This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R² of 1.0), with a dynamic range from 10²-10⁶ cells/ml. Genotypes with >/=~80% average nucleotide identity to those targeted crosshybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R²=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions.
Table of Contents - 6[-]1 Introduction - 8[-]2 Env and HIV transmission - 34[-] 2.1 Differential transmission of HIV-1 by distinct subsets of effector dendritic cells - 34[-]3 Env antigenicity - 52[-] 3.1 The mannose-dependent epitope for neutralizing antibody 2G12 on HIV-1 glycoprotein gp120 - 52[-]4 Env folding - 76[-] 4.1 Folding and functionality of HIV-1 envelope glycoprotein disulfide bond mutants: discrepancies between ER quality control verdicts and viral fitness requirements - 76[-] 4.2 A stable -sheet fold can substitute for a disulfide bond in HIV-1 gp120 - 98[-] 4.3 Local and distal compensatory changes upon evolution of the HIV-1 envelope glycoproteins lacking the N-terminal disulfide bond in gp120 - 118[-]5 Env modifications for vaccines - 128[-] 5.1 A recombinant HIV-1 envelope glycoprotein complex stabilized by an intermolecular disulfide bond between the gp120 and gp41 subunits is an antigenic mimic of the trimeric virion-associated structure - 128[-] 5.2 Variable loop-deleted variants of the HIV-1 envelope glycoprotein can be stabilized by the introduction of an intermolecular disulfide bridge between the gp120 and gp41 subunits - 162[-] 5.3 Biophysical and antigenic properties of a proteolytically mature, disulfide stabilized HIV-1 gp140 envelope glycoprotein - 182[-] 5.4 Evolution of the HIV-1 envelope glycoproteins with a disulfide bond between gp120 and gp41 - 212[-] 5.5 Enhancing the proteolytic maturation of HIV-1 envelope glycoproteins - 226[-] 5.6 Stabilization of the soluble, trimeric form of the envelope glycoprotein complex of HIV-1 - 248[-] 5.7 Evolutionary repair of HIV-1 gp41 with a kink in the N-terminal helix leads to restoration of the six-helix bundle structure - 276[-]6 Concluding remarks - 290[-]Appendix Mutational analyses and natural variability of the gp41 ectodomain - 296[-]Summary - 322[-]Samenvatting (Dutch) - 328[-]Dankwoord (Dutch) - 334[-]Publications - 336.
(source: Nielsen Book Data)
The need for a vaccine against HIV is obvious, but the development of an effective vaccine has met with frustrations. The HIV envelope glycoproteins, residing in the viral membrane, are the sole viral proteins exposed on the outside of virus particles and are therefore major targets for vaccine design. The first part of this thesis describes research aimed at understanding the folding and function of the HIV-1 envelope glycoproteins and their properties underlying the effective viral immune evasion. The second part of the thesis describes the design of modifications of the envelope glycoproteins that should improve their properties as vaccine antigens. (source: Nielsen Book Data) 9789053566671 20190128
The need for a vaccine against HIV is obvious, but the development of an effective vaccine has met with frustrations. The HIV envelope glycoproteins, residing in the viral membrane, are the sole viral proteins exposed on the outside of virus particles and. (source: Nielsen Book Data) 9781417583386 20190129