bluuebunny/crossref_metadata_2025_split huggingface dataset:
Berberine-INF55 (5-Nitro-2-Phenylindole) Hybrid Antimicrobials: Effects of Varying the Relative Orientation of the Berberine and INF55 Components
Authors: Tomkiewicz Danuta , Casadei Gabriele , Larkins-Ford Jonah , Moy Terence I. , Garner James , Bremner John B. , Ausubel Frederick M. , Lewis Kim , Kelso Michael J. 
Published: May 2010

ABSTRACT

Hybrid antimicrobials containing an antibacterial linked to a multidrug resistance (MDR) pump inhibitor make up a promising new class of agents for countering efflux-mediated bacterial drug resistance. This study explores the effects of varying the relative orientation of the antibacterial and efflux pump inhibitor components in three isomeric hybrids (SS14, SS14-M, and SS14-P) which link the antibacterial alkaloid and known substrate for the NorA MDR pump berberine to different positions on INF55 (5-nitro-2-phenylindole), an inhibitor of NorA. The MICs for all three hybrids against wild-type, NorA-knockout, and NorA-overexpressing
Staphylococcus aureus
cells were found to be similar (9.4 to 40.2 μM), indicating that these compounds are not effectively effluxed by NorA. The three hybrids were also found to have similar curing effects in a
Caenorhabditis elegans
live infection model. Each hybrid was shown to accumulate in
S. aureus
cells to a greater extent than either berberine or berberine in the presence of INF55, and the uptake kinetics of SS14 were found to differ from those of SS14-M and SS14-P. The effects on the uptake and efflux of the NorA substrate ethidium bromide into
S. aureus
cells in the presence or absence of the hybrids were used to confirm MDR inhibition by the hybrids. MDR-inhibitory activity was confirmed for SS14-M and SS14-P but not for SS14. Molecular dynamics simulations revealed that SS14 prefers to adopt a conformation that is not prevalent in either SS14-M or SS14-P, which may explain why some properties of SS14 diverge from those of its two isomers. In summary, subtle repositioning of the pump-blocking INF55 moiety in berberine-INF55 hybrids was found to have a minimal effect on their antibacterial activities but to significantly alter their effects on MDR pumps.
Human Antimicrobial Peptide LL-37 Induces MefE/Mel-Mediated Macrolide Resistance in
Streptococcus pneumoniae
Authors: Zähner Dorothea , Zhou Xiaoliu , Chancey Scott T. , Pohl Jan , Shafer William M. , Stephens David S. 
Published: May 2010

ABSTRACT

Macrolide resistance is a major concern in the treatment of
Streptococcus pneumoniae
. Inducible macrolide resistance in this pneumococcus is mediated by the efflux pump MefE/Mel. We show here that the human antimicrobial peptide LL-37 induces the
mefE
promoter and confers resistance to erythromycin and LL-37. Such induction may impact the efficacy of host defenses and of macrolide-based treatment of pneumococcal disease.
Salmonella enterica
Serovar Enteritidis
tatB
and
tatC
Mutants Are Impaired in Caco-2 Cell Invasion
In Vitro
and Show Reduced Systemic Spread in Chickens
Authors: Mickael Claudia Silva , Lam Po-King S. , Berberov Emil M. , Allan Brenda , Potter Andrew A. , Köster Wolfgang 
Published: May 2010

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Enteritidis is a leading causative agent of gastroenteritis in humans. This pathogen also colonizes the intestinal tracts of poultry and can spread systemically in chickens. Transfer to humans usually occurs through undercooked or improperly handled poultry meat or eggs. The bacterial twin-arginine transport (Tat) pathway is responsible for the translocation of folded proteins across the cytoplasmic membrane. In order to study the role of the Tat system in the infection and colonization of chickens by
Salmonella
Enteritidis, we constructed chromosomal deletion mutants of the
tatB
and
tatC
genes, which are essential components of the Tat translocon. We observed that the
tat
mutations affected bacterial cell morphology, motility, and sensitivity to albomycin, sodium dodecyl sulfate (SDS), and EDTA. In addition, the mutant strains showed reduced invasion of polarized Caco-2 cells. The wild-type phenotype was restored in all our
Salmonella
Enteritidis
tat
mutants by introducing episomal copies of the
tatABC
genes. When tested in chickens by use of a
Salmonella
Enteritidis Δ
tatB
strain, the Tat system inactivation did not substantially affect cecal colonization, but it delayed systemic infection. Taken together, our data demonstrated that the Tat system plays a role in
Salmonella
Enteritidis pathogenesis.
Ail Binding to Fibronectin Facilitates
Yersinia pestis
Binding to Host Cells and Yop Delivery
Authors: Tsang Tiffany M. , Felek Suleyman , Krukonis Eric S. 
Published: May 2010

ABSTRACT

Yersinia pestis
, the causative agent of plague, evades host immune responses and rapidly causes disease. The
Y. pestis
adhesin Ail mediates host cell binding and is critical for Yop delivery. To identify the Ail receptor(s), Ail was purified following overexpression in
Escherichia coli
. Ail bound specifically to fibronectin, an extracellular matrix protein with the potential to act as a bridge between Ail and host cells. Ail expressed by
E. coli
also mediated binding to purified fibronectin, and Ail-mediated
E. coli
adhesion to host cells was dependent on fibronectin. Ail expressed by
Y. pestis
bound purified fibronectin, as did the
Y. pestis
adhesin plasminogen activator (Pla). However, a KIM5 Δ
ail
mutant had decreased binding to host cells, while a KIM5 Δ
pla
mutant had no significant defect in adhesion. Furthermore, treatment with antifibronectin antibodies decreased Ail-mediated adhesion by KIM5 and the KIM5 Δ
pla
mutant, indicating that the Ail-fibronectin interaction was important for cell binding. Finally, antifibronectin antibodies inhibited the KIM5-mediated cytotoxicity of host cells in an Ail-dependent fashion. These data indicate that Ail is a key adhesin that mediates binding to host cells through interaction with fibronectin on the surface of host cells, and this interaction is important for Yop delivery by
Y. pestis
.
‘Acceptable rebellion’: marketing hipster aesthetics to sell Camel cigarettes in the US
Authors: Hendlin Yogi , Anderson Stacey J , Glantz Stanton A 
Published: May 2010

ObjectiveThe aim of the present work was to understand why and how RJ Reynolds and other tobacco companies have marketed tobacco products to young adult social trendsetting consumers (termed ‘hipsters’) to recruit trendsetters and average consumers to smoke.MethodsAnalysis of tobacco industry documents and industry marketing materials.ResultsSince 1995, RJ Reynolds developed its marketing campaigns to better suit the lifestyle, image identity and attitudes of hip trendsetters (so-called ‘hipsters’), and Camel's brand identity actively shifted to more closely convey the hipster persona. Camel emphasised in-venue events such as promotional music tours to link the brand and smoking to activities and symbols appealing to hipsters and their emulating masses.ConclusionsTo reach this targeted and socially valuable trend-setting population, public health advocates must tap into hipster psychology and expose to the targeted community the tobacco company's efforts to infiltrate the hipster community to turn hipsters into tobacco-using role models.
Advances in Extracting Cloud Composition Information from Spaceborne Infrared Radiances—A Robust Alternative to Brightness Temperatures. Part I: Theory
Authors: Pavolonis Michael J. 
Published: May 2010

Abstract
Infrared measurements can be used to obtain quantitative information on cloud microphysics, including cloud composition (ice, liquid water, ash, dust, etc.), with the advantage that the measurements are independent of solar zenith angle. As such, infrared brightness temperatures (BT) and brightness temperature differences (BTD) have been used extensively in quantitative remote sensing applications for inferring cloud composition. In this study it is shown that BTDs are fundamentally limited and that a more physically based infrared approach can lead to significant increases in sensitivity to cloud microphysics, especially for optically thin clouds. In lieu of BTDs, a derived radiative parameter β, which is directly related to particle size, habit, and composition, is used. Although the concept of effective absorption optical depth ratios β has been around since the mid-1980s, this is the first study to explore the use of β for inferring cloud composition in the total absence of cloud vertical boundary information. The results showed that, even in the absence of cloud vertical boundary information, one could significantly increase the sensitivity to cloud microphysics by converting the measured radiances to effective emissivity and constructing effective absorption optical depth ratios from a pair of spectral emissivities in the 8–12-μm “window.” This increase in sensitivity to cloud microphysics is relative to BTDs constructed from the same spectral pairs. In this article, the focus is on describing the physical concepts (which can be applied to narrowband or hyperspectral infrared measurements) used in constructing the β data space.
Convective Snowbands Downstream of the Rocky Mountains in an Environment with Conditional, Dry Symmetric, and Inertial Instabilities
Authors: Schumacher Russ S. , Schultz David M. , Knox John A. 
Published: May 2010

Abstract
Convective snowbands moved slowly over Wyoming and northern Colorado on 16–17 February 2007 and produced up to 71 mm (2.8 in.) of snow that was unpredicted by operational numerical weather prediction models and human forecasters. The northwest–southeast-oriented bands lasted for over 6 h, comprising both a single major band (more than 30 km wide) and multiple minor bands (about 10 km wide). The convective bands initiated within the ascending branch of a secondary circulation associated with both near-surface and elevated frontogenesis, but the bands remained nearly stationary while the near-surface frontogenesis moved quickly equatorward. The bands occurred downstream of complex terrain on the anticyclonic-shear side of a midlevel jet streak, where conditional, dry symmetric (negative potential vorticity), and inertial (negative absolute vorticity) instabilities were present.
To determine the mechanisms responsible for the development and organization of these bands, simulations using a convection-permitting numerical model are conducted. In contrast to the operational models, these simulations are able to produce convective bands in the same area and at about the same time as that observed. The simulated bands occurred in an environment with a nearly well-mixed, baroclinic boundary layer, positive convective available potential energy, and widespread negative potential vorticity. Individual bands initiated on the low-momentum side of vorticity banners downstream of mountains, and in association with frontogenetical ascent along two baroclinic zones. In addition, ascent caused by both frontogenesis and banded moist convection produced additional narrow regions of negative vorticity by transporting low-momentum air upward and creating strong horizontal gradients in wind speed. This event is similar to other observed instances of banded convection in the western United States on the anticyclonic-shear side of strong mid- and upper-tropospheric jets in environments lacking large-scale saturation. In contrast, these events differ from previously published banded precipitation events in the comma head of extratropical cyclones and downstream of mountains where large-scale saturation is present.
Dynamical Core of an Atmospheric General Circulation Model on a Yin–Yang Grid
Authors: Baba Yuya , Takahashi Keiko , Sugimura Takeshi , Goto Koji 
Published: May 2010

Abstract
The three-dimensional dynamical core of an atmospheric general circulation model employing Yin–Yang grid is developed and examined. Benchmark test cases based on the shallow-water model configuration are first performed to examine the validity of two-dimensional calculations. The experiments show that the model simulates reasonable flow fields with second-order accuracy. The model validation is then extended to three-dimensional features where the capability of the dynamical core on the Yin–Yang grid has not been tested before: the global mountain gravity wave, long-term integration, and life cycle experiments. The simulated flow fields are in good agreement with the results of original experiments in all three experiments. The sensitivity of the model flow field to the overset region is also tested. The experiments reveal that the presence of the overset region does not significantly affect the dynamics on both long and short time scales, if the number of overset grids is fixed to three and the high-order interpolation method is applied for data interpolation between the Yin–Yang grids.
Lack of glucose recycling between endoplasmic reticulum and cytoplasm underlies cellular dysfunction in glucose-6-phosphatase-β–deficient neutrophils in a congenital neutropenia syndrome
Authors: Jun Hyun Sik , Lee Young Mok , Cheung Yuk Yin , McDermott David H. , Murphy Philip M. , De Ravin Suk See , Mansfield Brian C. , Chou Janice Y. 
Published: May 2010

AbstractG6PC3 deficiency, characterized by neutropenia and neutrophil dysfunction, is caused by deficiencies in the endoplasmic reticulum (ER) enzyme glucose-6-phosphatase-β (G6Pase-β or G6PC3) that converts glucose-6-phosphate (G6P) into glucose, the primary energy source of neutrophils. Enhanced neutrophil ER stress and apoptosis underlie neutropenia in G6PC3 deficiency, but the exact functional role of G6Pase-β in neutrophils remains unknown. We hypothesized that the ER recycles G6Pase-β–generated glucose to the cytoplasm, thus regulating the amount of available cytoplasmic glucose/G6P in neutrophils. Accordingly, a G6Pase-β deficiency would impair glycolysis and hexose monophosphate shunt activities leading to reductions in lactate production, adenosine-5′-triphosphate (ATP) production, and reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity. Using annexin V–depleted neutrophils, we show that glucose transporter-1 translocation is impaired in neutrophils from G6pc3−/− mice and G6PC3-deficient patients along with impaired glucose uptake in G6pc3−/− neutrophils. Moreover, levels of G6P, lactate, and ATP are markedly lower in murine and human G6PC3-deficient neutrophils, compared with their respective controls. In parallel, the expression of NADPH oxidase subunits and membrane translocation of p47phox are down-regulated in murine and human G6PC3-deficient neutrophils. The results establish that in nonapoptotic neutrophils, G6Pase-β is essential for normal energy homeostasis. A G6Pase-β deficiency prevents recycling of ER glucose to the cytoplasm, leading to neutrophil dysfunction.
Metabolic flexibility revealed in the genome of the cyst-forming α-1 proteobacterium Rhodospirillum centenum
Authors: Lu Yih-Kuang , Marden Jeremiah , Han Mira , Swingley Wesley D , Mastrian Stephen D , Chowdhury Sugata Roy , Hao Jicheng , Helmy Tamer , Kim Sun , Kurdoglu Ahmet A , Matthies Heather J , Rollo David , Stothard Paul , Blankenship Robert E , Bauer Carl E , Touchman Jeffrey W 
Published: May 2010

Abstract

Background

Rhodospirillum centenum is a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic N2-fixing environment. It is emerging as a genetically amenable model organism for molecular genetic analysis of cyst formation, photosynthesis, phototaxis, and cellular development. Here, we present an analysis of the genome of this bacterium.

Results

R. centenum contains a singular circular chromosome of 4,355,548 base pairs in size harboring 4,105 genes. It has an intact Calvin cycle with two forms of Rubisco, as well as a gene encoding phosphoenolpyruvate carboxylase (PEPC) for mixotrophic CO2 fixation. This dual carbon-fixation system may be required for regulating internal carbon flux to facilitate bacterial nitrogen assimilation. Enzymatic reactions associated with arsenate and mercuric detoxification are rare or unique compared to other purple bacteria. Among numerous newly identified signal transduction proteins, of particular interest is a putative bacteriophytochrome that is phylogenetically distinct from a previously characterized R. centenum phytochrome, Ppr. Genes encoding proteins involved in chemotaxis as well as a sophisticated dual flagellar system have also been mapped.

Conclusions
Remarkable metabolic versatility and a superior capability for photoautotrophic carbon assimilation is evident in R. centenum.
Energy metabolism of Heliobacterium modesticaldum during phototrophic and chemotrophic growth
Authors: Tang Kuo-Hsiang , Yue Hai , Blankenship Robert E 
Published: May 2010

Abstract

Background

Heliobacterium modesticaldum is a gram-positive nitrogen-fixing phototrophic bacterium that can grow either photoheterotrophically or chemotrophically but not photoautotrophically. Surprisingly, this organism is lacking only one gene for the complete reverse tricarboxylic acid (rTCA) cycle required for autotrophic carbon fixation. Along with the genomic information reported recently, we use multiple experimental approaches in this report to address questions regarding energy metabolic pathways in darkness, CO2 fixation, sugar assimilation and acetate metabolism.

Results
We present the first experimental evidence that D-ribose, D-fructose and D-glucose can be photoassimilated by H. modesticaldum as sole carbon sources in newly developed defined growth medium. Also, we confirm two non-autotrophic CO2-fixation pathways utilized by H. modesticaldum: reactions catalyzed by pyruvate:ferredoxin oxidoreductase and phosphoenolpyruvate carboxykinase, and report acetate excretion during phototrophic and chemotrophic growth. Further, genes responsible for pyruvate fermentation, which provides reducing power for nitrogen assimilation, carbon metabolism and hydrogen production, are either active or up-regulated during chemotrophic growth. The discovery of ferredoxin-NADP+ oxidoreductase (FNR) activity in cell extracts provides the reducing power required for carbon and nitrogen metabolisms. Moreover, we show that photosynthetic pigments are produced by H. modesticaldum during the chemotrophic growth, and demonstrate that H. modesticaldum performs nitrogen fixation during both phototrophic and chemotrophic growth.

Conclusion
Collectively, this report represents the first comprehensive studies for energy metabolism in heliobacteria, which have the simplest known photosynthetic machinery among the entire photosynthetic organisms. Additionally, our studies provide new and essential insights, as well as broaden current knowledge, on the energy metabolism of the thermophilic phototrophic bacterium H. modesticaldum during phototrophic and chemotrophic growth.
The development of a 16S rRNA gene based PCR for the identification of Streptococcus pneumoniaeand comparison with four other species specific PCR assays
Authors: El Aila Nabil Abdullah , Emler Stefan , Kaijalainen Tarja , De Baere Thierry , Saerens Bart , Alkan Elife , Deschaght Pieter , Verhelst Rita , Vaneechoutte Mario 
Published: May 2010

Abstract

Background

Streptococcus pneumoniae is one of the most frequently encountered pathogens in humans but its differentiation from closely related but less pathogenic streptococci remains a challenge.

Methods
This report describes a newly-developed PCR assay (Spne-PCR), amplifying a 217 bp product of the 16S rRNA gene of S. pneumoniae, and its performance compared to other genotypic and phenotypic tests.

Results
The new PCR assay designed in this study, proved to be specific at 57°C for S. pneumoniae, not amplifying S. pseudopneumoniae or any other streptococcal strain or any strains from other upper airway pathogenic species. PCR assays (psaA, LytA, ply, spn9802-PCR) were previously described for the specific amplification of S. pneumoniae, but psaA-PCR was the only one found not to cross-react with S. pseudopneumoniae.

Conclusion
Spne-PCR, developed for this study, and psaA-PCR were the only two assays which did not mis-identify S. pseudopneumoniae as S. pneumoniae. Four other PCR assays and the AccuProbe assay were unable to distinguish between these species.
Human immunodeficiency virus type I-specific CD8+T cell subset abnormalities in chronic infection persist through effective antiretroviral therapy
Authors: Pohling Julia , Zipperlen Katrin , Hollett Natasha A , Gallant Maureen E , Grant Michael D 
Published: May 2010

Abstract

Background
Effective highly active antiretroviral therapy (HAART) reduces human immunodeficiency virus (HIV) replication, restores CD4+ T lymphocyte counts and greatly reduces the incidence of opportunistic infections. While this demonstrates improved generalized immune function, rapid rebound to pre-treatment viral replication levels following treatment interruption indicates little improvement in immune control of HIV replication. The extent to which HAART can normalize HIV-specific CD8+ T cell function over time in individuals with chronic infection remains an important unresolved issue. In this study, we evaluated the magnitude, general specificity and character of HIV specific CD8+ T cell responses at four time points across 2-9 years in 2 groups of chronically infected individuals separated on the basis of either effective antiretroviral suppression or ongoing replication of HIV.

Methods
Peripheral blood mononuclear cells (PBMC) were stimulated with overlapping 15mer peptides spanning HIV Gag, Pol, Env and Nef proteins. Cells producing interferon-γ (IFN-γ) or interleukin-2 (IL-2) were enumerated by ELISPOT and phenotyped by flow cytometry.

Results and Conclusions
The magnitude of the HIV-specific CD8+ T cell response ranged from < .01 to approximately 1.0% of PBMC and was significantly greater in the group with detectable viral replication. Stronger responses reflected higher numbers of CD8+CD45RA- effector memory cells producing IFN-γ, but not IL-2. Magnitude, general specificity and character of the HIV-specific CD8+ T cell response changed little over the study period. While antiretroviral suppression of HIV in chronic infection reduces HIV-specific CD8+ T cell response magnitude in the short term, it had no significant effect on response character over periods up to 9 years.