bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter
Authors: Ivars-Martinez Elena , Martin-Cuadrado Ana-Belen , D'Auria Giuseppe , Mira Alex , Ferriera Steve , Johnson Justin , Friedman Robert , Rodriguez-Valera Francisco 
Published: July 2008

Abstract
Alteromonas macleodii is a common marine heterotrophic γ-proteobacterium. Isolates from this microbe cluster by molecular analysis into two major genotypic groups or ecotypes, one found in temperate latitudes in the upper water column and another that is for the most part found in the deep water column of the Mediterranean. Here, we describe the genome of one strain of the ‘deep ecotype’ (AltDE) isolated from 1000 m in the Eastern Mediterranean and compare this genome with that of the type strain ATCC 27126, a representative of the global ‘surface’ ecotype. The genomes are substantially different with DNA sequence similarity values that are borderline for microbes belonging to the same species, and a large differential gene content, mainly found in islands larger than 20 kbp, that also recruit poorly to the Global Ocean Sampling project (GOS). These genomic differences indicate that AltDE is probably better suited to microaerophilic conditions and for the degradation of recalcitrant compounds such as urea. These, together with other features, and the distribution of this genotypic group, indicate that this microbe colonizes relatively large particles that sink rapidly to meso and bathypelagic depths. The genome of ATCC 27126 on the other hand has more potential for regulation (two component systems) and degrades more sugars and amino acids, which is consistent with a more transient particle attachment, as would be expected for lineages specialized in colonizing smaller particulate organic matter with much slower sinking rates. The genomic data are also consistent with a picture of incipient speciation driven by niche specialization.
Prospective Randomized Trial of 3 Antiseptic Solutions for Prevention of Catheter Colonization in an Intensive Care Unit for Adult Patients
Authors: Vallés J. , Fernández I. , Alcaraz D. , Chacón E. , Cazorla A. , Canals M. , Mariscal D. , Fontanals D. , Morón A. 
Published: July 2008

Objective.To compare the effectiveness for prevention of central venous and arterial catheter colonization of 3 skin antisepsis with 1 of 3 antiseptic solutions: 10% aqueous povidone iodine (aqueous PI), 2% aqueous chlorhexidine gluconate (aqueous CG), and 0.5% alcoholic chlorhexidine gluconate (alcoholic CG).Design.Prospective, randomized controlled trial.Setting.Intensive care unit in a teaching hospital.Methods.Patients were randomly assigned to 1 of the 3 skin antisepsis groups. The distal tips of catheters were semiquantitatively cultured when the catheters were no longer necessary or if there was a suspicion of catheter-related infection. Rates of catheter colonization, catheter-related sepsis, and catheter-related bacteremia were compared among the 3 groups.Results.A total of 631 catheters were included in the study (194 from the aqueous PI group, 211 from the aqueous CG group, and 226 from the alcoholic CG group). The incidence of catheter colonization was significantly lower in the alcoholic CG than in the aqueous PI group (14.2% vs 24.7%; relative risk, 0.5 [95% confidence interval, 0.3-0.8; P < .01]); it was also significantly lower in the aqueous CG group than in the aqueous PI group (16.1 % vs 24.7%; relative risk, 0.6 [95% confidence interval, 0.4-0.9; P = .03]). There were no significant differences between the aqueous CG and the alcoholic CG groups. Incidences of catheter-related bacteremia were similar for all 3 groups. The aqueous and alcoholic CG solutions were superior to the aqueous PI solution in preventing catheter colonization due to gram-positive bacteria.Conclusions.The aqueous and alcoholic CG solutions for cutaneous antisepsis were similarly effective in preventing colonization of central venous catheters and arterial catheters. Both had significantly lower incidences of colonization than did the aqueous PI solution; this effect seems to be related to the CG solutions' more efficacious prevention of colonization with gram-positive bacteria.
ExactFDR: exact computation of false discovery rate estimate in case-control association studies
Authors: Wojcik Jérôme , Forner Karl 
Published: July 2008

AbstractSummary: Genome-wide association studies require accurate and fast statistical methods to identify relevant signals from the background noise generated by a huge number of simultaneously tested hypotheses. It is now commonly accepted that exact computations of association probability value (P-value) are preferred to χ2 and permutation-based approximations. Following the same principle, the ExactFDR software package improves speed and accuracy of the permutation-based false discovery rate (FDR) estimation method by replacing the permutation-based estimation of the null distribution by the generalization of the algorithm used for computing individual exact P-values. It provides a quick and accurate non-conservative estimator of the proportion of false positives in a given selection of markers, and is therefore an efficient and pragmatic tool for the analysis of genome-wide association studies.Availability: A Java 1.6 (1.5-compatible) version is available on SourceForge: http://sourceforge.net/projects/exactfdr.Contact: Jerome.wojcik@merckserono.netSupplementary information: Supplementary data are available at Bioinformatics online.
dbNEI2.0: building multilayer network for drug–NEI–disease
Authors: Zhang Jing , Ma Tao , Li Yanda , Li Shao 
Published: July 2008

Abstract
Summary: The neuro-endocrine-immune (NEI) system plays a critical regulatory role in modulating host homeostasis and optimizing health. We created the dbNEI 2 years ago to collect NEI molecules and interactions. For transferring the conceptual NEI to the systematic NEI network and uncovering the NEI's medical function, we updated the dbNEI 2.0 in three ways: (i) extended NEI molecules to 2242 genes and 7657 chemical compounds by using gene ontology-based (GO-based) data mining strategy, (ii) added multilayer interactions of NEI molecules including KEGG signal transduction and metabolic pathways, HPRD protein–protein interactions (PPI), transcription factor and microRNA regulations and (iii) connected 611 drugs and 823 diseases through multilayer NEI interactions. The reconstructed drug–NEI–disease network will facilitate the systematic study of NEI system.
Availability: http://bioinfo.au.tsinghua.edu.cn/dbNEIweb/
Contact: shaoli@mail.tsinghua.edu.cn
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
Authors: Xiong Bing , Liu Ke , Wu Jie , Burk David L. , Jiang Hualiang , Shen Jingkang 
Published: July 2008

Abstract
Summary: DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome. DrugViz can import drug–target network information in an extended SIF file format to Cytoscape and display the two-dimensional (2D) structures of small molecule nodes in a unified visualization environment. It also can identify small molecule nodes by means of three different 2D structure searching methods, namely isomorphism, substructure and fingerprint-based similarity searches. After selections, users can furthermore conduct a two-side clustering analysis on drugs and targets, which allows for a detailed analysis of the active compounds in the network, and elucidate relationships between these drugs and targets. DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology.
Availability: DrugViz and data set used in Application are freely available for download at http://202.127.30.184:8080/software.html
Contact: jkshen@mail.shcnc.ac.cn
The CellML Model Repository
Authors: Lloyd Catherine M. , Lawson James R. , Hunter Peter J. , Nielsen Poul F. 
Published: July 2008

Abstract
Summary: The CellML Model Repository provides free access to over 330 biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval.
Availability: The CellML Model Repository is publicly accessible at http://www.cellml.org/models
Contact: c.lloyd@auckland.ac.nz
End-joining long nucleic acid polymers
Authors: van den Hout M. , Hage S. , Dekker C. , Dekker N. H. 
Published: July 2008

Abstract
Many experiments involving nucleic acids require the hybridization and ligation of multiple DNA or RNA molecules to form a compound molecule. When one of the constituents is single stranded, however, the efficiency of ligation can be very low and requires significant individually tailored optimization. Also, when the molecules involved are very long (&gt;10 kb), the reaction efficiency typically reduces dramatically. Here, we present a simple procedure to efficiently and specifically end-join two different nucleic acids using the well-known biotin-streptavidin linkage. We introduce a two-step approach, in which we initially bind only one molecule to streptavidin (STV). The second molecule is added only after complete removal of the unbound STV. This primarily forms heterodimers and nearly completely suppresses formation of unwanted homodimers. We demonstrate that the joining efficiency is 50 ± 25% and is insensitive to molecule length (up to at least 20 kb). Furthermore, our method eliminates the requirement for specific complementary overhangs and can therefore be applied to both DNA and RNA. Demonstrated examples of the method include the efficient end-joining of DNA to single-stranded and double-stranded RNA, and the joining of two double-stranded RNA molecules. End-joining of long nucleic acids using this procedure may find applications in bionanotechnology and in single-molecule experiments.
In Planta Analysis of the Cell Cycle-Dependent Localization of AtCDC48A and Its Critical Roles in Cell Division, Expansion, and Differentiation
Authors: Park Sookhee , Rancour David Michael , Bednarek Sebastian York 
Published: July 2008

AbstractCDC48/p97 is a conserved homohexameric AAA-ATPase chaperone required for a variety of cellular processes but whose role in the development of a multicellular model system has not been examined. Here, we have used reverse genetics, visualization of a functional Arabidopsis (Arabidopsis thaliana) CDC48 fluorescent fusion protein, and morphological analysis to examine the subcellular distribution and requirements for AtCDC48A in planta. Homozygous Atcdc48A T-DNA insertion mutants arrest during seedling development, exhibiting decreased cell expansion and displaying pleiotropic defects in pollen and embryo development. Atcdc48A insertion alleles show significantly reduced male transmission efficiency due to defects in pollen tube growth. Yellow fluorescent protein-AtCDC48A, a fusion protein that functionally complements the insertion mutant defects, localizes in the nucleus and cytoplasm and is recruited to the division mid-zone during cytokinesis. The pattern of nuclear localization differs according to the stage of the cell cycle and differentiation state. Inducible expression of an Atcdc48A Walker A ATPase mutant in planta results in cytokinesis abnormalities, aberrant cell divisions, and root trichoblast differentiation defects apparent in excessive root hair emergence. At the biochemical level, our data suggest that the endogenous steady-state protein level of AtCDC48A is dependent upon the presence of ATPase-active AtCDC48A. These results demonstrate that CDC48A/p97 is critical for cytokinesis, cell expansion, and differentiation in plants.
The EPIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION Is Sufficient to Induce Abscission inArabidopsisthrough the Receptor-Like Kinases HAESA and HAESA-LIKE2
Authors: Stenvik Grethe-Elisabeth , Tandstad Nora M. , Guo Yongfeng , Shi Chun-Lin , Kristiansen Wenche , Holmgren Asbjørn , Clark Steven E. , Aalen Reidunn B. , Butenko Melinka A. 
Published: July 2008

AbstractIn Arabidopsis thaliana, the final step of floral organ abscission is regulated by INFLORESCENCE DEFICIENT IN ABSCISSION (IDA): ida mutants fail to abscise floral organs, and plants overexpressing IDA display earlier abscission. We show that five IDA-LIKE (IDL) genes are expressed in different tissues, but plants overexpressing these genes have phenotypes similar to IDA-overexpressing plants, suggesting functional redundancy. IDA/IDL proteins have N-terminal signal peptides and a C-terminal conserved motif (extended PIP [EPIP]) at the C terminus (EPIP-C). IDA can, similar to CLAVATA3, be processed by an activity from cauliflower meristems. The EPIP-C of IDA and IDL1 replaced IDA function in vivo, when the signal peptide was present. In addition, synthetic IDA and IDL1 EPIP peptides rescued ida and induced early floral abscission in wild-type flowers. The EPIP-C of the other IDL proteins could partially substitute for IDA function. Similarly to ida, a double mutant between the receptor-like kinases (RLKs) HAESA (HAE) and HAESA-LIKE2 (HSL2) displays nonabscising flowers. Neither overexpression of IDA nor synthetic EPIP or EPIP-C peptides could rescue the hae hsl2 abscission deficiency. We propose that IDA and the IDL proteins constitute a family of putative ligands that act through RLKs to regulate different events during plant development.
TheCladosporium fulvumVirulence Protein Avr2 Inhibits Host Proteases Required for Basal Defense
Authors: van Esse H. Peter , van't Klooster John W. , Bolton Melvin D. , Yadeta Koste A. , van Baarlen Peter , Boeren Sjef , Vervoort Jacques , de Wit Pierre J.G.M. , Thomma Bart P.H.J. 
Published: July 2008

AbstractCladosporium fulvum (syn. Passalora fulva) is a biotrophic fungal pathogen that causes leaf mold of tomato (Solanum lycopersicum). During growth in the apoplast, the fungus establishes disease by secreting effector proteins, 10 of which have been characterized. We have previously shown that the Avr2 effector interacts with the apoplastic tomato Cys protease Rcr3, which is required for Cf-2–mediated immunity. We now show that Avr2 is a genuine virulence factor of C. fulvum. Heterologous expression of Avr2 in Arabidopsis thaliana causes enhanced susceptibility toward extracellular fungal pathogens, including Botrytis cinerea and Verticillium dahliae, and microarray analysis showed that Avr2 expression triggers a global transcriptome reflecting pathogen challenge. Cys protease activity profiling showed that Avr2 inhibits multiple extracellular Arabidopsis Cys proteases. In tomato, Avr2 expression caused enhanced susceptibility toward Avr2-defective C. fulvum strains and also toward B. cinerea and V. dahliae. Cys protease activity profiling in tomato revealed that, in this plant also, Avr2 inhibits multiple extracellular Cys proteases, including Rcr3 and its close relative Pip1. Finally, silencing of Avr2 significantly compromised C. fulvum virulence on tomato. We conclude that Avr2 is a genuine virulence factor of C. fulvum that inhibits several Cys proteases required for plant basal defense.
Phytoplankton response to light and internal phosphorus loading from sediment release
Authors: CYMBOLA JENNIFER , OGDAHL MARY , STEINMAN ALAN D. 
Published: July 2008

Summary1. A 2 × 2 factorial design was employed to look at the influence of two levels of phosphorus (P; high and low) and two levels of light (high and low) and their interactions, on phytoplankton abundance, elemental tissue composition and community structure in two seasons (April and June) of 2005.2. A novel feature of the experiment was the creation of high and low P levels by manipulating sediment core conditions in the laboratory. Sediment cores were incubated with their associated overlaying water column from four different sites in Mona Lake, Michigan, under anaerobic or aerobic conditions, respectively.3. After 24 days, the water overlaying the sediment cores was collected and used as growth media for phytoplankton collected from Mona Lake. Phytoplankton communities were grown in the laboratory in the high or low P water, and subjected to high (250 μmol m−2 s−1) or low (10 μmol m−2 s−1) light for 9 (April) or 14 (June) days.4. In the April experiment, high P treatments resulted in significantly higher chlorophyll‐a concentrations, significantly lower C : P ratios from two of the four sites, and greater dominance by Scenedesmus at all sites relative to low P treatments. High light generally led to higher chlorophyll‐a concentrations, higher C : P ratios and greater Scenedesmus and Fragilaria biovolume at all sites. A significant interaction was measured between P and light for chlorophyll‐a and Scenedesmus biovolume, suggesting the influence of P was more apparent at high light than at low light levels.5. In the June experiment, high P increased ash‐free dry mass (AFDM), lowered C : P ratios and resulted in increased Pediastrum biovolume. High light levels led to greater chlorophyll‐a concentrations, AFDM and C : P ratios, as well as increased biovolumes of Scendesmus, Pediastrum and Fragilaria. A significant interaction was found between P and light for all three taxa, as the positive influence of P was more pronounced at high light levels.6. The results of our study demonstrate that sediment‐derived P stimulates phytoplankton growth, but that its effect on phytoplankton dynamics is modulated by other factors, such as light.
Reflection across plant cell boundaries in confocal laser scanning microscopy
Authors: LIU D.Y.T. , KUHLMEY B.T. , SMITH P.M.C. , DAY D.A. , FAULKNER C.R. , OVERALL R.L. 
Published: July 2008

SummaryThe fluorescence patterns of proteins tagged with the green fluorescent protein (GFP) and its derivatives are routinely used in conjunction with confocal laser scanning microscopy to identify their sub‐cellular localization in plant cells. GFP‐tagged proteins localized to plasmodesmata, the intercellular junctions of plants, are often identified by single or paired punctate labelling across the cell wall. The observation of paired puncta, or ‘doublets’, across cell boundaries in tissues that have been transformed through biolistic bombardment is unexpected if there is no intercellular movement of the GFP‐tagged protein, since bombardment usually leads to the transformation of single, isolated cells. We expressed a putative plasmodesmal protein tagged with GFP by bombarding Allium porrum epidermal cells and assessed the nature of the doublets observed at the cell boundaries. Doublets were formed when fluorescent spots were abutting a cell boundary and were only observable at certain focal planes. Fluorescence emitted from the half of a doublet lying outside the transformed cells was polarized. Optical simulations performed using finite‐difference time‐domain computations showed a dramatic distortion of the confocal microscope's point spread function when imaging voxels close to the plant cell wall due to refractive index differences between the wall and the cytosol. Consequently, axially and radially out‐of‐focus light could be detected. A model of this phenomenon suggests how a doublet may form when imaging only a single real fluorescent body in the vicinity of a plant cell wall using confocal microscopy. We suggest, therefore, that the appearance of doublets across cell boundaries is insufficient evidence for plasmodesmal localization due to the effects of the cell wall on the reflection and scattering of light.
Transcriptional activation by MarA, SoxS and Rob of two tolC promoters using one binding site: a complex promoter configuration for tolC in Escherichia coli
Authors: Zhang Aixia , Rosner Judah L. , Martin Robert G. 
Published: July 2008

SummaryThe Escherichia coli tolC encodes a major outer membrane protein with multiple functions in export (e.g. diverse xenobiotics, haemolysin) and as an attachment site for phage and colicins. tolC is regulated in part by MarA, SoxS and Rob, three paralogous transcriptional activators which bind a sequence called the marbox and which activate multiple antibiotic and superoxide resistance functions. Two previously identified tolC promoters, p1 and p2, are not regulated by MarA, SoxS or Rob but p2 is activated by EvgAS and PhoPQ which also regulate other functions. Using transcriptional fusions and primer extension assays, we show here that tolC has two additional strong overlapping promoters, p3 and p4, which are downstream of p1, p2 and the marbox and are activated by MarA, SoxS and Rob. p3 and p4 are configured so that a single marbox suffices to activate transcription from both promoters. At the p3 promoter, the marbox is separated by 20 bp from the −10 hexamer for RNA polymerase but at the p4 promoter, the same marbox is separated by 30 bp from the −10 hexamer. The multiple tolC promoters may allow the cell to respond to diverse environments by co‐ordinating tolC transcription with other appropriate functions.
An international collaborative study to establish a replacement World Health Organization International Standard for human immunodeficiency virus 1 RNA nucleic acid assays
Authors: Davis C. , Berry N. , Heath A. , Holmes H. 
Published: July 2008

Background and Objectives An international collaborative study was undertaken to identify a replacement for the World Health Organization (WHO) 1st International Standard for human immunodeficiency virus 1 (HIV‐1) RNA for use in nucleic acid‐based techniques (NAT) (code 97/656). In the original study to establish the 1st International Standard, a second candidate material (code 97/650) had been shown to perform well and this was re‐evaluated to establish whether it would be a suitable replacement.Materials and Methods Eight laboratories from six different countries participated in the collaborative study to evaluate the candidate replacement standard. A total of eight different NATs were used, five in a quantitative format and three qualitative, of which five were commercially available.Results The results showed that the estimates of RNA copies in the current study were generally in line with those of the original study and there was no evidence of any drift in overall levels expressed in International Units (IU) for the candidate standard between the two studies. Furthermore, it was shown to be stable over long‐term storage at –20°C.Conclusions The candidate material code 97/650 was established by the WHO as the 2nd International Standard for HIV‐1 RNA for use in NAT and assigned a unitage of 5·56 log10(363 078) IU/vial.