The design of single-stranded nucleic acid knots

A general strategy is described for the synthesis of single-stranded nucleic acid knots. Control of nucleic acid sequence is used to direct the formation of secondary structures that produce the target topology. The key feature of the strategy is the equation of a half-turn of double helical DNA or RNA with a node in a knot. By forming nodes from complementary DNA sequences, it appears possible to direct the assembly of any simple knot. Stabilization of individual nodes may be achieved by constructing them from long regions containing both B-DNA and Z-DNA. Control over the braiding of DNA that acts as a link between node-forming domains can be realized by condensing the nodes into well-defined DNA structures, such as extended domains of linear duplex, branched junctions, antijunctions or mesojunctions. Further topological control may be derived from the pairing of linker regions to complementary single-stranded molecules, thereby preventing them from braiding in an undesirable fashion.     

Filament formation inThermus species in the presence of some D-amino acids or glycine

A number of strains ofThermus spp. changed morphology from rods of about 6 to 8 m long to multicellular filaments (unsheathed trichomes) up to many hundreds of micrometres long with the addition of glycine or certain D-amino acids to the growth medium. Associated with this change was the formation of braided trichomes and occasionally true knots. Filament formation was reversible by the removal of the causal agent, but only if growth was possible. Electron microscopy suggested that the wall structure was not changed, but only that cells did not separate due to the continuous nature of the outer membrane layer. The filaments were thus multicellular. The constituent cells were similar in length to the normal rod-shaped cells. Filament formation byThermus spp. may have applications in industrial scale culture of these extracellular enzymeproducing thermophilic bacteria.     

RNA-guided DNA assembly

We propose molecular models for homologous DNA recombination events that are guided by either double-stranded RNA (dsRNA) or single-stranded RNA (ssRNA) templates. The models are applied to explain DNA rearrangements in some groups of ciliates, such as Stylonychia or Oxytricha, where extensive gene rearrangement occurs during differentiation of a somatic macronucleus from a germline micronucleus. We describe a model for RNA template guided DNA recombination, such that the template serves as a catalyst that remains unchanged after DNA recombination. This recombination can be seen as topological braiding of the DNA, with the template-guided alignment proceeding through DNA branch migration. We show that a virtual knot diagram can provide a physical representation of the DNA at the time of recombination. Schematically, the braiding process can be represented as a crossing in the virtual knot diagram. The homologous recombination corresponds to removal of the crossings in the knot diagram (called smoothing). We show that if all recombinations are performed at the same time (i.e., simultaneous smoothings of the crossings) then one of the resulting DNA molecules will always contain all of the gene segments in their correct, linear order, which produces the mature DNA sequence.     

Geomorphic dynamics of floodplains: ecological implications and a potential modelling strategy

1.  The dynamics of channel migration and floodplain renewal constitute an important control of the ecological diversity of river corridors. Restoration initiatives should therefore assess whether these dynamics must be reinstated in order to address the cause rather than the symptoms of floodplain biodiversity decline.
2.  Restoration of reach-scale dynamism in rivers where this is a natural behavioural process will restore smaller-scale geomorphological and sedimentological processes that encourage vegetation regeneration, but may require catchment-scale management of material flows.
3.  Channel dynamics depend on the style of river–floodplain interaction, and this may be summarised in qualitative, classificatory, sedimentological models of floodplain architecture that have been somewhat neglected in the ecological literature.
4.  One approach to the assessment of floodplain biodiversity and its restoration would be through the development of simulation models based on specified channel styles, and involving simplified hydrodynamics and successional changes. Such models, currently the subject of research as a spin-off from modelling studies of landscape evolution, would permit evaluation of the consequences for ecological diversity of implementing various management options that may affect the dynamics of channel migration.