Chaim writes:
Dear TWiV Masters,
In episode 482, the paper discussed used the PacBio long read sequencing technology. However, Vincent referred to the machine as being “the size of a harmonica,” when the PacBio Sequel is actually about 5 and a half feet tall. The MinION, by Oxford Nanopore, is the small portable long read sequencer that had been mentioned on TWiEvo.
Pedantically yours,
Rob writes:
Dear Twivvers
A quick error correction email on your discussion on PacBio sequencing from the last TWiV, which mixed up two different systems.
There are two commercial long read sequencing technologies: PacBio and Oxford nanopore.
PacBio systems (covered last week) are the size of a US-style refrigerator (not a harmonica as Vincent suggested). They turn linear dsDNA into what is topologically a ssDNA circle by ligating a hairpin oligo to each end. They then sequence round and round the circle (covering fwd and reverse strands, sometimes more than once each) to reduce error.
Oxford nanopore systems (the minIONs) are the size of a harmonica, and reads the nucleotide sequence of linear DNA that is fed through a pore.
From Rob in London, where it’s -2C, snowing pretty heavily and everyone is hiding indoors because the UK can’t cope with snow.
(eg see https://www.youtube.com/watch?v=Nq9ay_K_YOU – not safe for work)
Dr Rob White
Lecturer In Virology
Imperial College London
Section of Virology
London
Kay writes:
Dear TWiV Team (and Nels) !
I am lagging behind by a few episodes, so chances are that somebody else has already made these comments, which should have been sent in more timely as a ‘follow up’.
In the last episode I listened to (TWiV 476, In ACOD1 we trust), you discussed an interesting paper wherein the authors claim that multiple viruses upregulate a particular lncRNA which in turn increases metabolic flux through the TCA cycle. You were totally enthusiastic about the immense workload done by the authors and the elegant experiments.
I must say that I am not totally convinced, because this paper dodges a number of important questions:
1) the induction of this lncRNA is reported to be IFN-independent (which makes sense) but to depend on NFkB. I find it hard to believe that viruses would trigger the NFkB response ‘on purpose’ to get a metabolic advantage. As a downside, the viruses would have to increase their defense against all the other nasty factors induced by NFkB
2) The authors don’t even discuss the fact that their lncRNA is sitting next to ACOD1, which has two important properties: First, ACOD1 (the protein!) is also known as IRG1 (immunoresponsive gene) and is a well known NFkB target and regulator of the inflammatory response. Second, ACOD1 acts on cis-aconitate, which is an important intermediate in the TCA cycle. ACOD1 generates itaconic acid, which inhibits the glyoxylate shunt. I don’t want to go into details, here is a good reference:
https://www.ncbi.nlm.nih.gov/pubmed/23610393
3) The neighbor relationship of the lncRNA and the ACOD1 gene raises a number of suspicions: Does the knock-out of the lnc-RNA really not affect the protein-coding ACOD1 gene? Wouldn’t it be obvious to at least check if the lncRNA acts by regulating the expression of the neighboring ACOD1 gene? It might be a total coincidence that both the lncRNA and the neighboring ACOD1 gene are NFkB targets, are anti-inflammatory and regulate the TCA cycle. But not even discuss this ??? I don’t know.
Ah, on a more positive note, here is an answer to a question raised by Rich Condit: Are there other proteins/enzymes that bind RNA? Yes, there are. One of them is particularly pertinent: The cytosolic form of aconitase (the enzyme that isomerizes citrate in the TCA) moonlights as a specific RNA-binding protein recognizing “iron response elements” in the mRNA. In this function, the protein is referred to as IRP1
https://en.wikipedia.org/wiki/Iron-responsive_element-binding_protein
but it is active as an aconitase nevertheless. And is has the same substrate as ACOD1. A coincidence?
Best Wishes,
Kay
Kay Hofmann
Institute for Genetics
University of Cologne
Justin writes:
Just wanted to say I absolutely loved the section of TWIV 480 where Scott Hensley was talking about the RBC assay and other tests they do on influenza, that’s exactly why I listen – as a total nerd who does method development in a pharmaceutical lab, thanks, hope to hear him back on the episode.
Bryn writes:
Hello!
My question is this: Although different species of viruses probably had very different origins, could one of those possible origins be that “viruses have come from cells as defense mechanisms?” (I’m watching all of twiv from the beginning and haven’t seen every episode yet, so sorry if this has already been covered.) I was wondering if it’s plausible that some single celled organism created a kind of chemical with the “intention” of warding off being eaten or destroying nearby cells and this “weapon’s” potency lay in its ability to behave as a virus? Maybe the cell was attacking another cell with a very similar genetic sequence but was just different enough to avoid also being infected. Or maybe built into an animal’s genetic code to discourage cannibalism or inbreeding sort of like a prion? Also, perhaps the cell didn’t create a virus for the purpose of defense, but as a means of reproduction that was so effective that it in itself became reproducing. As a side note, do you think it’s possible for a poison to behave like a virus? Somehow being able to create more of itself using an element of our biology and infect cells but with zero genetic code and be as simple as a chemical compound? I’m planning on going to school to become medical lab technician and am fascinated with virology and would like to keep working my way up through school to become a virologist. I’m incredibly fascinated by viruses and I think the key to learning about how life formed to begin with lies with them. I’m learning about them as a hobby but currently don’t have an education above a high school level.Thank you so much for reading!
Fernando writes:
Dear Vincent & The Virals,
(Couldn’t resist thinking of the TWiV crew as a pioneering rock & roll band) This bioinformatics paper just popped up in my Twitter feed, it shows some curious biases on how differential gene expression is reported in abstracts relative to the underlying expression data. It’s not virology, but I wonder whether the same phenomenon plays a role in bioinformatics-based studies you have reported recently.
Best wishes to the band 🙂
— F
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-017-0293-y