bluuebunny/crossref_metadata_2025_split huggingface dataset:
The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity
Authors: Bent Stephen J , Forney Larry J 
Published: May 2008

Abstract
Molecular microbial community analysis methods have revolutionized our understanding of the diversity and distribution of bacteria, archaea and microbial eukaryotes. The information obtained has adequately demonstrated that the analysis of microbial model systems can provide important insights into ecosystem function and stability. However, the terminology and metrics used in macroecology must be applied cautiously because the methods available to characterize microbial diversity are inherently limited in their ability to detect the many numerically minor constituents of microbial communities. In this review, we focus on the use of indices to quantify the diversity found in microbial communities, and on the methods used to generate the data from which those indices are calculated. Useful conclusions regarding diversity can only be deduced if the properties of the various methods used are well understood. The commonly used diversity metrics differ in the weight they give to organisms that differ in abundance, so understanding the properties of these metrics is essential. In this review, we illustrate important methodological and metric-dependent differences using simulated communities. We conclude that the assessment of richness in complex communities is futile without extensive sampling, and that some diversity indices can be estimated with reasonable accuracy through the analysis of clone libraries, but not from community fingerprint data.
PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways
Authors: Raman Karthik , Chandra Nagasuma 
Published: May 2008

AbstractStoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale metabolic models of several organisms such as Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus have already been constructed. Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the popular techniques for the constraint-based analysis of metabolic pathways.We have developed a computational tool, PathwayAnalyser, for the analysis of metabolic pathways, particularly by FBA and MoMA. PathwayAnalyser interfaces with the open-source GNU Linear Programming Toolkit (GLPK) for linear programming/FBA and Object Oriented Quadratic Programming (OOQP) for quadratic programming/MoMA. It gives a comprehensive report on gene deletions from the Systems Biology Markup Language (SBML) Model and objective function input for FBA. PathwayAnalyser is open-source and is available at "http://sourceforge.net/projects/pathwayanalyser":http://sourceforge.net/projects/pathwayanalyser
Stigmatizing Attitudes Toward Obesity in a Representative Population‐based Sample
Authors: Hilbert Anja , Rief Winfried , Braehler Elmar 
Published: May 2008

Objective: The aim of this study was to determine stigmatizing attitudes toward obesity in the population, and its related psychological and sociodemographic determinants.Methods and Procedures: In a representative population‐based survey (N = 1,000), computer‐assisted telephone interviewing was used to assess stigmatizing attitudes toward obesity, causal attributions of obesity, the labeling of obesity as an illness, perceptions about prevalence, severity, and chronicity of obesity, support of obesity prevention, and sociodemographic characteristics.Results: Of the 1,000 participants, 23.5% (n = 235) had stigmatizing attitudes toward obesity, 21.5% (n = 215) did not have stigmatizing attitudes toward obesity, and 55.0% (n = 550) had attitudes that were undetermined with respect to stigmatization. Predictors of greater stigmatization were more causal attributions of obesity to individual behavior, less education, and older age, while causal attributions of obesity to heredity and labeling obesity as an illness predicted less stigmatization. Stigmatizing attitudes were significantly associated with stronger overall support of obesity prevention, but less readiness to support prevention financially.Discussion: Our results indicate that stigmatizing attitudes toward obesity are prevalent in the population. Information about the etiology of obesity and the clinical relevance of this condition could prove useful for destigmatization efforts.
DNA molecule dynamics in converging–diverging microchannels
Authors: Hsieh Shou‐Shing , Liou Jian‐Heng 
Published: May 2008

The conformation and dynamics of double‐stranded DNA molecules in a pressure‐driven flow‐through sharp/gradual converging (contraction half)‐diverging (expansion half) square microchannels with a contraction/expansion ratio of 4:1/1:4 were examined using fluorescently labelled λ‐phage DNA at 2.2≤De≤30.7 (De is Deborah number, a dimensionless number used in rheology to characterize how fluid a material is). Both the diffusion and stretching of individual DNA molecules and their local flow velocity were visualized, recorded and measured with using MPIV (microparticle image velocimetry) and CLSM (confocal laser‐scanning microscopy). The onset of the coil‐stretch transition in DNA molecules and their time‐dependent velocity in the elongational flow were determined at the micro scale. Velocity distribution was measured via MPIV through orange fluorescent particles and carboylate‐modified microspheres of 1 μm diameter. The channel geometry effect in terms of the channel contraction/expansion angle, the mass flow rate and the solution viscosity on the conformation and diffusion were also studied and discussed.
Taxol production by Pestalotiopsis terminaliae, an endophytic fungus of Terminalia arjuna (arjun tree)
Authors: Gangadevi Venkatraman , Muthumary Johnpaul 
Published: May 2008

Terminalia arjuna is a medicinal plant (the arjun tree) that possesses anticancer activity. An endophytic fungus, Pestalotiopsis terminaliae, was isolated from the fresh healthy leaves of this tree and was screened for the production of taxol, an anticancer drug, in artificial culture medium. The taxol produced was analysed chromatographically and spectrometrically. The amount of taxol produced by the fungus was found to be 211.1 μg/litre. This was sufficient for the fungus to be considered as a potential source material for improvement, by engineering, the production of taxol. The fungal taxol extracted from an organic extract of the fungal culture had strong cytotoxic activity towards BT220, H116, Int 407, HL 251 and HLK 210 human cancer cells in vitro when tested using an apoptosis assay.
High‐level expression and single‐step purification of recombinant Bacillus anthracis protective antigen from Escherichia coli
Authors: Lu Jinbiao , Wei Dong , Wang Yefu , Wang Guozhi 
Published: May 2008

PA (protective antigen) is a major immunogen of the vaccine against anthrax. In the present study, a new expression system, Escherichia coli strain Rosetta™ 2(DE3), was used for high‐level expression of rPA (recombinant PA) whose gene contains 66 rare E. coli codons (9.0% of 733 total PA gene codons). The rPA‐formed inclusion bodies were washed with Triton X‐100 and 2 M urea and solubilized in 5 M urea, followed by a 60%‐satd.‐ammonium sulfate precipitation. Finally, the untagged rPA was efficiently and rapidly purified by single‐step hydrophobic‐interaction chromatography using Phenyl‐Sepharose High Performance resin on an AKTA Purifier 10 system. The yield was approx. 13 mg of high‐purity (>99%) biologically active rPA per litre of culture, which can be used for the detection of anthrax and as a potential component of a vaccine against anthrax.
Vascular endothelial cell antigen (VECA), a novel secreted protein: overexpression in Escherichia coli of the hexahistidine‐ tagged protein and production of polyclonal antibodies
Authors: Xiong Shao Quan , Yang Han Shuo , Chen Yi Yuan , Zhao Cheng Jian , Yuan Zhu , Zhao Xin Yu , Yan Fei , Wang Bai Ding , Tang Ming Hai , Yang Jin Liang , Wei Yu Quan 
Published: May 2008

A novel VECA (vascular endothelial cell antigen) was previously identified by using an antibody pool against antigens in HUVECs (human umbilical‐vein endothelial cells). VECA has been evolutionarily conserved in vertebrate species ranging from frog and fish to mouse and human. Bioinformatics analysis indicated that VECA was 10.1 kDa in size, with a predicted signal sequence and transmembrane domain, indicating that VECA may have important biological functions. The present paper describes a procedure for obtaining and purifying human recombinant VECA expressed in Escherichia coli as a fusion protein, via a human VECA cDNA linked pQE30 expression vector to DNA coding for hexahistidine. The purified protein was used to raise anti‐(human VECA) polyclonal antibodies, which were suitable for detecting the presence of VECA in cells, cell‐culture supernatant and tissues by immunoblotting and immunohistochemistry. To our knowledge, this is the first study on the protein expression and polyclonal‐antibody production for human VECA. In addition, we report for the first time the positive identification of VECA in humans at the protein and subcellular level and provide the first experimental verification that VECA was indeed a secreted protein. The anti‐(human VECA) polyclonal antibodies prepared may serve as a useful tool for future biological function studies on VECA.
The antibacterial efficacy of an aceraceous plant [Shantung maple (Acer truncatum Bunge)] may be related to inhibition of bacterial β‐oxoacyl‐acyl carrier protein reductase (FabG)
Authors: Zhang Feng , Luo Shi‐Yun , Ye Yan‐Bin , Zhao Wen‐Hua , Sun Xu‐Guang , Wang Zhi‐Qun , Li Ran , Sun Ying‐Hui , Tian Wei‐Xi , Zhang Ying‐Xia 
Published: May 2008

Polyphenols, including flavonoids, are the major components of the extracts from aceraceous plants. They possess remarkable antibacterial and antitumour activity. Our study focused on whether the inhibition of the bacterial type II fatty acid synthesis system is the mechanism for the antibacterial effect of the related plant polyphenols. Extracts obtained from the fallen leaves of the Shantung maple (Acer truncatum Bunge) using different solvents, and the related pure compound PGG (1,2,3,4,6‐penta‐O ‐galloyl‐β‐d‐glucose), potently inhibited the FabG (β‐oxoacyl‐ACP reductase) steps in the fatty‐acid‐elongation cycle with the IC50 values between 0.9 and 7.2 μg/ml. An ethyl acetate extract appeared to inhibit FabG reductase in a mixed manner with NADPH, as did PGG with NADPH, demonstrating that they interfered with the binding of the cofactor to the enzyme. Gram‐positive and Gram‐negative bacteria and some fungi were used to evaluate the antibacterial abilities of different extract samples. The experiments showed that a higher polyphenol content of the extracts led to a more potent inhibitory capacity against FabG, thus enhancing the antibacterial efficacy.
Generation of Affibody® ligands binding interleukin‐2 receptor α/CD25
Authors: Grönwall Caroline , Snelders Eveline , Palm Anna Jarelöv , Eriksson Fredrik , Herne Nina , Ståhl Stefan 
Published: May 2008

Affibody® molecules specific for human IL‐2Rα, the IL‐2 (interleukin‐2) receptor α subunit, also known as CD25, were selected by phage‐display technology from a combinatorial protein library based on the 58‐residue Protein A‐derived Z domain. The IL‐2R system plays a major role in T‐cell activation and the regulation of cellular immune responses. Moreover, CD25 has been found to be overexpressed in organ rejections, a number of autoimmune diseases and T‐cell malignancies. The phage‐display selection using Fc‐fused target protein generated 16 unique Affibody® molecules targeting CD25. The two most promising binders were characterized in more detail using biosensor analysis and demonstrated strong and selective binding to CD25. Kinetic biosensor analysis revealed that the two monomeric Affibody® molecules bound to CD25 with apparent affinities of 130 and 240 nM respectively. The Affibody® molecules were, on biosensor analysis, found to compete for the same binding site as the natural ligand IL‐2 and the IL‐2 blocking monoclonal antibody 2A3. Hence the Affibody® molecules were assumed to have an overlapping binding site with IL‐2 and antibodies targeting the IL‐2 blocking Tac epitope (for example, the monoclonal antibodies Daclizumab and Basiliximab, both of which have been approved for therapeutic use). Furthermore, immunofluorescence microscopy and flow‐cytometric analysis of CD25‐expressing cells demonstrated that the selected Affibody® molecules bound to CD4+ CD25+ PMBCs (peripheral‐blood mononuclear cells), the IL‐2‐dependent cell line NK92 and phytohaemagglutinin‐activated PMBCs. The potential use of the CD25‐binding Affibody® molecules as targeting agents for medical imaging and for therapeutic applications is discussed.
Collagen reorganization in leech wound healing
Authors: Tettamanti Gianluca , Grimaldi Annalisa , Congiu Terenzio , Perletti Gianpaolo , Raspanti Mario , Valvassori Roberto , de Eguileor Magda 
Published: May 2008

Background Information. Leeches respond to surgical lesions with the same sequence of events as that described for wound healing in vertebrates, where collagen is important for the development of tensions in healing wounds, functioning as an extracellular scaffold for accurate regeneration of the structures disrupted by surgical or traumatic actions.Results. In surgically lesioned leeches, newly synthesized collagen is arranged in hierarchical structures. Fibrils can be packed and shaped to form cords or tubular structures, thus acting as an extracellular scaffold that directs and organizes the outgrowth of new vessels and the migration of immune cells towards lesioned tissues. In these animals, the general architecture of collagen fibrils, generated during tissue regeneration, shows similarities to both the structural pattern of collagen bundles and assembly processes observed in several vertebrate systems (fish scales, amphibian skin and human cornea).Conclusions. The production of extracellular matrix during wound healing in leeches is a surprising example of conservation of an extremely close relationship between the structure and function of molecular structures. It could be hypothesized that collagen structures, characterized not only by a striking structural complexity, but also by multifunctional purposes, are anatomical systems highly conserved throughout evolution.
Sulphated glycoconjugates are powerful inhibitors of spermatozoa binding to the vitelline envelope in amphibian eggs
Authors: Caputo Mariangela , Riccio Stefania , Paglierucci Paolo , Tretola Loredana , Diglio Clementina , Carotenuto Rosa , De Marco Nadia , Campanella Chiara 
Published: May 2008

Background information. In amphibians, the role of sulphated glycans has not been determined in spermatozoa—egg interaction, although they are known to be involved in other systems. In previous studies, it was found that, in Discoglossus pictus, a VE (vitelline envelope) glycoprotein of 63 kDa exhibits high homology to Xenopus laevis gp69/gp64 and to ZP2 of mammals. gp63 and a glycoprotein of 75 kDa are both capable of binding the spermatozoa in in vitro assays and, having similar peptide maps and different glycosylation, are probably two glycoforms of the same protein.Results. In the present study, binding assays performed by treating dejellied eggs with metaperiodate suggest that hydroxy groups of sugars are not directly involved in spermatozoa—vitelline envelope binding. Competition assays between dejellied eggs and spermatozoa preincubated with dextran, dextran sulphate or fucoidan indicated that sulphated oligosaccharides have an inhibitory effect on spermatozoa binding. In similar competition assays, Lex (Lewisx) trisaccharide 3′‐sulphate inhibited spermatozoa binding to VE in contrast with 3′‐sialyl‐Lex tetrasaccharide. Assays performed with gp75‐ or gp63‐coated beads and spermatozoa treated with fucoidan or dextran sulphate indicated that sulphated oligosaccharides competitively inhibit spermatozoa binding to gp75‐coated beads, yet not to gp63‐coated beads. Finally, solubilized VE digested with N‐glycosidase F retains the inhibitory activity in spermatozoa—VE binding assays in contrast with VE treated with α‐N‐acetylgalactosaminidase.Conclusion. It was concluded that VE sulphate groups are involved in spermatozoa binding. These groups are present in gp75 glycoconjugates and are probably located in O‐linked glycoconjugates.
The role of Munc18‐1 in docking and exocytosis of peptide hormone vesicles in the anterior pituitary
Authors: Korteweg Niki , Maia Ascanio S. , Thompson Brenda , Roubos Eric W. , Burbach J. Peter H. , Verhage Matthijs 
Published: May 2008

Background information. Many neurons secrete classical transmitters from synaptic vesicles as well as peptide transmitters from LDCVs (large dense‐core vesicles). Little is known about the mechanistic differences between these two secretory pathways. The soluble protein Munc18‐1 is essential for synaptic vesicle secretion [Verhage, Maia, Plomp, Brussaard, Heeroma, Vermeer, Toonen, Hammer, van den Berg, Missler, et al. (2000) Science 287, 864–869.].Results. In the present study, we tested if Munc18 genes are also involved in peptidergic secretion from LDCVs using the anterior pituitary as a model system. We show that Munc18‐1 is the dominant isoform expressed in the anterior pituitary. In Munc18‐1 null mutant mice, the anterior pituitary developed normally and the five major endocrine cell types had a normal distribution. However, circulating peptide hormone levels were decreased by up to 50‐fold in the null mutant, whereas the intracellular levels were significantly higher than that in controls. Ultrastructural analysis using the tannic acid method revealed striking differences in the distribution of secretory vesicles: (i) the number of exocytotic figures was mostly decreased in the null mutants and (ii) the LDCVs accumulated near but not at their target membrane. This is in contrast with the apparently normal distribution of synaptic vesicles in developing synapses in the null mutant (Verhage et al., 2000).Conclusions. We conclude that Munc18‐1 is involved in the secretion of peptide hormones and in the docking of LDCVs. These results unmask an apparent mechanistic difference between LDCVs and synaptic vesicles.
Centrioles resist forces applied on centrosomes during G2/M transition
Authors: Abal Miguel , Keryer Guy , Bornens Michel 
Published: May 2008

Background information. Centrosome movements at the onset of mitosis result from a balance between the pulling and pushing forces mediated by microtubules. The structural stability of the centrosome core structure, the centriole pair, is correlated with a heavy polyglutamylation of centriole tubulin.Results. Using HeLa cells stably expressing centrin—green fluorescent protein as a centriole marker, we monitored the effect of microinjecting an anti‐(polyglutamylated tubulin) monoclonal antibody, GT335, in G1/S or G2 cells. In contrast with the slow effect of the monoclonal antibody GT335 during interphase, a dramatic and rapid centrosome fragmentation occurred in cells microinjected in G2 that was both Eg5‐ and dynein‐dependent. Inhibition of either one of these two motors significantly decreased the scattering of centrosome fragments, and inhibition of centrosome segregation by impairing microtubule dynamics abolished centrosome fragmentation.Conclusions. Our results demonstrate that the compact structure of the mitotic centrosome is capable of absorbing most of the pulling and pushing forces during G2/M transition and suggest that centrosomes could act as mechanosensors integrating tensions during cell division.
MIPDB: a relational database dedicated to MIP family proteins
Authors: El Karkouri Khalid , Gueuné Hervé , Delamarche Christian 
Published: May 2008

Background information. The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water‐transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota, and the rapid accumulation of new sequences in the database provides an opportunity for large‐scale analysis, to identify functional and/or structural signatures or to infer evolutionary relationships. To help perform such an analysis, we have developed MIPDB (database for MIP proteins), a relational database dedicated to members of the MIP family.Results. MIPDB is a motif‐oriented database that integrates data on 785 MIP proteins from more than 200 organisms and contains 230 distinct sequence motifs. MIPDB proposes the classification of MIP proteins into three functional subgroups: AQPs, glycerol‐uptake facilitators and aquaglyceroporins. Plant MIPs are classified into three specific subgroups according to their subcellular distribution in the plasma membrane, tonoplast or the symbiosome membrane. Some motifs of the database are highly selective and can be used to predict the transport function or subcellular localization of unknown MIP proteins.Conclusions. MIPDB offers a user‐friendly and intuitive interface for a rapid and easy access to MIP resources and to sequence analysis tools. MIPDB is a web application, publicly accessible at http:idefix.univ‐rennes1.fr:8080Protindex.html.
Phylogeny and evolution of the major intrinsic protein family
Authors: Zardoya Rafael 
Published: May 2008

Background information. MIPs (major intrinsic proteins) form channels across biological membranes that control recruitment of water and small solutes such as glycerol and urea in all living organisms. Because of their widespread occurrence and large number, MIPs are a sound model system to understand evolutionary mechanisms underlying the generation of protein structural and functional diversity. With the recent increase in genomic projects, there is a considerable increase in the quantity and taxonomic range of MIPs in molecular databases.Results. In the present study, I compiled more than 450 non‐redundant amino acid sequences of MIPs from NCBI databases. Phylogenetic analyses using Bayesian inference reconstructed a statistically robust tree that allowed the classification of members of the family into two main evolutionary groups, the GLPs (glycerol‐uptake facilitators or aquaglyceroporins) and the water transport channels or AQPs (aquaporins). Separate phylogenetic analyses of each of the MIP subfamilies were performed to determine the main groups of orthology. In addition, comparative sequence analyses were conducted to identify conserved signatures in the MIP molecule.Conclusions. The earliest and major gene duplication event in the history of the MIP family led to its main functional split into GLPs and AQPs. GLPs show typically one single copy in microbes (eubacteria, archaea and fungi), up to four paralogues in vertebrates and they are absent from plants. AQPs are usually single in microbes and show their greatest numbers and diversity in angiosperms and vertebrates. Functional recruitment of NOD26‐like intrinsic proteins to glycerol transport due to the absence of GLPs in plants was highly supported. Acquisition of other MIP functions such as permeability to ammonia, arsenite or CO2is restricted to particular MIP paralogues. Up to eight fairly conserved boxes were inferred in the primary sequence of the MIP molecule. All of them mapped on to one side of the channel except the conserved glycine residues from helices 2 and 5 that were found in the opposite side.