Bootstrap Confidence Regions for Canonical Variates: Application to Studies of Evolutionary Differentiation

Theory recently developed to construct confidence regions based on the parametric bootstrap is applied to add inferential information to graphical displays of sample centroids in canonical variate analysis. Problems of morphometric differentiation among subspecies and species are addressed using numerical resampling procedures.     

Classification of vegetation in the Western Australian wheatbelt using Landsat MSS data

We examined the use of Landsat multispectral scanner (MSS) data to provide preliminary information on broad vegetation types present within nature reserves in the wheatbelt region of Western Australia. We analysed Landsat data for an area of natural vegetation for which ground survey and aerial photographic data are available. We used canonical variate analysis to examine the degree of spectral separation between training sites selected in the main structural vegetation types. The training classes were then grouped into spectral classes and an allocation procedure used to map the pixels in the reserve into these classes. The analysis provided a good correspondence between spectral classes and broad vegetation types recognised from aerial photography, but did not discriminate between differences in dominant species (e.g. between different types of Eucalypt woodland). The classification derived from the study reserve was then applied successfully to two nearby reserves, indicating that the data can be used to provide initial information on the broad vegetation types present in wheatbelt reserves, although it is not suitable for finer resolution studies.Abbreviation MSS = Multi-spectral scanner     

Application of a canonical transformation to detection of quantitative trait loci with the aid of genetic markers in a multi-trait experiment

Effects of individual quantitative trait loci (QTLs) can be isolated with the aid of linked genetic markers. Most studies have analyzed each marker or pair of linked markers separately for each trait included in the analysis. Thus, the number of contrasts tested can be quite large. The experimentwise type-I error can be readily derived from the nominal type-I error if all contrasts are statistically independent, but different traits are generally correlated. A new set of uncorrelated traits can be derived by application of a canonical transformation. The total number of effective traits will generally be less than the original set. An example is presented for DNA microsatellite D21S4, which is used as a marker for milk production traits of Israeli dairy cattle. This locus had significant effects on milk and protein production but not on fat. It had a significant effect on only one of the canonical variables that was highly correlated with both milk and protein, and this variable explained 82% of the total variance. Thus, it can be concluded that a single QTL is affecting both traits. The effects on the original traits could be derived by a reverse transformation of the effects on the canonical variable.     

The morphometric relationship of Upper Cave 101 and 103 to modern Homo sapiens

Since the discovery of the Homo sapiens crania from the Upper Cave of Zhoukoudian in northern China (UC 101, UC 102, and UC 103), no clear consensus has arisen regarding their affinities with modern populations. We use linear craniofacial measurements to compare UC 101 and UC 103 to a worldwide sample of H. sapiens that includes Paleoamericans and Archaic Indians, and employ Mahalanobis distance analysis and associated unweighted, unrestricted canonical variate analysis for the comparisons. Analyses indicate that UC 101 has consistent affinities with Easter Island and European populations, whereas UC 103 has more tenuous similarities with Australo-Melanesian groups. Both fossils exhibit some similarities to certain Paleoamerican and Archaic Indian individuals, but rarely cluster together. Upper Cave 103 is more of an outlier to modern populations than is UC 101. The fossils are not representative of any group to which they have been compared, but may be part of the generalized population that was ancestral to Paleoamericans.     

Taxonomic status of the six-band morph of Cyphotilapia frontosa (Perciformes: Cichlidae) from Lake Tanganyika, Africa

Six- and seven-band morphs have been identified in a cichlid, Cyphotilapia frontosa, that is endemic to Lake Tanganyika. These color morphs have allopatric distributions; the six-band morph is widespread in the northern half of the lake while the seven-band morph is restricted to Kigoma on the east coast of the lake. Because no specimens of the seven-band morph have been available for taxonomic study except for the holotype of C. frontosa, the taxonomic status of these morphs has not been discussed. In a recent survey at the lake, 21 specimens of the seven-band morph were collected. A comparison of these with existing collection specimens of the six-band morph showed significant differences in morphometric and meristic characters; however, because all characters largely overlapped between these morphs, they are regarded as conspecific.     

The use of mean pool abundances to interpret 15N tracer experiments

A pulse dilution ¹⁵N technique was used in the field to determine the effect of the ammonium to nitrate ratio in a fertilizer application on the uptake of ammonium and nitrate by ryegrass and on gross rates of mineralization and nitrification. Two experiments were performed, corresponding approximately to the first and second cuts of grass. Where no substantial recent immobilization of inorganic nitrogen had occurred, mineralization was insensitive to the form of nitrogen applied, ranging from 2.1–2.6 kg N ha^-1 d^-1. The immobilization of ammonium increased as the proportion of ammonium in the application increased. In the second experiment there was evidence that high rates of immobilization in the first experiment were associated with high rates of mineralization in the second. The implication was that some nitrogen immobilized in the first experiment was re-mineralized during the second. Whether this was nitrogen taken up, stored in roots and released following defoliation was not clear. Nitrification rates in this soil were low (0.1–0.63 kg N ha^-1 d^-1), and as a result, varying the ratio of ammonium to nitrate applied markedly altered the relative uptake of ammonium and nitrate. In the first experiment, where temperatures were low, preferential uptake of ammonium occurred, but where >90% of the uptake was as ammonium, a reduction in yield and nitrogen uptake was observed. In the second experiment, where temperatures and growth rates were higher, the proportion of ammonium to nitrate taken up had no effect on yield or nitrogen uptake.     

On the use of size functions for shape analysis

According to a recent mathematical theory a shape can be represented by size functions, which convey information on both the topological and metric properties of the viewed shape. In this paper the relevance of the theory of size functions to visual perception is investigated. An algorithm for the computation of the size functions is presented, and many theoretical properties of the theory are demonstrated on real images. It is shown that the representation of shape in terms of size functions (1) can be tailored to suit the invariance of the problem at hand and (2) is stable against small qualitative and quantitative changes of the viewed shape. A distance between size functions is used as a measure of similarity between the representations of two different shapes. The results obtained indicate that size functions are likely to be very useful for object recognition. In particular, they seem to be well suited for the recognition of natural and articulated objects.     

Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action

The efficiency of canonical serine protease inhibitors is conventionally attributed to the rigidity of their protease binding loop with no conformational change upon enzyme binding, yielding an example of the lock-and-key model for biomolecular interactions. However, solution-state structural studies revealed considerable flexibility in their protease binding loop. We resolve this apparent contradiction by showing that enzyme binding of small, 35-residue inhibitors is actually a dynamic conformer selection process on the nanosecond-timescale. Thus, fast timescale dynamics enables the association rate to be solely diffusion-controlled just like in the rigid-body model.     

A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase.

The specificity of GalNAc-transferase is consistent with the existence of an extended site composed of nine subsites, denoted by R4, R3, R2, R1, R0, R1', R2', R3', and R4', where the acceptor at R0 is either Ser or Thr to which the reducing monosaccharide is being anchored. To predict whether a peptide will react with the enzyme to form a Ser- or Thr-conjugated glycopeptide, a new method has been proposed based on the vector-projection approach as well as the sequence-coupled principle. By incorporating the sequence-coupled effect among the subsites, the interaction mechanism among subsites during glycosylation can be reflected and, by using the vector projection approach, arbitrary assignment for insufficient experimental data can be avoided. The very high ratio of correct predictions versus total predictions for the data in both the training and the testing sets indicates that the method is self-consistent and efficient. It provides a rapid means for predicting O-glycosylation and designing effective inhibitors of GalNAc-transferase, which might be useful for targeting drugs to specific sites in the body and for enzyme replacement therapy for the treatment of genetic disorders.     

Environmental factors influence on chemical polymorphism of the essential oils of Lychnophora ericoides

Lychnophora ericoides is a Brazilian medicinal plant used in folk medicine as an anti-inflammatory and analgesic agent. The essential oils from leaves of two populations with and without scent, collected at 2-month intervals during an 1-year period, were analysed by GC-MS. The results were submitted to principal component and cluster analysis which allowed two groups of essential oils to be distinguished with respect to sampling site and scent: cluster I (Vianópolis site, with specimens exhibiting an aromatic scent) containing a high percentage of alpha-bisabolol (44.7-76.4%) and alpha-cadinol (10.9-23.5%), and cluster II (Cristalina site, with specimens without scent) characterised by a high content of (E)-nerolidol (31.3-47.1%) and ar-dihydro-turmerone (4.8-15.4%). The canonical discriminant analysis showed that using the data set of the seven sampling months and (E)-nerolidol and alpha-bisabolol as predictable variables, it was possible to distinguish between the samples harvested according to Cerrado seasons, dry winter (May-September) and humid summer (November-March). In addition, canonical correlation analysis between the soil sampling sites and the populations revealed a significant relationship between oil components and edaphic factors. Oxygenated sesquiterpenes and potential acidity, Al saturation, cationic exchange capacity, silt, and sand load as the first canonical variate were fairly strongly related to samples collected in Vianópolis site. On the other hand, monoterpenes and sesquiterpene hydrocarbons were strongly related to chemical balance in soils (organic matter, P and base saturation), which is related to samples at the Cristalina site. The chemovariation observed appears to be environmentally determined.     

Earthworm-serine protease: characterization, molecular cloning, and application of the catalytic functions

An earthworm, Lumbricus rubellus, produces alkaline serine proteases that are greater than trypsins in their activity and stability. The proteases which were purified from the earthworm were composed of six isozyme proteins. Each isozyme consisted of a single polypeptide chain which was derived from the different genes. The enzymes had activity and were stable at below 60 °C over a wide range of pH 2–11 and were strongly resistant to organic solvents and detergents. Moreover, they retain full activity for long years at room temperature. They acted on various proteins, such as elastin as well as fibrin, and some peptides, such as β-amyloid 1–40 and solubilized actual fibrin clots of whole blood in a rat’s vena cava. They also catalyzed the hydrolysis of various esters. The cDNAs encoding the proteases were cloned and sequenced. They showed similarity to mammalian serine proteases and conserved the catalytic amino acid residues, however, neither arginine nor lysine residues were present in the autolysis region. The gene encoding the native form of an isozyme protein was expressed in Pichia pastoris to produce the active protease in the culture medium. The proteases contributed to the production of the “earthworm autolysate”. The extracts of the autolysate could be used as a “peptone substitute” in media for the efficient growth of microorganisms.     

The use of fluorescence correlations spectroscopy to probe chromatin in the cell nucleus

All systems in thermodynamic equilibrium are subject to spontaneous fluctuations from equilibrium. For very small system, the fluctuations can be made apparent, and can be used to study the behavior of the system without introducing any external perturbations. The mean squared amplitude of these fluctuations contains information about the absolute size of the system. The characteristic time of the fluctuation autocorrelation function contains kinetic information. In the experiments reported here, these concepts are applied to the binding equilibrium between ethidium bromide and DNA, a system where the fluorescence properties of the dye greatly enhance the effect of spontaneous fluctuations in the binding equilibrium. Preliminary experiments employ well-characterized DNA preparations, including calif thymus DNa, SV40 DNA, and calf thymus nucleohistone particles. Additional measurements are described which have been made in small regions of individual nuclei, isolated from green monkey kidney cells, observing as few as 5000 dye molecules. The data indicate that the strength of dye binding increases in nuclei isolated from cells which have been stimulated to enter the cell growth cycle. The viscosity of nuclear material is inferred to be between one and two orders of magnitude greater than that of water, and it decreases as the cells leave the resting state and enter the cell growth cycle. Washing the nuclei also lowers the viscosity. These experiments demonstrate that fluorescence correlation spectroscopy can provide information at the subnuclear level that is otherwise unavailable.