A method for determining overall protein fold from NMR distance restraints

Summary We describe a simple method for determining the overall fold of a polypeptide chain from NOE-derived distance restraints. The method uses a reduced representation consisting of two particles per residue, and a force field containing pseudo-bond and pseudo-angle terms, an electrostatic term, but no van der Waals or hard shell repulsive terms. The method is fast and robust, requiring relatively few distance restraints to approximate the correct fold, and the correct mirror image is readily determined. The method is easily implemented using commercially available molecular modeling software.     

The tertiary structure of Aspergillus saitoi minor ribonuclease (Ms) predicted from the structure of RNase T1

Ribonuclease Ms from Aspergillus saitoi is a small acidic protein (11 714 Da) containing 106 amino acids of known sequence. Unlike other enzymes belonging to the RNase T₁ family this ribonuclease is base-unspecific. Using interactive computer graphics and energy minimisation we predicted the structure of RNase Ms on the basis of sequence homology to RNase T₁ of known structure. In this report the predicted structure of this protein is presented and characterised.     

Montane plant communities of Fynbos Biome

The vegetation of the mountains of the Fynbos Biome is classified and described, mostly on the basis of vegetation structure and higher taxa. Various gradients can be recognized. A gradient in soil conditions runs from coarse textured, nutrient-poor soils in non-grassy fynbos (Mountain Fynbos) through grassy fynbos and grassy non-fynbos (Eastern Fynbos and Grasslands & Grassy Shrubland) to finer textured and less nutrient-poor soils in the non-fynbos Karroid & Renoster Shrubland. Another gradient of significance can be likened to the tropical gradient running from the dry conditions of hot semi-deserts to savannas or grasslands to woodlands. At the dry extreme an open shrubland occurs (Karroid & Renoster Shrubland, Asteraceous Fynbos), at intermediate positions a herbland occurs (Restioid Fynbos) and at the wet extreme another type of shrubland occurs (Ericaceous Fynbos). This kind of moisture gradient occurs on individual mountains with the xeric end being at the base of the north slopes, and the mesic end being on the upper south aspects. Soil characteristics are closely linked to this gradient; the better developed soils being found on the south aspects. Another moisture gradient is apparent in the vegetation. This gradient runs from the mesic southern coastal mountains to the north west where summer droughts are extremely severe although total rainfall may be similar.Nomenclature follows that used in the Government Herbarium, Stellenbosch.I thank William Bond, Richard Cowling, John Rushworth, Eddy van der Maarel and Marinus Werger for critical comments and discussion.     

Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding

Summary Sixty-four eucaryotic nuclear DNA sequences, half of them coding and half noncoding, have been examined as expressions of first-, second-, or third-order Markov chains. Standard statistical tests found that most of the sequences required at least second-order Markov chains for their representation, and some required chains of third order. For all 64 sequences the observed one-step second-order transition count matrices were effective in predicting the two-step transition count matrices, and 56 of 64 were effective in predicting the three-step transition count matrices. The departure from random expectation of the observed first- and second-order transition count matrices meant that a considerable sample of eucaryotic nuclear DNA sequences, both protein coding and noncoding, have significant local structure over subsequences of three to five contiguous bases, and that this structure occurs throughout the total length of the sequence. These results suggested that present DNA sequences may have arisen from the duplication, concatenation, and gradual modification of very early short sequences.     

Species dispersion profiles of anthropogenic grasslands in the Italian Eastern Pre-Alps

A method is proposed to analyse the dispersion profiles of species in classes of environmental variables, based on the decomposition of the expected frequencies in contingency tables with many interacting species. The method has been applied to data of dominant or very frequent graminoid species in grasslands of the Natisone Valley (Friuli, Italy). It allowed to make predictions by removing the random component of variation.Nomenclature follows: P. Zangheri (1976). Flora Italica, CEDAM, Padua.The authors were recipients of an Italian CNR grant (E. Feoli) and a Canadian NSERC grant (L. Orlóci) during tenure of this project. The results are in partial fulfillment of a commitment to the Centro Regionale per la Sperimentazione Agraria per il Friuli-Venezia Giulia.     

A prediction model for parasitic gastro-enteritis in lambs

Paton G., Thomas R. J. and Waller P. J. 1984. A prediction model for parasitic gastroenteritis in lambs. International Journal for Parasitology14: 439–445. The parasite Ostertagia circumcincta is a major cause of parasitic gastro-enteritis in lambs in temperate countries. A prediction model is described, based on a mathematical representation of the external and internal stages of the life-cycle.The model is used to predict the numbers of infective larvae on a permanent experimental paddock grazed by ewes and lambs in 1973 and 1974. The “moisture status” of the surface layer of the pasture was found to be of fundamental importance for the successful prediction of the development and survival of the pre-infective larval stages. For the years studied the contribution to the summer wave of infection by lamb derived larvae was particularly significant.     

Full and reduced models for yield trials

Summary Empirical results routinely demonstrate that the reduced Additive Main effects and Multiplicative Interaction (AMMI) model achieves better predictive accuracy for yield trials than does the full treatment means model. It may seem mysterious that treatment means are not the most accurate estimates, but rather that the AMMI model is often more accurate than its data. The statistical explanation involves the Stein effect, whereby a small sacrifice in bias can produce a large gain in accuracy. The corresponding agricultural explanation is somewhat complex, beginning with a yield trial's design and ending with its research purposes and applications. In essence, AMMI selectively recovers pattern related to the treatment design in its model, while selectively relegating noise related to the experimental design in its discarded residual. For estimating the yield of a particular genotype in a particular environment, the AMMI model uses the entire yield trial, rather than only the several replications of this particular trial, as in the treatment means model. This use of more information is the source of AMMI's gain in accuracy.This research was supported by the Rhizobotany Project of the USDA-ARS     

Structure-activity relationships on hyperglycemia by representatives of the adipokinetic/hyperglycemic hormone family in Blaberus discoidalis cockroaches

Summary Several members of the adipokinetic/hyperglycemic neurohormone family from several different invertebrate species have been prepared by solid-phase peptide synthesis and assayed by a modified in vivo hyperglycemic bioassay in Blaberus discoidalis cockroaches. The hypertrehalosemic hormone (HrTH) is the endogenous hypertrehalosemic factor for B. discoidalis and was the most potent peptide in the assay. The more divergent the sequence of a family member from Blaberus HrTH, the less potent was the bioanalog. Manduca adipokinetic hormone is the most divergent peptide of the family and was totally inactive in the bioassay. Locusta adipokinetic hormone I had reduced maximum activity in the assay, which suggests that Ser⁵ is an important residue for the transduction of the hyperglycemic response. The direct relation between bioanalog similarity to Blaberus HrTH sequence and potency suggests that the hormone and target cell receptor for HrTH have evolved to maintain an optimal fit.Abbreviations AKH adipokinetic hormone - HrGH hyperglycemic hormone - HrTH hypertrehalosemic hormone - RPCH red pigmentconcentrating hormone - CAH cardioacceleratory hormone. Hormone abbreviations are according to the convention of Gäde and Raina (1989) except that the genus names are not abbreviated     

Assessing the risk of invasive success in Pinus and Banksia in South African mountain fynbos

Abstract. South African mountain fynbos has been severely invaded by trees and shrubs introduced from other mediterranean-climate regions. Management of these invasions should involve controlling current invaders and screening future introductions. Invasion windows are described and functional groups are defined for pines based on life history attributes important for invasion in the fire-prone mountain fynbos. The most successful invasive pines here (Pinus halepensis, P. pinaster and P. radiata) are fire-resilient and have small seeds, low seed-wing loadings, short juvenile periods, moderate to high degrees of serotiny and relatively poor fire-tolerance as adults. Other species with these attributes, especially from mediterranean-climate regions, wouldbe high-risk introductions. Taxa in other functional groups have not become major weeds even with widespread man-aided dissemination. Experience with pine invaders was used to define functional groups in western Australian Banksia species (Proteaceae), shrubs and trees which include taxa with similar attributes to fynbos invaders (e.g. Hakea and Pinus spp.). Banksias have only recently been introduced to the Cape, and are likely to be increasingly cultivated for the cut flower market. Tall serotinous shrubs with many small seeds per plant, short juvenile periods and low fire tolerance were identified as high risk introductions. This group includes thicket-forming species which maintain very large viable seed banks, e.g. Banksia burdettii, B. hookeriana and B. leptophylla. Low sprouting shrubs with few large seeds per plant and long juvenile periods are unlikely to become invasive in mountain fynbos. The approach of defining functional groups based on life history attributes and invasion windows is valuable for predicting the probability of invasive success. Chance interactions suchas an opportunistic dispersal mutualism between Pinus pinea and an introduced squirrel sometimes confound these predictions and underscore the idiosyncracies inherent in biological invasions.     

Evolutionary analysis of the multigene pregnancy-specific β1-Glycoprotein family: Separation of historical and nonhistorical signals

The pregnancy-specific ₁-glycoproteins (PSG) form a large family of closely related proteins. Using newly developed methods of sequence analysis, in combination with protein modeling, we provide a framework for investigating the evolution and biological function of genes like the PSG. Evolutionary trees, based on C-terminal sequence, group PSG genes in a manner consistent with their genomic organization. Trees constructed using the N-terminal domain sequences are unreliable as an indicator of phylogeny because of non-neutral processes of sequence change. During duplication of the PSG genes, evolutionary pressures have resulted in a gradient of constrained change across each gene. The N-terminal domains show a nonrandom pattern of amino acid substitutions clustered in the immunoglobulin complementarity-determining region (CDR)-like regions, which appear to be important in the function of the protein.