A comparison of reciprocal averaging and non-centred principal components analysis

Non-centred Principal Components Analysis (NPCA) ordinates sites and species simultaneously, and can be solved either by direct iteration or by eigenvector calculation. The weight of sites and species in the analysis is proportional to their overall abundance. Because of this, the method is not susceptible to distortion by rare species, as is the case with Reciprocal Averaging (RA). Detrending techniques can also be applied to this method to eliminate arch effects.When NPCA was tried with field data, it produced ordination axes that were significantly associated to independently measured environmental variables. In contrast, RA failed to produce axes related to environmental factors, even after the main rare species had been eliminated from the analysis.Abbreviations NPCA Non-centred Principal Components Analysis - RA Reciprocal Averaging     

Human erythrocyte catalase, isolation with an improved method, characterization and comparison to bovine liver catalase

Catalase enzyme was purified from human erythrocytes. The modified procedure of M?rikofer-Zwez et. al. [Eur. J. Biochem. 11: 49-57, 1969] yielded erythrocyte catalase with high specific activity and with one band on SDS polyacrylamide gel. Its other characteristics (isoelectric point; E405/280, E1%1cm at 280 nm and 405 nm) were in agreement with previously described findings. The results obtained for molecular mass, electrophoretic mobility, chromatographic behaviour on CM-Sepadex gel, addition test, and change of electrophoretic mobility in human serum showed differences between human erythrocyte catalase and bovine liver catalase. These results suggest that human erythrocyte catalase and bovine liver catalase are two distinct catalase forms.     

一种测量林窗面积的改良方法:等角椭圆扇形法

目前测量林窗面积较精确的方法为:测量从林窗中心沿8或16个罗盘方向到林窗林冠边缘的距离,再将林窗近似成等角8或16边形估测其面积(本文称这类方法为等角多边形法)。研究表明,等角8或16边形法均会低估林窗面积,本文提出一种改良方法:等角椭圆扇形法,野外测量与前者相同,计算时将相邻距离间的部分近似为椭圆扇形,以所有椭圆扇形面积之和估测林窗面积。用配对t检验对等角多边形法和等角椭圆扇形法的林窗面积进行比较,结果表明:(1)等角16边形法与等角8或4边形法存在极显著差异(P<0.001),比后两者,分别高10.96%和61.66%,这表明等角条边形法均会低估林窗面积;(2)等角椭圆扇形16分法比等角16边形法大10.16%,且二者之间存在极显著差异(P<0.001),因此,等角16边形法的测量值位于等角椭圆扇形16分法和等角8边形法之间;由(1)和(2)可推断等角椭圆扇形16分法比等角8边形法更准确;(3)等角椭圆扇形8分法与等角椭圆扇形16分法没有显著差异(P=0.715),但与等角8边形法存在显著差异(P<0.05),因此,等角椭圆扇形8分法比等角8边形法更准确。另外,本文的两个等角8边形法(基于两组不同罗盘方位的测量距离)求得的林窗面积之间存在极显著差异(P<0.01),而两个等角椭圆扇形8分法之间却没有差异(P=0.778),这表明等角椭圆扇形8分法的结果更稳定。     

Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages

Weighted averaging regression and calibration form a simple, yet powerful method for reconstructing environmental variables from species assemblages. Based on the concepts of niche-space partitioning and ecological optima of species (indicator values), it performs well with noisy, species-rich data that cover a long ecological gradient (>3 SD units). Partial least squares regression is a linear method for multivariate calibration that is popular in chemometrics as a robust alternative to principal component regression. It successively selects linear components so as to maximize predictive power. In this paper the ideas of the two methods are combined. It is shown that the weighted averaging method is a form of partial least squares regression applied to transformed data that uses the first PLS-component only. The new combined method, ast squares, consists of using further components, namely as many as are useful in terms of predictive power. The further components utilize the residual structure in the species data to improve the species parameters (optima) in the final weighted averaging predictor. Simulations show that the new method can give 70% reduction in prediction error in data sets with low noise, but only a small reduction in noisy data sets. In three real data sets of diatom assemblages collected for the reconstruction of acidity and salinity, the reduction in prediction error was zero, 19% and 32%.     

High resolution approach to the native state ensemble kinetics and thermodynamics

Many biologically interesting functions such as allosteric switching or protein-ligand binding are determined by the kinetics and mechanisms of transitions between various conformational substates of the native basin of globular proteins. To advance our understanding of these processes, we constructed a two-dimensional free energy surface (FES) of the native basin of a small globular protein, Trp-cage. The corresponding order parameters were defined using two native substructures of Trp-cage. These calculations were based on extensive explicit water all-atom molecular dynamics simulations. Using the obtained two-dimensional FES, we studied the transition kinetics between two Trp-cage conformations, finding that switching process shows a borderline behavior between diffusive and weakly-activated dynamics. The transition is well-characterized kinetically as a biexponential process. We also introduced a new one-dimensional reaction coordinate for the conformational transition, finding reasonable qualitative agreement with the two-dimensional kinetics results. We investigated the distribution of all the 38 native nuclear magnetic resonance structures on the obtained FES, analyzing interactions that stabilize specific low-energy conformations. Finally, we constructed a FES for the same system but with simple dielectric model of water instead of explicit water, finding that the results were surprisingly similar in a small region centered on the native conformations. The dissimilarities between the explicit and implicit model on the larger-scale point to the important role of water in mediating interactions between amino acid residues.     

Predicting alternate structure attainment and amyloidogenesis: a nonlinear signal analysis approach

Chain hydrophobicity values have been used in prediction of alternate structure attainment by a polypeptide. Nonlinear signal analysis on the hydrophobicity values gives important clues about the propensities of particular stretches of a protein to form local or nonlocal contacts. These contacts determine the folding behavior of a polypeptide and helps in predicting the final structure that can be attained. A nonlinear signal analysis called the recurrent quantification analysis has been carried out using the hydrophobicity values on a wide range of proteins obtained from human, plant, and fungal sources. Here, we show that such an analysis gives us an easy handle in determining sequences within the proteins that may be important in beta-sheet formation leading to amyloidosis.     

High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS

All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance both diagnosis and therapy of specific diseases. Proteomic methods can provide means to accomplish this grand medical vision. In this review, we will focus on the potential use of proteome analysis for clinical applications, such as disease diagnosis and assessment of response to therapy. We focus on CE coupled with MS (CE-MS) and review in detail different aspects of CE-MS coupling and the results obtained using CE-MS analysis of clinically relevant samples. We also discuss clinical applications of the technology for the diagnosis of renal diseases, urogenital cancer, and arteriosclerosis as well as monitoring the responses to therapeutic interventions.     

High resolution analysis and differential condensation in RBA-banded human chromosomes

Summary Human prophase, premetaphase, and mid-metaphase chromosomes are prepared and analyzed using the thymidine cell synchronization technique and R-banding patterns (RBA). Haploid sets with 700–1000 bands can be demonstrated. Sequences of chromosomes of different degrees of condensation are helpful for a better understanding and classification of regions of extended chromosomes. A considerable variation in the condensation of parts of homologous chromosomes is reflected in the variability of the arm ratio. This differential condensation of chromosomes is entirely effected by variation of the degree of condensation in AT rich interbands and can be attributed to the degree of labeling by BrdU.     

An improved method for searching plant functional types by numerical analysis

Abstract. The use of plant functional types (PFTs) to describe patterns and processes in plant communities has become essential to study and predict consequences of global change on vegetation and ecosystem processes. A PFT is a group of plants that, irrespective of phylogeny, are similar in a given set of traits and similar in their association to certain variables, which may be factors to which the plants are responding or effects of the plants in the ecosystem. To define PFTs relevant traits must be selected and an appropriate method must be used to classify plants into types. We critically review methods used for the analysis of PFT‐based data and describe a new recursive algorithm to numerically search for traits and find optimal PFTs. The algorithm uses three data matrices: describing populations by traits, communities by these populations and community sites by environmental factors or effects. It defines PFTs polythetically by cluster analysis, revealing plant types whose performance in communities is maximally associated to the specified environmental variables. We test the method with data from natural grassland communities of southern Brazil, which were experimentally subjected to combinations of grazing levels and N‐fertilizer. The new method is found to be better than similar analytical procedures previously described. Redundancy among traits is discussed and a procedure for comparing alternative solutions is presented based on the similarity in terms of PFT responses between different trait subsets. The concept of PFT response group is illustrated by example.