bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-Function Analysis of
Escherichia coli
MnmG (GidA), a Highly Conserved tRNA-Modifying Enzyme
Authors: Shi Rong , Villarroya Magda , Ruiz-Partida Rafael , Li Yunge , Proteau Ariane , Prado Silvia , Moukadiri Ismaïl , Benítez-Páez Alfonso , Lomas Rodrigo , Wagner John , Matte Allan , Velázquez-Campoy Adrián , Armengod M.-Eugenia , Cygler Miroslaw 
Published: October 2009

ABSTRACT

The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of
Escherichia coli
MnmG at 2.4-Å resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.
Differential Modulation ofBurkholderia cenocepaciaVirulence and Energy Metabolism by the Quorum-Sensing Signal BDSF and Its Synthase
Authors: Deng Yinyue , Boon Calvin , Eberl Leo , Zhang Lian-Hui 
Published: October 2009

ABSTRACTBurkholderia cenocepaciaproduces the moleculecis-2-dodecenoic acid (BDSF), which was previously shown to play a role in antagonism against the fungal pathogenCandida albicansby interfering with its morphological transition. In this study, we show that production of BDSF is under stringent transcriptional control and the molecule accumulates in a cell density-dependent manner, typically found with quorum-sensing (QS) signals.B. cenocepaciamutant strain J2315 with a deleted Bcam0581 gene, which encodes an enzyme essential for BDSF production, exhibited a growth defect in minimal medium but not in rich medium, decreased virulence gene expression, and attenuated virulence in a zebrafish infection model. Exogenous addition of BDSF to the mutant rescues virulence gene expression but fails to restore its growth defect in minimal medium. We show that Bcam0581, but not BDSF, is associated withB. cenocepaciaATP biogenesis. We also provide evidence that some of the BDSF-regulated genes are also controlled by the acyl-homoserine-lactone-dependent QS system and are thus coregulated by two cell-to-cell signaling systems. These data demonstrate that in addition to the role in cross-kingdom signal interference, BDSF and its synthase are also important for the virulence and physiology ofB. cenocepacia.
CbpA: a Polarly Localized Novel Cyclic AMP-Binding Protein in
Pseudomonas aeruginosa
Authors: Endoh Takayuki , Engel Joanne N. 
Published: October 2009

ABSTRACT

In
Pseudomonas aeruginosa
, cyclic AMP (cAMP) signaling regulates the transcription of hundreds of genes encoding diverse virulence factors, including the type II secretion system (T2SS) and type III secretion system (T3SS) and their associated toxins, type IV pili (TFP), and flagella. Vfr, a cAMP-dependent transcriptional regulator that is homologous to the
Escherichia coli
catabolite repressor protein, is thought to be the major cAMP-binding protein that regulates these important virulence determinants. Using a bioinformatic approach, we have identified a gene (PA4704) encoding an additional putative cAMP-binding protein in
P. aeruginosa
PAO1, which we herein refer to as CbpA, for
c
AMP-
b
inding
p
rotein
A
. Structural modeling predicts that CbpA is composed of a C-terminal cAMP-binding (CAP) domain and an N-terminal degenerate CAP domain and is structurally similar to eukaryotic protein kinase A regulatory subunits. We show that CbpA binds to cAMP-conjugated agarose via its C-terminal CAP domain. Using in vitro trypsin protection assays, we demonstrate that CbpA undergoes a conformational change upon cAMP binding. Reporter gene assays and electrophoresis mobility shift assays defined the
cbpA
promoter and a Vfr-binding site that are necessary for Vfr-dependent transcription. Although CbpA is highly regulated by Vfr, deletion of
cbpA
did not affect known Vfr-dependent functions, including the T2SS, the T3SS, flagellum- or TFP-dependent motility, virulence in a mouse model of acute pneumonia, or protein expression profiles. Unexpectedly, CbpA-green fluorescent protein was found to be localized to the flagellated old cell pole in a cAMP-dependent manner. These results suggest that polar localization of CbpA may be important for its function.
Identification of a Stress-Induced Factor ofCorynebacterineaeThat Is Involved in the Regulation of the Outer Membrane Lipid Composition
Authors: Meniche Xavier , Labarre Cécile , de Sousa-d'Auria Célia , Huc Emilie , Laval Françoise , Tropis Marielle , Bayan Nicolas , Portevin Damien , Guilhot Christophe , Daffé Mamadou , Houssin Christine 
Published: October 2009

ABSTRACTCorynebacterineaeare gram-positive bacteria that possess a true outer membrane composed of mycolic acids and other lipids. Little is known concerning the modulation of mycolic acid composition and content in response to changes in the bacterial environment, especially temperature variations. To address this question, we investigated the function of the Rv3802c gene, a gene conserved inCorynebacterineaeand located within a gene cluster involved in mycolic acid biosynthesis. We showed that the Rv3802 ortholog is essential inMycobacterium smegmatis, while itsCorynebacterium glutamicumortholog, NCgl2775, is not. We provided evidence that the NCgl2775 gene is transcriptionally induced under heat stress conditions, and while the corresponding protein has no detectable activity under normal growth conditions, the increase in its expression triggers an increase in mycolic acid biosynthesis concomitant with a decrease in phospholipid content. We demonstrated that these lipid modifications are part of a larger outer membrane remodeling that occurs in response to exposure to a moderately elevated temperature (42°C). In addition to showing an increase in the ratio of saturated corynomycolates to unsaturated corynomycolates, our results strongly suggested that the balance between mycolic acids and phospholipids is modified inside the outer membrane following a heat challenge. Furthermore, we showed that these lipid modifications help the bacteria to protect against heat damage. The NCgl2775 protein and its orthologs thus appear to be a protein family that plays a role in the regulation of the outer membrane lipid composition ofCorynebacterineaeunder stress conditions. We therefore propose to name this protein family the envelope lipids regulation factor (ElrF) family.
The effects of temperature, photoperiod, and vernalization on regrowth and flowering competence inEuphorbia esula(Euphorbiaceae) crown buds
Authors: Foley M. E. , Anderson J. V. , Horvath D. P. 
Published: October 2009

The herbaceous perennial weed Euphorbia esula L. (Euphorbiaceae) reproduces by vegetative and sexual means, characteristics that are key to its persistence and survival. In this study, we examined environmental effects on regrowth and flowering under controlled conditions to further validate field observations and set the stage for the future identification of molecular mechanisms involved in the regulation of these processes. Shoot cuttings were exposed to different combinations of decreasing temperatures, decreasing photoperiods, and vernalization, in growth chambers. Subsequently, shoots were removed and regrowth and flowering from new shoots were monitored in a warm temperature greenhouse under long-day conditions. Vernalization alone has no effect on regrowth and flowering. Plants required decreasing temperature followed by vernalization for rapid regrowth and flowering. Decreasing photoperiod at a constant temperature with or without vernalization had no significant effect on regrowth and flowering. In conjunction with previous field research, the results suggest that a gradually decreasing temperature is required as one of the components for flowering competence and vernalization is determinate for reproductive development under long-day conditions.
Patterns of defence gene expression in the tomato–Verticilliuminteraction
Authors: Robb Jane , Castroverde Christian D.M. , Shittu Hakeem O. , Nazar Ross N. 
Published: October 2009

In a tomato plant infected by Verticillium dahliae , race 1, compatibility or incompatibility appears to be determined in the stem, but little is known about the genes that either regulate or effect critical cellular events. In the present study, microarray and RT-PCR analyses were used to assess changes in tomato mRNA populations during both interactions. Initially, a commercially available DNA chip was used to screen gene expression at a single critical time point after inoculation of resistant and susceptible plants. From the results, the most-affected genes were selected to develop a tomato Verticillium response (TVR) DNA chip for detailed analyses of gene expression for 15 d after inoculation. Taken together, over half of the genes on the TVR array exhibited one of three distinct patterns of change, one reflecting a resistant phenotype and two being consistent with a susceptible phenotype. Of particular interest was a cluster of strongly expressed genes belonging to groups 2 and 3 that appeared to be co-ordinately down regulated in infected resistant plants relative to susceptible. Many of these genes encode pathogenesis related (PR) proteins. The data demonstrate that even though complex, the biological system can be standardized sufficiently to allow the reproducible analysis of gene expression in a whole plant system and provide patterns of transcriptional variation that can be used to assess the significance of specific genes in pathogenesis and resistance.
Spatial genetic structure of lowbush blueberry,Vaccinium angustifolium, in four fields in Maine
Authors: Bell Daniel J. , Rowland Lisa J. , Zhang Dapeng , Drummond Frank A. 
Published: October 2009

Expressed sequence tag – polymerase chain reaction (EST-PCR) molecular markers were used to infer spatial genetic structure of four lowbush blueberry ( Vaccinium angustifolium Ait.) fields in Maine. Genetic structure was quantified at three spatial scales: (1) within apparent clones (intrapatch), (2) among clones within a field, and (3) among fields separated by as much as 65 km. Of five “clones” or putative individuals examined in the intrapatch study, two showed complete genetic homogeneity within the patch, while three showed some band differences at their edges compared with their interiors. These differences at the edges, however, matched adjacent clones (so-called “intruders”), from which it was concluded that lowbush blueberry exhibits a fairly tight, phalanx clonal architecture with no evidence of invasive seedling establishment within clones. No significant correlation between genetic and physical distance was found among clones within fields via several statistical approaches. Significant among-field genetic differentiation was found via AMOVA (ΦPT= 8.4%; p ≤ 0.01) based upon transect samples across four fields ranging from 12.5 to 65 km apart. Principal component analysis and spatial autocorrelation (SA) corroborated these findings. Significant positive SA was found at the within-field distance class of <350 m, but SA decreased to an insignificant value by the first interfield distance of 12.5 km. A special form of SA analysis was employed to detect “hotspots” of genetic similarity between pairs of adjacent clones in two fields. Results indicated that 5 of 23 pairs of clones (21.7%) were genetically similar to each other, while the majority of pairs (18 of 23; 78.3%) showed random, decreasing patterns of genetic similarity. Results are discussed in terms of clonal dynamics including architecture, seedling recruitment, and inferred pollen or seed dispersal distances.
Low soil temperature reduces the positive effects of high nutrient supply on the growth and biomass of white birch seedlings in ambient and elevated carbon dioxide concentrations
Authors: Ambebe Titus Fondo , Dang Qing-Lai , Marfo Jacob 
Published: October 2009

To investigate the interactive effects of soil temperature (Tsoil) and nutrient supply on the responses of growth and biomass of white birch ( Betula papyrifera Marsh.) to atmospheric carbon dioxide concentration ([CO2]), seedlings were grown under two [CO2] (360 and 720 µmol·mol–1), three Tsoil (5, 15, and 25 °C initially, increased to 7, 17, and 27 °C one month later), and three nutrient regimes (Low: N–P–K = 4:1.8:3.3 mg·L–1; Intermediate: N–P–K = 80:35:66 mg·L–1; and High: N–P–K = 160:70:132 mg·L–1) for 4 months. Low Tsoil reduced leaf and total biomass at high nutrient supply and root biomass at intermediate and high nutrient supply. There were significant three-factor interactive effects on root collar diameter (RCD), stem biomass, and leaf mass ratio. Low Tsoil reduced RCD at high nutrient supply and stem biomass at intermediate and high nutrient supply in elevated [CO2] while intermediate and high Tsoil enhanced them. Values of leaf mass ratio were lowest at low Tsoil and low nutrient supply in elevated [CO2]. The effect of Tsoil was generally insignificant at low nutrient supply, but the responses of growth and biomass remained significantly higher under high than low nutrient supply at all Tsoil.
Tomato plant architecture as affected by salinity: Descriptive analysis and integration in a 3-D simulation model
Authors: Najla Safaa , Vercambre Gilles , Pagès Loïc , Grasselly Dominique , Gautier Hélène , Génard Michel 
Published: October 2009

Limited information is available on the effect of salinity on plant architecture; not only on final plant height, number of leaves, and leaf area, but also on plant growth and development from the leaflet to the whole plant scale. Tomato plants ( Solanum lycopersicum L. ‘Marmara’) were grown in greenhouses at four salinity levels (4, 7, 10, and 13 mS·cm–1). Plant development (leaf and inflorescence initiation), leaf growth rate, and final leaf dimensions were measured along the stem according to leaf rank and treatment. A decrease in leaflet growth and in the number of leaflets per leaf was associated with a lower growth rate and longer growth period in salinity stressed plants. Stem internode length was also reduced by salinity. At the plant scale, plant height and leaf area decreased with an increase in salinity. These parameters were the main inputs of a 3-D model of plant architecture, which enabled a complete description of plant architecture from the elementary to the canopy scale. This model of plant architecture was evaluated by comparing hemi-spherical photos of the plant taken with a camera with those generated by the model. The model was used to estimate light interception which should be useful to calculate photosynthesis at the plant scale.
Post-Keynesian Theories of the Firm under Financialization
Authors: Dallery Thomas 
Published: October 2009

Financialization is studied here from a microeconomic viewpoint. Following Stockhammer (2004a), the theory of the firm has been amended by introducing agency problems and class analysis between shareholders and managers. Further to that, I propose two alternative configurations for incorporation into the theory: the first views financialization as a constraint for the managerial firm, while the second discusses shareholders’ interests and integrates them as an end in itself for the finance-dominated firm. My conclusions focus on finance-oppressed accumulation, financial fragility, and potential macroeconomic instability. JEL classification: D21, E12, G30
Sox7-sustained expression alters the balance between proliferation and differentiation of hematopoietic progenitors at the onset of blood specification
Authors: Gandillet Arnaud , Serrano Alicia G. , Pearson Stella , Lie-A-Ling Michael , Lacaud Georges , Kouskoff Valerie 
Published: October 2009

AbstractThe molecular mechanisms that regulate the balance between proliferation and differentiation of precursors at the onset of hematopoiesis specification are poorly understood. By using a global gene expression profiling approach during the course of embryonic stem cell differentiation, we identified Sox7 as a potential candidate gene involved in the regulation of blood lineage formation from the mesoderm germ layer. In the present study, we show that Sox7 is transiently expressed in mesodermal precursors as they undergo specification to the hematopoietic program. Sox7 knockdown in vitro significantly decreases the formation of both primitive erythroid and definitive hematopoietic progenitors as well as endothelial progenitors. In contrast, Sox7-sustained expression in the earliest committed hematopoietic precursors promotes the maintenance of their multipotent and self-renewing status. Removal of this differentiation block driven by Sox7-enforced expression leads to the efficient differentiation of hematopoietic progenitors to all erythroid and myeloid lineages. This study identifies Sox7 as a novel and important player in the molecular regulation of the first committed blood precursors. Furthermore, our data demonstrate that the mere sustained expression of Sox7 is sufficient to completely alter the balance between proliferation and differentiation at the onset of hematopoiesis.
Difference in the regulation of IL-8 expression induced by uropathogenic E. coli between two kinds of urinary tract epithelial cells
Authors: Tsai Kun-Wei , Lai Hong-Thih , Tsai Tzung-Chieh , Wu Yi-Chien , Yang Ya-Ting , Chen Kwei-Yi , Chen Chun-Ming , Li Yi-Shuan J , Chen Cheng-Nan 
Published: October 2009

AbstractBacterial adherence to epithelial cells is a key virulence trait of pathogenic bacteria. The type 1 fimbriae and the P-fimbriae of uropathogenicEscherichia coli(UPEC) have both been described to be important for the establishment of urinary tract infections (UTI). To explore the interactions between the host and bacterium responsible for the different environments of UPEC invasion, we examined the effect of pH and osmolarity on UPEC strain J96 fimbrial expression, and subsequent J96-induced interleukin-8 (IL-8) expression in different uroepithelial cells. The J96 strain grown in high pH with low osmolarity condition was favorable for the expression of type 1 fimbriae; whereas J96 grown in low pH with high osmolarity condition was beneficial for P fimbriae expression. Type 1 fimbriated J96 specifically invaded bladder 5637 epithelial cells and induced IL-8 expression. On the contrary, P fimbriated J96 invaded renal 786-O epithelial cells and induced IL-8 expression effectively. Type 1 fimbriated J96-induced IL-8 induction involved the p38, as well as ERK, JNK pathways, which leads to AP-1-mediated gene expression. P fimbriated J96-induced augmentation of IL-8 expression mainly involved p38-mediated AP-1 and NF-κB transcriptional activation. These results indicate that different expression of fimbriae in J96 trigger differential IL-8 gene regulation pathways in different uroepithelial cells.
An editor for pathway drawing and data visualization in the Biopathways Workbench
Authors: Byrnes Robert W , Cotter Dawn , Maer Andreia , Li Joshua , Nadeau David , Subramaniam Shankar 
Published: October 2009

Abstract

Background
Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface.

Results
The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system.

Conclusion
Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.
Early over expression of messenger RNA for multiple genes, including insulin, in the Pancreatic Lymph Nodes of NOD mice is associated with Islet Autoimmunity
Authors: Regnault Béatrice , Osorio y Fortea José , Miao Dongmei , Eisenbarth George , Melanitou Evie 
Published: October 2009

AbstractBackgroundAutoimmune diabetes (T1D) onset is preceded by a long inflammatory process directed against the insulin-secreting β cells of the pancreas. Deciphering the early autoimmune mechanisms represents a challenge due to the absence of clinical signs at early disease stages. The aim of this study was to identify genes implicated in the early steps of the autoimmune process, prior to inflammation, in T1D. We have previously established that insulin autoantibodies (E-IAA) predict early diabetes onset delineating an early phenotypic check point (window 1) in disease pathogenesis. We used this sub-phenotype and applied differential gene expression analysis in the pancreatic lymph nodes (PLN) of 5 weeks old Non Obese Diabetic (NOD) mice differing solely upon the presence or absence of E-IAA. Analysis of gene expression profiles has the potential to provide a global understanding of the disease and to generate novel hypothesis concerning the initiation of the autoimmune process.MethodsAnimals have been screened weekly for the presence of E-IAA between 3 and 5 weeks of age. E-IAA positive or negative NOD mice at least twice were selected and RNAs isolated from the PLN were used for microarray analysis. Comparison of transcriptional profiles between positive and negative animals and functional annotations of the resulting differentially expressed genes, using software together with manual literature data mining, have been performed.ResultsThe expression of 165 genes was modulated between E-IAA positive and negative PLN. In particular, genes coding for insulin and for proteins known to be implicated in tissue remodelling and Th1 immunity have been found to be highly differentially expressed. Forty one genes showed over 5 fold differences between the two sets of samples and 30 code for extracellular proteins. This class of proteins represents potential diagnostic markers and drug targets for T1D.ConclusionOur data strongly suggest that the immune related mechanisms taking place at this early age in the PLN, correlate with homeostatic changes influencing tissue integrity of the adjacent pancreatic tissue. Functional analysis of the identified genes suggested that similar mechanisms might be operating during pre-inflammatory processes deployed in tissues i) hosting parasitic microorganisms and ii) experiencing unrestricted invasion by tumour cells.