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Tobacco necrosis virus (TNV) interfered with cucumber necrosis virus (CNV) replication in mixed infections. TNV inhibited both the initiation of CNV infections and subsequent CNV multiplication. Evidence of interference was found in qualitative evaluations of symptoms on a wide host range and by quantitative evaluations (lesion counts and incidence of systemic symptoms) on cucumber, cowpea, and bean. Fresh weight measurements similarly indicated antagonism in mixed infections. Some evidence of CNV interfering with TNV replication was found, in the form of a reduction in the occurrence of systemic symptoms. Photometric scanning of sucrose density gradient columns after centrifugation revealed that in mixed infections CNV reached only half the concentration attained in single infections while TNV was unaffected or even very slightly increased in concentration. This interference continued even when high temperatures greatly limited TNV replication. Only at 3° C, where its replication was barely detectable, did TNV have no effect on the CNV concentration attained. CNV did not significantly aid TNV replication at any temperature. In serial passage of mixed infections TNV quickly gained in concentration relative to CNV. Although CNV and TNV symptoms could not readily be distinguished from one another on most hosts, Phaseolus vulgaris var. Topcrop kept at 23 C and Chenopodium capitaturn kept at 18 C were established as reliable indicators of CNV and TNV respectively. One preparation from doubly infected tissue showed evidence of possible phenotypic mixing based on polyacrylamide gel electrophoresis and on reactions with antisera, although this could not be confirmed by infectivity tests. Through use of the antigen-antibody neutralization test, another virus preparation from doubly infected tissue gave evidence of possible genomic masking of TNV RNA in CNV coat protein. No evidence of possible genomic masking in the opposite direction was found. / Land and Food Systems, Faculty of / Graduate

Knowledge about structure and dynamics of the important biological macromolecules — proteins, nucleic acids, lipids and sugars — helps to understand their function. Atomic-resolution structures of macromolecules are routinely captured with X-ray crystallography and other techniques. In this thesis, simulations are used to explore the dynamics of the molecules beyond the static structures. Viruses are machines constructed from macromolecules. Crystal structures of them reveal little to no information about their genomes. In simulations of empty capsids, we observed a correlation between the spatial distribution of chloride ions in the solution and the position of RNA in crystals of satellite tobacco necrosis virus (STNV) and satellite tobacco mosaic virus (STMV). In this manner, structural features of the non-symmetric RNA could also be inferred. The capsid of STNV binds calcium ions on the icosahedral symmetry axes. The release of these ions controls the activation of the virus particle upon infection. Our simulations reproduced the swelling of the capsid upon removal of the ions and we quantified the water permeability of the capsid. The structure and dynamics of the expanded capsid suggest that the disassembly is initiated at the 3-fold symmetry axis. Several experimental methods require biomolecular samples to be injected into vacuum, such as mass-spectrometry and diffractive imaging of single particles. It is therefore important to understand how proteins and molecule-complexes respond to being aerosolized. In simulations we mimicked the dehydration process upon going from solution into the gas phase. We find that two important factors for structural stability of proteins are the temperature and the level of residual hydration. The simulations support experimental claims that membrane proteins can be protected by a lipid micelle and that a non-membrane protein could be stabilized in a reverse micelle in the gas phase. A water-layer around virus particles would impede the signal in diffractive experiments, but our calculations estimate that it should be possible to determine the orientation of the particle in individual images, which is a prerequisite for three-dimensional reconstruction. / BMC B41, 25/5, 9:15