A comparison of clustering methods for river benthic community analysis

Four commonly used clustering methods (UPGMA, Ward Linkage,Complete Linkage and TWINSPAN) were compared in their abilitytorecognise the structure of three river macroinvertebratesdatasetswhich were pre-determined based on habitat and biologicalcharacteristics or chemical water quality of sampling sites.DCA,NMDS and ANOSIM were applied to the same datasets to providefurther information about data structure, and nonparametrictestswere also undertaken on major chemical variables to justifythepredeterminations. The modified Rand Index was used to measuretheagreement between a particular solution and the pre-determinedclassification. The results showed that Ward Linkage performedbestwhen its use was broadened and used with the CY DissimilarityMeasure, followed by TWINSPAN and Complete Linkage with UPGMAbeingleast successful. There was evidence to suggest that theeffectiveness of some clustering methods (e.g. UPGMA) may varyatdifferent clustering levels, and simulation techniques whichhavebeen used to assess clustering methods could leave somepropertiesof clustering methods unexamined.     

Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines

Dominant phenotype of a genetic marker provides incomplete information about the marker genotype of an individual. A consequence of using this incomplete information for mapping quantitative trait loci (QTL) is that the inference of the genotype of a putative QTL flanked by a marker with dominant phenotype will depend on the genotype or phenotype of the next marker. This dependence can be extended further until a marker genotype is fully observed. A general algorithm is derived to calculate the probability distribution of the genotype of a putative QTL at a given genomic position, conditional on all observed marker phenotypes in the region with dominant and missing marker information for an individual. The algorithm is implemented for various populations stemming from two inbred lines in the context of mapping QTL. Simulation results show that if only a proportion of markers contain missing or dominant phenotypes, QTL mapping can be almost as efficient as if there were no missing information in the data. The efficiency of the analysis, however, may decrease substantially when a very large proportion of markers contain missing or dominant phenotypes and a genetic map has to be reconstructed first on the same data as well. So it is important to combine dominant markers with codominant markers in a QTL mapping study. This revised version was published online in July 2006 with corrections to the Cover Date.     

Computational Sequence Analysis of the Tissue Inhibitor of Metalloproteinase Family

The tissue inhibitor of metalloproteinase (TIMP) family regulates extracellular matrix turnover and tissue remodeling by forming tight-binding inhibitory complexes with matrix metalloproteinases (MMPs). MMPs and TIMPs have been implicated in many normal and pathological processes, such as morphogenesis, development, angiogenesis, and cancer metastasis. This minireview provides information that would aid in classification of the TIMP family and in understanding the similarities and differences among TIMP members according to the physical data, primary structure, and homology values. Calculations of molecular weight, isoelectric point values, and molar extinction coefficients are reported. This study also compares sequence similarities and differences among the TIMP members through calculations of homology within their individual loop regions and the mature region of the molecule. Lastly, this report examines structure–function relationships of TIMPs. Thorough knowledge of TIMP primary and tertiary structure would facilitate the uncovering of the molecular mechanisms underlying metalloproteinase, inhibitory activities and biological functions of TIMPs.     

A method of selecting data points for fitting the maximum biomass-density line for stands undergoing self-thinning

Abstract A problem that has always existed in self-thinning studies is the lack of objectivity in determining which data points to include when fitting the maximum biomass-density line. This paper demonstrates a more objective method of selecting data points using data from 12 even-aged Pinus radiata stands undergoing self-thinning. The method involves the division of a cluster of data points into a specified number of intervals. From each interval, that point having the maximum stand biomass is selected to contribute to the fitting process. This process is repeated a specified number of times using an increasing number of intervals. Each time an estimate of the line is obtained. From these estimates, one can be chosen to represent the maximum biomass-density line. The method may also be useful in other areas involving the definition of a boundary condition.     

纵向资料回归系数的新估计

本文研究纵向资料中回归系数的估计,借助于相依回归模型中的信息迭加法,给出了一个新估计,它改进了最小二乘估计．     

The diverse world of coenzyme A binding proteins

Coenzyme A is involved in a number of important metabolic pathways. Recently the structures of several coenzyme A binding proteins have been determined. We compare in some detail the structures of seven different coenzyme A protein complexes. These seven proteins all have distinctly different folds.     

Evolutionary processes in the genusCapsella (Brassicaceae)

Capsella comprises diploid (C. grandiflora andC. rubella) and tetraploid taxa. It is argued that the tetraploidC. bursa-pastoris is of intraspecific origin despite disomic inheritance and fixed heterozygosity. It is of considerable age as evidenced by the fossil record and molecular data. Gene duplication by polyploidization and a mixed mating system provided the genetic flexibility for greatest colonizing success. Pronounced variation patterns at a micro- and macrogeographic scale are observed inC. bursa-pastoris for many characters including life history traits, leaf morphology and allozymes. This variation pattern can be explained by several components comprising phylogenetic age, random processes, ecotypic variation and colonization history. The adaptive strategy ofC. bursa-pastoris cannot be assigned to either ecotypic differentiation or phenotypic plasticity alone. It depends on the trait under study.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

Recording long‐term heart rate in Paranotothenia angustata using an electronic datalogger

A unique heart beat datalogging device was either surgically implanted into the peritoneal cavity (internal‐fish) or attached by nylon anchor tags to the dorsal fin rays (external‐fish) of the black cod Paranotothenia angustata . Both groups had a mean ±  s . e . heart rate of c . 46 beats min⁻¹ after 24 h, and by 20 days external‐fish showed a significant reduction (34 ± 3 beats min⁻¹) whereas internal‐fish did not (44 ± 2 beats min⁻¹). In demersal fishes external attachment of an electronic recording device may be preferable to surgical implantation.     

Characteristics of plant communities containing rare conifers in Poyang Lake Basin,China

The endangerment mechanism of rare conifer species is a very critical problem in conservation biodiversity. Thus, the studies on the protection of the rare and endangered coniferous trees have received extensive attention. The objective of this study was to understand the survival and distribution of the rare coniferous tree species in natural forests of the Poyang Lake Basin. Field investigations on plant communities were conducted in 21 plots from Oct. 2014 to Oct. 2015. These plots were distributed in the Nanling Mountains, Luoxiao Mountains, Wuyi Mountains, Huangshan Mountains, and Jiuling Mountain. The dimensions of each plot were 20 m × 20 m. Community species composition and quantitative characteristics in each plot were recorded. The importance values of trees, shrubs and herbs were computed, respectively. The community types and structural properties were analyzed. A total of 23 sets of community sampling data were obtained in details. A number of 11 species of rare conifers were found in 14 different formations. Rare conifer trees mainly occurred in the communities as co-edificatos or companion species. The formations included Form. Taxus wallichiana var. mairei, Form. Pseudotsuga sinensis, Form. Fokienia hodginsii and Form. Torreya grandis, where the dominant species was coniferous trees. In conclusion, our study provides valuable field investigation data of rare coniferous in Poyang Lake basin, which could provide insight into the protection and management of these species.