tag:blogger.com,1999:blog-9057886603931233717.post348383309212929372..comments2023-09-19T06:13:42.354-07:00Comments on Official O'Keefe Lab blog & (other) cool stuff: Next Gen sequencing provides evidence for MLVs and XMRV in prostate cancer! Eh? What's this all aboot?Denise S. O'Keefe, PhD.http://www.blogger.com/profile/10878930814538170550noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-9057886603931233717.post-8749778901884423502012-10-24T00:32:08.961-07:002012-10-24T00:32:08.961-07:00This comment has been removed by a blog administrator.Anonymoushttps://www.blogger.com/profile/16671195978168816842noreply@blogger.comtag:blogger.com,1999:blog-9057886603931233717.post-67663668859498916772012-07-19T15:49:01.966-07:002012-07-19T15:49:01.966-07:00Hi Denise,
With regards to Grossberg's findin...Hi Denise,<br /><br />With regards to Grossberg's findings, here's the patent: http://www.patentstorm.us/patents/5827750/description.html?forumid=331851<br /><br />And Grossberg's bio: http://www.mcw.edu/microbiology/SidneyGrossberg.htm#.UAiOO7S41y0<br /><br />I have been fascinated by the mysterious JHK virus ever since knowledge of a Human Gamma Retrovirus was discovered by Mikovits in 2009.<br /><br />JHK was isolated from a patient with ME in 1989, yet nothing was published until 1997 with no mention of ME.<br /><br />Its sequence was only added to Genbank last year, over 20 years after its discovery, and was classified a "XMRV": http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1133973<br /><br />And it is produced by the same human B-lymphoblastoid cell line that also produces EBV, which also causes mono/glandular fever, a common ailment that precedes M.E.<br /><br />I hope you find this information as interesting as I have.<br /><br />Best wishes, <br /><br />BBAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-9057886603931233717.post-75757674154550129112011-12-15T07:00:34.555-08:002011-12-15T07:00:34.555-08:00hey thanks for the info and refs anon...regarding ...hey thanks for the info and refs anon...regarding whether or not the RNA/DNA-seq was sequence independent, they say they used illumina...but that's it...Denise S. O'Keefe, PhD.https://www.blogger.com/profile/10878930814538170550noreply@blogger.comtag:blogger.com,1999:blog-9057886603931233717.post-43176810280198769122011-12-14T15:14:32.096-08:002011-12-14T15:14:32.096-08:00Hi Denise
Has anyone told you about the positive ...Hi Denise<br /><br />Has anyone told you about the positive CFS MLV-related retrovirus findings that were made in 1989? It wasn't published until 1997 but a sequence was added this year to the GenBank from that paper.<br /><br />Res Virol. 1997 May-Jun;148(3):191-206.<br />A human B-lymphoblastoid cell line constitutively producing Epstein-Barr herpesvirus and JHK retrovirus.<br />Grossberg SE, Kushnaryov VM, Cashdollar LW, Raisch KP, Miller G, Sun HY.<br />Source<br />Department of Microbiology, Medical College of Wisconsin, Milwaukee 53226, USA.<br /><br />Abstract<br />The human B-lymphoblastoid cell line, designated JHK-3, with pre-B-cell characteristics, chronically produces two viruses, Epstein-Barr virus (EBV) and JHK virus, an apparently novel retrovirus. The JHK-3 cells are much more productive of extracellular EBV than the high-producer marmoset line B95-8. The extracellular virus of the JHK-3 EBV strain is relatively fragile, more broadly dispersed in an ultracentrifuged sucrose gradient than the B95-8 EBV and more susceptible to disruption by combined treatment with urea and dithiothreitol. By restriction fragment length polymorphism analysis, the JHK-3 EBV strain resembles the EBV strain FF-41. The JHK-3 cells also produce an incompletely characterized, relatively fragile, enveloped, icosahedral RNA virus that contains Mn(++)-dependent reverse transcriptase. JHK virions measure 85 nm in ultrathin sections, much smaller than other Retroviridae. The JHK virus exhibits a distinctive morphogenesis, most nearly resembling C-type retroviruses. The JHK-3 cell line provides a human cell model for investigating virus/virus interactions and their pathogenetic affects on host cells which chronically and simultaneously produce DNA and RNA viruses.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-9057886603931233717.post-77373401377454421002011-12-14T14:51:39.047-08:002011-12-14T14:51:39.047-08:00sorry I meant to add that I,m not sure that this w...sorry I meant to add that I,m not sure that this was sequence independent amplification or notAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-9057886603931233717.post-26593227861235570972011-12-14T14:49:53.229-08:002011-12-14T14:49:53.229-08:00The coverage here was only 4x which was woefully i...The coverage here was only 4x which was woefully inadequate. Thw chances of detecting relatively rare integration sites at this level of coverage is very low indeed.MLVs tend to integrate into CpG islands and even at 10x coverage many of these regions are grossly unrepresented or missed altogether.Kim et al indeed only found 14 integration sites from the DNA of 9 patients. The authors may have been confused and only considered the results from the VP-62 clone interating into the DNA of the cell line du-145 which is entirely different from the in vivo pictureAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-9057886603931233717.post-25980607322733776302011-12-14T13:33:02.127-08:002011-12-14T13:33:02.127-08:00Hi Denise.
The Chow paper (Kim et al.) found onl...Hi Denise.<br /><br /><br />The Chow paper (Kim et al.) found only 14 integration sites in 9 patients. So XMRV does not integrate on every chromosome in every infected cell. <br /><br />MLV viruses and HTLV-1 have also been found to have integrated into the same nucleotide in a cell line as it did in host DNA.<br /><br /><br />The primary structure of the putative oncogene pim-1 shows extensive homology with protein kinases. http://www.cell.com/abstract/0092-8674%2886%2990886-X<br /><br />Weinstein et al. Insertion and truncation of c-myb by murine leukemia virus in a myeloid cell line derived from cultures of normal hematopoietic cells. http://jvi.asm.org/content/61/7/2339.abstract<br /><br />HTLV-1 Integration into Transcriptionally Active Genomic Regions Is Associated with Proviral Expression and with HAM/TSP. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000027Anonymousnoreply@blogger.com