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Dr O'Keefe - Paper accepted for publication

VillageLife

Senior Member
Messages
674
Location
United Kingdom

FancyMyBlood

Senior Member
Messages
189
I don't think this paper has anything to do with MLVs honestly. It's quite common that labs are involved in several different research projects. If it was really about MLVs I'd quess such a signifcant finding would be mentioned in the title.
 

currer

Senior Member
Messages
1,409
This is unlikely to be about a virus other than MLVs given what we know from Dr O'Keefe's blog.
 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
I don't think this paper has anything to do with MLVs honestly. It's quite common that labs are involved in several different research projects. If it was really about MLVs I'd quess such a signifcant finding would be mentioned in the title.

Just like the Italian paper?

On the face of it. MRVs might not be mentioned in the paper, but there is little doubt that is what they are finding, as O'Keefe has mentioned previously in relation to this work. What did she say: not XMRV, but related? Sounds awfully like an MRV to me.
 

Firestormm

Senior Member
Messages
5,055
Location
Cornwall England
Activation of innate anti-viral immune response genes in symptomatic benign prostatic hyperplasia

'A big CONGRATS to Allison Atwood-Madigan in the lab, the above paper has just been accepted for publication in Genes & Immunity (a Nature journal)! Bring on the celebratory laser-tag'

Has to be worth celebrating wherever one gets a paper published I would imagine, or whatever it's content.
 

FancyMyBlood

Senior Member
Messages
189
Just like the Italian paper?

On the face of it. MRVs might not be mentioned in the paper, but there is little doubt that is what they are finding, as O'Keefe has mentioned previously in relation to this work. What did she say: not XMRV, but related? Sounds awfully like an MRV to me.

It might be something like the Rnase L findings earlier implicated in prostate cancer. Yes, O'Keefe may believe these finding can be explained by MLVs, but until she publishes a paper where MLVs are actually found in PC, her findings are replicated and she's able to demonstrate cause-and-effect I'll just take the paper as it is: activation of innate anti-viral immune response genes in PC.
 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
It might be something like the Rnase L findings earlier implicated in prostate cancer. Yes, O'Keefe may believe these finding can be explained by MLVs, but until she publishes a paper where MLVs are actually found in PC, her findings are replicated and she's able to demonstrate cause-and-effect I'll just take the paper as it is: activation of innate anti-viral immune response genes in PC.

As far as I know, MRVs have already been found in PC, so if O'Keefe's lab was to publish a paper on the discovery of MRVs, it would in fact be a replication of the earlier studies. Besides, it's not PC in this case.but benign prostatic hyperplasia.

BTW I didn't dispute your first comment about whether MRVs were in the study, rather your comment about the study title not referring to MRVs. I was making the observation that previous studies have found MRVs, but gone to some some length to say the opposite in the title, and the abstract of the study.

I might also mention that O'Keefe has stated that papers finding MRVs are having trouble getting published.
 
Messages
646
As far as I know, MRVs have already been found in PC, so if O'Keefe's lab was to publish a paper on the discovery of MRVs, it would in fact be a replication of the earlier studies.

In science, replication requires that the reproducibility of results is demonstrated via research that is independent of earlier work - a different study by the same researcher doesn't meet the 'independent' qualification. For useful points on replication and reproducibility see: http://www.sciencemag.org/content/334/6060/1225.full (multiple articles in right hand menu (may require login) and http://sciencecareers.sciencemag.or...s_issues/articles/2011_12_02/caredit.a1100133

For the cart and horse problem in cancers see: ftp://130.94.180.226/pub/pca/inflammation/palapattu_etal_carcinogenesis_2004.pdf

IVI
 

Mula

Senior Member
Messages
131
Comparatively few sequences have been completely cloned, with most being similar to the reference sequence of xmrv. When pol and env are not detectable using primers targeting these sequences, then the sequence of the primers is not the type which is present.
 

Mula

Senior Member
Messages
131
I dont know if this is the right place to post this but the O'keefe scientist said that maybe they are using the wrong primiers cuz they find MLV gag but not pol or env. what does this mean? can it still be found by lipkin by NGS? sorry i dont know anything about this

http://okeefe-lab.blogspot.ca/2012/...of-mlv-gag.html?showComment=1346005326877&m=1

Dr Lipkin is not using next generation sequencing (NGS) to look for retroviruses in MECFS patients. He is to use it to look for EBV, HHV-6, about thirty in total, for the CFI project.
 

Daffodil

Senior Member
Messages
5,875
Thanks, Mula. So, if finding a new pathogen depends on the sequences we already know of, how can we find new ones? What if its a new pathogen with completely different sequences?

sorry perhaps this is a dumb question
 

Mula

Senior Member
Messages
131
It is typical to pull out one sequence with a particular test and differing versions with others. As is found with the retroviruses no two sequences are produced from a single test. To then find unknown sequences that infect below the ability of PCR next generation sequencing is the preferred choice. When a sequence is identified this can be searched for using primers that match, and if they are unknown then SISPA primers are used. Ideally both are required in this scenario.

The same pathogen can have different sequences both identified and unknown. Classification of sequences however could then be many years in discovery.