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Re: Re: Where are the experiments which prove HIV isolation, sexual transmission and antibody specificit

Many of these infectious molecular clones can be purchased from the AIDS Reagent Repositories:

If the Perth Group would like to claim that density gradient ultracentrfugation is the ONLY acceptable method of isolating a virus, they should provide some evidence that any virus has ever been isolated by that method to their satisfaction, preferably another retrovirus. Density gradient centrifugation is just one of hundreds of methods of seperating biological (and other) materials. It seperates materials based on their boyant densities which is just one of many proterties. Before the biolgocical revolutions which ocurred in the late 20th century, such as Lambda phage library construction, monoclonal antibody production (including binding monoclonal antibodies to various matrices for the purposes of immunopurification), and DNA sequencing electron microscopy and crude serology (with polyclonal sera) were considered cutting-edge tools in virological identification. However, times have changed and many far more accurate technologies now exist.

Below are just a few of thousands of papers published on HIVs and SIVs that illustrate why infectious molecular clones (and techniques such as site-driected mutagenesis which can be used to identify individual amino acids that contribute to pathogenicity) are useful, indeed critical, to AIDS research.

Virology 2003 Mar 15;307(2):328-40
Analysis of the functional relationship between V3 loop and gp120 context with regard to human immunodeficiency virus coreceptor usage using naturally selected sequences and different viral backbones.
Bagnarelli P, Fiorelli L, Vecchi M, Monachetti A, Menzo S, Clementi M.
Istituto di Microbiologia, Universita di Ancona, Ancona, Italy.
ABSTRACT:
The human immunodeficiency virus type 1 (HIV-1) gp120 V3 loop plays a predominant role in chemokine receptor usage; however, other linear and nonlinear gp120 domains are involved in this step of the HIV-1 replication cycle. At present, the functional relationship between V3 and these domains with regard to coreceptor usage is unclear. To gain insights into the nature of this relationship in naturally selected viral variants, we developed a recombinant strategy based on two different gp120 backbones derived from CXCR4 (X4)- and CCR5 (R5)-tropic viral strains, respectively. Using this recombinant model system, we evaluated the phenotype patterns conferred to chimeric viruses by exogenous V3 loops from reference molecular clones and samples from infected subjects. In 13 of 17 recombinants (76%), a comparable phenotype was observed independently of the gp120 backbone, whereas in a minority of the recombinant viruses (4/17, 24%) viral infectivity depended on the gp120 context. No case of differential tropism using identical V3 sequence in the two gp120 contexts was observed. Site-directed mutagenesis experiments were performed to evaluate the phenotypic impact of specific V3 motifs. The data indicate that while the interaction of HIV-1 with chemokine receptors is driven by V3 loop and influenced by its evolutionary potential, the gp120 context plays a role in influencing the replication competence of the variants, suggesting that compensatory mutations occurring at sites other than V3 are necessary in some cases.
PMID: 12667802

Sevilya Z, Loya S, Duvshani A, Adir N, Hizi A.
Mutagenesis of cysteine 280 of the reverse transcriptase of human immunodeficiency virus type-1: the effects on the ribonuclease H activity.
J Mol Biol. 2003 Mar 14;327(1):19-30.
PMID: 12614605

Brunelle MN, Brakier-Gingras L, Lemay G. Replacement of murine leukemia virus readthrough mechanism by human immunodeficiency virus frameshift allows synthesis of viral proteins and virus replication. J Virol. 2003 Mar;77(5):3345-50. PMID: 12584361

Wei X, Liang C, Gotte M, Wainberg MA. The M184V mutation in HIV-1 reverse transcriptase reduces the restoration of wild-type replication by attenuated viruses. AIDS. 2002 Dec 6;16(18):2391-8. PMID: 12461412

J Virol 2002 Dec;76(23):12173-84
Direct binding of human immunodeficiency virus type 1 Nef to the major histocompatibility complex class I (MHC-I) cytoplasmic tail disrupts MHC-I trafficking. ,br>Williams M, Roeth JF, Kasper MR, Fleis RI, Przybycin CG, Collins KL.
Graduate Program in Cellular and Molecular Biology, University of Michigan. University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA.
ABSTRACT:
Nef, an essential pathogenic determinant for human immunodeficiency virus type 1, has multiple functions that include disruption of major histocompatibility complex class I molecules (MHC-I) and CD4 and CD28 cell surface expression. The effects of Nef on MHC-I have been shown to protect infected cells from cytotoxic T-lymphocyte recognition by downmodulation of a subset of MHC-I (HLA-A and -B). The remaining HLA-C and -E molecules prevent recognition by natural killer (NK) cells, which would otherwise lyse cells expressing small amounts of MHC-I. Specific amino acid residues in the MHC-I cytoplasmic tail confer sensitivity to Nef, but their function is unknown. Here we show that purified Nef binds directly to the HLA-A2 cytoplasmic tail in vitro and that Nef forms complexes with MHC-I that can be isolated from human cells. The interaction between Nef and MHC-I appears to be weak, indicating that it may be transient or stabilized by other factors. Supporting the fact that these molecules interact in vivo, we found that Nef colocalizes with HLA-A2 molecules in a perinuclear distribution inside cells. In addition, we demonstrated that Nef fails to bind the HLA-E tail and also fails to bind HLA-A2 tails with deletions of amino acids necessary for MHC-I downmodulation. These data provide an explanation for differential downmodulation of MHC-I allotypes by Nef. In addition, they provide the first direct evidence indicating that Nef functions as an adaptor molecule able to link MHC-I to cellular trafficking proteins. PMID: 12414957

Competing interests:   None declared