bluuebunny/crossref_metadata_2025 huggingface dataset:
ORIGINAL ARTICLE: Coinfection rates in φ6 bacteriophage are enhanced by virus‐induced changes in host cells
Authors: Joseph Sarah B. , Hanley Kathryn A. , Chao Lin , Burch Christina L.
Published: December 2008

Two or more viruses infecting the same host cell can interact in ways that profoundly affect disease dynamics and control, yet the factors determining coinfection rates are incompletely understood. Previous studies have focused on the mechanisms that viruses use to suppress coinfection, but recently the phenomenon of enhanced coinfection has also been documented. In the experiments described here, we explore the hypothesis that enhanced coinfection rates in the bacteriophage φ6 are achieved by virus‐induced upregulation of the φ6 receptor, which is the bacterial pilus. First, we confirmed that coinfection enhancement in φ6 is virus‐mediated by showing that φ6 attaches significantly faster to infected cells than to uninfected cells. Second, we explored the hypothesis that coinfection enhancement in φ6 depends upon changes in the expression of an inducible receptor. Consistent with this hypothesis, the closely related phage, φ12, that uses constitutively expressed lipopolysaccharide as its receptor, attaches to infected and uninfected cells at the same rate. Our results, along with the previous finding that coinfection in φ6 is limited to two virions, suggest that viruses may closely regulate rates of coinfection through mechanisms for both coinfection enhancement and exclusion.
State of Mind, State of Order: Reactions to Ethnic Unrest in the Islamic Republic of Iran
Authors: Elling Rasmus Christian
Published: December 2008

By analysing the symbols and language employed in official statements on two cases of ethnic minority unrest in Iran in 2005–6, the article shows how the Islamic Republic's ideologues and leaders are responding to threats against national security and to alternative definitions of identity. In this emerging discourse, religious and secular notions of patriotism and loyalty are interwoven and an Islamist/nationalist conceptualisation of Iranian nationhood is defended. This interesting process of paradoxical dynamics is an important part of the ongoing struggle to define the identity of Iran in a region boiling with political and cultural conflicts.
Civic and Ethnic Conceptions of Nationhood in the First Czechoslovak Republic: Emanuel Rádl's Theories of Nationalism1
Authors: Novotna Tereza
Published: December 2008

External forces are often seen as a source of the break‐up of Czechoslovakia before World War II. This paper, however, argues that no less significant were the tensions between Czechs and Germans. One of the Czech thinkers who saw the fragility of Czechoslovakia was Emanuel Rádl. The author examines Rádl's concepts of nation and nationality, and introduces his idea of the contractual state. The author criticises certain incongruities in Rádl's theoretical suggestions. Nevertheless, she finds prescient Rádl's vision that the solution of the relation between Czechs and Germans would affect the entire Central European region.
Michelia viridipetala sp. nov. (Magnoliaceae) from Yunnan, China
Authors: Yi Qi‐Fei , Zhou Ren‐Zhang , Zeng Qing‐Wen , Xing Fu‐Wu
Published: December 2008

Michelia viridipetala Law, R. Z. Zhou & Q. F. Yi, a new species of M. sect. Micheliopsis (Magnoliaceae) from Yunnan, China, is described and illustrated. Notes are also presented on the pollen morphology, phenology, ecology and conservation status of the new species. The new species was found growing in the evergreen broad‐leaved forest at altitudes of 1500–1650 m a.s.l. in Faduo Xiang, Xichou County, Yunnan Province, China. It is closely related to M. figo Sprengel, but differs in its higher habit (up to 15 m), densely brown villose indumentum with straight hairs, larger narrowly elliptic or elliptic leaves (12–29.5×4.0–8.5 cm), abaxially pale green outer 3 tepals, densely pubescent ellipsoid–ovoid gynoecia, and 2–3 ovulate carpels.
Gadolinium inhibits group III but not group IV muscle afferent responses to dynamic exercise
Authors: Hayes Shawn G. , McCord Jennifer L. , Koba Satoshi , Kaufman Marc P.
Published: December 2008

Dynamic exercise has been shown to stimulate rapidly both group III and IV muscle afferents. The often rapid (i.e. 2 s) onset latencies of the group IV afferents is particularly surprising because these unmyelinated afferents are thought to respond to the gradual accumulation of metabolites signalling a mismatch between blood/oxygen demand and supply in exercising muscles. One explanation for the rapid onset to exercise by group IV afferents is that they are mechanosensitive, a concept that has been supported by the finding that these afferents were stimulated by vasodilatation induced by injection of vasoactive drugs. We therefore examined in decerebrated cats the effect of gadolinium, a blocker of mechanogated channels, on the responses of group III and IV muscle afferents to dynamic exercise induced by electrical stimulation of the mesencephalic locomotor region. We found that gadolinium (10 mm; 1 ml) injected into the abdominal aorta had no significant effect (P> 0.05) on the responses of 11 group IV afferents to dynamic exercise. In contrast, gadolinium markedly attenuated the responses of 11 group III afferents to exercise (P< 0.05). Our findings suggest that group IV afferents are not responding to a mechanical stimulus during exercise. Instead their rapid response to dynamic exercise might be caused by a chemical substance whose concentration is directly proportional to blood flow, which increases in the skeletal muscles when they are dynamically exercising.
The late gestation fetal cardiovascular response to hypoglycaemia is modified by prior peri‐implantation undernutrition in sheep
Authors: Burrage Deborah M. , Braddick Lucy , Cleal Jane K. , Costello Paula , Noakes David E. , Hanson Mark A. , Green Lucy R.
Published: December 2008

Undernourished late gestation fetuses display asymmetric growth restriction, suggestive of a redistribution of nutritional resources. The modification of fetal organ blood supply in response to acute hypoxia is well characterized, but it is not known whether similar responses occur in response to acute reductions in nutrition, or if such late gestation responses can be influenced by early gestation nutrition. In pregnant sheep, total nutrient requirements were restricted during the peri‐implantation period (PI40, 40%; PI50, 50% of total, days 1–31) or in late gestation (L, 50% total, days 104–postmortem). Control animals were fed 100% nutrient requirements. Fetal organ blood flows were measured at baseline, and during acute fetal hypoglycaemia induced by maternal insulin infusion at 125 dGA. Baseline heart rate was increased in PI40 fetuses. During hypoglycaemia, an initial rise in fetal heart rate was followed by a slower fall. Fetal femoral artery blood flow decreased, and adrenal blood flow and femoral vascular resistance increased in all fetuses during hypoglycaemia. These changes were accompanied by increased fetal plasma adrenaline and cortisol, and reduced plasma insulin levels. The maximum femoral artery blood flow response to hypoglycaemia occurred earlier in PI50 and PI40 compared with control fetuses. The late gestation fetal cardiovascular response to acute hypoglycaemia was consistent with a redistribution of combined ventricular output away from the periphery and towards central organs. One element of the peripheral vascular response was modified by peri‐implantation nutrient restriction, indicating that nutritional challenges early in gestation can have an enduring impact on cardiovascular control.
Characterization of Structural Embrittlement of Creep Crack Growth for W-Added 12%Cr Ferritic Heat-Resistant Steel Related to the Multiaxial Stress
Authors: Sugiura Ryuji , Yokobori A. Toshimitsu , Tabuchi Masaaki , Fuji Akio , Adachi Takeshi
Published: December 2008

In components under static creep loading condition, the multiaxial stress fields appear due to the plastic constraint and they produce a more brittle type cracking behavior. From a practical standpoint, the characterizations of creep crack growth rates under the multiaxial stress field are important to improve the methods for creep life extension. In this paper, creep crack growth tests were conducted using round bar specimens with sharp circular notches for tungsten-added 12%Cr ferritic heat-resistant steel (W12%Cr steel), and the effect of multiaxiality on creep ductility and creep crack growth rate were investigated. Furthermore, three-dimensional elastic-plastic creep finite element analyses were conducted to clarify the effect of multiaxiality on creep crack growth.
Inelastic Contact Behavior of Crystalline Asperities in rf MEMS Devices
Authors: Rezvanian O. , Zikry M. A.
Published: December 2008

Microelectromechanical systems (MEMS), particularly those with radio frequency (rf) applications, have demonstrated significantly better performance over current electromechanical and solid-state technologies. Surface roughness and asperity microcontacts are critical factors that can affect contact behavior at scales ranging from the nano to the micro in MEMS devices. Recent investigations at the continuum level have underscored the importance of microstructural effects on the inelastic behavior of asperity microcontacts. Hence, a microstructurally based approach that accounts for the inhomogeneous deformation of the asperity microcontacts under cyclic loading and that is directly related to asperity physical scales and anisotropies can provide a detailed understanding of the deformation mechanisms associated with asperity microcontacts so that guidelines can be incorporated in the design and fabrication process to effectively size critical components and forces for significantly improved device durability and performance. A physically based microstructural representation of fcc crystalline materials that couples a multiple-slip crystal plasticity formulation to dislocation densities is used in a specialized finite-element modeling framework. The asperity model and the loading conditions are based on realistic service conditions consistent with rf MEMS with metallic normal contacts. The evolving microstructure, stress fields, contact width, hardness, residual effects, and the localized phenomena that can contribute to failure initiation and evolution in the flattening of single crystal gold asperity microcontacts are characterized for a loading-unloading cycle. It is shown that the nonuniform loading conditions due to asperity geometry and contact loading and the size effects due to asperity dimensions result in significant contribution of the geometrically necessary dislocation densities to stress, deformation, and microstructural evolution of crystalline asperities. This is not captured in modeling efforts based on von Mises continuum plasticity formulations. Residual strains and stresses are shown to develop during the cyclic loading. Localized tensile stress regions are shown to develop due to stress reversal and strain hardening during both loading and unloading regimes. Hardness predictions also indicate that nano-indentation hardness values of the contact material can overestimate the contact force in cases, where a rigid flat surface is pressed on a surface roughness asperity.
Purinergic Control of T Cell Activation by ATP Released Through Pannexin-1 Hemichannels
Authors: Schenk Ursula , Westendorf Astrid M. , Radaelli Enrico , Casati Anna , Ferro Micol , Fumagalli Marta , Verderio Claudia , Buer Jan , Scanziani Eugenio , Grassi Fabio
Published: December 2008

Pannexin hemichannel–mediated release of ATP provides an autocrine, costimulatory signal for T cell activation.
Analysis of Metagene Portraits Reveals Distinct Transitions During Kidney Organogenesis
Authors: Tsigelny Igor F. , Kouznetsova Valentina L. , Sweeney Derina E. , Wu Wei , Bush Kevin T. , Nigam Sanjay K.
Published: December 2008

Grouping microarray expression data into metagenes, followed by organization of these gene clusters into self-organizing maps, reveals distinct stages of kidney organogenesis.
γ-Secretase Limits the Inflammatory Response Through the Processing of LRP1
Authors: Zurhove Kai , Nakajima Chikako , Herz Joachim , Bock Hans H. , May Petra
Published: December 2008

Cleavage of the intracellular domain of the lipoprotein receptor LRP1 allows it to transcriptionally inhibit inflammatory responses.
Rethinking Cancer Metastasis
Authors: Kiberstis Paula A.
Published: December 2008

In mice, normal mammary cells can colonize the lung, suggesting that metastases might arise from displaced normal cells acquiring genetic changes that confer malignancy.
More Than Just Constitutively Active
Authors: VanHook Annalisa M.
Published: December 2008

EGFR and EGFRvIII activate target gene expression through distinct mechanisms.
Kinase-Independent Signaling from TGF-β Receptors to TAK1
Authors: Gough Nancy R.
Published: December 2008

TGF-β signals through the type I receptor to trigger Lys63-linked ubiquitylation and activation of the kinase TAK1.
Stressing the Response to an Inflamed Hypothalamus
Authors: Adler Elizabeth M.
Published: December 2008

Hypothalamic IKKβ-NF-κB signaling plays a critical role in the metabolic response to overnutrition.
Mapping Out Redundancy
Authors: Ray L. Bryan
Published: December 2008

Data from an RNAi screen combined with genetic interaction analysis allows construction of a comprehensive kinase cellular signaling network in
Drosophila
.
Probing Pathways Periodically
Authors: Elston Timothy C.
Published: December 2008

Monitoring the response to periodic input signals reveals dynamic properties of a MAPK pathway.
Blood Pressure Control: It’s (Another) Gas!
Authors: Kiberstis Paula A.
Published: December 2008

Hydrogen sulfide gas regulates blood pressure and blood vessel function in mice.
Can You Hear Me Now?
Authors: Ray L. Bryan
Published: December 2008

Adenylyl cyclase molecules appear to shout their message to neighboring inositol 1,4,5-trisphosphate receptors.
Chloride Channel Clinched
Authors: Kelner Katrina L.
Published: December 2008

A transmembrane protein induced in cytokine-treated bronchial epithelial cells seems to be a long-sought primary carrier of a voltage- and calcium-dependent chloride current.
High-Resolution Imaging of Redox Signaling in Live Cells Through an Oxidation-Sensitive Yellow Fluorescent Protein
Authors: Maulucci Giuseppe , Labate Valentina , Mele Marina , Panieri Emiliano , Arcovito Giuseppe , Galeotti Tommaso , Østergaard Henrik , Winther Jakob R. , De Spirito Marco , Pani Giovambattista
Published: December 2008

Measure and visualize intracellular changes in redox state.
The Importance of Meeting at the Pole
Authors: Ray L. Bryan
Published: December 2008

A feedback loop that integrates multiple signaling mechanisms controls bacterial cell division.
NAADP: A Universal Ca
2+
Trigger
Authors: Guse Andreas H. , Lee Hon Cheung
Published: December 2008

NAADP elicits an initial release of calcium, which is subsequently amplified through the action of other calcium messengers.
GSK-3β Masters TLR4 Responses
Authors: Foley John F.
Published: December 2008

GSK-3β inhibits the production of IFN-β by macrophages treated with LPS.
Reproductive Competence Reduces Life Span
Authors: VanHook Annalisa
Published: December 2008

The reproductive system affects life span in
C. elegans
by regulating fat metabolism.
Protein Lifetimes
Authors: Ray L. Bryan
Published: December 2008

A method that determines the half-lives of all cellular proteins has been used to identify targets of a ubiquitin ligase that controls the cell cycle through protein degradation.
Dscam’s Double Duty
Authors: VanHook Annalisa M.
Published: December 2008

The cell adhesion molecule Dscam is also a netrin receptor.
Ubiquitin’s Pup(py)?
Authors: Hurtley Stella M.
Published: December 2008

A prokaryotic version of ubiquitin, a eukaryotic tag for protein degradation, is linked to lysines in prokaryotic proteins destined for destruction, a process called pupylation.
No Oxygen, No Wnt
Authors: Wong Wei
Published: December 2008

Hypoxia inhibits the interaction of Wnt3a with a molecular chaperone, leading to improper processing of Wnt3a and proteosomal degradation.
Fat Roots Implicate New Plant Hormone
Authors: Ray L. Bryan
Published: December 2008

Characterization of receptor-like kinases in
Arabidopsis
links the ethylene synthetic pathway and regulation of cell wall biosynthesis.
Science Signaling
Podcast: 25 November 2008
Authors: May Petra , VanHook Annalisa M.
Published: December 2008

Petra May discusses new findings about a role for LRP1 in inhibiting inflammation.
An Upgrade in the Processor
Authors: Wong Wei
Published: December 2008

Activin treatment of pituitary cells increases its own production, as well as that of an opposing hormone.
The Yin Yang of Root Regulation
Authors: Hines Pamela J.
Published: December 2008

The number of stem cells in plant roots is controlled by an auxin-cytokine feedback loop in which a particular gene integrates signals from both hormones.
Science Signaling
Podcast: 02 December 2008
Authors: Lee Sam W. , Ongusaha Pat P. , VanHook Annalisa M.
Published: December 2008

Sam Lee and Pat Ongusaha discuss their research on the mechanisms by which ultraviolet B radiation induces cell death.
Blue Light Response
Authors: Hines Pamela J.
Published: December 2008

Blue light triggers the association of a photoreceptor, transcription factor, and DNA site, thus inducing expression for the gene
FT
(flowering time) and initiating flowering.
De Novo Organ Formation from Differentiated Cells: Root Nodule Organogenesis
Authors: Crespi Martin , Frugier Florian
Published: December 2008

Root nodule organogenesis in legumes is initiated by bacterial signals and
directed by plant signaling pathways.
Damage Control for Mitochondria
Authors: Wong Wei
Published: December 2008

Parkin translocates to mitochondria with low membrane potentials and causes their autophagic removal.
Ontologies of Cellular NetworksA report on the workshop “Ontologies of Cellular Networks,” Newark, New Jersey, 27 to 28 March 2008.
Authors: Arp Robert , Smith Barry
Published: December 2008

A meeting of philosophers and biologists reveals the great diversity in ideas about how pathway information can be organized.
Turning to the DARC Side
Authors: Adler Elizabeth M.
Published: December 2008

The Duffy antigen receptor for chemokines promotes leukocyte migration.
Controlling Ectodomain Shedding from the Inside
Authors: Gough Nancy R.
Published: December 2008

The GTPase Rab5 acts as a cytosolic molecular switch controlling release of the ectodomain of syndecan-1 from the extracellular surface.
Fault Diagnosis Engineering of Digital Circuits Can Identify Vulnerable Molecules in Complex Cellular Pathways
Authors: Abdi Ali , Tahoori Mehdi Baradaran , Emamian Effat S.
Published: December 2008

An engineering approach reveals the weakest links in cellular signaling networks.
Debio 025, a Cyclophilin Binding Molecule, Is Highly Efficient in Clearing Hepatitis C Virus (HCV) Replicon-Containing Cells When Used Alone or in Combination with Specifically Targeted Antiviral Therapy for HCV (STAT-C) Inhibitors
Authors: Coelmont Lotte , Kaptein Suzanne , Paeshuyse Jan , Vliegen Inge , Dumont Jean-Maurice , Vuagniaux Grégoire , Neyts Johan
Published: December 2008

Debio 025 is a potent inhibitor of hepatitis C virus (HCV) replication (J. Paeshuyse et al., Hepatology 43:761-770, 2006). In phase I clinical studies, monotherapy (a Debio 025 dose of 1,200 mg twice a day) resulted in a mean maximal decrease in the viral load of 3.6 log10units (R. Flisiak et al., Hepatology 47:817-826, 2008), whereas a reduction of 4.6 log10units was obtained in phase II studies when Debio 025 was combined with interferon (R. Flisiak et al., J. Hepatol., 48:S62, 2008). We here report on the particular characteristics of the in vitro anti-HCV activities of Debio 025. The combination of Debio 025 with either ribavirin or specifically targeted antiviral therapy for HCV (STAT-C) inhibitors (NS3 protease or NS5B [nucleoside and nonnucleoside] polymerase inhibitors) resulted in additive antiviral activity in short-term antiviral assays. Debio 025 has the unique ability to clear hepatoma cells from their HCV replicon when it is used alone or in combination with interferon and STAT-C inhibitors. Debio 025, when it was used at concentrations that have been observed in human plasma (0.1 or 0.5 μM), was able to delay or prevent the development of resistance to HCV protease inhibitors as well as to nucleoside and nonnucleoside polymerase inhibitors. Debio 025 forms an attractive drug candidate for the treatment of HCV infections in combination with standard interferon-based treatment and treatments that directly target the HCV polymerase and/or protease.
Roles of the Extraintestinal Pathogenic
Escherichia coli
ZnuACB and ZupT Zinc Transporters during Urinary Tract Infection
Authors: Sabri Mourad , Houle Sébastien , Dozois Charles M.
Published: December 2008

Roles of the ZnuACB and ZupT transporters were assessed in
Escherichia coli
K-12 and uropathogenic
E. coli
(UPEC) CFT073. K-12 and CFT073 Δ
znu
Δ
zupT
mutants demonstrated decreased
65
Zn
2+
uptake and growth in minimal medium. CFT073Δ
znu
demonstrated an intermediate decrease of
65
Zn
2+
uptake and growth in minimal medium, whereas the CFT073Δ
zupT
mutant grew as well as CFT073 and exhibited a less marked decrease in
65
Zn
2+
uptake. CFT073 mutants grew as well as the wild type in human urine. In competitive infections in CBA/J mice, the Δ
zupT
mutant demonstrated no disadvantage during urinary tract infection. In contrast, the UPEC Δ
znu
and Δ
znu
Δ
zupT
strains demonstrated significantly reduced numbers in the bladders (mean 4.4- and 30-fold reductions, respectively) and kidneys (mean 41- and 48-fold reductions, respectively). In addition, in single-strain infection experiments, the Δ
znu
and Δ
znu
Δ
zupT
mutants were reduced in the kidneys (
P
= 0.0012 and
P
< 0.0001, respectively). Complementation of the CFT073 Δ
znu
Δ
zupT
mutant with the
znuACB
genes restored growth in Zn-deficient medium and bacterial numbers in the bladder and kidneys. The loss of the zinc transport systems decreased both motility and resistance to hydrogen peroxide, which could be restored by supplementation with zinc. Overall, the results indicate that Znu and ZupT are required for growth in zinc limited-conditions, that Znu is the predominant zinc transporter, and that the loss of Znu and ZupT has a cumulative effect on fitness during UTI, which may in part be due to reduced resistance to oxidative stress and motility.
Salmonella
-Containing Vacuoles Display Centrifugal Movement Associated with Cell-to-Cell Transfer in Epithelial Cells
Authors: Szeto Jason , Namolovan Anton , Osborne Suzanne E. , Coombes Brian K. , Brumell John H.
Published: December 2008

Intracellular
Salmonella enterica
serovar Typhimurium (serovar Typhimurium) occupies a
Salmonella
-containing vacuole (SCV) where bacterial effector proteins are secreted into the host cell using type III secretion systems (T3SS). Cytoskeletal motor proteins and T3SS-delivered effector proteins facilitate SCV positioning to juxtanuclear positions where bacterial replication occurs. Here, we show that this characteristic SCV positioning is not maintained by all SCVs during infection of HeLa cells. Notably, juxtanuclear SCV localization that occurs by 8 to 14 h postinfection is followed by significant centrifugal displacement of a subset of SCVs toward the host cell periphery by 24 h postinfection. This novel phenotype requires bacterial protein synthesis, a functional
Salmonella
pathogenicity island 2 (SPI-2)-encoded T3SS, intact microtubules, and kinesin-1 motor protein. Bacteria lacking PipB2, a kinesin-recruiting T3SS effector, did not exhibit centrifugal displacement and remained at juxtanuclear positions throughout 24 h of infection. While levels of the SPI-2 effectors PipB2 and SifA increased during 24 h postinfection, a corresponding decrease in levels of the SPI-1 T3SS effectors SipA and SopB, both known to mediate juxtanuclear SCV positioning, was observed. A fluorescence-based assay indicated that wild-type serovar Typhimurium transferred from infected to uninfected epithelial cells while strains deficient in SPI-2 T3SS secretion or PipB2 did not. Our results reveal a novel SCV phenotype implicated in the cell-to-cell spread of serovar Typhimurium during infection.
Major Surface Protein LipL32 Is Not Required for Either Acute or Chronic Infection with
Leptospira interrogans
Authors: Murray Gerald L. , Srikram Amporn , Hoke David E. , Wunder Elsio A. , Henry Rebekah , Lo Miranda , Zhang Kunkun , Sermswan Rasana W. , Ko Albert I. , Adler Ben
Published: December 2008

Leptospira interrogans
is responsible for leptospirosis, a zoonosis of worldwide distribution. LipL32 is the major outer membrane protein of pathogenic leptospires, accounting for up to 75% of total outer membrane protein. In recent times LipL32 has become the focus of intense study because of its surface location, dominance in the host immune response, and conservation among pathogenic species. In this study, an
lipL32
mutant was constructed in
L. interrogans
using transposon mutagenesis. The
lipL32
mutant had normal morphology and growth rate compared to the wild type and was equally adherent to extracellular matrix. Protein composition of the cell membranes was found to be largely unaffected by the loss of LipL32, with no obvious compensatory increase in other proteins. Microarray studies found no obvious stress response or upregulation of genes that may compensate for the loss of LipL32 but did suggest an association between LipL32 and the synthesis of heme and vitamin B
12
. When hamsters were inoculated by systemic and mucosal routes, the mutant caused acute severe disease manifestations that were indistinguishable from wild-type
L. interrogans
infection. In the rat model of chronic infection, the LipL32 mutant colonized the renal tubules as efficiently as the wild-type strain. In conclusion, this study showed that LipL32 does not play a role in either the acute or chronic models of infection. Considering the abundance and conservation of LipL32 among all pathogenic
Leptospira
spp. and its absence in saprophytic
Leptospira
, this finding is remarkable. The role of this protein in leptospiral biology and pathogenesis thus remains elusive.
Characterization of the Cpx Regulon inEscherichia coliStrain MC4100
Authors: Price Nancy L. , Raivio Tracy L.
Published: December 2008

The Cpx two-component signal transduction pathway ofEscherichia colimediates adaptation to envelope protein misfolding. However, there is experimental evidence that at least 50 genes in 34 operons are part of the Cpx regulon and many have functions that are undefined or unrelated to envelope protein maintenance. No comprehensive analysis of the Cpx regulon has been presented to date. In order to identify strongly Cpx-regulated genes that might play an important role(s) in envelope protein folding and/or to further define the role of the Cpx response and to gain insight into what makes a gene subject to strong Cpx regulation, we have carried out a uniform characterization of a Cpx-regulatedluxreporter library in a single-strain background. Strongly Cpx-regulated genes encode proteins that are directly linked to envelope protein folding, localized to the envelope but uncharacterized, or involved in limiting the cellular concentration of noxious molecules. Moderately Cpx-regulated gene clusters encode products implicated in biofilm formation. An analysis of CpxR binding sites in strongly regulated genes indicates that while neither a consensus match nor their orientation predicts the strength of Cpx regulation, most genes contain a CpxR binding site within 100 bp of the transcriptional start site. Strikingly, we found that while there appears to be little overlap between the Cpx and Bae envelope stress responses, the σEand Cpx responses reciprocally regulate a large group of strongly Cpx-regulated genes, most of which are uncharacterized.
The Membrane Lipoprotein LppX of
Paenibacillus
sp. Strain W-61 Serves as a Molecular Chaperone for Xylanase of Glycoside Hydrolase Family 11 during Secretion across the Cytoplasmic Membrane
Authors: Fukuda Mutsumi , Watanabe Seiji , Kaneko Jun , Itoh Yoshifumi , Kamio Yoshiyuki
Published: December 2008

Paenibacillus
sp. strain W-61, which can utilize xylan as the sole source of carbon and energy, produces extracellular xylanases 1 and 3 (Xyn1 and Xyn3) and cell surface xylanase 5. In this study we found that
lppX
, immediately downstream of
xyn1
, encodes a lipoprotein located on the outer layer of the cytoplasmic membrane and that the LppX lipoprotein is essential for the secretion of active Xyn1 across the cytoplasmic membranes. In
Escherichia coli
, wild-type LppX was destined for the inner layer of the outer membrane. Mutant LppX(C19A), in which Cys-19, a possible lipomodification residue, is replaced with Ala, was located in the periplasm without being anchored to the membranes. Another mutant, LppX(S20D S21D), with substitutions of Asp for Ser-20 and Ser-21 (conversion to an Asp-Asp signal for sorting to the inner membrane), resided on the outer layer of the inner membrane, demonstrating that LppX has the sorting property of a lipoprotein.
E. coli
harboring both
xyn1
and
lppX
secreted active Xyn1 into the periplasm. In contrast,
E. coli
carrying
xyn1
alone failed to do so, accumulating inactive Xyn1 in the cytoplasmic membranes. Exogenous LppX(C19A) liberated the inactive Xyn1, which had been stagnating in the inner membrane, into the medium as an active enzyme. Thus, we propose that LppX is a novel type of lipoprotein that assists Xyn1 in making the proper fold necessary for traveling across the cytoplasmic membranes to be secreted as an active enzyme.
COUPLED DOUBLE-DISTRIBUTION-FUNCTION LATTICE BOLTZMANN MODEL WITH AN ADJUSTABLE BULK VISCOSITY
Authors: LI Q. , HE Y. L. , GAO Y. J.
Published: December 2008

A coupled double-distribution-function (DDF) lattice Boltzmann method was recently developed for the compressible Navier–Stokes equations. In this method, the specific-heat ratio and the Prandtl number can be easily adjusted. However, the ratio between the bulk and shear viscosities is fixed at a value related to the specific-heat ratio. In order to obtain a bulk viscosity satisfying the Stokes' hypothesis or an adjustable bulk viscosity in the recovered momentum and energy equations, correction terms, which are proportional to the divergence of macroscopic velocity, are incorporated into the microscopic evolution equations. The constraints imposed on these correction terms can be derived from the Chapman–Enskog analysis. With these constraints, the forms of the correction terms can be determined, and then a coupled DDF lattice Boltzmann model with adjustable specific-heat ratio, Prandtl number, and bulk viscosity can be obtained. Numerical simulations are performed for the attenuation of sound waves. The numerical results are found to be in good agreement with the theoretical solutions.
A MULTI-AGENT-BASED APPROACH TO TAX MORALE
Authors: LIMA F. W. S. , ZAKLAN GEORG
Published: December 2008

We embed the behavior of tax evasion into the standard two-dimensional Ising model. In the presence of an external magnetic field, the Ising model is able to generate the empirically observed effect of tax morale, i.e., the phenomenon that in some countries tax evasion is either rather high or low. The external magnetic field captures the agents' trust in governmental institutions. We also find that tax authorities may curb tax evasion via appropriate enforcement mechanisms. Our results are robust for the Barabási–Albert and Voronoi–Delaunay networks.
MODELING THE TOPOLOGY OF SDH NETWORKS
Authors: SANTIAGO A. , CÁRDENAS J. P. , MOURONTE M. L. , FELIU V. , BENITO R. M.
Published: December 2008

SDH (Synchronous Digital Hierarchy) is the standard technology for the information transmission in broadband optical networks. Unlike the Internet, SDH networks are strictly planned; rings, meshes, stars, or tree-branches topologies are designed to connect their basic elements. In spite of that, we have found that the SDH network operated by Telefónica in Spain shares remarkable topological properties with other real complex networks empirically analyzed, such as the worldwide web network. In particular, we have found power-law scaling in the degree distribution (P(k) ~ k-γ) and properties of small world networks. Considering real planning directives that take into account geographical and technological variables, we propose an ad hoc computational model that reproduces the aforementioned topological traits observed in the Spanish SDH network.
VALIDATING RANGE-DEPENDENT, FULL-FIELD MODELS OF THE ACOUSTIC VECTOR FIELD IN SHALLOW WATER ENVIRONMENTS
Authors: SMITH KEVIN B.
Published: December 2008

Numerical algorithms for computing acoustic particle velocity from a pressure propagation model are introduced. Implementation using both a parabolic equation and normal mode approach are considered. The parabolic equation model employed uses a split-step Fourier algorithm, although application of the technique is general to other parabolic equation models. Expressions for the normal mode equations are also presented, for both coupled and adiabatic mode models. Results for a Pekeris waveguide are presented for a point source, prompting a brief discussion of multipath influence on the estimation of the direction of energy flow. Approximate analytic solutions are used to validate the general results of both the models. Results for the range-dependent benchmark wedge are then presented, which show generally good agreement between the two types of models. The results from the two-way, coupled normal mode model provide potential benchmark solutions for the wedge and a means of confirming the accuracy of other models.
How are we doing?
Authors: Vardi Moshe Y.
Published: December 2008

A rabbinical story tells about an angry reader who stormed into a newspaper office waving the day's paper, asking to see the editor of the obituary column.
Technology strategy and managementThe legacy of Bill Gates
Authors: Cusumano Michael
Published: December 2008

Assessing the pluses and minuses of the helmsmanship of Microsoft Corporation since its inception.
The long road to 64 bits
Authors: Mashey John
Published: December 2008

Double, double toil and trouble ---Shakespeare,
Macbeth
, Act 4, Scene 1
Engineering rural development
Authors: Parikh Tapan S.
Published: December 2008

Information systems enable rural development by increasing the accountability of nongovernmental organizations.
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Pad services for vision-, hearing-, and speech-impaired users
Authors: Jutla Dawn N. , Kanevsky Dimitri
Published: December 2008

They promise mobile information access and assistive Web services for tens of millions worldwide.
Computational challenges in e-commerce
Authors: Feigenbaum Joan , Parkes David C. , Pennock David M.
Published: December 2008

Economic and social sciences will drive Internet protocols and services into the future.
Q&AThe upper limit
Authors: Hoffmann Leah
Published: December 2008

Jeannette Wing talks about clusters, creativity, and the power of computational thinking.
TIMELINESSound in computing
Authors: Robare Paul , Forlizzi Jodi
Published: December 2008

This account of ways in which computers have interacted with us via our ears is a welcome first, an over-the-transom, unsolicited Timelines contribution.---Jonathan Grudin
ALCAT1 is a polyglycerophospholipid acyltransferase potently regulated by adenine nucleotide and thyroid status
Authors: Cao Jingsong , Shen Weiqun , Chang Zhijie , Shi Yuguang
Published: December 2008

Acyl-CoA:lysocardiolipin acyltransferase-1 (ALCAT1) catalyzes acylation of lysocardiolipin back to cardiolipin, an important step in cardiolipin remodeling. The present study reports the catalytic properties of ALCAT1 in vitro and its regulation by thyroid hormone status in mouse liver and heart. Recombinant ALCAT1 expressed in Sf9 cells preferred basic pH conditions and did not require divalent cations or integrity of the subcellular membrane for its enzymatic activity. Recombinant ALCAT1 was potently inhibited by ADP and ATP, but not by adenosine nucleotide analogs or other nucleotides, such as UTP and GTP, suggesting that ALCAT1 does not require ATP hydrolysis for its enzyme activity. In addition to cardiolipin, ALCAT1 also catalyzed acylation of other members of the polyglycerophospholipid family, including phosphatidylglycerol, a precursor for cardiolipin synthesis, and bis(monoacylglycero)phosphate, a structural isomer of lysophosphatidylglycerol and a metabolic intermediate of cardiolipin. These findings suggest that ALCAT1 plays a role in the remodeling of other polyglycerophospholipids. In support of a regulatory role of ALCAT1 in cardiolipin remodeling in response to oxidative stress, ALCAT1 expression in liver and heart was significantly downregulated in mice with hypothyroidism and upregulated in mice treated with thyroid hormone, which is known to stimulate mitochondrial activity, oxidative stress, and cardiolipin remodeling.
Glomerular surface area is normalized in mice born with a nephron deficit: no role for AT1receptors
Authors: Shweta Amany , Cullen-McEwen Luise A. , Kett Michelle M. , Evans Roger G. , Denton Kate M. , Fitzgerald Sharyn M. , Anderson Warwick P. , Bertram John F.
Published: December 2008

We examined whether deficits in glomerular capillary surface area associated with a congenital nephron deficit could be corrected by glomerular hypertrophy. Using unbiased stereological techniques, we examined the time course and mode of glomerular hypertrophy in mice lacking one allele for glial cell line-derived neurotrophic factor (GDNF). These GDNF heterozygous (Het) mice are born with ∼30% less nephrons than wild-type (WT) littermates. An additional group of GDNF Het mice received the angiotensin type 1 (AT1)-receptor antagonist candesartan (Cand; 10 mg·kg−1·day−1) from 5 wk of age to determine the role of AT1receptors in the compensatory hypertrophy. At 10 wk of age, the total volume of renal corpuscles, glomerular capillary surface area, and length of glomerular capillaries in the kidneys of GDNF Het mice were all markedly (∼45%) less than that of WT mice ( P < 0.001). However, by 30 wk, and persisting at 60 wk of age, GDNF Het and WT mice did not significantly differ in any of these parameters. Furthermore, conscious 24-h mean arterial pressure (MAP) did not differ between GDNF Het and WT mice at any time point. MAP of GDNF Het-Cand mice was 20–30 mmHg less than that of GDNF Het-vehicle mice at all three ages, but Cand treatment did not significantly alter glomerular capillary dimensions. In conclusion, we have demonstrated that the deficit in glomerular capillary surface area associated with a congenital nephron deficit can be corrected for in adulthood by an increase in the total length of glomerular capillaries. This process does not require AT1receptor activation.
Role of cytosolic NADP+-dependent isocitrate dehydrogenase in ischemia-reperfusion injury in mouse kidney
Authors: Kim Jinu , Kim Ki Young , Jang Hee-Seong , Yoshida Takumi , Tsuchiya Ken , Nitta Kosaku , Park Jeen-Woo , Bonventre Joseph V. , Park Kwon Moo
Published: December 2008

Cytosolic NADP+-dependent isocitrate dehydrogenase (IDPc) synthesizes reduced NADP (NADPH), which is an essential cofactor for the generation of reduced glutathione (GSH), the most abundant and important antioxidant in mammalian cells. We investigated the role of IDPc in kidney ischemia-reperfusion (I/R) in mice. The activity and expression of IDPc were highest in the cortex, modest in the outer medulla, and lowest in the inner medulla. NADPH levels were greatest in the cortex. IDPc expression in the S1 and S2 segments of proximal tubules was higher than in the S3 segment, which is much more susceptible to I/R. IDPc protein was also highly expressed in the mitochondrion-rich intercalated cells of the collecting duct. IDPc activity was 10- to 30-fold higher than the activity of glucose-6-phosphate dehydrogenase, another producer of cytosolic NADPH, in various kidney regions. This study identifies that IDPc may be the primary source of NADPH in the kidney. I/R significantly reduced IDPc expression and activity and NADPH production and increased the ratio of oxidized glutathione to total glutathione [GSSG/(GSH+GSSG)], resulting in kidney dysfunction, tubular cell damage, and lipid peroxidation. In LLC-PK1cells, upregulation of IDPc by IDPc gene transfer protected the cells against hydrogen peroxide, enhancing NADPH production, inhibiting the increase of GSSG/(GSH+GSSG), and reducing lipid peroxidation. IDPc downregulation by small interference RNA treatment presented results contrasting with the upregulation. In conclusion, these results demonstrate that IDPc is expressed differentially along tubules in patterns that may contribute to differences in susceptibility to injury, is a major enzyme in cytosolic NADPH generation in kidney, and is downregulated with I/R.
Staphylococcus aureusand MRSA Colonization Rates among Gravidas Admitted to Labor and Delivery: A Pilot Study
Authors: Beigi R. , Hanrahan J.
Published: December 2008

Objective. To determine colonization rates ofStaphylococcus aureusgiven the potential for future intervention trials aimed at reducing surgical-site infectious morbidity, and to estimate methicillin-resistantStaphylococcus aureus(MRSA) rates in our patient population.Study design. Prospective pilot investigation comprising data from 104 gravidas admitted to an urban labor and delivery unit. All underwent anterior nares culture collection with a subset also undergoing vaginal culture collection.Results. Twenty-two percent of women were colonized in the anterior nares. Of the 28 women who had vaginal cultures collected, 4/28 (14.2%) demonstratedStaphylococcus aureuscolonization. There was 82% concordance between the nares and vagina. Nine percent of isolates were MRSA strains. Overall, 2/96 (2.1%) of women were MRSA-colonized.Conclusions. Rates ofStaphylococcus aureuscolonization among gravidas entering labor and delivery are modest and consistent with the general population. MRSA rates among gravidas appear to be reassuringly low in this pilot study.
Permanence of a Discrete Predator‐Prey Systems with Beddington‐DeAngelis Functional Response and Feedback Controls
Authors: Li Xuepeng , Yang Wensheng
Published: December 2008

We propose a discrete predator‐prey systems with Beddington‐DeAngelis functional response and feedback controls. By applying the comparison theorem of difference equation, sufficient conditions are obtained for the permanence of the system.
Inhibition of Angiogenic Factor Production from Murine Mast Cells by an Antiallergic Agent (Epinastine Hydrochloride) In Vitro
Authors: Asano K. , Furuta A. , Kanai K. , Sakaue S. , Suzaki H. , Hisamitsu T.
Published: December 2008

Angiogenesis is an important event both in the development of allergic inflammatory responses and in the pathophysiology of tissue remodeling in allergic diseases. In the present study, therefore, we examined the influence of antihistamines on angiogenesis through the choice of epinastine hydrochloride (EP) and murine mast cells in vitro. Mast cells (5 × 105 cells/mL) presensitized with murine IgE specific for ovalbumin (OVA) were stimulated with 10 ng/mL OVA in the presence of various concentrations of EP for 4 hours. The levels of angiogenesis factors, keratinocyte‐derived chemokine (KC), tumor necrosis factor‐α (TNF), and vascular endothelial growth factor (VEGF) in culture supernatants, were examined by ELISA. We also examined mRNA expression for the angiogenesis factors by RT‐PCR. EP significantly inhibited the production of KC, TNF, and VEGF induced by IgE‐dependent mechanism at more than 25 ng/mL. Semiquantitative analysis using RT‐PCR showed that EP also significantly reduced mRNA expressions for KC, TNF, and VEGF. These results strongly suggest that EP suppresses angiogenesis factor production through the inhibition of mRNA expression in mast cells and results in favorable modification of clinical conditions of allergic diseases.
Estimation of Subpixel Motion Using Bispectrum
Authors: Ismaili Aalaoui El Mehdi , Ibn-Elhaj Elhassane
Published: December 2008

Motion estimation techniques are widely used in today′s video processing systems. The frequently used techniques are frequency‐domain motion estimation methods, most notably phase correlation (PC). If the image frames are corrupted by Gaussian noises, then cross‐correlation and related techniques do not work well. In this paper, however, we have studied this topic from a viewpoint different from the above. Our scheme is based on the bispectrum method for sub‐pixel motion estimation of noisy image sequences. Experimental results show that our proposed method performs significantly better than PC technique.
Elliptic Equations in Weighted Sobolev Spaces on Unbounded Domains
Authors: Boccia Serena , Monsurrò Sara , Transirico Maria
Published: December 2008

We study in this paper a class of second‐order
linear elliptic equations in weighted Sobolev spaces on unbounded
domains of ℝn, n ≥ 3. We obtain an a priori bound, and a regularity
result from which we deduce a uniqueness theorem.
Pulmonary Tuberculosis in a Young Pregnant Female: Challenges in Diagnosis and Management
Authors: Maddineni Manogna , Panda Mukta
Published: December 2008

Background. With the world becoming a global village, tuberculosis is no longer limited to endemic areas. Our case emphasizes the impact of immigration on infectious disease epidemiology and challenges associated with diagnosis and treatment in pregnancy.Case. A 21-year-old Hispanic female presented in preterm labor and was found to be hypoxic. Chest X-ray revealed a paratracheal mass which a CT scan confirmed. PPD test was positive. Bronchoalveolar lavage did not reveal acid-fast bacilli and biopsy revealed caseating granulomas. Diagnosis and treatment were challenging due to constraints in radiological investigations, lack of initial evidence of acid-fast bacilli, and toxic profile of medications. Due to her high risk, she was started on antituberculosis regimen. The diagnosis was confirmed on Day 26 whenMycobacterium tuberculosiswas isolated by DNA probe.Conclusion. A high index of suspicion is required to recognize the changing face and disease spectrum of tuberculosis and initiate treatment for better outcomes.
Strong Convergence Theorem of Implicit Iteration Process for Generalized Asymptotically Nonexpansive Mappings in Hilbert Space
Authors: He Lili , Deng Lei , Liu Jianjun
Published: December 2008

Let C be a nonempty closed and convex subset of a Hilbert space H, let T and S : C → C be two commutative generalized asymptotically nonexpansive mappings. We introduce an implicit iteration process of S and T defined by , and then prove that {xn} converges strongly to a common fixed point of S and T. The results generalize and unify the corresponding results.
Nonlocal Boundary Value Problems for Elliptic‐Parabolic Differential and Difference Equations
Authors: Ashyralyev Allaberen , Gercek Okan
Published: December 2008

The abstract nonlocal boundary value problem −d2u(t)/dt2 + Au(t) = g(t), 0 < t < 1, du(t)/dt − Au(t) = f(t), 1 < t < 0, u(1) = u(−1) + μ
for differential equations in a Hilbert space H with the self‐adjoint positive definite
operator A is considered. The well‐posedness of this problem in Hölder spaces with
a weight is established. The coercivity inequalities for the solution of boundary value
problems for elliptic‐parabolic equations are obtained. The first order of accuracy difference
scheme for the approximate solution of this nonlocal boundary value problem
is presented. The well‐posedness of this difference scheme in Hölder spaces is established.
In applications, coercivity inequalities for the solution of a difference scheme
for elliptic‐parabolic equations are obtained.