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Viral vector nomenclature

Viral vector nomenclature - Protocols and Methods Forum

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  #1  
Old 06-05-2007, 05:36 PM
Tom Anderson
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Default Viral vector nomenclature



Hi all,

This may be a stupid question, but it's one that really bugs me.

Gutless viral vectors, right? Basically, a plasmid with an MCS, viral
packaging signals, and one or two other bits and bobs. You clone a gene
in, do some kind of packaging reaction, and you get out a load of little
blobs that have your construct in the middle and all the viral machinery
needed to deliver it into a cell on the outside.

What do you call those blobs?

I guess most people call them viruses, but to me, a virus means something
that's capable of infecting cells and making copies of itself, which these
things aren't. Some might call them vectors, but a vector is the piece of
DNA you put your gene into at the start, not the finished product. One guy
i worked with called them amplicons, which just seems completely wrong.
Any advances?

Can you call them viruses even though it can't cause a productive
infeection? I mean, just being unable to replicate in normal cells doesn't
disqualify AAV from being a virus. It's just that the only true host for
these blobs is the packaging cell line ...

Also: proteins go into solution, cells go into suspension, but what do
viruses do? Where's the borderline?

tom

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Tom Anderson, MRC Laboratory for Molecular Cell Biology, UCL, London WC1E 6BT
(t) +44 (20) 76797264 (f) +44 (20) 76797805 (e) [Only registered users see links. ]

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  #2  
Old 06-05-2007, 09:32 PM
Kyle Legate
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Default Viral vector nomenclature

Tom Anderson wrote:
Attenuated viri.
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  #3  
Old 06-06-2007, 01:17 AM
Aawara Chowdhury
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Default Viral vector nomenclature

In <[Only registered users see links. ].net> ,
Tom Anderson <[Only registered users see links. ].uk> wrote:


The correct term would be "viral vector", just as what that you refer
to as a "piece of DNA" should really be "plasmid vector", and not just
vector. The plasmid that you transfect to make a viral vector, should be
termed "viral vector DNA" or "viral vector plasmid".

The term "amplicon" is correctly applied to self-amplifying flavivirus
vector RNAs, but not to retroviral vectors, adenoviral vectors, and their
ilk.


Perhaps. You could call them replication-deficient mutant viruses.


Viruses go into suspension, I think.

AC
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  #4  
Old 06-06-2007, 01:43 AM
Ian A. York
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Default Viral vector nomenclature

In article <[Only registered users see links. ]>,
Kyle Legate <[Only registered users see links. ]> wrote:

You might conveivably call them attenuuated, but you wouldn't call them
"viri" under any circumstances, since only illiterates (and, increasingly,
computer techs -- but I repeat myself) use "viri" as the plural for
"viruses". "Virus" in Latin is a mass noun, and as such has no plural in
Latin; as an English word it follows the usual English rule and uses the
plural "viruses". People who, either attempting to show off their
non-existent Latin, or attempting to blindly follow a rule they don't
understand, use "viri" as the plural are, if anything, using the plural or
"vir" ("man").

I have nothing but pity for the poor pathetic wretches who use "virii",
thus desperately attempting to use an incorrect rule to pluralize the
non-existent word "virius".

Ian
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Ian York ([Only registered users see links. ]) <http://www.panix.com/~iayork/>
"-but as he was a York, I am rather inclined to suppose him a
very respectable Man." -Jane Austen, The History of England
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  #5  
Old 06-06-2007, 07:01 AM
Peter Ellis
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Default Viral vector nomenclature

Tom Anderson wrote:

Whether you can make a pellet by centrifugation?

Peter


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  #6  
Old 06-06-2007, 08:20 AM
DK
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Default Viral vector nomenclature

In article <[Only registered users see links. ].net> , Tom Anderson <[Only registered users see links. ].uk> wrote:

That's changed. Today, most people use "vector" synonymously
with "piece of DNA designed to get your favorite piece of DNA to
perform in the cells". I would call it "viral vector" (or "viral construct"
if you are that strict in your definition of vector).


There is no borderline. Just as there is no borderline between blue
and green. It's all about the conventions. At 1 g, viruses behave like
proteins - they don't sediment.

DK
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  #7  
Old 06-06-2007, 08:21 AM
DK
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Default Viral vector nomenclature

In article <f453gi$ini$[Only registered users see links. ]>, [Only registered users see links. ] (Ian A. York) wrote:

Heh-heh. I aways wondered if people who use "virii" also use "busi"
for more than one bus :-)

DK


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  #8  
Old 06-06-2007, 02:02 PM
Tom Anderson
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Default Viral vector nomenclature

On Wed, 6 Jun 2007, Peter Ellis wrote:


You can make a pellet of anything by centrifugation if you spin it hard
enough. Perhaps the position of the borderline depends on how big a
centrifuge you have!

tom

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(t) +44 (20) 76797264 (f) +44 (20) 76797805 (e) [Only registered users see links. ]
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  #9  
Old 06-06-2007, 02:41 PM
Tom Anderson
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Default Viral vector nomenclature

On Wed, 6 Jun 2007, Aawara Chowdhury wrote:


Hang on, though, the vector is the thing that does the carrying, not the
thing you eventually use. pRK5 is a vector; pRK5 with actin cloned into
the MCS is no longer a vector, it's a construct. You might say that pRK5
is the vector of this construct, but the construct itself is not a vector.

In my case, deleted type 5 adenovirus is a vector, but the things i'm
using aren't. 'Viral constructs' maybe? But that sounds like i'm talking
about the DNA with which i make the blobs (even though i'd actually call
that a genome, or a genomic construct).


Right. I could even accept that the genomes of my blobs are amplicons,
since they're units of nucleic acid which get replicated, but to call the
blobs themselves amplicons is surely wrong.


I'm going to go with this. It does everything a virus does except
reproduce; you wouldn't stop calling me person if i had a vasectomy,
right? No different!

Truly gutless systems are a bit different. I might suggest 'viroid', but
that means something else; 'virus-like particle' might do, but again, has
other connotations (it means at least two different things, to mycologists
and HIV people). 'Pseudovirus' also means something quite different
(infuriatingly, it's a kind of actual virus). How about 'virid'? Doesn't
seem to be used scientifically so far (as a noun), and at least sounds a
bit like 'plasmid'; the only trouble is that the particles themselves
would be viridions, which sounds like something out of a particularly bad
Star Trek: Voyager episode. I know! I'll call it a virius, just to annoy
Dr York.


Well, it seems like we're lacking a consensus here! I think, as DK said,
there's no hard and fast rule. I quite like the 'does it sediment at 1g?'
test, but i'm not sure it's strong enough - how do you define 'sediment'?

tom

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Tom Anderson, MRC Laboratory for Molecular Cell Biology, UCL, London WC1E 6BT
(t) +44 (20) 76797264 (f) +44 (20) 76797805 (e) [Only registered users see links. ]

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  #10  
Old 06-06-2007, 08:24 PM
Kyle Legate
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Default Viral vector nomenclature

Ian A. York wrote:
I wish I could understand what you're saying, but I a little illiterate.
Thanks for the pity.
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