bluuebunny/crossref_metadata_2025 huggingface dataset:
Toll-Like Receptor 2- and MyD88-Dependent Phosphatidylinositol 3-Kinase and Rac1 Activation Facilitates the Phagocytosis ofListeria monocytogenesby Murine Macrophages
Authors: Shen Yanna , Kawamura Ikuo , Nomura Takamasa , Tsuchiya Kohsuke , Hara Hideki , Dewamitta Sita R. , Sakai Shunsuke , Qu Huixin , Daim Sylvia , Yamamoto Takeshi , Mitsuyama Masao
Published: April 2010

Toll-like receptors (TLRs) play a key role in the innate immune response by sensing bacterial ligands. The mechanisms involved in the TLR-mediated cytokine response are well established; however, the possible contribution of TLR-dependent recognition of bacteria to macrophage phagocytosis remains unclear.Listeria monocytogenesis an intracellular, parasitic, Gram-positive bacterium recognized mainly by TLR2. In this study, we investigated whether TLR2-dependent signaling is involved in the phagocytosis ofL. monocytogenesby macrophages. We found no difference in the number ofL. monocytogenescells associating with wild-type (WT) and TLR2−/−macrophages 1 h after infection. However, the number ofL. monocytogenescells phagocytosed in TLR2−/−and MyD88−/−macrophages was significantly lower than that of WT macrophages. In addition, lipopolysaccharide (LPS) treatment restored impaired phagocytic activity of TLR2−/−macrophages but did not enhance the activity of MyD88−/−macrophages. The efficiency of phagocytosis was suppressed by inhibitors of phosphatidylinositol 3-kinase (PI3K) and the small Rho GTPases but not by cycloheximide. Moreover, functional activation of PI3K and Rac1 was impaired in TLR2−/−and MyD88−/−macrophages. In anin vivoinfection model, we found significantly lower numbers ofL. monocytogenescells phagocytosed in peritoneal macrophages of TLR2−/−and MyD88−/−mice after intraperitoneal infection. Moreover, a lower number of bacteria were detected in the spleens of TLR2−/−mice 1 day after intravenous infection than in WT mice. These results clearly indicated that TLR2-MyD88-dependent signaling enhances the basal level of phagocytosis ofL. monocytogenesby macrophages through activation of PI3K and Rac1, not by synthesis of proinflammatory cytokines or expression of phagocytic receptors.
Importance of CXC Chemokine Receptor 2 in Alveolar Neutrophil and Exudate Macrophage Recruitment in Response to Pneumococcal Lung Infection
Authors: Herbold Wiebke , Maus Regina , Hahn Ines , Ding Nadine , Srivastava Mrigank , Christman John W. , Mack Matthias , Reutershan Jörg , Briles David E. , Paton James C. , Winter Christine , Welte Tobias , Maus Ulrich A.
Published: April 2010

Sustained neutrophilic infiltration is known to contribute to organ damage, such as acute lung injury. CXC chemokine receptor 2 (CXCR2) is the major receptor regulating inflammatory neutrophil recruitment in acute and chronic inflamed tissues. Whether or not the abundant neutrophil recruitment observed in severe pneumonia is essential for protective immunity againstStreptococcus pneumoniaeinfections is incompletely defined. Here we show that CXCR2 deficiency severely perturbs the recruitment of both neutrophils and exudate macrophages associated with a massive bacterial outgrowth in distal airspaces after infection withS. pneumoniae, resulting in 100% mortality in knockout (KO) mice within 3 days. Moreover, irradiated wild-type mice reconstituted with increasing amounts of CXCR2 KO bone marrow (10, 25, 50, and 75% KO) have correspondingly decreased numbers of both neutrophils and exudate macrophages, which is associated with a stepwise increase in bacterial burden and a reciprocal stepwise decrease in survival inS. pneumoniae-induced pulmonary infection. Finally, application of the CXCR2 antagonist SB-225002 resulted in decreased alveolar neutrophil and exudate macrophage recruitment in mice along with increased lung bacterial loads after infection withS. pneumoniae. Together, these data show that CXC chemokine receptor 2 serves a previously unrecognized nonredundant role in the regulation of both neutrophil and exudate macrophage recruitment to the lung in response toS. pneumoniaeinfection. In addition, we demonstrate that a threshold level of 10 to 25% of reduced neutrophil recruitment is sufficient to cause increased mortality in mice infected withS. pneumoniae.
Transcriptome of Swarming
Proteus mirabilis
Authors: Pearson Melanie M. , Rasko David A. , Smith Sara N. , Mobley Harry L. T.
Published: April 2010

Swarming motility by the urinary tract pathogen
Proteus mirabilis
has been a long-studied but little understood phenomenon. On agar, a
P. mirabilis
colony grows outward in a bull's-eye pattern formed by consecutive waves of rapid swarming followed by consolidation into shorter cells. To examine differential gene expression in these growth phases, a microarray was constructed based on the completed genome sequence and annotation. RNA was extracted from broth-cultured, swarming, and consolidation-phase cells to assess transcription during each of these growth states. A total of 587 genes were differentially expressed in broth-cultured cells versus swarming cells, and 527 genes were differentially expressed in broth-cultured cells versus consolidation-phase cells (consolidate). Flagellar genes were highly upregulated in both swarming cells and consolidation-phase cells. Fimbriae were downregulated in swarming cells, while genes involved in cell division and anaerobic growth were upregulated in broth-cultured cells. Direct comparison of swarming cells to consolidation-phase cells found that 541 genes were upregulated in consolidate, but only nine genes were upregulated in swarm cells. Genes involved in flagellar biosynthesis, oligopeptide transport, amino acid import and metabolism, cell division, and phage were upregulated in consolidate. Mutation of
dppA
,
oppB
, and
cysJ
, upregulated during consolidation compared to during swarming, revealed that although these genes play a minor role in swarming,
dppA
and
cysJ
are required during ascending urinary tract infection. Swarming on agar to which chloramphenicol had been added suggested that protein synthesis is not required for swarming. These data suggest that the consolidation phase is a state in which
P. mirabilis
prepares for the next wave of swarming.
Discordant Influence of
Blastomyces dermatitidis
Yeast-Phase-Specific Gene
BYS1
on Morphogenesis and Virulence
Authors: Krajaejun Theerapong , Wüthrich Marcel , Gauthier Gregory M. , Warner Thomas F. , Sullivan Thomas D. , Klein Bruce S.
Published: April 2010

Blastomyces dermatitidis
is a thermally induced dimorphic fungus capable of causing lung and systemic infections in immunocompetent animal hosts. With the publication of genomic sequences from three different strains of
B
.
dermatitidis
and the development of RNA interference as a gene-silencing tool, it has become possible to easily ascertain the virulence and morphological effects of knocking down the expression of candidate genes of interest.
BYS1
(
Blastomyces
yeast-phase-specific 1), first identified by Burg and Smith, is expressed at high levels in yeast cells and is undetectable in mold. The deduced protein sequence of
BYS1
has a putative signal sequence at its N terminus, opening the possibility that the
BYS1
-encoded protein is associated with the yeast cell wall. Herein, strains of
B
.
dermatitidis
with silenced expression of
BYS1
were engineered and tested for morphology and virulence. The silenced strains produced rough-surfaced cultures on agar medium and demonstrated a propensity to form pseudohyphal cells on prolonged culture
in vitro
and
in vivo
, as measured in the mouse lung. Tests using a mouse model of blastomycosis with either yeast or spore inocula showed that the
bys1
-silenced strains were as virulent as control strains. Thus, although silencing of
BYS1
alters morphology at 37°C, it does not appear to impair the pathogenicity of
B
.
dermatitidis
.
Temperature-Induced Changes in the Lipopolysaccharide ofYersinia pestisAffect Plasminogen Activation by the Pla Surface Protease
Authors: Suomalainen Marjo , Lobo Leandro Araujo , Brandenburg Klaus , Lindner Buko , Virkola Ritva , Knirel Yuriy A. , Anisimov Andrey P. , Holst Otto , Korhonen Timo K.
Published: April 2010

The Pla surface protease ofYersinia pestisactivates human plasminogen and is a central virulence factor in bubonic and pneumonic plague. Pla is a transmembrane β-barrel protein and member of the omptin family of outer membrane proteases which require bound lipopolysaccharide (LPS) to be proteolytically active. Plasminogen activation and autoprocessing of Pla were dramatically higher inY. pestiscells grown at 37°C than in cells grown at 20°C; the difference in enzymatic activity by far exceeded the increase in the cellular content of the Pla protein.Y. pestismodifies its LPS structure in response to growth temperature. We purified His6-Pla under denaturing conditions and compared various LPS types for their capacity to enhance plasmin formation by His6-Pla solubilized in detergent. Reactivation of His6-Pla was higher withY. pestisLPSs isolated from bacteria grown at 37°C than with LPSs from cells grown at 25°C. Lack of O antigens and the presence of the outer core region as well as a lowered level of acylation in LPS were found to enhance the Pla-LPS interaction. Genetic substitution of arginine 138, which is part of a three-dimensional protein motif for binding to lipid A phosphates, decreased both the enzymatic activity of His6-Pla and the amount of Pla inY. pestiscells, suggesting the importance of the Pla-lipid A phosphate interaction. The temperature-induced changes in LPS are known to helpY. pestisto avoid innate immune responses, and our results strongly suggest that they also potentiate Pla-mediated proteolysis.
Salmonella entericaSerovar Typhimurium Invades Fibroblasts by Multiple Routes Differing from the Entry into Epithelial Cells
Authors: Aiastui Ana , Pucciarelli M. Graciela , García-del Portillo Francisco
Published: April 2010

Fibroblasts are ubiquitous cells essential to tissue homeostasis. Despite their nonphagocytic nature, fibroblasts restrain replication of intracellular bacterial pathogens such asSalmonella entericaserovar Typhimurium. The extent to which the entry route of the pathogen determines this intracellular response is unknown. Here, we analyzedS.Typhimurium invasion in fibroblasts obtained from diverse origins, including primary cultures and stable nontransformed cell lines derived from normal tissues. Features distinct to the invasion of epithelial cells were found in all fibroblasts tested. In some fibroblasts, bacteria lacking the type III secretion system encoded in theSalmonellapathogenicity island 1 displayed significant invasion rates and induced the formation of lamellipodia and filopodia at the fibroblast-bacteria contact site. Other bacterial invasion traits observed in fibroblasts were the requirement of phosphatidylinositol 3-kinase, mitogen-activated protein kinase MEK1, and both actin filaments and microtubules. RNA interference studies showed that different Rho family GTPases are targeted byS.Typhimurium to enter into distinct fibroblasts. Rac1 and Cdc42 knockdown affected invasion of normal rat kidney fibroblasts, whereas none of the GTPases tested (Rac1, Cdc42, RhoA, or RhoG) was essential for invasion of immortalized human foreskin fibroblasts. Collectively, these data reveal a marked diversity in the modes used byS.Typhimurium to enter into fibroblasts.
A Deficiency in Arabinogalactan Biosynthesis AffectsCorynebacterium glutamicumMycolate Outer Membrane Stability
Authors: Bou Raad Roland , Méniche Xavier , de Sousa-d'Auria Celia , Chami Mohamed , Salmeron Christophe , Tropis Marielle , Labarre Cecile , Daffé Mamadou , Houssin Christine , Bayan Nicolas
Published: April 2010

Corynebacterineaeis a specific suborder of Gram-positive bacteria that includesMycobacterium tuberculosisandCorynebacterium glutamicum. The ultrastructure of the cell envelope is very atypical. It is composed of a heteropolymer of peptidoglycan and arabinogalactan (AG) covalently associated to an outer membrane. Five arabinosyltransferases are involved in the biosynthesis of AG inC. glutamicum. AftB catalyzes the transfer of Araf(arabinofuranosyl) onto the arabinan domain of the arabinogalactan to form terminal β(1 → 2)-linked Arafresidues. Here we show that ΔaftBcells lack half of the arabinogalactan mycoloylation sites but are still able to assemble an outer membrane. In addition, we show that a ΔaftBmutant grown on a rich medium has a perturbed cell envelope and sheds a significant amount of membrane fragments in the external culture medium. These fragments contain mono- and dimycolate of trehalose and PorA/H, the major porin ofC. glutamicum, but lack conventional phospholipids that typify the plasma membrane, suggesting that they are derived from the atypical mycolate outer membrane of the cell envelope. This is the first report of outer membrane destabilization in theCorynebacterineae, and it suggests that a strong interaction between the mycolate outer membrane and the underlying polymer is essential for cell envelope integrity. The presence of outer membrane-derived fragments (OMFs) in the external medium of the ΔaftBmutant is also a very promising tool for outer membrane characterization. Indeed, fingerprint analysis of major OMF-associated proteins has already led to the identification of 3 associated mycoloyltransferases and an unknown protein with a C-terminal hydrophobic anchoring domain reminiscent of that found for the S-layer protein PS2 ofC. glutamicum.
BacA Is Essential for Bacteroid Development in Nodules of Galegoid, but not Phaseoloid, Legumes
Authors: Karunakaran Ramakrishnan , Haag Andreas F. , East Alison K. , Ramachandran Vinoy K. , Prell Jurgen , James Euan K. , Scocchi Marco , Ferguson Gail P. , Poole Philip S.
Published: April 2010

BacA is an integral membrane protein, the mutation of which leads to increased resistance to the antimicrobial peptides bleomycin and Bac7
1-35
and a greater sensitivity to SDS and vancomycin in
Rhizobium leguminosarum
bv.
viciae
,
R. leguminosarum
bv.
phaseoli
, and
Rhizobium etli
. The growth of
Rhizobium
strains on dicarboxylates as a sole carbon source was impaired in
bacA
mutants but was overcome by elevating the calcium level. While
bacA
mutants elicited indeterminate nodule formation on peas, which belong to the galegoid tribe of legumes, bacteria lysed after release from infection threads and mature bacteroids were not formed. Microarray analysis revealed almost no change in a
bacA
mutant of
R. leguminosarum
bv.
viciae
in free-living culture. In contrast, 45 genes were more-than 3-fold upregulated in a
bacA
mutant isolated from pea nodules. Almost half of these genes code for cell membrane components, suggesting that BacA is crucial to alterations that occur in the cell envelope during bacteroid development. In stark contrast,
bacA
mutants of
R. leguminosarum
bv.
phaseoli
and
R. etli
elicited the formation of normal determinate nodules on their bean host, which belongs to the phaseoloid tribe of legumes. Bacteroids from these nodules were indistinguishable from the wild type in morphology and nitrogen fixation. Thus, while
bacA
mutants of bacteria that infect galegoid or phaseoloid legumes have similar phenotypes in free-living culture, BacA is essential only for bacteroid development in indeterminate galegoid nodules.
ThePseudomonas aeruginosaPathogenicity Island PAPI-1 Is Transferred via a Novel Type IV Pilus
Authors: Carter Michelle Qiu , Chen Jianshun , Lory Stephen
Published: April 2010

Pseudomonas aeruginosais a major cause of nosocomial infections, particularly in immunocompromised patients or in individuals with cystic fibrosis. The notable ability ofP. aeruginosato inhabit a broad range of environments, including humans, is in part due to its large and diverse genomic repertoire. The genomes of most strains contain a significant number of large and small genomic islands, including those carrying virulence determinants (pathogenicity islands). The pathogenicity island PAPI-1 of strain PA14 is a cluster of 115 genes, and some have been shown to be responsible for virulence phenotypes in a number of infection models. We have previously demonstrated that PAPI-1 can be transferred to otherP. aeruginosastrains following excision from the chromosome of the donor. Here we show that PAPI-1 is transferred into recipientP. aeruginosaby a conjugative mechanism, via a type IV pilus, encoded in PAPI-1 by a 10-gene cluster which is closely related to the genes in the enterobacterial plasmid R64. We also demonstrate that the precursor of the major pilus subunit, PilS2, is processed by the chromosomally encoded prepillin peptidase PilD but not its paralog FppA. Our results suggest that the pathogenicity island PAPI-1 may have evolved by acquisition of a conjugation system but that because of its dependence on an essential chromosomal determinant, its transfer is restricted toP. aeruginosaor other species capable of providing a functional prepilin peptidase.
Visualization of Flagella during Bacterial Swarming
Authors: Turner Linda , Zhang Rongjing , Darnton Nicholas C. , Berg Howard C.
Published: April 2010

When cells of
Escherichia coli
are grown in broth and suspended at low density in a motility medium, they swim independently, exploring a homogeneous, isotropic environment. Cell trajectories and the way in which these trajectories are determined by flagellar dynamics are well understood. When cells are grown in a rich medium on agar instead, they elongate, produce more flagella, and swarm. They move in coordinated packs within a thin film of fluid, in intimate contact with one another and with two fixed surfaces, a surfactant monolayer above and an agar matrix below: they move in an inhomogeneous, anisotropic environment. Here we examine swarm-cell trajectories and ways in which these trajectories are determined by flagellar motion, visualizing the cell bodies by phase-contrast microscopy and the flagellar filaments by fluorescence microscopy. We distinguish four kinds of tracks, defining stalls, reversals, lateral movement, and forward movement. When cells are stalled at the edge of a colony, they extend their flagellar filaments outwards, moving fluid over the virgin agar; when cells reverse, changes in filament chirality play a crucial role; when cells move laterally, they are pushed sideways by adjacent cells; and when cells move forward, they are pushed by flagellar bundles in the same way as when they are swimming in bulk aqueous media. These maneuvers are described in this report.
Genetic, Structural, and Antigenic Analyses of Glycan Diversity in the O-Linked Protein Glycosylation Systems of HumanNeisseriaSpecies
Authors: Børud Bente , Aas Finn Erik , Vik Åshild , Winther-Larsen Hanne C. , Egge-Jacobsen Wolfgang , Koomey Michael
Published: April 2010

Bacterial capsular polysaccharides and lipopolysaccharides are well-established ligands of innate and adaptive immune effectors and often exhibit structural and antigenic variability. Although many surface-localized glycoproteins have been identified in bacterial pathogens and symbionts, it not clear if and how selection impacts associated glycoform structure. Here, a systematic approach was devised to correlate gene repertoire with protein-associated glycoform structure inNeisseriaspecies important to human health and disease. By manipulating the protein glycosylation (pgl) gene content and assessing the glycan structure by mass spectrometry and reactivity with monoclonal antibodies, it was established that protein-associated glycans are antigenically variable and that at least nine distinct glycoforms can be expressedin vitro. These studies also revealed that in addition toNeisseria gonorrhoeaestrain N400, one other gonococcal strain and isolates ofNeisseria meningitidisandNeisseria lactamicaexhibit broad-spectrum O-linked protein glycosylation. Although a strong correlation betweenpglgene content, glycoform expression, and serological profile was observed, there were significant exceptions, particularly with regard to levels of microheterogeneity. This work provides a technological platform for molecular serotyping of neisserial protein glycans and for elucidatingpglgene evolution.
Haloferax volcanii
Flagella Are Required for Motility but Are Not Involved in PibD-Dependent Surface Adhesion
Authors: Tripepi Manuela , Imam Saheed , Pohlschröder Mechthild
Published: April 2010

Although the genome of
Haloferax volcanii
contains genes (
flgA1
-
flgA2
) that encode flagellins and others that encode proteins involved in flagellar assembly, previous reports have concluded that
H. volcanii
is nonmotile. Contrary to these reports, we have now identified conditions under which
H. volcanii
is motile. Moreover, we have determined that an
H. volcanii
deletion mutant lacking flagellin genes is not motile. However, unlike flagella characterized in other prokaryotes, including other archaea, the
H. volcanii
flagella do not appear to play a significant role in surface adhesion. While flagella often play similar functional roles in bacteria and archaea, the processes involved in the biosynthesis of archaeal flagella do not resemble those involved in assembling bacterial flagella but, instead, are similar to those involved in producing bacterial type IV pili. Consistent with this observation, we have determined that, in addition to disrupting preflagellin processing, deleting
pibD
, which encodes the preflagellin peptidase, prevents the maturation of other
H. volcanii
type IV pilin-like proteins. Moreover, in addition to abolishing swimming motility, and unlike the
flgA1
-
flgA2
deletion, deleting
pibD
eliminates the ability of
H. volcanii
to adhere to a glass surface, indicating that a nonflagellar type IV pilus-like structure plays a critical role in
H. volcanii
surface adhesion.
Biochemical Characterization of the C
4
-Dicarboxylate Transporter DctA from
Bacillus subtilis
Authors: Groeneveld Maarten , Detert Oude Weme Ruud G. J. , Duurkens Ria H. , Slotboom Dirk Jan
Published: April 2010

Bacterial secondary transporters of the DctA family mediate ion-coupled uptake of C
4
-dicarboxylates. Here, we have expressed the DctA homologue from
Bacillus subtilis
in the Gram-positive bacterium
Lactococcus lactis
. Transport of dicarboxylates
in vitro
in isolated membrane vesicles was assayed. We determined the substrate specificity, the type of cotransported ions, the electrogenic nature of transport, and the pH and temperature dependence patterns. DctA was found to catalyze proton-coupled symport of the four C
4
-dicarboxylates from the Krebs cycle (succinate, fumurate, malate, and oxaloacetate) but not of other mono- and dicarboxylates. Because (i) succinate-proton symport was electrogenic (stimulated by an internal negative membrane potential) and (ii) the divalent anionic form of succinate was recognized by DctA, at least three protons must be cotransported with succinate. The results were interpreted in the light of the crystal structure of the homologous aspartate transporter Glt
Ph
from
Pyrococcus horikoshii
.
Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in
Rhodobacter capsulatus
Authors: Mercer Ryan G. , Callister Stephen J. , Lipton Mary S. , Pasa-Tolic Ljiljana , Strnad Hynek , Paces Vaclav , Beatty J. Thomas , Lang Andrew S.
Published: April 2010

The purple nonsulfur photosynthetic bacterium
Rhodobacter capsulatus
has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in
Caulobacter crescentus
has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in
R. capsulatus
shares a high degree of sequence similarity with the
C. crescentus
protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and
ctrA
mutant cultures to identify the genes dysregulated by the loss of CtrA in
R. capsulatus
. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of ∼6% of genes in the
R. capsulatus
genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral
ctrA
gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.
Genome Sequence of
Lentisphaera araneosa
HTCC2155
T
, the Type Species of the Order
Lentisphaerales
in the Phylum
Lentisphaerae
Authors: Thrash J. Cameron , Cho Jang-Cheon , Vergin Kevin L. , Morris Robert M. , Giovannoni Stephen J.
Published: April 2010

Information on the genome content of deeply branching phyla with very few cultured members is invaluable for expanding understanding of microbial evolution.
Lentisphaera araneosa
HTCC2155
T
was isolated from the Oregon coast using dilution-to-extinction culturing. It is a marine heterotroph found in surface and mesopelagic waters in both the Pacific and Atlantic oceans and has the unusual property of producing a net-like matrix of secreted exopolysaccharide. Here we present the genome sequence of
L. araneosa
HTCC2155
T
, importantly, one of only two sequenced members of the phylum
Lentisphaerae
.
Direct Targets of CodY in
Staphylococcus aureus
Authors: Majerczyk Charlotte D. , Dunman Paul M. , Luong Thanh T. , Lee Chia Y. , Sadykov Marat R. , Somerville Greg A. , Bodi Kip , Sonenshein Abraham L.
Published: April 2010

More than 200 direct CodY target genes in
Staphylococcus aureus
were identified by genome-wide analysis of
in vitro
DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules, and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the
agr
locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the
agr
locus. Since
S. aureus
CodY was activated
in vitro
by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence.
The LysR-Type Nitrogen Assimilation Control Protein Forms Complexes with Both Long and Short DNA Binding Sites in the Absence of Coeffectors
Authors: Rosario Christopher J. , Frisch Ryan L. , Bender Robert A.
Published: April 2010

Most LysR-type transcriptional regulators (LTTRs) function as tetramers when regulating gene expression. The nitrogen assimilation control protein (NAC) generally functions as a dimer when binding to DNA and activating transcription. However, at some sites, NAC binds as a tetramer. Like many LTTRs, NAC tetramers can recognize sites with long footprints (74 bp for the site at
nac
) with a substantial DNA bend or short footprints (56 bp for the site at
cod
) with less DNA bending. However, unlike other LTTRs, NAC can recognize both types of sites in the absence of physiologically relevant coeffectors, suggesting that the two conformers of the NAC tetramer (extended and compact) are interchangeable without the need for any modification to induce or stabilize the change. In order for NAC to bind as a tetramer, three interactions must exist: an interaction between the two NAC dimers and an interaction between each NAC dimer and its corresponding binding site. The interaction between one dimer and its DNA site can be weak (recognizing a half-site rather than a full dimer-binding site), but the other two interactions must be strong. Since the conformation of the NAC tetramer (extended or compact) is determined by the nature of the DNA site without the intervention of a small molecule, we argue that the coeffector that determines the conformation of the NAC tetramer is the DNA site to which it binds.
Glucose Metabolism in
Legionella pneumophila
: Dependence on the Entner-Doudoroff Pathway and Connection with Intracellular Bacterial Growth
Authors: Harada Eiji , Iida Ken-Ichiro , Shiota Susumu , Nakayama Hiroaki , Yoshida Shin-Ichi
Published: April 2010

Glucose metabolism in
Legionella pneumophila
was studied by focusing on the Entner-Doudoroff (ED) pathway with a combined genetic and biochemical approach. The bacterium utilized exogenous glucose for synthesis of acid-insoluble cell components but manifested no discernible increase in the growth rate. Assays with permeabilized cell preparations revealed the activities of three enzymes involved in the pathway, i.e., glucokinase, phosphogluconate dehydratase, and 2-dehydro-3-deoxy-phosphogluconate aldolase, presumed to be encoded by the
glk
,
edd
, and
eda
genes, respectively. Gene-disrupted mutants for the three genes and the
ywtG
gene encoding a putative sugar transporter were devoid of the ability to metabolize exogenous glucose, indicating that the pathway is almost exclusively responsible for glucose metabolism and that the
ywtG
gene product is the glucose transporter. It was also established that these four genes formed part of an operon in which the gene order was
edd-glk-eda-ywtG
, as predicted by genomic information. Intriguingly, while the mutants exhibited no appreciable change in growth characteristics
in vitro
, they were defective in multiplication within eukaryotic cells, strongly indicating that the ED pathway must be functional for the intracellular growth of the bacterium to occur. Curiously, while the deficient glucose metabolism of the
ywtG
mutant was successfully complemented by the
ywtG
+
gene supplied in
trans
via plasmid, its defect in intracellular growth was not. However, the latter defect was also manifested in wild-type cells when a plasmid carrying the mutant
ywtG
gene was introduced. This phenomenon, resembling so-called dominant negativity, awaits further investigation.
A Novel Hydrolytic Dehalogenase for the Chlorinated Aromatic Compound Chlorothalonil
Authors: Wang Guangli , Li Rong , Li Shunpeng , Jiang Jiandong
Published: April 2010

Dehalogenases play key roles in the detoxification of halogenated aromatics. Interestingly, only one hydrolytic dehalogenase for halogenated aromatics, 4-chlorobenzoyl-coenzyme A (CoA) dehalogenase, has been reported. Here, we characterize another novel hydrolytic dehalogenase for a halogenated aromatic compound from the 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil)-degrading strain of
Pseudomonas
sp. CTN-3, which we have named Chd. Chd catalyzes a hydroxyl substitution at the 4-chlorine atom of chlorothalonil. The metabolite of the Chd dehalogenation, 4-hydroxy-trichloroisophthalonitrile, was identified by reverse-phase high-performance liquid chromatography (HPLC), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR). Chd dehalogenates chlorothalonil under anaerobic and aerobic conditions and does not require the presence of cofactors such as CoA and ATP. Chd contains a putative conserved domain of the metallo-β-lactamase superfamily and shows the highest identity with several metallohydrolases (24 to 29%). Chd is a monomer (36 kDa), and the isoelectric point (pI) of Chd is estimated to be 4.13. Chd has a dissociation constant (

K
m

) of 0.112 mM and an overall catalytic rate (
k
cat
) of 207 s
−1
for chlorothalonil. Chd is completely inhibited by 1,10-phenanthroline, diethyl pyrocarbonate, and
N
-bromosuccinic acid. Site-directed mutagenesis of Chd revealed that histidines 128 and 157, serine 126, aspartates 45, 130 and 184, and tryptophan 241 were essential for the dehalogenase activity. Chd differs from other reported hydrolytic dehalogenases based on the analysis of amino acid sequences and catalytic mechanisms. This study provides an excellent dehalogenase candidate for mechanistic study of hydrolytic dehalogenation of halogenated aromatic compound.
Multiple Interaction Domains in FtsL, a Protein Component of the Widely Conserved Bacterial FtsLBQ Cell Division Complex
Authors: Gonzalez Mark D. , Akbay Esra A. , Boyd Dana , Beckwith Jon
Published: April 2010

A bioinformatic analysis of nearly 400 genomes indicates that the overwhelming majority of bacteria possess homologs of theEscherichia coliproteins FtsL, FtsB, and FtsQ, three proteins essential for cell division in that bacterium. These three bitopic membrane proteins form a subcomplexin vivo, independent of the other cell division proteins. Here we analyze the domains ofE. coliFtsL that are involved in the interaction with other cell division proteins and important for the assembly of the divisome. We show that FtsL, as we have found previously with FtsB, packs an enormous amount of information in its sequence for interactions with proteins upstream and downstream in the assembly pathway. Given their size, it is likely that the sole function of the complex of these two proteins is to act as a scaffold for divisome assembly.
Mutagenesis and Functional Characterization of the Four Domains of GlnD, a Bifunctional Nitrogen Sensor Protein
Authors: Zhang Yaoping , Pohlmann Edward L. , Serate Jose , Conrad Mary C. , Roberts Gary P.
Published: April 2010

GlnD is a bifunctional uridylyltransferase/uridylyl-removing enzyme (UTase/UR) and is believed to be the primary sensor of nitrogen status in the cell by sensing the level of glutamine in enteric bacteria. It plays an important role in nitrogen assimilation and metabolism by reversibly regulating the modification of P
II
protein; P
II
in turn regulates a variety of other proteins. GlnD appears to have four distinct domains: an N-terminal nucleotidyltransferase (NT) domain; a central HD domain, named after conserved histidine and aspartate residues; and two C-terminal ACT domains, named after three of the allosterically regulated enzymes in which this domain is found. Here we report the functional analysis of these domains of GlnD from
Escherichia coli
and
Rhodospirillum rubrum
. We confirm the assignment of UTase activity to the NT domain and show that the UR activity is a property specifically of the HD domain: substitutions in this domain eliminated UR activity, and a truncated protein lacking the NT domain displayed UR activity. The deletion of C-terminal ACT domains had little effect on UR activity itself but eliminated the ability of glutamine to stimulate that activity, suggesting a role for glutamine sensing by these domains. The deletion of C-terminal ACT domains also dramatically decreased UTase activity under all conditions tested, but some of these effects are due to the competition of UTase activity with unregulated UR activity in these variants.
BOUNDING THE ELECTROMAGNETIC AND WEAK DIPOLE MOMENTS OF THE TAU–LEPTON IN A SIMPLEST LITTLE HIGGS MODEL
Authors: GUTIÉRREZ-RODRÍGUEZ A.
Published: April 2010

From the total cross-section for the reaction e+e-→τ+τ-γ at the Z1 pole and in the framework of a simplest little Higgs model (SLHM), we get a limit on the characteristic energy scale of the model f, f ≥ 5.4 TeV , which in turn induces bounds on the electromagnetic and weak dipole moments of the tau–lepton. Our bounds on the electromagnetic moments are consistent with the bounds obtained by the L3 and OPAL collaborations for the reaction e+e-→τ+τ-γ. We also obtained bounds on the tau weak dipole moments which are consistent with the bounds obtained recently by the DELPHI and ALEPH collaborations from the reaction e+e-→τ+τ-.
BOSONIC SEESAW AND A SOLUTION TO THE μ PROBLEM IN THE UNPARTICLE PHYSICS
Authors: KIKUCHI TATSURU
Published: April 2010

Recently, conceptually new physics beyond the Standard Model has been proposed by Georgi, where a new physics sector becomes conformal and provides "unparticle" which couples to the Standard Model sector through higher dimensional operators in low energy effective theory. Among several possibilities, we focus on operators involving the unparticle and Higgs boson. Once the Higgs develops the vacuum expectation value (VEV), the conformal symmetry is broken and as a result, the mixing between the unparticle and the Higgs boson emerges. In the former part of this paper, we consider a natural realization of bosonic seesaw in the context of unparticle physics. In this framework, the negative mass squared or the electroweak symmetry breaking vacuum is achieved as a result of mass matrix diagonalization. So, the bosonic seesaw mechanism for the electroweak symmetry breaking can naturally be understood in the framework of unparticle physics. In the latter part of this paper, we consider the unparticle as a hidden sector of supersymmetry breaking, and give some phenomenological consequences of this scenario. The result shows that there is a possibility for the unparticle as a hidden sector in SUSY breaking sector, and can provide a solution to the μ problem in SUSY models.
QFT AS PILOT-WAVE THEORY OF PARTICLE CREATION AND DESTRUCTION
Authors: NIKOLIĆ HRVOJE
Published: April 2010

States in quantum field theory (QFT) are represented by many-particle wave functions, such that a state describing n particles depends on n space–time positions. Since a general state is a superposition of states with different numbers of particles, the wave function lives in the configuration space identified with a product of an infinite number of four-dimensional Minkowski space–times. The squared absolute value of the wave function is interpreted as the probability density in the configuration space, from which the standard probabilistic predictions of QFT can be recovered. Such a formulation and probabilistic interpretation of QFT allows one to interpret the wave function as a pilot wave that describes deterministic particle trajectories, which automatically includes a deterministic and continuous description of particle creation and destruction. In particular, when the conditional wave function associated with a quantum measurement ceases to depend on one of the space–time coordinates, then the 4-velocity of the corresponding particle vanishes, describing a trajectory that stops at a particular point in space–time. In a more general situation a dependence on this space–time coordinate is negligibly small but not strictly zero, in which case the trajectory does not stop but the measuring apparatus still behaves as if this particle has been destroyed.
HAWKING RADIATION VIA ANOMALY AND TUNNELING METHOD BY UNRUH'S AND CANONICAL ACOUSTIC BLACK HOLE
Authors: BÉCAR RAMÓN , GONZÁLEZ PABLO , PULGAR GUSTAVO , SAAVEDRA JOEL
Published: April 2010

We study the Hawking radiation by Unruh's and canonical acoustic black hole from the viewpoint of anomaly cancelation method developed by Robinson and Wilczek and by the simple and physically intuitive picture given by the tunneling mechanism.
BLACK HOLE ENTROPY AND AREA QUANTUM ENTANGLEMENT ORIGINATED FROM SPIN NETWORKS
Authors: SHAO D. , SHAO L. , SHAO C. G. , NODA H.
Published: April 2010

By making use of the grasping action of the area operator as an antisymmetrizer of the grasped strands in spin network and the Penrose binor identity, an equidistant area spectrum [Formula: see text] is deduced. Utilizing the spectrum to calculate the quantized area of black hole horizon, we recalculate the entropy of black hole H(A) = (8πℏGN)-1kA ln 2. By taking advantage of the smallest area quantum "½" excited by the spectrum via the Wilson loop in edge of spin network to approach the possible origin of qubit, the existences of entanglement of the area quanta in quantum space, as well as the nonlocal property of the entangled states are demonstrated.
TIMELIKE GEODESIC MOTION IN HORAVA–LIFSHITZ SPACE–TIME
Authors: CHEN JUHUA , WANG YONGJIU
Published: April 2010

Recently a nonrelativistic renormalizable theory of gravitation has been proposed by P. Horava. When restricted to satisfy the condition of detailed balance, this theory is intimately related to topologically massive gravity in three dimensions, and the geometry of the Cotton tensor. At long distances, this theory is expected to flow to the relativistic value λ = 1, and could therefore serve as a possible candidate for a UV completion of Einstein's general relativity or an infrared modification thereof. In this paper under allowing the lapse function to depend on the spatial coordinates xias well as t, we obtain the spherically symmetric solutions. And then by analyzing the behavior of the effective potential for the particle, we investigate the timelike geodesic motion of particle in the Horava–Lifshitz space–time. We find that the nonradial particle falls from a finite distance to the center along the timelike geodesics when its energy is in an appropriate range. However, we find that it is complexity for radial particle along the timelike geodesics. There are three different cases due to the energy of radial particle: (i) when the energy of radial particle is higher than a critical value EC, the particle will fall directly from infinity to the singularity; (ii) when the energy of radial particle equals to the critical value EC, the particle orbit at r = rCis unstable, i.e. the particle will escape from r = rCto the infinity or to the singularity, depending on the initial conditions of the particle; (iii) when the energy of radial particle is in a proper range, the particle will rebound to the infinity or plunge to the singularity from a infinite distance, depending on the initial conditions of the particle.
THE CMS PIXEL DETECTOR
Authors: ERDMANN W.
Published: April 2010

The inner tracking detectors at the LHC operate in a region of unprecedented particle rates. Thousands of hits must be detected, time-stamped and stored in every 25 ns bunch crossing interval. The silicon pixel detector for the CMS experiment has been designed to meet the requirements of position resolution, rate capability and radiation tolerance with a minimal amount of material. Its unique ability to provide three-dimensional high precision space points plays an important role in the tracking system of the CMS detector.
PALINDROMES AND ORDERINGS IN ARTIN GROUPS
Authors: DELOUP FLORIAN
Published: April 2010

The braid group Bn, endowed with Artin's presentation, admits two distinguished involutions. One is the anti-automorphism rev : Bn→Bn, [Formula: see text], defined by reading braids in the reverse order (from right to left instead of left to right). Another one is the conjugation τ : x ↦ Δ-1xΔ by the generalized half-twist (Garside element).

More generally, the involution rev is defined for all Artin groups (equipped with Artin's presentation) and the involution τ is defined for all Artin groups of finite type. A palindrome is an element invariant under rev. We study palindromes and palindromes invariant under τ in Artin groups of finite type. Our main results are the injectivity of the map [Formula: see text] in all finite-type Artin groups, the existence of a left-order compatible with rev for Artin groups of type A, B, D, and the existence of a decomposition for general palindromes. The uniqueness of the latter decomposition requires that the Artin groups carry a left-order.
A MODIFIED FINITE DIFFERENCES METHOD FOR ANALYSIS OF ULTRASONIC PROPAGATION IN NONHOMOGENEOUS MEDIA
Authors: RENTERIA LUCIANO ALONSO , ORIA JUAN M. PEREZ
Published: April 2010

The propagation of ultrasonic waves is generally studied in homogeneous media, although in certain industrial applications the conditions of propagation differ from the ideal conditions and the predicted results are not valid. This work is focused on the resolution of the Helmholtz equation for the study of the ultrasonic propagation in nonhomogeneous media. In this way, the solution of the Helmholtz equation has been obtained by means of Finite Differences, using a nonconventional scheme that substantially improves the results obtained with other techniques such as standard Finite Differences or Finite Elements. Moreover, it decreases the computational cost in the calculation of the coefficients about 85%. The effects on the ultrasonic echoes in propagation environments with high gradients of propagation's speed have been analyzed by simulation using the method presented, and the results obtained have been experimentally validated through a set of measurements.
FLUCTUATION AND VARIABILITY OF SHALLOW WATER AMBIENT NOISE FROM TIME SERIES MEASUREMENTS
Authors: SANJANA M. C. , LATHA G. , THIRUNAVUKKARASU A. , RAJENDRAN V.
Published: April 2010

Medium period variations of ambient noise from time series measurements at two sites in shallow Bay of Bengal is reported. The noise at site1 is contributed by local shipping as well as wind, while at site2 wind is the dominant noise source. The data is analyzed for noise properties in the 0.1–7.5 kHz band. An increase in average noise level of up to 10 dB is noted for site1 owing to ship traffic contribution. The statistics of noise samples is reported in terms of standard deviation σ of the measured levels relative to the mean. Standard deviation values exhibit a wide range and decreases from 5 dB at low frequencies to 1.5 dB at 7.5 kHz. For site2, the standard deviation varies from 4.0 dB at low frequencies to 2 dB at 7.5 kHz and consistency is seen in the frequency band 2.0–6 kHz thus ascertaining strong influence of uniform noise source wind in this band. Wind speed dependence on noise variability is checked and it shows a decrease in standard deviation for increase in wind speeds and drops down to 1–2 dB for 5 beau fort. For higher wind speeds highly variable local shipping noise is better masked by wind/sea state noise which is uniform in nature.
DISTRIBUTION OF TWISTED KLOOSTERMAN SUMS MODULO PRIME POWERS
Authors: KELMER DUBI
Published: April 2010

In this paper, we study Kloosterman sums twisted by multiplicative characters modulo a prime power. We show, by an elementary calculation, that these sums become equidistributed on the real line with respect to a suitable measure.
KORSELT NUMBERS AND SETS
Authors: BOUALLÈGUE KAIS , ECHI OTHMAN , PINCH RICHARD G. E.
Published: April 2010

Let α ∈ ℤ\{0}. A positive integer N is said to be an α-Korselt number (Kα-number, for short) if N ≠ α and p - α divides N - α for each prime divisor p of N. We are concerned, here, with both a numerical and theoretical study of composite squarefree Korselt numbers.

The paper contains two main results. The first one shows that for α ∈ ℤ\{0}, the following properties hold:

(i) If α ≤ 1, then each composite squarefree Kα-number has at least three prime factors.

(ii) Suppose that α > 1. Let p < q be two prime numbers and N ≔ pq. If N is an α-Korselt number, then p < q ≤ 4α - 3. In particular, there are only finitely many α-Korselt numbers with exactly two prime factors.

Let α ∈ ℕ\{0}; by an α-Williams number (Wα-number, for short) we mean a positive integer which is both a Kα-number and a K-α-number. Our second main result shows that if p, 3p - 2, 3p + 2 are all prime, then their product is a (3p)-Williams number.
CONGRUENCES FOR ANDREWS' SMALLEST PARTS PARTITION FUNCTION AND NEW CONGRUENCES FOR DYSON'S RANK
Authors: GARVAN F. G.
Published: April 2010

Let spt (n) denote the total number of appearances of smallest parts in the partitions of n. Recently, Andrews showed how spt (n) is related to the second rank moment, and proved some surprising Ramanujan-type congruences mod 5, 7 and 13. We prove a generalization of these congruences using known relations between rank and crank moments. We obtain explicit Ramanujan-type congruences for spt (n) mod ℓ for ℓ = 11, 17, 19, 29, 31 and 37. Recently, Bringmann and Ono proved that Dyson's rank function has infinitely many Ramanujan-type congruences. Their proof is non-constructive and utilizes the theory of weak Maass forms. We construct two explicit nontrivial examples mod 11 using elementary congruences between rank moments and half-integer weight Hecke eigenforms.