The effects of clipping and fertilization on nitrogen nutrition and allocation by mycorrhizal and nonmycorrhizal Panicum coloratum L., a C4 grass

Summary Mycorrhizal and nonmycorrhizal plants of Panicum coloratum L. were grown in a factorial treatment design under two nitrogen levels and two clipping heights with an unclipped control. The nitrogen concentration in different plant components was determined following 9 weeks of growth under experimental conditions. Mycorrhizal infection increased green leaf and sheath nitrogen concentration by a relatively small, but significant percentage and had no effect on nitrogen allocation to the various plant components. Clipping increased leaf nitrogen concentration but inhibited growth to the extent that, when compared with the unclipped controls, less nitrogen remained in residual plant biomass with up to half of the total nitrogen allocated to offtake (the material removed by clipping). Plants receiving the higher nitrogen fertilization had higher tissue concentration of N and more N allocated to above-ground living tissues. Mycorrhizal infection interacted with clipping height and also with N availability significantly. Infection was unable to ameliorate the negative effects of the most severe clipping regime and of the low nitrogen availability on leaf and sheath N content. This is possibly due to mycorrhizal demand for carbohydrates competing with the carbohydrate requirement of roots for nitrogen uptake.     

Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci

The phylogeny of Celastraceae subfamily Hippocrateoideae (～ 100 species and 19 genera in the Old and New World tropics) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. The subfamily is easily recognized by the synapomorphies of transversely flattened, deeply lobed capsules and seeds with membranous basal wings or narrow stipes together with bisexual, 5-merous flowers that generally have an extrastaminal disk and three stamens. Hippocrateoideae, like Salacioideae, are inferred to have an Old World origin. The narrow stipes of Neotropical species that are water-dispersed are inferred to be derived within the subfamily from ancestral species with wind-dispersed winged seeds. Helictonema, a monotypic genus endemic to tropical Africa, has a small, white, spongy aril that is located at the base of the seed wing and appears to be unique within Hippocrateoideae. Our inference that Helictonema is sister to the remaining members of the subfamily, considered in the context of Sarawakodendron being sister to Salacioideae, suggests that small arils and capsular fruit were primitive within both subfamilies. The aril became dramatically enlarged within Salacioideae, in which the fruits are berries, and lost entirely within Hippocrateoideae, in which the fruits are transversely flattened capsules. All five Old World taxa of Prionostemma and all eight currently recognized species within Simirestis are transferred to Pristimera, one South African variety of Pristimera is raised to species level, and all three taxa in Pristimera subgenus Trochantha are transferred to the new genus Trochantha.     

<Emphasis Type="Italic">Scoredist</Emphasis>: A simple and robust protein sequence distance estimator

Background  

Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used.     

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

Background  

Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling are not fully known. In the present work we approached this by using two of the most popular HMM packages: SAM and HMMER. The programs' abilities to build models and score sequences were compared on a SCOP/Pfam based test set. The comparison was done separately for local and global HMM scoring.