Calculations of the CD spectrum of bovine pancreatic ribonuclease

CD spectra of bovine pancreatic ribonuclease A (RNase A) and its subtilisin-modified form (RNase S) have been calculated, based upon high-resolution structures from x-ray diffraction. All known transitions in the peptide and side-chain groups, especially the aromatic and disulfide groups, have been included. Calculations have been performed with both the matrix method and with first-order perturbation theory. A newly developed method for treating the electrostatic interactions among transition charge densities and between static charge distributions and transition charge densities is used. The effects of local electrostatic fields upon the group transition energies are included for all transitions. Rotational strengths generated by the matrix method were combined with Gaussian band shapes to generate theoretical CD spectra. The calculated spectra reproduce the signs and approximate magnitudes of the near-uv CD bands of both RNase A and S. Agreement is most satisfactory for the negative 275 nm band, dominated by tyrosine contributions. In agreement with two previous studies by other workers, coupling between Tyr 73 and Tyr 115 is the single most important factor in this band. The positive band observed near 240 nm is dominated by disulfide contributions, according to our results. The far-uv CD spectrum is poorly reproduced by the calculations. The observed 208 nm band, characteristic of α-helices, is absent from the calculated spectrum, probably because the helices in RNase are short. A strong positive couplet centered near 190 nm is predicted but not observed. Possible reasons for these incorrect predictions of the current theoretical model in the far-uv are discussed. © 1997 John Wiley & Sons, Inc.     

The local‐regional species richness relationship: new perspectives on the null‐hypothesis

Despite considerable criticism in recent years, the use of local (SL) and regional species richness (SR) plots has a long tradition to test for community saturation. The traditional approach has been to compare linear and polynomial regression models of untransformed measures of SL and SR with a statistically significant linear or polynomial model indicating unsaturated and saturated communities, respectively. This approach has been the target of much controversy owing to statistical issues, the confounding effects of the arbitrary choice for the size of the local and regional area, and the difficulty in attributing ecological processes to the underlying SL SR pattern. The statistical issues and effects of scale stem from the lack of statistical independence and induced correlation between SL SR arising from the mathematical constraint, SL<SR. However, by removing this mathematical constraint by means of a logratio transformation, SL SR relationships can be calculated using ordinary linear regression and with a logical and definitive null‐hypothesis based solely on the presence of a statistically significant slope, which provides a quantitative measure of curvature. Simulations of SL SR relationships with varying curvature and SL:SR ratio demonstrate that the logratio model can accurately measure curvature independent of the SL:SR ratio. Therefore, the tendency for studies with high local:regional area ratio to result in linear SL SR trends when analysed by traditional regression methods may be mitigated by reanalysis by the logratio model. By alleviating the effects of scale, the logratio model offers a more statistically sound assessment of the SL SR relationship, which in turn can serve as an effective tool to complement emerging process‐based models.     

Transactivation of the human c-myc gene by c-Myb.

We analyse the contribution of six Myb-binding sites in the upstream c-myc sequences to transactivation by co-transfection assays. Surprisingly, deletion of the six Myb-binding sites did not influence the transactivation of c-myc by c-Myb protein. Instead, the strongest transactivation was observed with a c-myc reporter plasmid which contains only 450 bp of exon 1 including the c-myc promoter P2. An exchange of the DNA binding domain of c-Myb by that of GAL4 led only to small transactivation effects indicating that the DNA binding domain of c-Myb is essential for transactivation of the c-myc gene. These results suggest either an indirect transactivation mechanism of the c-myc gene by c-Myb proteins or a role of the DNA binding domain for additional effects than DNA binding.     

Modelling of Polarization-Dependent Loss in Plasmonic Nanowire Waveguides

We have investigated the potential of using gold nanowires embedded in a dielectric cladding environment as polarization-independent long-range surface plasmon polariton waveguides at telecom wavelengths. We performed finite-element analysis on various symmetric and close-to-symmetric cross-sectional geometries and evaluated the effects of cladding thickness on the propagation and coupling loss. The calculations confirm that fabrication of polarization-independent waveguides with reasonable tolerances is feasible and that straight-waveguide insertion losses around 1.5 dB for short (0.5 mm) devices can be realized when coupling to and from conventional dielectric waveguide geometries.     

Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages

We investigated whether arbuscular mycorrhizal fungal (AMF) communities in plant roots are random subsets of the local taxon pool or whether they reflect the action of certain community assembly rules. We studied AMF small subunit rRNA gene sequence groups in the roots of plant individuals belonging to 11 temperate forest understorey species. Empirical data were compared with null models assuming random association. Distinct fungal species pools were present in young and old successional forest. In both forest types, the richness of plant-AMF associations was lower than expected by chance, indicating a degree of partner selectivity. AMF communities were generally not characteristic of individual plant species, but those associated with ecological groups of plant species - habitat generalists and forest specialists - were nonrandom subsets of the available pool of fungal taxa and differed significantly from each other. Moreover, these AMF communities were the least distinctive in spring, but developed later in the season. Comparison with a global database showed that generalist plants tend to associate with generalist AMF. Thus, the habitat range of the host and a possible interaction with season played a role in the assembly of AMF communities in individual plant root systems.     

Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing

Variation in plant species richness has been described using only aboveground vegetation. The species richness of roots and rhizomes has never been compared with aboveground richness in natural plant communities. We made direct comparisons of grassland plant richness in identical volumes (0.1 × 0.1 × 0.1 m) above and below the soil surface, using conventional species identification to measure aboveground richness and 454 sequencing of the chloroplast trnL(UAA) intron to measure belowground richness. We described above- and belowground richness at multiple spatial scales (from a neighbourhood scale of centimetres to a community scale of hundreds of metres), and related variation in richness to soil fertility. Tests using reference material indicated that 454 sequencing captured patterns of species composition and abundance with acceptable accuracy. At neighbourhood scales, belowground richness was up to two times greater than aboveground richness. The relationship between above- and belowground richness was significantly different from linear: beyond a certain level of belowground richness, aboveground richness did not increase further. Belowground richness also exceeded that of aboveground at the community scale, indicating that some species are temporarily dormant and absent aboveground. Similar to other grassland studies, aboveground richness declined with increasing soil fertility; in contrast, the number of species found only belowground increased significantly with fertility. These results indicate that conventional aboveground studies of plant richness may overlook many coexisting species, and that belowground richness becomes relatively more important in conditions where aboveground richness decreases. Measuring plant belowground richness can considerably alter perceptions of biodiversity and its responses to natural and anthropogenic factors.