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Nice jimm.
So the isolated 4 different gene sequences from CFS and 4 diffrent gene sequences from healthy diners (BD set) but state in the paper that there are only 6 unique virii. Can you tell which two match up?? I'm a bit foggy today.
George - you had going with 'diners' instead of 'doners'. I'm not making fun, I substitute vowels (that aren't right next to each other on the keyboard!) to make new and interesting words all the time.
egads, don't make me laugh I'm too tired today. Dang it! O.k. so they had 4 unique sequences from the CFSer's and 4 from um. . .Them healty people (grins) but only 6 unique virii so I'm wondering which ones match. Cause I'm thinking if the CFSer's match up that would me a specific type of virus for us and then I would think that those might be like really like the XMRV one.
Then I'm thinkin' do the ones that show up in the healthy people look like the ones in the CFSer's??? Cause what if they kinda look like FMlV or MoMLV ya know where I'm going with this???
I'm going to wander off an eat some doners now. . . . .
egads, don't make me laugh I'm too tired today. Dang it! O.k. so they had 4 unique sequences from the CFSer's and 4 from um. . .Them healty people (grins) but only 6 unique virii so I'm wondering which ones match. Cause I'm thinking if the CFSer's match up that would me a specific type of virus for us and then I would think that those might be like really like the XMRV one.
Then I'm thinkin' do the ones that show up in the healthy people look like the ones in the CFSer's??? Cause what if they kinda look like FMlV or MoMLV ya know where I'm going with this???
I'm going to wander off an eat some doners now. . . . .
1. MLV-related virus CFS isolate CFS-type1 polyprotein gene, partial cds
2. MLV-related virus CFS isolate BD-26 polyprotein-like gene, partial sequence
3. MLV-related virus CFS isolate BD-22 polyprotein gene, partial cds
4. MLV-related virus CFS isolate CFS-type3 polyprotein-like gene, partial sequence
5. MLV-related virus CFS isolate CFS-type2 polyprotein gene, partial cds
6. MLV-related virus CFS isolate BD-28 polyprotein-like gene, partial sequence
7. MLV-related virus CFS envelope glycoprotein gene, partial cds
8. MLV-related virus CFS isolate BD26 envelope glycoprotein gene, partial cds
OK I'm out of my depth I know, but I recollect that CFS1-3 are the 3 found in CFSers and the 4th they found was in those healthy diners (that's a classic btw!). Don't recall if there was any overlap, ie whether any of those were found in both. This may all be obvious but thought I'd post in case it helped...O.k. so they had 4 unique sequences from the CFSer's and 4 from um. . .Them healty people (grins) but only 6 unique virii so I'm wondering which ones match.
I'd like to know...I think...are you going towards bits of these sequences look like maybe they could be just those known 'harmless' MLVs you mention, or are you going towards hmm maybe those MLVs aren't so friendly as was thought? None of them can actually be FMIV or MoMLV surely, since they've said that all four are new PMRVs? Is the possibility of some of the new HGRVs being formed using bits of the harmless MLVs looking at all likely do you think?Then I'm thinkin' do the ones that show up in the healthy people look like the ones in the CFSer's??? Cause what if they kinda look like FMlV or MoMLV ya know where I'm going with this???
I wish I could vote this thread HOT
I love to see your brains unravelling all the pieces
Thank you
Yes my brain has completely unravelled and is now in pieces. (grins)
O.k. now what the heck to do with the information that two of the sequences match 100 % to lab mouse 129 XMRV viral strain and one has a 96% sequence match to lab mouse C57 black/ C57 black 6 (same mouse line evidentaly) ?????????????????????????????????????????????????
Otis my brain is in so many pieces at thsi ponit thta I fogret what the hekc I was thniking in the fisrt place. (bleh)
Is it just me or is there no problem at all here?
Because non of the viruses that Alter, Lo et al. found are identical to a mouse virus. They might be very close - but they are not identical. So, what's the problem? And alter et al. already proved that these viruses are more closely related to polytropic murine leukemia viruses than to endogenous murine leukemia viruses.
Exciting! Will they give you a result from the test?
Hi Otis
Sorry I've been so brain dead lately. It comes and goes and when it's bad it's very bad. Just got up from about a 3 day nap (grins) I currently have 3 working brain cells and thought I'd try to use them.
The whole BLAST thing sounds really cool. I'm guessing here that what is needed to do BLAST is the gene sequences so that you can run two against each other?????
http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239
Looks like a primer on the BLAST
http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide
This looks like where to get the nucleotide sequences like the ones from the Alter Paper
When I typed in XMRV I got 638 hit's some with patents????? and the complete genomes of VP 62/42/35 (these are at the very end of the 638 listed)
http://www.ncbi.nlm.nih.gov/nuccore/EF185282.1
This link is the entire nucleotide sequence, I think you can use the Accession number in the BLAST????? and it loads the sequence?????
On the Friend Murine Leukemia virus there is a whole genome on the FB29 it's link is here http://www.ncbi.nlm.nih.gov/nuccore/Z11128.1 there does seem to be a lot of variants of this virus, A LOT of variants.
The Moloney MLV (which is classed as a PMLV) is here http://www.ncbi.nlm.nih.gov/nuccore/J02255.1
Now what I can't figure out is how to find out if a MLV sequence comes from a particular mouse strain. Like what Vince was talking about with the, and here's another fuzzy, either an MLV sequence from Alter/Lo paper was a match for the 129 mouse strain or XMRV is a match for the 129 mouse strain. But where does one find MLV's listed with reference to specific lab mice???? (head scratch)
I did find this information on the Jackson Laboratories site http://jaxmice.jax.org/strain/004178.html about the 129 strain. (if you click on the tabs it get's into some facinating reading if you have time to read through it, grins) and that lead to this page http://jaxmice.jax.org/protocolsdb/...P2_MASTER_PROTOCOL_ID,P2_JRS_CODE:5200,004178 which list's phenotyping, primers and other information for laboratory use but I still don't know how to match it all up and come to a reasonable piece of information that we can use. ?????
You probably have all the above information and are happily BLASTING away. (grins) but just in case I could add anything I though I toss this stuff out there. Who knows maybe the links will come in handy down the road. (big grins)