bluuebunny/crossref_metadata_2025 huggingface dataset:
Vendor development and control:its linkage with demand chain
Authors: Seetharaman A. , Khatibi A. Ali , Swee Ting Wu
Published: June 2004

Explains the linkage of vendor development and control as an integral factor of value on demand chain logistics. Presents a comparison of the traditional purchasing function with vendor development in. Provides the missing link of value chain by demand chain. Describes the supplier integration approach as a competitive corporate strategy in a conceptual synthesis by linking demand chain with order management, marketing, sales, channel management, pricing, service, etc. Analyses the vendor development strategy from three key dimensions. Further discusses the advantages of vendor development in the short run, bottom line performance increase, and long run revenue enhancing the value of an organisation. Also discusses the impact on demand chain from the costing point of view with elaboration on cost and pricing activities involving total cost of ownership, understanding supplier costs and target costing with target pricing commensurate with expectations of customers. Concludes with an emphasis on the importance of providing e‐learning and upgrading the skills of staff in order to expedite the adoption of vendor integration strategy in its demand chain logistics management.
The advent of manufacturing technology and its implications for the development of the value chain
Authors: Agrawal Rakesh K. , Hurriyet Hilal
Published: June 2004

This world has moved into the “Organic Era” requiring the development of “organic organisations” that would have characteristics similar to those in the “natural systems”. The factory of the future may be a virtual organisation or a physical entity with bricks and mortar, but it would be holistic and value‐driven with lean outfit, flexibility and agility as its essential characteristics. The process of value chain development would incorporate an organic approach for the transformation of the current organisations or the development of new organisations. The future organisations would have a focus on the development of self‐based characteristics for self‐actualisation, a necessary condition for their survival in the environment of declining resources, increasing customer expectations, extended organisation forms, and boundary less markets. Appropriate manufacturing technology would be used to support the organic process.
A business model for the new economy
Authors: Walters David
Published: June 2004

The new economy brought with it a new approach to designing business models. Not too many years ago the familiar organisation structure was dominated by a traditional view of managers that was based on asset ownership and vertical organisation structures. The prevalent view was that ownership enhanced control and profit margins. More recently flexibility, co‐operation and collaboration have become important features for success. The success of organisations such as Dell and the move by some of the largest corporations in the world towards a model within which assets are managed rather than owned has led to significant changes not only in structure, but also in attitudes and managerial behaviour. As a result the “new business model” has five common attributes, the firm should: be cash flow driven; focus on return on investment; function with distributed (leveraged) assets or low capital intensity; do so with a single minded view on core assets and distinctive capabilities; and develop competitive advantage by relevant positioning within its industry value chain. Reviews these developments, using the Australian wine industry as an example of the new business model.
The two‐fluid modelling of gas‐particle transport phenomenon in confined systems considering inter particle collision effects
Authors: Mitter A. , Malhotra J.P. , Jadeja H.T.
Published: June 2004

A modelling approach of gas solid flow, considering different physical phenomenon such as fluid turbulence, particle turbulence and interparticle collision effects are presented. The approach is based on the two‐fluid model formulation where both phases are treated as continuum. This implies that the gas phase as well as the particle phase are weighted by their separate volumetric fractions. According to the experimental results and numerical simulations, the inter‐particle collision possesses a significant influence of turbulence level on particle transport properties in gas solid turbulent flow even for dispersed phase volume fraction (α<0.01). Comparisons in predictions have been depicted with inclusion of interparticle collision effect in the equation of particle turbulent kinetic energy and with exclusion of this effect. Experimental research has been conducted in a thermal power plant depicting higher erosion resistance of noncircular square sectioned coal pipe bends in comparison with those with circular cross section, the salient features of the experimental work are presented in this paper. Experiments have been conducted to determine, pressure drop in straight and curved portions of conduits conveying air coal mixtures in a thermal power plant. Validation of this experimental data with numerical predictions have been presented.
Effectiveness of several turbulence models in natural convection
Authors: Walsh P.C. , Leong W.H.
Published: June 2004

Heat transfer due to natural convection inside a closed cavity must be modeled to include the effects of turbulence if the Rayleigh number is sufficiently large. This study assesses the performance of several commonly used numerical turbulence models such as k‐ε, Renormalized Group k‐ε and Reynolds stress model, in predicting heat transfer due to natural convection inside an air‐filled cubic cavity. The cavity is maintained at 307 K on one side and 300 K on the opposite side with a linear temperature variation between these values on the remaining walls. Two cases are considered, one in which the heated side is vertical, and the other in which it is inclined at 45° from the horizontal. Rayleigh numbers of 107, 108, 109 and 1010 are considered. Results of the three turbulence models are compared to experimentally determined values or values from correlations. It was found that the standard k‐ε model was the most effective model in terms of accuracy and computational economy.
Molecular dynamics simulation of micro‐Poiseuille flow for liquid argon in nanoscale
Authors: Xu J.L. , Zhou Z.Q. , Xu X.D.
Published: June 2004

The molecular dynamics simulation of micro‐Poiseuille flow for liquid argon in nanoscale was performed in non‐dimensional unit system with the control parameters of channel size, coupling parameters between solid wall and liquid particles, and the gravity force. The molecular forces are considered not only among the liquid molecules, but also between the solid wall and liquid molecules. The simulation shows that a larger gravity force produces a larger shear rate and a higher velocity distribution. In terms of the gravity force, there are three domain regions each with distinct flow behaviors: free molecule oscillation, coupling and gravity force domain regions. Stronger fluid/wall interactions can sustain a larger coupling region, in which the flow is controlled by the balance of the intermolecular force and the gravity force. Strong surface interaction leads to small slip lengths and the slip lengths are increased slightly with increasing the shear rate. Weak surface interaction results in higher slip lengths and the slip lengths are dramatically decreased with increasing the shear rate. The viscosities are nearly kept constant (Newton flow behavior) if the non‐dimensional shear rate is below 2.0. At higher non‐dimensional shear rate larger than 2.0, the viscosities have a sharp increase with increasing the shear rate, and the non‐Newton flow appears.
Medical quality management: the case for action learning as a quality initiative
Authors: Jackson Vance M.
Published: June 2004

This paper explores how medical quality management has developed in the USA since the 1900s reviewing and summarizing the history of the movement through an extensive literature review. With a particular emphasis on action learning as a theoretical construct, the paper then assesses the extent to which action learning can be applied to the quality process. Using two case studies from the literature, the paper suggests that the action learning process, can in fact overcome some of the problems related to the implementation of quality initiatives in medical settings, and in particular those related to the fear expressed often by physicians that quality procedures emphasize cost cutting at the expense of patient care.
Commodity Price Volatility, Vulnerability and Development
Authors: Combes Jean‐Louis , Guillaumont Patrick
Published: June 2004

This article examines the meaning and consequences of the developing countries’ vulnerability to the volatility of commodity prices. It first considers how to define and measure a country’s shocks and exposure arising from commodity price volatility in order to identify structural as distinct from policy vulnerability. The main channels through which price vulnerability influences economic growth are then presented. Finally, the policy implications for development aid, its allocation and design, are outlined. It is found that, while structural vulnerability is bad for growth, a policy of openness contributes to resilience. With the right rules, aid could play an important growth‐enhancing and poverty‐reducing role if allocated at least partly on the basis of vulnerability.
The New European Trade Preferences: Does ‘Everything But Arms’ (EBA) Help the Poor?
Authors: Page Sheila , Hewitt Adrian
Published: June 2004

The EU’s offer of tariff‐ and quota‐free access for all exports from the Least Developed Countries (for Everything but Arms) has been welcomed as part of the WTO‐led initiative to assist these countries. But it is not without problems. As the Least Developed compete more with other developing countries than with the EU, trade is likely to be diverted from other, sometimes poorer, countries. (‘Least Developed’ is an official classification, not a neutral measure of poverty.) EBA contradicts and impedes the EU’s policies of reciprocity and promotion of regions: it not only creates an alternative trade regime, but seems unilaterally to break existing agreements. The article concludes that the policy was adopted for essentially political, not developmental, motives.
Possible role of Hes5 for the rostrocaudal polarity formation of the tectum
Authors: Kimura Jun , Katahira Tatsuya , Araki Isato , Nakamura Harukazu
Published: June 2004

The alar plate of the mesencephalon differentiates into the optic tectum. Retinal fibers project to the tectum topographically in a retinotopic manner. Engrailed (En) is responsible for the tectum polarity formation and regionalization. Former study indicated the presence of the molecule whose expression is repressed by En and that represses the isthmus‐related gene expression. To isolate such molecules, we constructed a subtracted library between cDNA population of the normal rostral mesencephalon and of the rostral mesencephalon that misexpresses En2. From the library, we isolated cHes5, a chicken homolog of Drosophila hairy/Enhancer of split. cHes5 begins to be expressed in the rostral part of the E2 mesencephalon, and spreads to caudal mesencephalon by E3. To our expectation, cHes5 expression was repressed by En2. Furthermore, misexpression of cHes5 in the mesencephalon inhibited expression of ephrinA2, a marker of caudal mesencephalon. An active repressor form of Hes5, which is a chimeric molecule of Hes5 and repressor domain of En2, showed a similar but more severe phenotype. The results indicate that Hes5 is regulated by En and is responsible for rostral identity of mesencephalon by repressing ephrinA2.
The role of Pax7 in determining the cytoarchitecture of the superior colliculus
Authors: Thompson Jennifer , Lovicu Frank , Ziman Mel
Published: June 2004

Pax genes are a family of transcriptional regulators vital for embryonic development. One member of the family, Pax7, functions early in neural development to establish dorsal polarity of the neural tube, and continuous refinement of its expression affords regional identity to brain nuclei, in particular the superior colliculus. Pax7 expression within the superior colliculus is eventually restricted to the stratum griseum et fibrosum superficiale (SGFS), the retinorecipient layer to which the optic nerve projects. The key role of Pax7 in specification of the superior colliculus has been highlighted by misexpression studies which result in ectopic formation of superior collicular tissue with characteristic laminae innervated by retinal ganglion cell axons. Here we review the role of Pax7 in formation of the superior colliculus and discuss the possibility that Pax7 may also assist in refinement of correct topographic mapping.
Retinoic acid decreases fetal lung mesenchymal cell proliferation in vivo and in vitro
Authors: Dalvin Sussie , Komatsuzaki Katsumi , Anselmo Mark A. , Kling David E. , Schnitzer Jay J. , Kinane T. Bernard
Published: June 2004

Retinoic acid (RA) is an important coordinator of mammalian organogenesis. RA is implicated in critical lung developmental events. Cell proliferation is precisely regulated during development. We investigated the effect of RA on proliferating mesenchymal cells in both whole organ lung cultures and cell cultures. The potential pathways required for the response were studied in cultures of lung mesenchymal cells from embryonic day (e) 12. We observed an RA‐dependent reduction in proliferation of mesenchymal cells in both whole organ and in cell culture. In mesenchymal cell cultures, RA decreased proliferation in lung mesenchymal cells by 72%. This was associated with a decrease of erk‐1/2 activity by 68%. Mesenchymal cell proliferation is erk‐1/2 dependent. Erk‐1/2 can be activated by G‐protein coupled receptors (GPCR) or tyrosine kinase receptors (RTK). RA treatment altered both the RTK and the GPCR pathways in primary lung mesenchymal cells. The Epidermal Growth Factor (EGF) dependent erk‐1/2 activation was increased by 35% whereas the Gi‐protein cascade was inhibited by 44% in cells treated with RA. Our results suggest that RA decreases proliferation of lung mesenchyme via a Gi‐protein and the erk‐1/2 signaling cascade.
Expression and function of class B scavenger receptor type I on both apical and basolateral sides of the plasma membrane of polarized testicular Sertoli cells of the rat
Authors: Nakagawa Akihisa , Nagaosa Kaz , Hirose Tomoe , Tsuda Kayoko , Hasegawa Kunio , Shiratsuchi Akiko , Nakanishi Yoshinobu
Published: June 2004

Class B scavenger receptor type I (SR‐BI), a multiligand membrane protein, exists in various organs and cell types. In the testis, SR‐BI is expressed in two somatic cell types: Leydig cells and Sertoli cells. Unlike interstitially localized Leydig cells, Sertoli cells present within the seminiferous tubules keep contact with spermatogenic cells and form the tight junction to divide the seminiferous epithelium into the basal and adluminal compartments. In this study, the expression and function of SR‐BI in rat Sertoli cells were examined with respect to dependency on the spermatogenic cycle, the plasma membrane polarity, and the pituitary hormone follicle‐stimulating hormone (FSH). When the expression of SR‐BI was histochemically examined with testis sections, both protein and mRNA were already present in Sertoli cells during the first‐round spermatogenesis and continued to be detectable thereafter. The level of SR‐BI mRNA expression in Sertoli cells was lower at spermatogenic stages I–VI than at other stages. SR‐BI was present and functional (in mediating cellular incorporation of lipids of high density lipoprotein) at both the apical and basolateral surfaces of polarized Sertoli cells. Finally, SR‐BI expression at both the protein and mRNA levels was stimulated by FSH in cultured Sertoli cells. These results indicate that SR‐BI functions on both the apical and basolateral plasma membranes of Sertoli cells, and that SR‐BI expression in Sertoli cells changes during the spermatogenic cycle and is stimulated, at least in cultures, by FSH.
Four Simple Tests of Campaign Contributions and Trade Policy Preferences
Authors: Beaulieu Eugene , Magee Christopher
Published: June 2004

This paper uses campaign contribution data to examine trade policy preferences among political action committees. With perfect factor mobility, as the Heckscher–Ohlin (HO) model assumes, interest group trade positions should depend on their factor of production but not on their industry. We show, consistent with the 2 × 2 HO model, that capital groups consistently back representatives supporting trade liberalization while labor groups favor protectionists. Unlike previous work, we also measure the variation in trade policy preferences within capital and labor groups. We find evidence that the industry net export position significantly affects labor unions' trade policy preferences. Industry characteristics have no impact on capital group lobbying. The former result suggests that empirical analyses of labor PAC contributions that exclude industry characteristics may be misspecified.
Promotion of B Cell Immune Responses via an Alum-Induced Myeloid Cell Population
Authors: Jordan Michael B. , Mills David M. , Kappler John , Marrack Philippa , Cambier John C.
Published: June 2004

Exposure of naïve B cells to the cytokine interleukin-4 (IL-4) and/or antigen leads to a state of “priming,” in which subsequent aggregation of major histocompatibility complex class II molecules induces the mobilization of calcium ions and cell proliferation. However, it is not clear how critical this priming is for immune responses or how it is normally induced in vivo. Injection of mice with the commonly used adjuvant alum led to priming of splenic B cells and to the accumulation in the spleen of a previously unknown population of IL-4–producing, Gr1
+
cells. These cells and IL-4 were both required for in vivo priming and expansion of antigen-specific B cells, as well as for optimal production of antibody. These studies reveal a key role for a previously unknown accessory myeloid cell population in the generation of humoral immune responses.
Long-Term Memory Requires PolyADP-ribosylation
Authors: Cohen-Armon Malka , Visochek Leonid , Katzoff Ayelet , Levitan David , Susswein Abraham J. , Klein Rodika , Valbrun Mireille , Schwartz James H.
Published: June 2004

PolyADP-ribose-polymerase 1 is activated in neurons that mediate several forms of long-term memory in
Aplysia
. Because polyADP-ribosylation of nuclear proteins is a response to DNA damage in virtually all eukaryotic cells, it is surprising that activation of the polymerase occurs during learning and is required for long-term memory. We suggest that fast and transient decondensation of chromatin structure by polyADP-ribosylation enables the transcription needed to form long-term memory without strand breaks in DNA.
Modeling the Nucleus and Jets of Comet 81P/Wild 2 Based on the Stardust Encounter Data
Authors: Sekanina Zdenek , Brownlee Donald E. , Economou Thanasis E. , Tuzzolino Anthony J. , Green Simon F.
Published: June 2004

We interpret the nucleus properties and jet activity from the Stardust spacecraft imaging and the onboard dust monitoring system data. Triangulation of 20 jets shows that 2 emanate from the nucleus dark side and 16 emanate from sources that are on slopes where the Sun's elevation is greater than predicted from the fitted triaxial ellipsoid. Seven sources, including five in the Mayo depression, coincide with relatively bright surface spots. Fitting the imaged jets, the spikelike temporal distribution of dust impacts indicates that the spacecraft crossed thin, densely populated sheets of particulate ejecta extending from small sources on the rotating nucleus, consistent with an emission cone model.
Guidebook for a Grand Tour
Authors: Burke Kevin
Published: June 2004

The Earth
An Intimate History. by Richard Fortey. HarperCollins, London, 2004. 511 pp. £25. ISBN 0-00-257011-4. Forthcoming from Knopf, ISBN 0-375-40626-3.

The author uses visits to particular places (including Newfoundland, the San Andreas fault, Hawaii, Oman, and the Alps) as a framework for discussing plate tectonics and its effects on Earth's history.
Characterization of
Mycobacterium smegmatis
Expressing the
Mycobacterium tuberculosis
Fatty Acid Synthase I (
fas1
) Gene
Authors: Zimhony Oren , Vilchèze Catherine , Jacobs William R.
Published: June 2004

Unlike most other bacteria, mycobacteria make fatty acids with the multidomain enzyme eukaryote-like fatty acid synthase I (FASI). Previous studies have demonstrated that the tuberculosis drug pyrazinamide and 5-chloro-pyrazinamide target FASI activity. Biochemical studies have revealed that in addition to C
16:0
,
Mycobacterium tuberculosis
FASI synthesizes C
26:0
fatty acid, while the
Mycobacterium smegmatis
enzyme makes C
24:0
fatty acid. In order to express
M. tuberculosis
FASI in a rapidly growing
Mycobacterium
and to characterize the
M. tuberculosis
FASI in vivo, we constructed an
M. smegmatis
Δ
fas1
strain which contained the
M. tuberculosis fas1
homologue. The
M. smegmatis
Δ
fas1
(
attB
::
M. tuberculosis fas1
) strain grew more slowly than the parental
M. smegmatis
strain and was more susceptible to 5-chloro-pyrazinamide. Surprisingly, while the
M. smegmatis
Δ
fas1
(
attB
::
M. tuberculosis fas1
) strain produced C
26:0
, it predominantly produced C
24:0
. These results suggest that the fatty acid elongation that produces C
24:0
or C
26:0
in vivo is due to a complex interaction among FASI, FabH, and FASII and possibly other systems and is not solely due to FASI elongation, as previously suggested by in vitro studies.
A Gene from the Mesophilic BacteriumDehalococcoides ethenogenesEncodes a Novel Mannosylglycerate Synthase
Authors: Empadinhas Nuno , Albuquerque Luciana , Costa Joana , Zinder Stephen H. , Santos Manuel A. S. , Santos Helena , da Costa Milton S.
Published: June 2004

Mannosylglycerate (MG) is a common compatible solute found in thermophilic and hyperthermophilic prokaryotes. In this study we characterized a mesophilic and bifunctional mannosylglycerate synthase (MGSD) encoded in the genome of the bacteriumDehalococcoides ethenogenes. mgsDencodes two domains with extensive homology to mannosyl-3-phosphoglycerate synthase (MPGS, EC 2.4.1.217) and to mannosyl-3-phosphoglycerate phosphatase (MPGP, EC 3.1.3.70), which catalyze the consecutive synthesis and dephosphorylation of mannosyl-3-phosphoglycerate to yield MG inPyrococcus horikoshii,Thermus thermophilus, andRhodothermus marinus. The bifunctional MGSD was overproduced inEscherichia coli, and we confirmed the combined MPGS and MPGP activities of the recombinant enzyme. The optimum activity of the enzyme was at 50°C. To examine the properties of each catalytic domain of MGSD, we expressed them separately inE. coli. The monofunctional MPGS was unstable, while the MPGP was stable and was characterized.Dehalococcoides ethenogenescannot be grown sufficiently to identify intracellular compatible solutes, andE. coliharboring MGSD did not accumulate MG. However,Saccharomyces cerevisiaeexpressingmgsDaccumulated MG, confirming that this gene product can synthesize this compatible solute and arguing for a role in osmotic adjustment in the natural host. We did not detect MGSD activity in cell extracts ofS. cerevisiae. Here we describe the first gene and enzyme for the synthesis of MG from a mesophilic microorganism and discuss the possible evolution of this bifunctional MGSD by lateral gene transfer from thermophilic and hyperthermophilic organisms.
Identification of σB-Dependent Genes inBacillus cereusby Proteome and In Vitro Transcription Analysis
Authors: van Schaik Willem , Zwietering Marcel H. , de Vos Willem M. , Abee Tjakko
Published: June 2004

The alternative sigma factor σBof the food pathogenBacillus cereusis activated upon stress exposure and plays a role in the adaptive response of vegetative cells. This study describes the identification of σB-dependent genes inB. cereus. Two-dimensional gel electrophoresis was performed with protein extracts from a σB-overproducingB. cereusstrain. Nine protein spots, which were absent from the negative control, were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry or N-terminal sequencing. The σB-dependent expression of the corresponding genes was confirmed by Northern blot analysis with RNA isolated fromB. cereusATCC 14579 and itssigBnull mutant. Northern blot analysis also revealed that six other genes were part of σB-dependent operons. The proteins that are predicted to be encoded by the σB-dependent genes include an intracellular protease, a Mg2+transporter, and a thiamine biosynthesis protein (ThiG). Highly conserved promoter sites were found to precede all σB-dependent genes, with the exception ofthiG. By searching theB. cereusgenome for this conserved promoter sequence, five more candidate σB-dependent genes were identified. Northern blot analysis and in vitro transcription experiments with a reconstitutedB. cereusσB-RNA polymerase holoenzyme confirmed the σBdependency of two of these genes and strongly suggested that two other genes, encoding an oligopeptide-binding OppA-like protein and subunit II of the cytochromedubiquinol oxidase, are also σBdependent. In conclusion, σBofB. cereusnot only regulates genes directly involved in the stress response but may also control specific metabolic rearrangements.
The YopD Translocator of
Yersinia pseudotuberculosis
Is a Multifunctional Protein Comprised of Discrete Domains
Authors: Olsson Jan , Edqvist Petra J. , Bröms Jeanette E. , Forsberg Åke , Wolf-Watz Hans , Francis Matthew S.
Published: June 2004

To establish an infection,
Yersinia pseudotuberculosis
utilizes a plasmid-encoded type III translocon to microinject several anti-host Yop effectors into the cytosol of target eukaryotic cells. YopD has been implicated in several key steps during Yop effector translocation, including maintenance of
yop
regulatory control and pore formation in the target cell membrane through which effectors traverse. These functions are mediated, in part, by an interaction with the cognate chaperone, LcrH. To gain insight into the complex molecular mechanisms of YopD function, we performed a systematic mutagenesis study to search for discrete functional domains. We highlighted amino acids beyond the first three N-terminal residues that are dispensable for YopD secretion and confirmed that an interaction between YopD and LcrH is essential for maintenance of
yop
regulatory control. In addition, discrete domains within YopD that are essential for both pore formation and translocation of Yop effectors were identified. Significantly, other domains were found to be important for effector microinjection but not for pore formation. Therefore, YopD is clearly essential for several discrete steps during efficient Yop effector translocation. Recognition of this modular YopD domain structure provides important insights into the function of YopD.
The PmrA-Regulated
pmrC
Gene Mediates Phosphoethanolamine Modification of Lipid A and Polymyxin Resistance in
Salmonella enterica
Authors: Lee Hyunwoo , Hsu Fong-Fu , Turk John , Groisman Eduardo A.
Published: June 2004

The PmrA/PmrB regulatory system of
Salmonella enterica
controls the modification of lipid A with aminoarabinose and phosphoethanolamine. The aminoarabinose modification is required for resistance to the antibiotic polymyxin B, as mutations of the PmrA-activated
pbg
operon or
ugd
gene result in strains that lack aminoarabinose in their lipid A molecules and are more susceptible to polymyxin B. Additional PmrA-regulated genes appear to participate in polymyxin B resistance, as
pbgP
and
ugd
mutants are not as sensitive to polymyxin B as a
pmrA
mutant. Moreover, the role that the phosphoethanolamine modification of lipid A plays in the resistance to polymyxin B has remained unknown. Here we address both of these questions by establishing that the PmrA-activated
pmrC
gene encodes an inner membrane protein that is required for the incorporation of phosphoethanolamine into lipid A and for polymyxin B resistance. The PmrC protein consists of an N-terminal region with five transmembrane domains followed by a large periplasmic region harboring the putative enzymatic domain. A
pbgP pmrC
double mutant resembled a
pmrA
mutant both in its lipid A profile and in its susceptibility to polymyxin B, indicating that the PmrA-dependent modification of lipid A with aminoarabinose and phosphoethanolamine is responsible for PmrA-regulated polymyxin B resistance.
HutZ Is Required for Efficient Heme Utilization inVibrio cholerae
Authors: Wyckoff Elizabeth E. , Schmitt Michael , Wilks Angela , Payne Shelley M.
Published: June 2004

Vibrio cholerae, the causative agent of cholera, requires iron for growth. One mechanism by which it acquires iron is the uptake of heme, and several heme utilization genes have been identified inV. cholerae. These include three distinct outer membrane receptors, two TonB systems, and an apparent ABC transporter to transfer heme across the inner membrane. However, little is known about the fate of the heme after it enters the cell. In this report we show that a novel heme utilization protein, HutZ, is required for optimal heme utilization.hutZ(open reading frame [ORF] VCA0907) is encoded with two other genes,hutW(ORF VCA0909) andhutX(ORF VCA0908), in an operon divergently transcribed from thetonB1operon. AhutZmutant grew poorly when heme was provided as the sole source of iron, and the poor growth was likely due to the failure to use heme efficiently as a source of iron, rather than to heme toxicity. Heme oxygenase mutants of bothCorynebacterium diphtheriaeandC. ulceransfail to use heme as an iron source. When thehutWXZgenes were expressed in the heme oxygenase mutants, growth on heme was restored, andhutZwas required for this effect. Biochemical characterization indicated that HutZ binds heme with high efficiency; however, no heme oxygenase activity was detected for this protein. HutZ may act as a heme storage protein, and it may also function as a shuttle protein that increases the efficiency of heme trafficking from the membrane to heme-containing proteins.
Sinorhizobium meliloti
Sulfotransferase That Modifies Lipopolysaccharide
Authors: Cronan Glen E. , Keating David H.
Published: June 2004

Sinorhizobium meliloti
is a gram-negative soil bacterium found either in free-living form or as a nitrogen-fixing endosymbiont of a plant structure called the nodule. Symbiosis between
S. meliloti
and its plant host alfalfa is dependent on bacterial transcription of
nod
genes, which encode the enzymes responsible for synthesis of Nod factor.
S. meliloti
Nod factor is a lipochitooligosaccharide that undergoes a sulfate modification essential for its biological activity. Sulfate also modifies the carbohydrate substituents of the bacterial cell surface, including lipopolysaccharide (LPS) and capsular polysaccharide (K-antigen) (R. A. Cedergren, J. Lee, K. L. Ross, and R. I. Hollingsworth, Biochemistry
34:
4467-4477, 1995). We utilized the genomic sequence of
S. meliloti
to identify an open reading frame, SMc04267 (which we now propose to name
lpsS
), which encodes an LPS sulfotransferase activity. We expressed LpsS in
Escherichia coli
and demonstrated that the purified protein functions as an LPS sulfotransferase. Mutants lacking LpsS displayed an 89% reduction in LPS sulfotransferase activity in vitro. However,
lpsS
mutants retain approximately wild-type levels of sulfated LPS when assayed in vivo, indicating the presence of an additional LPS sulfotransferase activity(ies) in
S. meliloti
that can compensate for the loss of LpsS. The
lpsS
mutant did show reduced LPS sulfation, compared to that of the wild type, under conditions that promote
nod
gene expression, and it elicited a greater number of nodules than did the wild type during symbiosis with alfalfa. These results suggest that sulfation of cell surface polysaccharides and Nod factor may compete for a limiting pool of intracellular sulfate and that LpsS is required for optimal LPS sulfation under these conditions.
Dps Protects Cells against Multiple Stresses during Stationary Phase
Authors: Nair Sudha , Finkel Steven E.
Published: June 2004

Dps, the nonspecific DNA-binding protein from starved cells, is the most abundant protein in stationary-phaseEscherichia coli. Dps homologs are found throughout the bacteria and in at least one archaeal species. Dps has been shown to protect cells from oxidative stress during exponential-phase growth. During stationary phase, Dps organizes the chromosome into a highly ordered, stable nucleoprotein complex called the biocrystal. We show here that Dps is required for long-term stationary-phase viability under competitive conditions and thatdpsmutants have altered lag phases compared to wild-type cells. We also show that during stationary phase Dps protects the cell not only from oxidative stress but also from UV and gamma irradiation, iron and copper toxicity, thermal stress, and acid and base shock. The protective roles of Dps are most likely achieved through a combination of functions associated with the protein-DNA binding and chromosome compaction, metal chelation, ferroxidase activity, and regulation of gene expression.
Involvement of
Streptococcus gordonii
Beta-Glucoside Metabolism Systems in Adhesion, Biofilm Formation, and In Vivo Gene Expression
Authors: Kiliç Ali O. , Tao Lin , Zhang Yongshu , Lei Yu , Khammanivong Ali , Herzberg Mark C.
Published: June 2004

Streptococcus gordonii
genes involved in beta-glucoside metabolism are induced in vivo on infected heart valves during experimental endocarditis and in vitro during biofilm formation on saliva-coated hydroxyapatite (sHA). To determine the roles of beta-glucoside metabolism systems in biofilm formation, the loci of these induced genes were analyzed. To confirm the function of genes in each locus, strains were constructed with gene inactivation, deletion, and/or reporter gene fusions. Four novel systems responsible for beta-glucoside metabolism were identified, including three phosphoenolpyruvate-dependent phosphotransferase systems (PTS) and a binding protein-dependent sugar uptake system for metabolizing multiple sugars, including beta-glucosides. Utilization of arbutin and esculin, aryl-beta-glucosides, was defective in some mutants. Esculin and oligochitosaccharides induced genes in one of the three beta-glucoside metabolism PTS and in four other genetic loci. Mutation of genes in any of the four systems affected in vitro adhesion to sHA, biofilm formation on plastic surfaces, and/or growth rate in liquid medium. Therefore, genes associated with beta-glucoside metabolism may regulate
S. gordonii
in vitro adhesion, biofilm formation, growth, and in vivo colonization.
Multilocus Sequence Typing ofStreptococcus pyogenesRepresenting Most KnownemmTypes and Distinctions among Subpopulation Genetic Structures
Authors: McGregor Karen F. , Spratt Brian G. , Kalia Awdhesh , Bennett Alicia , Bilek Nicole , Beall Bernard , Bessen Debra E.
Published: June 2004

A long-term goal is to characterize the full range of genetic diversity withinStreptococcus pyogenesas it exists in the world today. Since theemmlocus is subject to strong diversifying selection,emmtype was used as a guide for identifying a genetically diverse set of strains. This report contains a description of multilocus sequence typing based on seven housekeeping loci for 495 isolates representing 158emmtypes, yielding 238 unique combinations of sequence type andemmtype. A genotypic marker for tissue site preference (emmpattern) revealed that only 17% of theemmtypes displayed the marker representing strong preference for infection at the throat and that 39% ofemmtypes had the marker for skin tropism, whereas 41% ofemmtypes harbored the marker for no obvious tissue site preference. As a group, theemmtypes bearing theemmpattern marker indicative of no obvious tissue site preference were far less likely to have two distinctemmtypes associated with the same sequence type than either of the two subpopulations having markers for strong tissue tropisms (P< 0.002). In addition, all genetic diversification events clearly ascribed to a recombinational mechanism involved strains of only two of theemmpattern-defined subpopulations, those representing skin specialists and generalists. The findings suggest that the population genetic structure differs for the tissue-defined subpopulations ofS. pyogenes. The observed differences may partly reflect differential host immune selection pressures.
P Pilus Assembly Motif Necessary for Activation of the CpxRA Pathway by PapE in
Escherichia coli
Authors: Lee Yvonne M. , DiGiuseppe Patricia A. , Silhavy Thomas J. , Hultgren Scott J.
Published: June 2004

P pilus biogenesis occurs via the highly conserved chaperone-usher pathway, and assembly is monitored by the CpxRA two-component signal transduction pathway. Structural pilus subunits consist of an N-terminal extension followed by an incomplete immunoglobulin-like fold that is missing a C-terminal seventh beta strand. In the pilus fiber, the immunoglobulin-like fold of each pilin is completed by the N-terminal extension of its neighbor. Subunits that do not get incorporated into the pilus fiber are driven “OFF-pathway.” In this study, we found that PapE was the only OFF-pathway nonadhesin P pilus subunit capable of activating Cpx. Manipulation of the PapE structure by removing, relocating within the protein, or swapping its N-terminal extension with that of other subunits altered the protein's self-associative and Cpx-activating properties. The self-association properties of the new subunits were dictated by the specific N-terminal extension provided and were consistent with the order of the subunits in the pilus fiber. However, these aggregation properties did not directly correlate with Cpx induction. Cpx activation instead correlated with the presence or absence of an N-terminal extension in the PapE pilin structure. Removal of the N-terminal extension of PapE was sufficient to abolish Cpx activation. Replacement of an N-terminal extension at either the amino or carboxyl terminus restored Cpx induction. Thus, the data presented in this study argue that PapE has features inherent in its structure or during its folding that act as specific inducers of Cpx signal transduction.
Genomic DNA Microarray Analysis: Identification of New Genes Regulated by Light Color in the CyanobacteriumFremyella diplosiphon
Authors: Stowe-Evans Emily L. , Ford James , Kehoe David M.
Published: June 2004

Many cyanobacteria use complementary chromatic adaptation to efficiently utilize energy from both green and red regions of the light spectrum during photosynthesis. Although previous studies have shown that acclimation to changing light wavelengths involves many physiological responses, research to date has focused primarily on the expression and regulation of genes that encode proteins of the major photosynthetic light-harvesting antennae, the phycobilisomes. We have used two-dimensional gel electrophoresis and genomic DNA microarrays to expand our understanding of the physiology of acclimation to light color in the cyanobacteriumFremyella diplosiphon. We found that the levels of nearly 80 proteins are altered in cells growing in green versus red light and have cloned and positively identified 17 genes not previously known to be regulated by light color in any species. Among these are homologs of genes present in many bacteria that encode well-studied proteins lacking clearly defined functions, such astspO, which encodes a tryptophan-rich sensory protein, and homologs of genes encoding proteins of clearly defined function in many species, such asnblAandchlL, encoding phycobilisome degradation and chlorophyll biosynthesis proteins, respectively. Our results suggest novel roles for several of these gene products and highly specialized, unique uses for others.
Mutational Analysis and Biochemical Characterization of theBurkholderia thailandensisDW503 Quorum-Sensing Network
Authors: Ulrich Ricky L. , Hines Harry B. , Parthasarathy N. , Jeddeloh Jeffrey A.
Published: June 2004

Numerous gram-negative bacteria communicate and regulate gene expression through a cell density-responsive mechanism termed quorum sensing (QS), which involves the synthesis and perception of diffusibleN-acyl-homoserine lactones (AHL). In this study we genetically and physiologically characterized theBurkholderia thailandensisDW503 QS network. In silico analysis of theB. thailandensisgenome revealed the presence of at least three AHL synthases (AHS) and five transcriptional regulators belonging to the LuxIR family of proteins. Mass spectrometry demonstrated that wild-typeB. thailandensissynthesizesN-hexanoyl-homoserine lactone (C6-HSL),N-octanoyl-homoserine lactone (C8-HSL), andN-decanoyl-homoserine lactone (C10-HSL). Mutation of thebtaI1(luxI) AHS gene prevented accumulation of C8-HSL in culture supernatants, enhanced beta-hemolysis of sheep erythrocytes, increased lipase production, and altered colony morphology on swarming and twitching motility plates. Disruption of thebtaI3(luxI) AHS prevented biosynthesis of C6-HSL and increased lipase production and beta-hemolysis, whereas mutagenesis of thebtaI2(luxI) allele eliminated C10-HSL accumulation and reduced lipase production. Complementation of thebtaI1andbtaI3mutants fully restored the synthesis of C8-HSL and C6-HSL to parental levels. In contrast, mutagenesis of thebtaR1,btaR3,btaR4, andbtaR5(luxR) transcriptional regulators had no effect on AHL accumulation, enhanced lipase production, and resulted in extensive beta-hemolysis on sheep blood agar plates. Furthermore, interruption of thebtaI1,btaR1, andbtaR3genes altered colony morphology on twitching and swarming motility plates and induced pigmentation. Additionally, phenotypic microarray analysis indicated that QS inB. thailandensisboth positively and negatively affects the metabolism of numerous substrates, including citric acid, formic acid, glucose 6-phosphate, capric acid, γ-hydroxybutyric acid, andd-arabinose. These results demonstrate that mutagenesis of theB. thailandensisQS system affects various cellular processes, including lipase production, swarming and twitching motility, beta-hemolysis of sheep erythrocytes, and carbon metabolism and/or transport.
σ54Enhancer Binding Proteins andMyxococcus xanthusFruiting Body Development
Authors: Jakobsen Jimmy S. , Jelsbak Lars , Jelsbak Lotte , Welch Roy D. , Cummings Craig , Goldman Barry , Stark Elizabeth , Slater Steve , Kaiser Dale
Published: June 2004

A search of the M1genome sequence, which includes 97% of theMyxococcus xanthusgenes, identified 53 sequence homologs of σ54-dependent enhancer binding proteins (EBPs). A DNA microarray was constructed from the M1genome that includes those homologs and 318 otherM. xanthusgenes for comparison. To screen the developmental program with this array, an RNA extract from growing cells was compared with one prepared from developing cells at 12 h. Previous reporter studies had shown thatM. xanthushas initiated development and has begun to express many developmentally regulated genes by 12 h. The comparison revealed substantial increases in the expression levels of 11 transcription factors that may respond to environmental stimuli. Six of the 53 EBP homologs were expressed at significantly higher levels at 12 h of development than during growth. Three were previously unknown genes, and they were inactivated to look for effects on fruiting body development. One knockout mutant produced fruiting bodies of abnormal shape that depended on the composition of the medium.
tonB3
Is Required for Normal Twitching Motility and Extracellular Assembly of Type IV Pili
Authors: Huang Bixing , Ru Kelin , Yuan Zheng , Whitchurch Cynthia B. , Mattick John S.
Published: June 2004

Three mutants with Tn
5
-B21 insertion in
tonB3
(PA0406) of
Pseudomonas aeruginosa
exhibited defective twitching motility and reduced assembly of extracellular pili. These defects could be complemented with wild-type
tonB3
.
Point Mutations in Transmembrane Helices 2 and 3 of ExbB and TolQ Affect Their Activities inEscherichia coliK-12
Authors: Braun Volkmar , Herrmann Christina
Published: June 2004

Replacement of glutamate 176, the only charged amino acid in the third transmembrane helix of ExbB, with alanine (E176A) abolished ExbB activity in all determined ExbB-dependent functions ofEscherichia coli. Combination of the mutations T148A in the second transmembrane helix and T181A in the third transmembrane helix, proposed to form part of a proton pathway through ExbB, also resulted in inactive ExbB. E176 and T148 are strictly conserved in ExbB and TolQ proteins, and T181 is almost strictly conserved in ExbB, TolQ, and MotA.
Haemophilus somnus
Possesses Two Systems for Acquisition of Transferrin-Bound Iron
Authors: Ekins Andrew , Bahrami Fariborz , Sijercic Ada , Maret Deborah , Niven Donald F.
Published: June 2004

Haemophilus somnus
strain 649 was found to acquire iron from ovine, bovine, and goat transferrins (Tfs). Expression of Tf receptors, as evaluated by solid-phase binding assays, required the organisms to be grown under iron-restricted conditions in the presence of Tf. Competition binding assays revealed the presence of two distinct Tf-binding receptor systems, one specific for bovine Tf and the other capable of binding all three ruminant Tfs. Affinity isolation procedures using total membranes yielded three putative bovine Tf-binding polypeptides and one putative ovine and goat Tf-binding polypeptide. PCR amplification followed by DNA sequence analyses revealed that
H. somnus
strain 649 possesses genes that encode a bipartite TbpA-TbpB receptor along with a homolog of the
Histophilus ovis
single-component TbpA receptor. Expression of TbpB and the single-component TbpA would appear to be subject to a form of phase variation involving homopolymeric nucleotide tracts within the structural genes.
Nitrosomonas europaea
Expresses a Nitric Oxide Reductase during Nitrification
Authors: Beaumont Hubertus J. E. , van Schooten Bas , Lens Sylvia I. , Westerhoff Hans V. , van Spanning Rob J. M.
Published: June 2004

In this paper, we report the identification of a
norCBQD
gene cluster that encodes a functional nitric oxide reductase (Nor) in
Nitrosomonas europaea
. Disruption of the
norB
gene resulted in a strongly diminished nitric oxide (NO) consumption by cells and membrane protein fractions, which was restored by the introduction of an intact
norCBQD
gene cluster in
trans
. NorB-deficient cells produced amounts of nitrous oxide (N
2
O) equal to that of wild-type cells. NorCB-dependent activity was present during aerobic growth and was not affected by the inactivation of the putative
fnr
gene. The findings demonstrate the presence of an alternative site of N
2
O production in
N. europaea
.
CORE SYMMETRIES OF A FLOW
Authors: KISHIMOTO AKITAKA
Published: June 2004

For a flow α on a C*-algebra one defines a symmetry as the group of automorphisms γ such that γαγ-1 is a cocycle perturbation of α. We propose to define a core of this symmetry, which acts trivially on the set of equivalence classes of KMS state representations, but may act non-trivially on the set of equivalence classes of covariant irreducible representations. In particular this core acts transitively on the set of those which induce faithful representations of the crossed product by α.
ON THE HESSIAN OF THE ENERGY FORM IN THE GINZBURG–LANDAU MODEL OF SUPERCONDUCTIVITY
Authors: COMTE MYRIAM , SAUVAGEOT MYRTO
Published: June 2004

The purpose of this work is to study the stability of radial solutions of degree d for the Ginzburg–Landau model of superconductivity with an applied magnetic field in a disk of radius [Formula: see text]. We consider the branch of solutions introduced in [24] as a branch with the radius of the ball as parameter. We prove that for small radii the branch is stable while it is unstable for large radii, see [6]. We then study in detail the Hessian of the energy at the symmetric vortex at the stability transition. Finally under a couple of extra assumptions, we construct a branch of solutions bifurcating from the radial one at this point, and describe it.