Theodoropoulos, D.I. Invasion biology. Critique of a pseudoscience.

The back cover of this book states that ‘contrary to theclaims of the nativists, research shows that man-dispersed speciesincrease biological diversity, benefit ecosystems, and act asan important force for healing the planet’. This is anuncompromising statement, and David Theodoropoulos divides hisdevelopment of the arguments supporting this statement intothree parts. Part I (Chapters 1–6) is ‘Nature, Dispersaland Reaction’. Part II (Chapters 7 and 8) is ‘Why?Psychology, Politics and Pseudoscience’. Part III (Chapters9–11) is ‘Humanity and Diversity’. There isalso an ‘Introduction’ including a summary of findingsand ‘An outline for a new theory of anthropogenic dispersal’,     

System, trends and perspectives of proteomics in dicot plants Part I: Technologies in proteome establishment

The first 3 years of the 21st century have seen the impact of plant proteomics on functional genomics that has enhanced our understanding, not only on the plant genome(s), but also more importantly, on the functional aspect of proteins. This is mainly due to availability of the complete genome sequence of the Arabidopsis thaliana-a dicotyledoneous (dicot) model plant-and technological advancements in proteomics. Proteomic analyses of a variety of dicot plants, including both Arabidopsis and the model legume species, barrel medic (Medicago truncatula), have greatly helped in an efficient separation, identification and cataloguing of a large number of proteins, and thereby defining their proteomes. Therefore, we have composed an inclusive review on dicot plant materials, as of February 2004, that provides system, trends and perspectives of proteomics in growth and development and the environment. The review is summarized and discussed as three individual, but interlinked, entities: Part I, technologies in proteome establishment (this review), Part II, proteomes of the complex developmental stages [G.K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, R. Rakwal, J. Chromatogr. B (2004)], and Part III, unraveling the proteomes influenced by the environment, and at the levels of function and genetic relationships [G.K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, R. Rakwal, J. Chromatogr. B (2004)]. This review deals with the diverse proteomic technologies being used in proteome development of different dicot plants.     

Highly efficient peptide separations in proteomics Part 1. Unidimensional high performance liquid chromatography

Sample complexity and dynamic range constitute enormous challenges in proteome analysis. The back-end technology in typical proteomics platforms, namely mass spectrometry (MS), can only tolerate a certain complexity, has a limited dynamic range per spectrum and is very sensitive towards ion suppression. Therefore, component overlap has to be minimized for successful mass spectrometric analysis and subsequent protein identification and quantification. The present review describes the advances that have been made in liquid-based separation techniques with focus on the recent developments to boost the resolving power. The review is divided in two parts; the first part deals with unidimensional liquid chromatography and the second part with bi- and multidimensional liquid-based separation techniques. Part 1 mainly focuses on reversed-phase HPLC due to the fact that it is and will, in the near future, remain the technique of choice to be hyphenated with MS. The impact of increasing the column length, decreasing the particle diameter, replacing the traditional packed beds by monolithics, amongst others, is described. The review is complemented with data obtained in the laboratories of the authors.     

Seasonal changes in contents of phenolic compounds and sugar inRhus,Euonymus andAcer leaves with special reference to anthocyanin formation in autumn

Seasonal variation in sugar, total phenol and flavanol contents was examined inRhus, Euonymus andAcer leaves. In all plant leaves, the total phenol and flavanol content per leaf increased rapidly at the early growth stages but thereafter the content was kept rather constant. Later on, sugar content increased to a high level, and the autumnal reddening began. An excessive accumulation of sugar just before the reddening indicated that the accumulation related to the anthocyanin formation. The incorporation of radioactivity into anthocyanin in autumn leaves from glucose-[U-¹⁴C] and phenylalanine-[U-¹⁴C] was also observed. Part III in the series “The Autumnal Reddening of Leaves”. For Part II, see Kumamoto J. Sci., Biol.11: 43–50 (1973).     

Biological characteristics ofSalmonella weltevreden typing phages

The important biological characteristics ofSalmonella weltevreden (3,10∶r∶z₆) typing phages were studied. On the basis of these, the phages could be classified into three groups: phages Φ I and Φ II, phages Φ III, Φ IV and Φ VI, and phage Φ V. Part of the work was done at the National Salmonella and Escherichia Centre, Central Research Institute, Kasauli, India.     

Glucose catabolism during aging and differentiation in hypocotyls ofPhaseolus mungo seedlings

Changes in activities of the glycolytic and pentose phosphate (PP) pathways in glucose catabolism in various parts of the hypocotyls obtained from 4-day-old etiolatedPhaseolus mungo seedlings were investigated by measuring the inhibition rates of respiration by iodoacetate and malonate, and the release of¹⁴CO₂ from [1-¹⁴C]- and [6-¹⁴C]glucose. The relative activity of the PP pathway in glucose catabolism was higher in the immature part (Part I) and the aged part (Part V) of the hypocotyls than in the intermediary one (Part III), while the activity of the glycolytic pathway decreased with aging. On a fresh weight basis, the enzyme activities of the glycolytic and PP pathways were higher in Part I than in Parts III and V. On a protein content basis, however, activities of the enzymes of the PP pathway increased with aging and differentiation of the hypocotyls whereas those of the glycolytic pathway decreased. Levels of nicotinamide adenine nucleotides were found to be in the following order: Part I>Part III> Part V for NAD⁺+NADH; Part I>Part V>Part III for NADP⁺+NADPH. The stimulative effect of methylene blue on decreasing the C₆/C₁ ratio was greater in Part III than in Part I, and No effect was observed in Part V. These data suggest that a decrease in the activity of the glycolytic pathway with aging and differentiation may be due to the decreasing glycolytic enzyme activities and NAD(H) content. The higher activity of the PP pathway in the immature part is attributable to larger amounts of NADP(H) and enzymes of the PP pathway. The greater contribution of the PP pathway to glucose catabolism in the aged part than in the intermediary part seems to results from a more active turnover of NADP and the relatively higher activity of the enzymes of the PP pathway than those of the glycolytic pathway.     

Secretion of flagellin by the LEE-encoded type III secretion system of enteropathogenic Escherichia coli

Background  

Enteropathogenic Escherichia coli (EPEC) is an attaching and effacing (A/E) pathogen that possesses a type III secretion system (T3SS) encoded within the locus of enterocyte effacement (LEE). The LEE is essential for A/E lesion formation and directs the secretion and translocation of multiple LEE-encoded and non-LEE encoded effector proteins into the cytosol of infected cells. In this study we used proteomics to compare proteins exported to the culture supernatant by wild type EPEC E2348/69, a ΔespADB mutant and a ΔescF T3SS mutant.     

Proteomic Studies on the Development of the Central Nervous System and Beyond

Neuroproteomics has become a ‘symbol’ or even a ‘sign’ for neuroscientists in the post-genomic era. During the last several decades, a number of proteomic approaches have been used widely to decipher the complexity of the brain, including the study of embryonic stages of human or non-human animal brain development. The use of proteomic techniques has allowed for great scientific advancements, including the quantitative analysis of proteomic data using 2D-DIGE, ICAT and iTRAQ. In addition, proteomic studies of the brain have expanded into fields such as subproteomics, synaptoproteomics, neural plasma membrane proteomics and even mitochondrial proteomics. The rapid progress that has been made in this field will not only increase the knowledge based on the neuroproteomics of the developing brain but also help to increase the understanding of human neurological diseases. This paper will focus on proteomic studies in the central nervous system and especially those conducted on the development of the brain in order to summarize the advances in this rapidly developing field.     

A designed glycopeptide array for characterization of sugar-binding proteins toward a glycopeptide chip technology

For the realization of a practical high-throughput protein detection and analysis system, a novel peptide array has been constructed using a designed glycopeptide model library with an α-helical secondary structure. This study will contribute the increment of the diversity of such an array system and the application to focused proteomics and ligand screening by effective detection of sugar-binding proteins. Fluorescent glycopeptides with an α-helix, a β-strand, or a loop structure were designed initially to select a suitable scaffold for the detection of a model protein. After selection of the α-helical structure as the best scaffold, a small model library with various saccharides was constructed to have charge and hydrophobicity variations in the peptide sequences. When various sugar-binding proteins were added to the peptide library array, the fluorescent peptides showed different responses in fluorescence intensities depending on their sequences as well as saccharides. The patterns of these responses could be regarded as “protein fingerprints” (PFPs), which are able to establish the identities of the target proteins. The resulting PFPs reflected the recognition properties of the proteins. Furthermore, statistical data analysis from obtained PFPs was performed using a cluster analysis. The PFPs of sugar-binding proteins were clustered successfully depending on their families and binding properties. These studies demonstrate that arrays with glycopeptide libraries based on designed structures can be promising tools to detect and analyze the target proteins. Designed peptides with functional groups such as sugars will play roles as the capturing agents of high-throughput protein nano/micro arrays for focused proteomics and ligand screening studies.     

Hemoprotein models based on a covalent helix-heme-helix sandwich. 3. Coordination properties, reactivity and catalytic application of Fe(III)- and Fe(II)-mimochrome I

 The coordination state of Fe(III)- and Fe(II)-mimochrome I, a covalent peptide-deuteroheme sandwich involving two nonapeptides bearing a histidine residue in a central position, was studied by UV-visible, EPR, and resonance Raman spectroscopy. The ferric and ferrous states of this new iron species mainly exist, at pH 7, in a low-spin hexacoordinate form with two axial histidine ligands coming from the peptide chains. A minor amount of high-spin form for the ferric state is also present at pH 7. However, it is mainly high-spin at pH 2 or in DMSO. Fe(II)-mimochrome I binds CO with an affinity comparable to that of myoglobin and hemoglobin. Fe(III)-mimochrome I reacts with alkylhydroxylamine and arylhydrazines, leading to the corresponding Fe(II)-nitrosoalkyl and Fe(III)-σ-aryl complexes, respectively. These reactions were greatly dependent on the solvent used and on the pH, and were much slower than the corresponding reactions performed by deuterohemin in the presence of excess imidazole. All these results indicate that the reactivity of iron-mimochrome I is controlled by the binding of the peptide chains to the iron. The reactivity shown by this complex at neutral pH is intermediate between that observed for iron porphyrins in the presence of excess imidazole and that of hemoproteins characterized by a strong bis-histidine axial coordination, such as cytochrome b ₅. Fe(III)-mimochrome I is able to catalyze styrene epoxidation by using a [Fe(III)-mimochrome I]/[H₂O₂]/[stryrene] ratio of 1 : 10 : 2000 in phosphate buffer solution (pH 7.2) containing 2% CTAB both under strictly anaerobic conditions and in the presence of oxygen, at 0  °C. Received: 26 May 1998 / Accepted: 20 August 1998     

Enhanced nuclear factor-kappa B-associated Wnt-1 expression in hepatitis B- and C-related hepatocarcinogenesis: identification by functional proteomics

Summary Chronic infections with hepatitis B and C viruses (HBV and HCV) are etiologically linked to hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Both viruses may induce activation of nuclear factor-kappa B (NF-κB) in hepatocytes that plays a crucial role in the regulation of cell growth and apoptosis. Functional proteomics analysis of proteins associated with NF-κB signaling complexes in both viruses-related HCC tumor and non-tumor tissues may disclose possible common mechanisms in hepatocarcinogenesis. By functional proteomics, we analyzed proteins associated with NF-κB-signaling complexes in four-paired human HCC tumor and non-tumor tissues from HBV- and HCV-infected patients, respectively, and in one-paired tissue with dual viral infection. The quantity of NF-κB-associated proteins was semi-quantitatively measured by protein spot intensity on the gels of two-dimensional polyacrylamide gel electrophoresis. The results showed that overexpression of NF-κB-associated Wnt-1 protein in tumor part was detected in the␣majority of HBV- and HCV-infected HCC samples. These data suggest that enhanced expression of NF-κB-associated Wnt-1 protein might be a mechanism of hepatocarcinogenesis common to HBV- and HCV-infected patients. NF-κB signaling pathway and Wnt-1 protein could be potential targets for designing highly effective therapeutic agents in treating HCC and for chemoprevention of hepatocarcinogenesis.     

Molecular biologist's guide to proteomics.

The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems.     

Evaluation of the effectiveness of EEG neurofeedback training for ADHD in a clinical setting as measured by changes in T.O.V.A. scores,behavioral ratings,and WISC-R performance

A study with three component parts was performed to assess the effectiveness of neurofeedback treatment for Attention Deficit/Hyperactivity Disorder (ADHD). The subject pool consisted of 23 children and adolescents ranging in age from 8 to 19 years with a mean of 11.4 years who participated in a 2-to 3-month summer program of intensive neurofeedback training. Feedback was contingent on the production of 16–20 hertz (beta) activity in the absence of 4–8 hertz (theta) activity. Posttraining changes in EEG activity, T.O.V.A. performance, (ADDES) behavior ratings, and WISC-R performance were assessed. Part I indicated that subjects who successfully decreased theta activity showed significant improvement in T.O.V.A. performance; Part II revealed significant improvement in parent ratings following neurofeedback training; and Part III indicated significant increases in WISC-R scores following neurofeedback training. This study is significant in that it examines the effects of neurofeedback training on both objective and subjective measures under relatively controlled conditions. Our findings corroborate and extend previous research, indicating that neurofeedback training can be an appropriate and efficacious treatment for children with ADHD.The first author (Joel F. Lubar) has provided consultative services for both Lexicor and Stoelting-Autogenics Corporations in order to help them develop appropriate protocols for neurofeedback. He is not an owner, stockholder, or employee for either organization.     

A review of the enforcement regime for vessel‐source oil pollution control

Abstract

The purpose of this article is to identify the currently applicable international law intended to regulate vessel‐source pollution. Part I delineates the elements relevant for this study. Part II discusses the development of a sequence of incremental conventions. Part III examines the significance and weaknesses of the 1973 MARPOL Convention with its 1978 Protocol and of the 1982 UN. Convention on the Law of the Sea. Part IV explores alternative and/or supplementary legal approaches for handling the vessel‐source oil pollution threat.     

Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae.

Enological strains of Saccharomyces cerevisiae display a high level of chromosome length polymorphism, but the molecular basis of this phenomenon has not yet been clearly defined. In order to gain further insight into the molecular mechanisms responsible for the karyotypic variability, we examined the chromosomal constitution of a strain known to possess aberrant chromosomes. Our data revealed that the strain carries four rearranged chromosomes resulting from two reciprocal translocations between chromosomes III and I, and chromosomes III and VII. The sizes of the chromosomal fragments exchanged through translocation range from 40 to 150 kb. Characterization of the breakpoints indicated that the translocations involved the RAHS of chromosome III, a transposition hot-spot on the right arm of chromosome I and a region on the left arm of chromosome VII. An analysis of the junctions showed that in all cases Ty elements were present and suggested that the translocations result from recombination between transposable Ty elements. The evidence for multiple translocations mediated by Ty elements in a single strain suggests that spontaneous Ty-driven rearrangement could be quite common and may play a major role in the alteration of karyotypes in natural and industrial yeasts. Received: 18 December 1998 / Accepted: 26 March 1999     

设施黄瓜育成品种果实外观品质的遗传多样性分析

对我国新育成的不同生态类型的138个设施黄瓜品种的19个果实外观性状进行了调查分析,研究其遗传多样性。结果表明,参试品种质量性状的遗传多样性指数都小于数量性状,不同生态类型黄瓜品种果实外观性状的遗传多样性指数为华北型(1.33)>华南型(1.25)>欧洲温室型(1.0)。质量性状的遗传多样性指数为华南型(0.91)>华北型(0.65)>欧洲温室型(0.48);数量性状的遗传多样性指数为华北型(1.94)>华南型(1.56)>欧洲温室型(1.47)。华南型品种果实数量性状的变异系数均高于华北型和欧洲温室型品种。主坐标轴分析(PCO)将所有种质划分为3个区组,即1区为华北型种质优势区、2区为华北型华南型和欧洲温室型种质混合分布区、3区为华南型种质区。PCO结果表明,1区和2区发生了基因渗透。对交流区域中华北型品种自交分离,后代中出现的稀刺瘤和光皮种质的情况进一步验证了基因渗透的结果。参照育成品种的果实性状信息对黄瓜以后的育种工作提出了建议。     

One of the possible mechanisms for the inhibition effect of Tb(III) on peroxidase activity in horseradish (<Emphasis Type="Italic">Armoracia rusticana</Emphasis>) treated with Tb(III)

One of the possible mechanisms for the inhibition effect of Tb(III) on peroxidase activity in horseradish (Armoracia rusticana) treated with Tb(III) was investigated using some biophysical and biochemical methods. Firstly, it was found that a large amount of Tb(III) can be distributed on the cell wall, that some Tb(III) can enter into the horseradish cell, indicating that peroxidase was mainly distributed on cell wall, and thus that Tb(III) would interact with horseradish peroxidase (HRP) in the plant. In addition, peroxidase bioactivity was decreased in the presence of Tb(III). Secondly, a new peroxidase-containing Tb(III) complex (Tb–HRP) was obtained from horseradish after treatment with Tb(III); the molecular mass of Tb–HRP is near 44 kDa and the pI is about 8.80. Thirdly, the electrocatalytic activity of Tb–HRP is much lower than that of HRP obtained from horseradish without treatment with Tb(III). The decrease in the activity of Tb–HRP is due to the destruction (unfolding) of the conformation in Tb–HRP. The planarity of the heme active center in the Tb–HRP molecule was increased and the extent of exposure of Fe(III) in heme was decreased, leading to inhibition of the electron transfer. The microstructure change in Tb–HRP might be the result of the inhibition effect of Tb(III) on peroxidase activity in horseradish.