Circular and linear DNA molecules in the Entamoeba histolytica complex molecular karyotype

Entamoeba histolytica genome was analysed by pulsed field gel electrophoresis under conditions to separate linear chromosomes in the 170–1400 kb range. We identified linear DNA molecules of 227, 366, 631, 850, 1112 and 1361 kb (mean sizes obtained by three different methods) and we estimated their reorientation times and migration velocities at various experimental conditions. DNA shift mobility assays, using ethidium bromide, suggested that bands migrating at 227 and 631 kb contain linear and circular DNA, whereas a band at 436 kb has only circular DNA. We obtained a regression equation relating sizes of supercoiled DNA molecules with their migration velocities during a pulse at constant electric field and temperature. We also developed a computer program (EHPATTERNS) that predicts the migration per pulse and the resolution order of circular and linear E. histolytica DNA at different pulse times and constant driving and frictional forces. The simulation showed that linear DNA molecules frequently co-migrate with circular molecules, but circular molecules change when the pulse time varies. This molecular mixture generates broad bands and difficulties in the interpretation of the molecular karyotype of E. histolytica. Received: 19 January 1999 / Revised version: 3 November 1999 / Accepted: 22 November 1999     

The use of a hybrid linear trap/FT-ICR mass spectrometer for on-line high resolution/high mass accuracy bottom-up sequencing.

In this work we present a hybrid linear trap/Fourier transform ion cyclotron resonance (ICR) mass spectrometer to perform protein sequencing using the bottom-up approach. We demonstrate that incorporation of the linear trap greatly enhances the overall performance of the hybrid system for the study of complex peptide mixtures separated by fast high-performance liquid chromatography gradients. The ability to detect in the linear trap enables employment of automatic gain control to greatly reduce space charging in the ICR cell irregardless of ion flux. Resulting accurate mass measurements of 2 ppm or better using external calibration are achieved for the base peak as well as ions at 2% relative abundance. The linear trap is used to perform ion accumulation and activation prior to detection in the ICR cell which increases the scan rate. The increased duty cycle allows for data-dependent mass analysis of coeluting peptides to be acquired increasing protein sequence coverage without increasing the gradient length. In addition, the linear trap could be used as an ion detection device to perform simultaneous detection of tandem mass spectra with full scan mass spectral detection in the ICR cell resulting in the fastest scan cycles for performing bottom-up sequencing of protein digests. Comparisons of protein sequence coverage are presented for product ion detection in the linear trap and ICR cell.     

Measurement errors and regression to the mean cannot explain bias in average Ellenberg indicator values

Smart & Scott (2004, this is sue) criticized our paper (Wamelink et al. 2002) about the bias in average Ellenberg indicator values. Their main criticism concerns the method we used, regression analysis. They state the bias can be mimicked by the construction of an artificial data set and that regression analysis is not a suited tool to investigate underlying phenomena. Moreover they claim that the present bias is caused by the distribution of Ellenberg indicator values between syntaxa, instead of a bias in average Ellenberg indicator values per species. We show that their criticism of the use of regression analysis does not hold. We selected average Ellenberg values per vegetation group for several pH classes and applied an F‐test to determine whether or not the vegetation groups within each pH class differed significantly from each other. This was the case for all tested classes (P < 0.001). Moreover we simulated an artificial data set, of which the F‐test for varying measurement error could not explain the magnitude of the F‐value we found earlier. This indicates that the bias we found in average Ellenberg indicator values cannot be explained by measurement errors or by regression to the mean. In the end, Smart & Scott, as we did, come to the conclusion that there is a bias present and that separate regression lines per vegetation type are necessary, but the debate remains open on whether or not this is caused by the bias in Ellenberg indicator values per species.     

Synthesis, crystal structure and magnetic properties of cubane and linear trinuclear nickel complexes formed by 3,5-dichloro-2-hydroxybenzylaminoacetic acid

The reaction of Ni(ClO₄)₂·6H₂O with 3,5-dichloro-2-hydroxy-benzylaminoacetic acid (H₂dchaa), NaN₃ and triethylamine in methanol solution or water solution under solvothermal methods leads to the formation of two completely different Ni^II compounds: [HN(C₂H₅)₃]₈·[Ni₄(dchaa)₄(N₃)₄]₂ (1) and [HN(C₂H₅)₃]₂·[Ni₃(dchaa)₄(H₂O)₄]₂·(H₂O)₂ (2). The complexes 1 and 2 have been characterized by elemental analyses, IR spectra and single-crystal X-ray diffraction. Structure analyses reveal that complex 1 is a cubane cluster, while the complex 2 is a linear trinuclear cluster. The magnetic investigation shows that complexes 1 and 2 exhibit a ferromagnetic coupling between Ni^II ions. Ac susceptibilities of 1 and 2 reveal no frequency-dependent out-of-phase signals and the corresponding magnetic properties were discussed.     

An effective method for accurate nymphal-stage delimitation of the cicada Hyalessa fuscata

Subterranean nymphal development in cicadas presents challenges to researchers in accurately estimating the number of their developmental stages, although such information is crucial to understanding and predicting their population dynamics. While most studies have relied on head width as an attribute for life-stage determination to date, such character in cicadas can be highly variable and thus differentiation solely based on such morphology is prone to subjectivity in practice. Here, we propose a reliable method for instar estimation that is applicable to Hyalessa fuscata nymphs. We first obtained morphometrics of nymphs in all stages. Second, we computed logarithm-transformation and principal component analysis to extract a transformed variable that captures most of the variance of morphological characteristics. Third, k-means were computed to divide the dataset into distinct clusters assuming four-, five- and six life-stage scenarios for the best interferences of life stages. Finally, simple linear regression analysis was conducted to compare and select the best fit model. Our result shows that five nymphal stages best fit for H. fuscata nymphs. This method is expected to provide an easy-to-handle ecological tool for the study of life history of cicadas as well as other insects that have long life cycles and multiple developmental stages.     

Spatial pattern characterization of linear polarization-sensitive backscattering Mueller matrix elements of human serum albumin sphere suspension

Human serum albumin (HSA) nanometer or micron particles represent promising drug-carrier systems. The azimuthal and radial variations of a linear polarization-sensitive backscattering Mueller matrix were experimentally studied in two cases: the scattering particle was smaller or larger in size to the probing wavelength of 780 nm. The results show that the twofold and fourfold structures are characteristic of small particle size suspension, whereas the eightfold structure is characteristic of large particle size suspension. Moreover, for both particle size suspensions, the element patterns have strong radial dependence when the suspension concentration and the incident power of laser change. In addition, for both particle size suspensions, the rotational symmetry of each element is lost in the case of oblique incidence but the multifold structure is maintained. Some suggestions for applications of Mueller matrix imaging in biomedical optics are provided.     

The frequency of the perfect genotype in a population subject to pleiotropic mutation

We consider a large population of asexual organisms characterised by a number of quantitative traits that are subject to stabilising selection. Mutation is taken to act pleiotropically, with every mutation generally changing all of the traits under selection. We focus on the equilibrium distribution of the population, where mutation and selection are in balance. It has been previously established that the equilibrium distribution of genotypic effects may be anomalous, as it may contain a singular spike--a Dirac delta function--corresponding to a non-zero proportion of the population having exactly optimal genotypic values. In the present work, we present exact results for the case where three traits are under selection. These results give the equilibrium genetic variance of the population, and the proportion of the population that have the optimal genotype. This is achieved for two different spherically symmetric distributions of mutant effects. Additionally, a simple and robust numerical approach is also presented that allows the treatment of some other mutation distributions, where there are an arbitrary number of selected traits.     

共生菌Hebeloma sp.的线形质粒DNA的分子克隆及测序的研究

共生担子菌滑菇 H ebeloma circinas携带两个线形的染色体外 DNA分子 .全部的菌丝 DNA经蛋白酶 K处理后 ,通过琼脂凝胶电泳观察到 :在染色体 DNA旁有两个大小不等的 DNA带 ,命名为 p HCl和 p HC2 ,其分子量分别为 1 0 .3kb和 9.1 kb.用核酸外切酶处理 p HC DNA,确认其 5′端被保护 .对 p HC2用不同的内切酶处理并确定其内切酶图谱 ,对其 3.2 kb H ind 片段进行克隆 ,亚克隆和测序 .结果表明 :其片段有两个开读框 ( open reading frames) ,携带类似于病毒 B型的DNA和 RNA多聚酶基因编码 .p HC2为该菌携带的一个典型的线形质粒 ,这也是首次在共生担子菌中发现的线形质粒 .     

Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.