed to purify the protein from the crude extracts by about 1 million fold to achieve apparent homogeneity, which is nearly impossible (without an antibody).
HeLa and 293 cells do not have this cytosolic DNA sensing pathway (i.e., cGAS and/or STING are not expressed in these cells); we think this may be one of the reasons these cells are so popular for plasmid transfection.
Open access in an anarchy
The solution to open access is the non-violence of anarchy: laying down the gun of coercive violence of enforcement by the state (and that of all petty oligarchs/gangs).
Sans state, there would be no copyright, no corporate charters, and therefore no corporations. Interactions would be horizontal, voluntary, non-coercive instead of vertical and coercive. An interaction cannot be deemed voluntary when it is at the gunpoint of the state, no matter how heavily cloaked.
In answer to the standard response “Who would build the roads?”, it would be the same people who do so now, but the money to pay them would not be confiscated at the state’s gunpoint.
A “phytometazoan” would be a combination of a metazoan and a “metaphyton”.
The nearest I could think of was corals:
In response to TWIV 222, which contained a large discussion about how to deal with scientific corruption, I would like to voice my own humble opinion. It is certainly true that those who discuss clear problems with the scientific process can unintentionally alert the public and give them ammunition to hinder the scientific process. Also, those naysayers, negative nellys, also have a knack of bruising the egos of scientists, who need that ego to keep them motivated in the face of the technical and intellectual challenges that face them from the time they wake up to the time their head hits the pillow. But we should certainly not dismiss those problems as not real or whacko, just because we cannot think of a solution. Indeed, a huge problem in science is people not revealing their own negative findings. How many scientists must hopefully press on, repeating experiments and trying to prove hypotheses that have already been disproven in the hands of multiple people? How often do we not provide advice to people when they present their research just because we fear that we will either bruise their ego or tip our own hand and be scooped in the process? We must ultimately ask ourselves the question, are we here to build our own careers, or are we here to advance our understanding of disease and the world around us?
Dear Vincent, Alan, Rich, Alan, Kathy & Dick,
At the beginning of TWiV #222 you mentioned the 60th anniversary of announcement of the structure of DNA. At Cold Spring Harbor Laboratory a meeting was organized to celebrate the event with a plethora of esteemed seminar speakers, including several Nobel laureates. Though the meeting concluded on Sunday James Watson, Sydney Brenner, Matthew Meselson and Wally Gilbert were invited to speak on Saturday evening. They recounted the heady the heady days of the discovery, events that led up to it and followed. It was punctuated with some irreverent humor too. But something Matt Meselson said struck a chord with me though he said it slightly tongue in cheek. He said that someone should really get this four, and by extension more people of their era, together to talk for a week and recount the way things were done, how, why, and the life of scientists back then. It reminded me of all the times you talk about getting people on before they die and their oral history is lost. Please instigate a regular feature on TWiV, TWiM and TWiP, alongside Virology 101, in which you talk to someone with such an oral history. I think it’s vital. It need not be a for a regularly scheduled TWi either, it could be a special episode as I’m sure they’d be very popular.
Secondly, with regards to the DNA GASsy sensor papers – a real tour de force as you said – I do share some concerns regarding how exactly some DNA viruses are sensed in the cytoplasm. But I would also contend there is still much to be understood about how GAS and other purported DNA sensors interact or play separate parts in this process. The proteins DAI (ZBP1), RNA pol III, AIM2, IFI16, and DDX41 have also been implicated as DNA sensors. How do their mechanism of sensing differ from each other? Do they; act in concert or in different subcellular locations or compartments, induce different signaling outcomes, recognize different DNA or DNA/protein complexes as substrates? If each were a sensor for one pathogen vs another that might give a clue, but this information seems lacking compared to the vigor it was pursued with regards to sensors that recognize foreign (viral) RNA.
Pick: Archiving the history of molecular biology, really a group of picks:
Edward Brydon, Ph.D.
Public Affairs, Cold Spring Harbor Laboratory
From Doc Ricky (@drricky) on Twitter:
listening to TWIV – yes, there’s evidence of retroviruses in “Protozoa”. Problem stems from incorrect use of the term.
Protozoa is a morphological classification, not evolutionary. At least 5 lineages are lumped in there.
at least in the amoebozoa, a sister clade to animals and fungi, yes, genomes are littered with retroviral copies.
Mind you, I don’t think a retrovirus has been observed “in action” among amoebozoa, but the tracks are there.
but this is also the lineage where mimivirus was discovered.
Dear Fellow Virologists,
To be fair to my european colleagues, I just wanted to give a short notice that you missed one name for IPS-1/VISA/MAVS in the last episode of TWIV. Meylan et al published the same protein in Nature in the fall of 2005 (the same period as the other articles) but the called it “Cardif”, because it is a CARD-containing adaptor protein that recruits IKK kinases (http://www.ncbi.nlm.nih.gov/pubmed/16177806).
A couple of years ago on a conference, one of the authors the Cardif paper mentioned in a presentation that all the authors from the four different papers had agreed on using the name: MAVS.
So that is what I have done since. It at least seemed like a reliable source, since he was not on the MAVS paper.
Thanks for an easy way to broaden my knowledge about other viruses than the specialized field I am doing my research on.
Best regards, Jonas
Jonas Söderholm, PhD
Department of Infectious diseases
University of Gothenburg
Dear family Twiv-ideae
I had a question before about scientific writing and I tried to solve it in twiv-o and I wanted to thank you that the answer was helpful and to the point, so I would like to take the chance to encourage enthusiast virologists to try the in twiv-o system if they have any inquiries or virus-related problems. I would certainly also refer microbiologists and parasitologist to check out the in twim-o and in twip-o systems too.
A follow-up TWiV 222: Last time when Dr. Racaniello asked why would be the DNA sensor in the cytoplasm instead of being in the nucleus? he said he was told that because the system is leaky and some viral DNA might reach the cytoplasm during infection and this is when the viruses are being sensed. He also that he just simply doesn’t buy it. (I also don’t). It seemed to me that it is just pure speculation not based on any evidence to think so, I mean it seems that there are no experiments done to quantify viral DNA “leakiness” to the cytoplasm during the course of an infection and whether this is a phenomenon that would push a cell to develop viral DNA sensors in the cytoplasm to fight infection. But anyways knowing that people speculate without evidence I want to take my turn. I think that may be this sensor is not in the cytoplasm specifically for viral DNA, may be it is just for ANY DNA and that presence of DNA in the cytoplasm is completely prohibited, therefore the sensor is just there and viral DNA is being treated as any other criminal DNA being in the wrong place.
Next, I have a Flu question that I think having the answer to it in on shot with the previous question would help me take my dose of virology for this week.
Influenza virus particles are covered by spikes of HA and NA with contradictory functions, HA binds sialic acid receptors to allow the virus envelope to fuse with the cell and allow for entry of the virus. NA is a sialidase that catalyzes the release of sialic acid both from cells and virus particles during virus release to allow for release of virus particles from the infected cell.
My question is: why not NA functions during entry of viruses preventing entry? i.e. if HA binds to sialic acid receptors on the cell surface to allow for entry, wouldn’t it be that NA then comes into action preventing this binding from being established? and if the answer is that there are more HA than NA on the virus particle surface, then why at the time of release NA is successfull in releasing virus particles from the infected cell, when also HA at this stage binds to sialic acid when it is leaving the cell?
If my question is not clear, just neglect it .
I am a PhD candidate waiting in the queue to get my VISA into graduate school to be allowed access to the land of thoughts and experiments.
The weather in Egypt … (I would not tell numbers not to make some people feel bad) but it is always sunny always nice
Thanks for the great show
Keep up the good work
Ain Shams University,
Cairo – Egypt
I saw this article in The Wall Street Journal that summarized a study in which researchers used publicly available information to find the identities of research participants who “anonymously” donated their genetic material. Do you think stories of this kind will become more common as research about (and the practice of) personalized medicine becomes more common? Will this make people more hesitant to embrace later medical breakthroughs or less willing to participate in research projects?
Science article (behind a paywall): http://www.sciencemag.org/content/339/6117/262.summary
Thank you all for the time and effort you put into the This-Week-in series.
(Undergraduate biology student)
How about Active Attenuated?
Often times you briefly talk about if a virus is alive. I enjoy hearing each members explanation for their stance. I’d like to hear this go in the other direction though. Take a bee hive for instance. Are the workers, having no reproductive future, alive? I assume you would, as anyone would consider a human with no children alive, and depending on your experience with children perhaps even more alive. But all of your talks that go this way tend to having the definition of life be more inclusive, virus, prion, etc. I’m interested on what your thoughts are towards making the definition of life less inclusive. For these ‘cultural’ modalities where not all members have a chance of reproduction could they be excluded. The idea will certainly be shot down, but I’m eager to hear why. For the bee example you’d likely say other members of the species can reproduce, but for colonial bee’s is the colony the minimal sustainable unit? Wouldn’t that be analogous to say a yeast cell being composed of living and ‘nonliving’ organelles.
Anyway, I’m currently working though a giant backlog due to ipod death, I hope to someday catch up to your thoughts on this.
Thanks for the time,
Love the show