bluuebunny/crossref_metadata_2025 huggingface dataset:
Interleukin 11 expression in the normal canine eye
Authors: Richards Tara R. , Mortlock Jessica H. H. , Pinard Chantale L. , Whelan Nick C. , Revay Tamas , LaMarre Jonathan
Published: April 2013

Objectives

The purpose of this study was to characterize the expression of interleukin‐11 (IL‐11), a cytokine with anti‐inflammatory, cytoprotective, and immune‐modulating characteristics, in the canine eye.

Procedures

Normal canine eyes were collected from clinically healthy dogs that had been euthanized for reasons unrelated to this study. The distribution of IL‐11 expression in the different ocular layers was evaluated by immunofluorescence (eight eyes). Expression levels were quantified (based on fluorescence intensity) using pixel density analysis. Primary cell cultures were derived from all three corneal cell layers. IL‐11 mRNA expression was assessed in these cultures using quantitative RT‐PCR before and after treatment with TGF‐β1, a known inducer of IL‐11 expression. IL‐11 protein expression was also assessed in the media of these cells by Western blot analysis.

Results

IL‐11 protein was detected in the corneal epithelium, keratocytes, and the corneal endothelium of the normal canine eyes examined using immunofluorescence. Baseline IL‐11 mRNA expression was noted in the corneal epithelium, fibroblasts, and endothelium using quantitative RT‐PCR. Treatment of canine corneal cell lines with TGF‐β1 resulted in statistically significant increases in IL‐11 expression in the corneal epithelium, endothelial and fibroblast cell lines with strongest induction noted in the fibroblasts and endothelium.

Conclusion

This is the first description of IL‐11 expression in the canine eye. The protein and mRNA appear to be constitutively present throughout all layers of the cornea and are increased by TGF‐β1, a cytokine important in ocular inflammation and disease.
A New Dynamical Model of Flexible Cracked Wind Turbines for Health Monitoring
Authors: Ben Hassena M. A. , Najar F. , Aydi B. , Choura S. , Ghorbel F. H.
Published: March 2013

We develop a mathematical model of a large-scale cracked horizontal axis wind turbine (HAWT) describing the flapping flexure of the flexible tower and blades. The proposed model has enough fidelity to be used in health monitoring applications. The equations of motion account for the effect of the applied aerodynamic forces, modeled using the blade element momentum (BEM) theory, and the location and shape of a crack introduced into one of the blades. We first examine the static response of the HAWT in presence of the crack, and then we formulate the eigenvalue problem and determine the natural frequencies and associated mode shapes. We show that both shape and location of the crack influence the first four natural frequencies. The dynamic response of the HAWT subjected to wind and gravity is obtained using a Galerkin procedure. We conduct a parametric analysis to investigate the influence of the crack on the eigenstructure and overall dynamics. The simulations depict that the first four natural frequencies are reduced as the crack size become more important. We also conclude that the tower root moment may be considered as potential indicators for health monitoring purposes.
Optimal Restraint for the Thoracic Compression of the SID-IIs Crash Dummy Using a Linear Spring-Mass Model
Authors: Shi Yibing , Wu Jianping , Nusholtz Guy S.
Published: March 2013

The optimal restraint for minimizing the peak thoracic compression of the SID-IIs side crash test dummy subjected to a prescribed impact is studied using a linear spring-mass model. This model consists of the thoracic and pelvic masses and three springs which connect the masses and interface them with an impacting surface through the restraint. The problem is posed as an optimal control problem, with the restraint, which could be any physical structure (e.g., an airbag) operating in a finite allowable space, treated as a displacement control element. Via an assumption of the linearity of the dummy model and a discretization scheme, the problem is approximated and transformed into a linear programming problem for numerical solution. Numerical solutions are obtained under different prescribed impacting surface motion histories, different restraint space values, and constraints on dummy responses. Results show that the general characteristics of the optimal restraint response is a rapid ramp up in velocity in the very beginning of the event, followed by a period of lower level of loading where the thoracic compression builds up, and then an approximately constant acceleration to maintain the compression. The corresponding theoretically minimum thoracic compression values under the various conditions studied are presented.
On the Existence of Controlled Maximal Contractive Sets for Multi Input Linear Systems
Authors: Cristofaro Andrea
Published: March 2013

In this work, the existence of maximal contractive sets for unstable multi input linear systems is discussed. It is shown that, under suitable algebraic conditions, linear feedback laws can be designed such that the set of values satisfying the saturation constraints is an invariant set for the closed-loop system, which is asymptotically stable.
Orexin Receptor Antagonists Differ from Standard Sleep Drugs by Promoting Sleep at Doses That Do Not Disrupt Cognition
Authors: Uslaner Jason M. , Tye Spencer J. , Eddins Donnie M. , Wang Xiaohai , Fox Steven V. , Savitz Alan T. , Binns Jacquelyn , Cannon Christopher E. , Garson Susan L. , Yao Lihang , Hodgson Robert , Stevens Joanne , Bowlby Mark R. , Tannenbaum Pamela L. , Brunner Joseph , Mcdonald Terrence P. , Gotter Anthony L. , Kuduk Scott D. , Coleman Paul J. , Winrow Christopher J. , Renger John J.
Published: April 2013

Selective orexin receptor antagonism promotes sleep at doses lower than those that impair attention and memory in contrast to the GABA receptor–positive allosteric modulators currently in use.
From Waste to Plastic: Synthesis of Poly(3-Hydroxypropionate) in Shimwellia blattae
Authors: Heinrich Daniel , Andreessen Bjï¿½rn , Madkour Mohamed H. , Al-Ghamdi Mansour A. , Shabbaj Ibrahim I. , Steinbï¿½chel Alexander
Published: March 2013

In recent years, glycerol has become an attractive carbon source for microbial processes, as it accumulates massively as a by-product of biodiesel production, also resulting in a decline of its price. A potential use of glycerol in biotechnology is the synthesis of poly(3-hydroxypropionate) [poly(3HP)], a biopolymer with promising properties which is not synthesized by any known wild-type organism. In this study, the genes for 1,3-propanediol dehydrogenase (
dhaT
) and aldehyde dehydrogenase (
aldD
) of
Pseudomonas putida
KT2442, propionate-coenzyme A (propionate-CoA) transferase (
pct
) of
Clostridium propionicum
X2, and polyhydroxyalkanoate (PHA) synthase (
phaC1
) of
Ralstonia eutropha
H16 were cloned and expressed in the 1,3-propanediol producer
Shimwellia blattae
. In a two-step cultivation process, recombinant
S. blattae
cells accumulated up to 9.8% ï¿½ 0.4% (wt/wt [cell dry weight]) poly(3HP) with glycerol as the sole carbon source. Furthermore, the engineered strain tolerated the application of crude glycerol derived from biodiesel production, yielding a cell density of 4.05 g cell dry weight/liter in a 2-liter fed-batch fermentation process.
Synthesis of Fucosyl-
N
-Acetylglucosamine Disaccharides by Transfucosylation Using α-l-Fucosidases from Lactobacillus casei
Authors: Rodrï¿½guez-Dï¿½az Jesï¿½s , Carbajo Rodrigo J. , Pineda-Lucena Antonio , Monedero Vicente , Yebra Marï¿½a J.
Published: March 2013

AlfB and AlfC α-l-fucosidases from
Lactobacillus casei
were used in transglycosylation reactions, and they showed high efficiency in synthesizing fucosyldisaccharides. AlfB and AlfC activities exclusively produced fucosyl-α-1,3-
N
-acetylglucosamine and fucosyl-α-1,6-
N
-acetylglucosamine, respectively. The reaction kinetics showed that AlfB can convert 23%
p
-nitrophenyl-α-
l
-fucopyranoside into fucosyl-α-1,3-
N
-acetylglucosamine and AlfC at up to 56% into fucosyl-α-1,6-
N
-acetylglucosamine.
Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns
Authors: Bougouffa S. , Yang J. K. , Lee O. O. , Wang Y. , Batang Z. , Al-Suwailem A. , Qian P. Y.
Published: March 2013

Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the
Alphaproteobacteria
-dominated deep sea to the
Planctomycetaceae
- or
Deferribacteres
-dominated interfaces to the
Gammaproteobacteria-
dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.
Characterization of a Wild, Novel Nisin A-Producing Lactococcus Strain with an L. lactis subsp.
cremoris
Genotype and an L. lactis subsp.
lactis
Phenotype, Isolated from Greek Raw Milk
Authors: Parapouli Maria , Delbès-Paus Céline , Kakouri Athanasia , Koukkou Anna-Irini , Montel Marie-Christine , Samelis John
Published: March 2013

Several molecular taxonomic studies have revealed that many natural (wild)
Lactococcus lactis
strains of dairy origin which are phenotypically representative of the
L. lactis
subspecies
lactis
cluster genotypically within subspecies
cremoris
and
vice versa
. Recently, we isolated two wild nisin-producing (Nis
+
)
L. lactis
strains, M78 and M104, of the
lactis
phenotype from Greek raw milk (J. Samelis, A. Lianou, A. Kakouri, C. Delbès, I. Rogelj, B. B. Matijašic, and M. C. Montel, J. Food Prot. 72:783–790, 2009); strain M78 possess a novel nisin A sequence (GenBank accession number
HM219853
). In this study, the actual subspecies identity of M78 and M104 isolates was elucidated, using 16S rRNA and
acmA
(encoding lactococcal
N
-acetylmuramidase) gene and histidine biosynthesis operon polymorphisms and 16S rRNA and
ldh
(encoding lactate dehydrogenase) gene phylogenies. Except the
acmA
gene analysis, molecular tools revealed that isolates M78 and M104 clustered with strains of the
cremoris
genotype, including the LMG 6897
T
strain, while they were distant from strains of the
lactis
genotype, including the LMG 6890
T
strain. The two wild isolates had identical repetitive sequence-based PCR (rep-PCR), randomly amplified polymorphic DNA (RAPD), plasmid, and whole-cell protein profiles and shared high 16S rRNA (99.9%) and
ldh
(100%) gene sequence homologies. In contrast, they exhibited identical sugar fermentation and enzymatic patterns which were similar to those of the subspecies
lactis
LMG 6890
T
strain. To our knowledge, this is the first complete identification report on a wild
L. lactis
subsp.
cremoris
genotype of the
lactis
phenotype which is capable of nisin A production and, thus, has strong potential for use as a novel dairy starter and/or protective culture.
Physiological and Transcriptional Responses of Saccharomyces cerevisiae to
d
-Limonene Show Changes to the Cell Wall but Not to the Plasma Membrane
Authors: Brennan Timothy C. R. , Krï¿½mer Jens O. , Nielsen Lars K.
Published: March 2013

Monoterpenes can, upon hydrogenation, be used as light-fraction components of sustainable aviation fuels. Fermentative production of monoterpenes in engineered microorganisms, such as
Saccharomyces cerevisiae
, has gained attention as a potential route to deliver these next-generation fuels from renewable biomass. However, end product toxicity presents a formidable problem for microbial synthesis. Due to their hydrophobicity, monoterpene inhibition has long been attributed to membrane interference, but the molecular mechanism remains largely unsolved. In order to gain a better understanding of the mode of action, we analyzed the composition and structural integrity of the cell envelope as well as the transcriptional response of yeast cells treated with an inhibitory amount of
d
-limonene (107 mg/liter). We found no alterations in membrane fluidity, structural membrane integrity, or fatty acid composition after the solvent challenge. A 4-fold increase in the mean fluorescence intensity per cell (using calcofluor white stain) and increased sensitivity to cell wall-degrading enzymes demonstrated that limonene disrupts cell wall properties. Global transcript measurements confirmed the membrane integrity observations by showing no upregulation of ergosterol or fatty acid biosynthesis pathways, which are commonly overexpressed in yeast to reinforce membrane rigidity during ethanol exposure. Limonene shock did cause a compensatory response to cell wall damage through overexpression of several genes (
ROM1
,
RLM1
,
PIR3
,
CTT1
,
YGP1
,
MLP1
,
PST1
, and
CWP1
) involved with the cell wall integrity signaling pathway. This is the first report demonstrating that cell wall, rather than plasma membrane, deterioration is the main source of monoterpene inhibition. We show that limonene can alter the structure and function of the cell wall, which has a clear effect on cytokinesis.
Genotypic Diversity and Virulence Characteristics of Clinical and Environmental Vibrio vulnificus Isolates from the Baltic Sea Region
Authors: Bier Nadja , Bechlars Silke , Diescher Susanne , Klein Florian , Hauk Gerhard , Duty Oliver , Strauch Eckhard , Dieckmann Ralf
Published: March 2013

The genetic diversity of
Vibrio vulnificus
isolates from clinical and environmental sources originating from the Baltic Sea region was evaluated by multilocus sequence typing (MLST), and possible relationships between MLST clusters, potential genotypic and phenotypic traits associated with pathogenicity, and source of isolation were investigated. The studied traits included genotyping of polymorphic loci (16S rRNA,
vcg
, and
pilF
), presence/absence of potential virulence genes, including
nanA
,
nab
, and genes of pathogenicity regions, metabolic features, hemolytic activity, resistance to human serum, and cytotoxicity to human intestinal cells. MLST generated 35 (27 new) sequence types and divided the 53 isolates (including four reference strains) into two main clusters, with cluster I containing biotype 1 and 2 isolates of mainly environmental origin and cluster II containing biotype 1 isolates of mainly clinical origin. Cluster II isolates were further subdivided into two branches. Branch IIB included isolates from recent cases of wound infections that were acquired at the German Baltic Sea coastline between 2010 and 2011 and isolates from seawater samples of the same regions isolated between 1994 and 2010. Comparing the MLST data with the results of genotyping and phenotyping showed that strains of MLST cluster II possess a number of additional pathogenicity-associated traits compared to cluster I strains. Rapid microbiological methods such as matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry combined with typing of selected virulence-associated traits (e.g., serum resistance, mannitol fermentation,
nanA
, and pathogenicity region XII) could be used for risk assessment purposes regarding
V. vulnificus
strains isolated from the Baltic Sea region.
Identification and Expression of Genes Involved in the Conversion of Daidzein and Genistein by the Equol-Forming Bacterium Slackia isoflavoniconvertens
Authors: Schröder Christine , Matthies Anastasia , Engst Wolfram , Blaut Michael , Braune Annett
Published: March 2013

Gut bacteria play a key role in the metabolism of dietary isoflavones, thereby influencing the availability and bioactivation of these polyphenols in the intestine. The human intestinal bacterium
Slackia isoflavoniconvertens
converts the main soybean isoflavones daidzein and genistein to equol and 5-hydroxy-equol, respectively. Cell extracts of
S. isoflavoniconvertens
catalyzed the conversion of daidzein via dihydrodaidzein to equol and that of genistein to dihydrogenistein. Growth of
S. isoflavoniconvertens
in the presence of daidzein led to the induction of several proteins as observed by two-dimensional difference gel electrophoresis. Based on determined peptide sequences, we identified a cluster of eight genes encoding the daidzein-induced proteins. Heterologous expression of three of these genes in
Escherichia coli
and enzyme activity tests with the resulting cell extracts identified the corresponding gene products as a daidzein reductase (DZNR), a dihydrodaidzein reductase (DHDR), and a tetrahydrodaidzein reductase (THDR). The recombinant DZNR also converted genistein to dihydrogenistein at higher rates than were observed for the conversion of daidzein to dihydrodaidzein. Higher rates were also observed with cell extracts of
S. isoflavoniconvertens
. The recombinant DHDR and THDR catalyzed the reduction of dihydrodaidzein to equol, while the corresponding conversion of dihydrogenistein to 5-hydroxy-equol was not observed. The DZNR, DHDR, and THDR were expressed as
Strep
-tag fusion proteins and subsequently purified by affinity chromatography. The purified enzymes were further characterized with regard to their activity, stereochemistry, quaternary structure, and content of flavin cofactors.
Importance of Relating Efficacy Measures to Unbound Drug Concentrations for Anti-Infective Agents
Authors: Gonzalez Daniel , Schmidt Stephan , Derendorf Hartmut
Published: April 2013

For the optimization of dosing regimens of anti-infective agents, it is imperative to have a good understanding of pharmacokinetics (PK) and pharmacodynamics (PD). Whenever possible, drug efficacy needs to be related to unbound concentrations at the site of action. For anti-infective drugs, the infection site is typically located outside plasma, and a drug must diffuse through capillary membranes to reach its target. Disease- and drug-related factors can contribute to differential tissue distribution. As a result, the assumption that the plasma concentration of drugs represents a suitable surrogate of tissue concentrations may lead to erroneous conclusions. Quantifying drug exposure in tissues represents an opportunity to relate the pharmacologically active concentrations to an observed pharmacodynamic parameter, such as the MIC. Selection of an appropriate specimen to sample and the advantages and limitations of the available sampling techniques require careful consideration. Ultimately, the goal will be to assess the appropriateness of a drug and dosing regimen for a specific pathogen and infection.
Detection and Characterization of Megasatellites in Orthologous and Nonorthologous Genes of 21 Fungal Genomes
Authors: Tekaia Fredj , Dujon Bernard , Richard Guy-Franck
Published: March 2013

Megasatellites are large DNA tandem repeats, originally described inCandida glabrata, in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
Diverse Hap43-Independent Functions of the Candida albicans CCAAT-Binding Complex
Authors: Hsu Po-Chen , Chao Chun-Cheih , Yang Cheng-Yao , Ye Ya-Ling , Liu Fu-Chen , Chuang Yung-Jen , Lan Chung-Yu
Published: March 2013

The CCAAT motif is ubiquitous in promoters of eukaryotic genomes. The CCAAT-binding complex (CBC) is conserved across a wide range of organisms, specifically recognizes the CCAAT motif, and modulates transcription directly or in cooperation with other transcription factors. In
Candida albicans
, CBC is known to interact with the repressor Hap43 to negatively regulate iron utilization genes in response to iron deprivation. However, the extent of additional functions of CBC is unclear. In this study, we explored new roles of CBC in
C. albicans
and found that CBC pleiotropically regulates many virulence traits
in vitro
, including negative control of genes responsible for ribosome biogenesis and translation and positive regulation of low-nitrogen-induced filamentation. In addition,
C. albicans
CBC is involved in utilization of host proteins as nitrogen sources and in repression of cellular flocculation and adhesin gene expression. Moreover, our epistasis analyses suggest that CBC acts as a downstream effector of Rhb1-TOR signaling and controls low-nitrogen-induced filamentation via the Mep2-Ras1-protein kinase A (PKA)/mitogen-activated protein kinase (MAPK) pathway. Importantly, the phenotypes identified here are all independent of Hap43. Finally, deletion of genes encoding CBC components slightly attenuated
C. albicans
virulence in both zebrafish and murine models of infection. Our results thus highlight new roles of
C. albicans
CBC in regulating multiple virulence traits in response to environmental perturbations and, finally, suggest potential targets for antifungal therapies as well as extending our understanding of the pathogenesis of other fungal pathogens.
Multiple Roles of RNase Y in Streptococcus pyogenes mRNA Processing and Degradation
Authors: Chen Zhiyun , Itzek Andreas , Malke Horst , Ferretti Joseph J. , Kreth Jens
Published: March 2013

Control over mRNA stability is an essential part of gene regulation that involves both endo- and exoribonucleases. RNase Y is a recently identified endoribonuclease in Gram-positive bacteria, and an RNase Y ortholog has been identified in
Streptococcus pyogenes
(group A streptococcus [GAS]). In this study, we used microarray and Northern blot analyses to determine the
S. pyogenes
mRNA half-life of the transcriptome and to understand the role of RNase Y in global mRNA degradation and processing. We demonstrated that
S. pyogenes
has an unusually high mRNA turnover rate, with median and mean half-lives of 0.88 min and 1.26 min, respectively. A mutation of the RNase Y-encoding gene (
rny
) led to a 2-fold increase in overall mRNA stability. RNase Y was also found to play a significant role in the mRNA processing of virulence-associated genes as well as in the rapid degradation of
rnpB
read-through transcripts. From these results, we conclude that RNase Y is a pleiotropic regulator required for mRNA stability, mRNA processing, and removal of read-through transcripts in
S. pyogenes
.
Three of Four GlnR Binding Sites Are Essential for GlnR-Mediated Activation of Transcription of the
Amycolatopsis mediterranei nas
Operon
Authors: Wang Ying , Wang Jing-Zhi , Shao Zhi-Hui , Yuan Hua , Lu Yin-Hua , Jiang Wei-Hong , Zhao Guo-Ping , Wang Jin
Published: March 2013

In
Amycolatopsis mediterranei
U32, genes responsible for nitrate assimilation formed one operon,
nasACKBDEF
, whose transcription is induced by the addition of nitrate. Here, we characterized GlnR as a direct transcriptional activator for the
nas
operon. The GlnR-protected DNA sequences in the promoter region of the
nas
operon were characterized by DNase I footprinting assay, the previously deduced
Streptomyces coelicolor
double 22-bp GlnR binding consensus sequences comprising
a1
,
b1
,
a2
, and
b2
sites were identified, and the sites were then mutated individually to test their roles in both the binding of GlnR
in vitro
and the GlnR-mediated transcriptional activation
in vivo
. The results clearly showed that only three GlnR binding sites (
a1
,
b1
, and
b2
sites) were required by GlnR for its specific binding to the
nas
promoter region and efficient activation of the transcription of the
nas
operon in U32, while the
a2
site seemed unnecessary.
Characterization of the
ospZ
Promoter in Shigella flexneri and Its Regulation by VirB and H-NS
Authors: Basta David W. , Pew Krystle L. , Immak Joy A. , Park Hiromichi S. , Picker Michael A. , Wigley Amanda F. , Hensley Christopher T. , Pearson Jaclyn S. , Hartland Elizabeth L. , Wing Helen J.
Published: March 2013

OspZ is an effector protein of the type III secretion system in
Shigella
spp. that downregulates the human inflammatory response during bacterial infection. The
ospZ
gene is located on the large virulence plasmid of
Shigella
. Many genes on this plasmid are transcriptionally repressed by the nucleoid structuring protein H-NS and derepressed by VirB, a DNA-binding protein that displays homology to the plasmid partitioning proteins ParB and SopB. In this study, we characterized the
ospZ
promoter and investigated its regulation by H-NS and VirB in
Shigella flexneri
. We show that H-NS represses and VirB partially derepresses the
ospZ
promoter. H-NS-mediated repression requires sequences located between −731 and −412 relative to the beginning of the
ospZ
gene. Notably, the VirB-dependent derepression of
ospZ
requires the same VirB binding sites as are required for the VirB-dependent derepression of the divergent
icsP
gene. These sites are centered 425 bp upstream of the
ospZ
gene but over 1 kb upstream of the
icsP
transcription start site. Although these VirB binding sites lie closer to
ospZ
than
icsP
, the VirB-dependent increase in
ospZ
promoter activity is lower than that observed at the
icsP
promoter. This indicates that the proximity of VirB binding sites to
Shigella
promoters does not necessarily correlate with the level of VirB-dependent derepression. These findings have implications for virulence gene regulation in
Shigella
and other pathogens that control gene expression using mechanisms of transcriptional repression and derepression.
Rapid Detection of HIV-1 Proviral DNA for Early Infant Diagnosis Using Recombinase Polymerase Amplification
Authors: Boyle David S. , Lehman Dara A. , Lillis Lorraine , Peterson Dylan , Singhal Mitra , Armes Niall , Parker Mathew , Piepenburg Olaf , Overbaugh Julie
Published: April 2013

Early diagnosis and treatment of human immunodeficiency virus type 1 (HIV-1) infection in infants can greatly reduce mortality rates. However, current infant HIV-1 diagnostics cannot reliably be performed at the point of care, often delaying treatment and compromising its efficacy. Recombinase polymerase amplification (RPA) is a novel technology that is ideal for an HIV-1 diagnostic, as it amplifies target DNA in <20 min at a constant temperature, without the need for complex thermocycling equipment. Here we tested 63 HIV-1-specific primer and probe combinations and identified two RPA assays that target distinct regions of the HIV-1 genome (long terminal repeat [LTR] andpol) and can reliably detect 3 copies of proviral DNA by the use of fluorescence detection and lateral-flow strip detection. Thesepoland LTR primers amplified 98.6% and 93%, respectively, of the diverse HIV-1 variants tested. This is the first example of an isothermal assay that consistently detects all of the major HIV-1 global subtypes.

IMPORTANCEDiagnosis of HIV-1 infection in infants cannot rely on the antibody-based tests used in adults because of the transfer of maternal HIV-1 antibodies from mother to child. Therefore, infant diagnostics rely on detection of the virus itself. However, current infant HIV-1 diagnostic methods require a laboratory setting with complex equipment. Here we describe the initial development of an HIV-1 diagnostic for infants that may be performed at the point of care in rural health clinics. We utilize a method that can amplify and detect HIV-1 DNA at an incubation temperature within the range of 25 to 42°C, eliminating the need for thermocycling equipment. HIV-1 diagnostics are challenging to develop due to the high diversity seen in HIV-1 strains worldwide. Here we show that this method detects the major HIV-1 strains circulating globally.
Bacterial Bioluminescence Regulates Expression of a Host Cryptochrome Gene in the Squid-Vibrio Symbiosis
Authors: Heath-Heckman Elizabeth A. C. , Peyer Suzanne M. , Whistler Cheryl A. , Apicella Michael A. , Goldman William E. , McFall-Ngai Margaret J.
Published: April 2013

The symbiosis between the squidEuprymna scolopesand its luminous symbiont,Vibrio fischeri, is characterized by daily transcriptional rhythms in both partners and daily fluctuations in symbiont luminescence. In this study, we sought to determine whether symbionts affect host transcriptional rhythms. We identified two transcripts in host tissues (E. scolopes cry1[escry1] andescry2) that encode cryptochromes, proteins that influence circadian rhythms in other systems. Both genes cycled daily in the head of the squid, with a pattern similar to that of other animals, in which expression of certaincrygenes is entrained by environmental light. In contrast,escry1expression cycled in the symbiont-colonized light organ with 8-fold upregulation coincident with the rhythms of bacterial luminescence, which are offset from the day/night light regime. Colonization of the juvenile light organ by symbionts was required for induction ofescry1cycling. Further, analysis with a mutant strain defective in light production showed that symbiont luminescence is essential for cycling ofescry1; this defect could be complemented by presentation of exogenous blue light. However, blue-light exposure alone did not induce cycling in nonsymbiotic animals, but addition of molecules of the symbiont cell envelope to light-exposed animals did recover significant cycling activity, showing that light acts in synergy with other symbiont features to induce cycling. While symbiont luminescence may be a character specific to rhythms of the squid-vibrio association, resident microbial partners could similarly influence well-documented daily rhythms in other systems, such as the mammalian gut.

IMPORTANCEIn mammals, biological rhythms of the intestinal epithelium and the associated mucosal immune system regulate such diverse processes as lipid trafficking and the immune response to pathogens. While these same processes are affected by the diverse resident microbiota, the extent to which these microbial communities control or are controlled by these rhythms has not been addressed. This study provides evidence that the presentation of three bacterial products (lipid A, peptidoglycan monomer, and blue light) is required for cyclic expression of a cryptochrome gene in the symbiotic organ. The finding that bacteria can directly influence the transcription of a gene encoding a protein implicated in the entrainment of circadian rhythms provides the first evidence for the role of bacterial symbionts in influencing, and perhaps driving, peripheral circadian oscillators in the host.
Paraspinal arteriovenous malformation Onyx embolization via an Ascent balloon
Authors: Martínez-Galdámez Mario , Rodriguez-Arias Carlos A , Utiel Elena , Arreba Emilio , Gonzalo Miguel , Arenillas Juan F
Published: March 2013

Purely extradural lumbar spinal arteriovenous malformations (AVMs) are rare lesions that have diverse presentations and imaging features. The treatment of a symptomatic high flow paraspinal AVM with multiple feeders remains a challenge. We report the first use of an Ascent balloon (dual lumen balloon catheter) to deliver Onyx with excellent penetration to a paraspinal AVM.
ON THE SUPERSYMMETRY OF THE DIRAC–KEPLER PROBLEM PLUS A COULOMB-TYPE SCALAR POTENTIAL IN (D+1) DIMENSIONS AND THE GENERALIZED LIPPMANN–JOHNSON OPERATOR
Authors: MARTÍNEZ D. , SALAZAR-RAMÍREZ M. , MOTA R. D. , GRANADOS V. D.
Published: April 2013

We will study the Dirac–Kepler problem plus a Coulomb-type scalar potential by generalizing the Lippmann–Johnson operator to D spatial dimensions. From this operator, we construct the supersymmetric generators to obtain the energy spectrum for discrete excited eigenstates and the radial spinor for the SUSY ground state.
A REALIZATION OF THE HOLOGRAPHIC ENTROPY
Authors: XIAO YONG , YANG GUANG
Published: April 2013

The entropy bound for the conventional quantum field theory is known as A3/4. Thus, there is an entropy gap from A3/4 to the holographic entropy A. In this paper, we show that the entropy gap can be overcome by introducing internal degrees of freedom to the system. Using a state counting method, we show explicitly how the familiar holographic thermodynamics with area entropy can be realized. It may help in the understanding of the microscopic origin of the holographic entropy.
IMPROVING SHORTEST PATHS IN THE DELAUNAY TRIANGULATION
Authors: ABELLANAS MANUEL , CLAVEROL MERCÈ , HERNÁNDEZ GREGORIO , HURTADO FERRAN , SACRISTÁN VERA , SAUMELL MARIA , SILVEIRA RODRIGO I.
Published: April 2013

We study a problem about shortest paths in Delaunay triangulations. Given two nodes s, t in the Delaunay triangulation of a point set S, we look for a new point p ∉ S that can be added, such that the shortest path from s to t, in the Delaunay triangulation of S∪{p}, improves as much as possible. We study several properties of the problem, and give efficient algorithms to find such a point when the graph-distance used is Euclidean and for the link-distance. Several other variations of the problem are also discussed.
STOCHASTIC SEISMIC RESPONSE OF BASE-ISOLATED BUILDINGS
Authors: JACOB C. , SEPAHVAND K. , MATSAGAR V. A. , MARBURG S.
Published: April 2013

The stochastic response of base-isolated building considering the uncertainty in the characteristics of the earthquakes is investigated. For this purpose, a probabilistic ground motion model, for generating artificial earthquakes is developed. The model is based upon a stochastic ground motion model which has separable amplitude and spectral non-stationarities. An extensive database of recorded earthquake ground motions is created. The set of parameters required by the stochastic ground motion model to depict a particular ground motion is evaluated for all the ground motions in the database. Probability distributions are created for all the parameters. Using Monte Carlo (MC) simulations, the set of parameters required by the stochastic ground motion model to simulate ground motions is obtained from the distributions and ground motions. Further, the bilinear model of the isolator described by its characteristic strength, post-yield stiffness and yield displacement is used, and the stochastic response is determined by using an ensemble of generated earthquakes. A parametric study is conducted for the various characteristics of the isolator. This study presents an approach for stochastic seismic response analysis of base-isolated building considering the uncertainty involved in the earthquake ground motion.
Ceramide 1-phosphate induces macrophage chemoattractant protein-1 release: involvement in ceramide 1-phosphate-stimulated cell migration
Authors: Arana Lide , Ordoñez Marta , Ouro Alberto , Rivera Io-Guané , Gangoiti Patricia , Trueba Miguel , Gomez-Muñoz Antonio
Published: April 2013

The bioactive sphingolipid ceramide 1-phosphate (C1P) is implicated in inflammatory responses and was recently shown to promote cell migration. However, the mechanisms involved in these actions are poorly described. Using J774A.1 macrophages, we have now discovered a new biological activity of C1P: stimulation of monocyte chemoattractant protein-1 (MCP-1) release. This novel effect of C1P was pertussis toxin (PTX) sensitive, suggesting the intervention of Giprotein-coupled receptors. Treatment of the macrophages with C1P caused activation of the phosphatidylinositol 3-kinase (PI3K)/Akt, mitogen-activated protein kinase kinase (MEK)/extracellularly regulated kinases (ERK), and p38 pathways. Inhibition of these kinases using selective inhibitors or specific siRNA blocked the stimulation of MCP-1 release by C1P. C1P stimulated nuclear factor-κB activity, and blockade of this transcription factor also resulted in complete inhibition of MCP-1 release. Also, C1P stimulated MCP-1 release and cell migration in human THP-1 monocytes and 3T3-L1 preadipocytes. A key observation was that sequestration of MCP-1 with a neutralizing antibody or treatment with MCP-1 siRNA abolished C1P-stimulated cell migration. Also, inhibition of the pathways involved in C1P-stimulated MCP-1 release completely blocked the stimulation of cell migration by C1P. It can be concluded that C1P promotes MCP-1 release in different cell types and that this chemokine is a major mediator of C1P-stimulated cell migration. The PI3K/Akt, MEK/ERK, and p38 pathways are important downstream effectors in this action.
Cardiac function and lipid distribution in rats fed a high-fat diet: in vivo magnetic resonance imaging and spectroscopy
Authors: Nagarajan Vijayasarathi , Gopalan Venkatesh , Kaneko Manami , Angeli Veronique , Gluckman Peter , Richards Arthur Mark , Kuchel Philip W. , Velan S. Sendhil
Published: March 2013

Obesity is a major risk factor in the development of cardiovascular disease, type 2 diabetes, and its pathophysiological precondition insulin resistance. Very little is known about the metabolic changes that occur in the myocardium and consequent changes in cardiac function that are associated with high-fat accumulation. Therefore, cardiac function and metabolism were evaluated in control rats and those fed a high-fat diet, using magnetic resonance imaging, magnetic resonance spectroscopy, mRNA analysis, histology, and plasma biochemistry. Analysis of blood plasma from rats fed the high-fat diet showed that they were insulin resistant ( P < 0.001). Our high-fat diet model had higher heart weight ( P = 0.005) and also increasing trend in septal wall thickness ( P = 0.07) compared with control diet rats. Our results from biochemistry, magnetic resonance imaging, and mRNA analysis confirmed that rats on the high-fat diet had moderate diabetes along with mild cardiac hypertrophy. The magnetic resonance spectroscopy results showed the extramyocellular lipid signal only in the spectra from high-fat diet rats, which was absent in the control diet rats. The intramyocellular lipids in high-fat diet rats was higher (8.7%) compared with rats on the control diet (6.1%). This was confirmed by electron microscope and light microscopy studies. Our results indicate that lipid accumulation in the myocardium might be an early indication of the cardiovascular pathophysiology associated with type 2 diabetes.
Nonantibiotic macrolides prevent human neutrophil elastase-induced mucus stasis and airway surface liquid volume depletion
Authors: Tarran Robert , Sabater Juan R. , Clarke Tainya C. , Tan Chong D. , Davies Catrin M. , Liu Jia , Yeung Arthur , Garland Alaina L. , Stutts M. Jackson , Abraham William M. , Phillips Gary , Baker William R. , Wright Clifford D. , Wilbert Sibylle
Published: March 2013

Mucus clearance is an important component of the lung's innate defense system. A failure of this system brought on by mucus dehydration is common to both cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). Mucus clearance rates are regulated by the volume of airway surface liquid (ASL) and by ciliary beat frequency (CBF). Chronic treatment with macrolide antibiotics is known to be beneficial to both CF and COPD patients. However, chronic macrolide usage may induce bacterial resistance. We have developed a novel macrolide, 2′-desoxy-9-( S)-erythromycylamine (GS-459755), that has significantly diminished antibiotic activity against Staphylococcus aureus, Streptococcus pneumonia, Moraxella catarrhalis, and Haemophilus influenzae. Since neutrophilia frequently occurs in chronic lung disease and human neutrophil elastase (HNE) induces mucus stasis by activating the epithelial sodium channel (ENaC), we tested the ability of GS-459755 to protect against HNE-induced mucus stasis. GS-459755 had no effect on HNE activity. However, GS-459755 pretreatment protected against HNE-induced ASL volume depletion in human bronchial epithelial cells (HBECs). The effect of GS-459755 on ASL volume was dose dependent (IC50∼3.9 μM) and comparable to the antibacterial macrolide azithromycin (IC50∼2.4 μM). Macrolides had no significant effect on CBF or on transepithelial water permeability. However, the amiloride-sensitive transepithelial voltage, a marker of ENaC activity, was diminished by macrolide pretreatment. We conclude that GS-459755 may limit HNE-induced activation of ENaC and may be useful for the treatment of mucus dehydration in CF and COPD without inducing bacterial resistance.
Quasi-Bézier Curves with Shape Parameters
Authors: Chen Jun
Published: March 2013

The universal form of univariate Quasi-Bézier basis functions with multiple shape parameters and a series of corresponding Quasi-Bézier curves were constructed step-by-step in this paper, using the method of undetermined coefficients. The series of Quasi-Bézier curves had geometric and affine invariability, convex hull property, symmetry, interpolation at the endpoints and tangent edges at the endpoints, and shape adjustability while maintaining the control points. Various existing Quasi-Bézier curves became special cases in the series. The obvious geometric significance of shape parameters made the adjustment of the geometrical shape easier for the designer. The numerical examples indicated that the algorithm was valid and can easily be applied.
Fast Disinfection ofEscherichia coliBacteria Using Carbon Nanotubes Interaction with Microwave Radiation
Authors: Al-Hakami Samer M. , Khalil Amjad B. , Laoui Tahar , Atieh Muataz Ali
Published: March 2013

Water disinfection has attracted the attention of scientists worldwide due to water scarcity. The most significant challenges are determining how to achieve proper disinfection without producing harmful byproducts obtained usually using conventional chemical disinfectants and developing new point-of-use methods for the removal and inactivation of waterborne pathogens. The removal of contaminants and reuse of the treated water would provide significant reductions in cost, time, liabilities, and labour to the industry and result in improved environmental stewardship. The present study demonstrates a new approach for the removal ofEscherichia coli(E. coli) from water using as-produced and modified/functionalized carbon nanotubes (CNTs) with 1-octadecanol groups (C18) under the effect of microwave irradiation. Scanning/transmission electron microscopy, thermogravimetric analysis, and FTIR spectroscopy were used to characterise the morphological/structural and thermal properties of CNTs. The 1-octadecanol (C18) functional group was attached to the surface of CNTs via Fischer esterification. The produced CNTs were tested for their efficiency in destroying the pathogenic bacteria (E. coli) in water with and without the effect of microwave radiation. A low removal rate (3–5%) of (E. coli) bacteria was obtained when CNTs alone were used, indicating that CNTs did not cause bacterial cellular death. When combined with microwave radiation, the unmodified CNTs were able to remove up to 98% of bacteria from water, while a higher removal of bacteria (up to 100%) was achieved when CNTs-C18was used under the same conditions.
Modification of Phospholipid Bilayers Induced by Sulfurated Naphthoquinones
Authors: Di Vitta Claudio , Marzorati Liliana , Funari Sérgio S.
Published: March 2013

New thionaphthoquinones and their hydroxyl derivatives, bearing alkyl side chains that match the phospholipids POPC and POPE, were synthesized in order to investigate their interactions with lipids. It was observed that, in general, these additives destabilize the lipid bilayer and induce less organized structures with higher curvature, in particular the induction of an hexagonal phase on aqueous POPC mixtures. Moreover, cubic phases, not normally observed in the pure lipids when fully hydrated, were detected. Coexistence of lamellar phases was interpreted as a consequence of microsegregation of the components in the mixtures. These results are in line with previous observations on the effect of structurally similar (hydro)quinones in phase behavior of these lipids.
Matrix Metalloproteinases in Cerebral Vasospasm following Aneurysmal Subarachnoid Hemorrhage
Authors: Mehta Vivek , Russin Jonathan , Spirtos Alexandra , He Shuhan , Adamczyk Peter , Amar Arun P. , Mack William J.
Published: April 2013

Delayed cerebral vasospasm is a significant cause of morbidity and mortality following aneurysmal subarachnoid hemorrhage (SAH). While the cellular mechanisms underlying vasospasm remain unclear, it is believed that inflammation may play a critical role in vasospasm. Matrix metalloproteinasees (MMPs) are a family of extracellular and membrane-bound proteases capable of degrading the blood-rain barrier (BBB). As such, MMP upregulation following SAH may result in a proinflammatory extravascular environment capable of inciting delayed cerebral vasospasm. This paper presents an overview of MMPs and describes existing data pertinent to delayed cerebral vasospasm.
Acquired Resistance to EGFR Inhibitors Is Associated with a Manifestation of Stem Cell–like Properties in Cancer Cells
Authors: Shien Kazuhiko , Toyooka Shinichi , Yamamoto Hiromasa , Soh Junichi , Jida Masaru , Thu Kelsie L. , Hashida Shinsuke , Maki Yuho , Ichihara Eiki , Asano Hiroaki , Tsukuda Kazunori , Takigawa Nagio , Kiura Katsuyuki , Gazdar Adi F. , Lam Wan L. , Miyoshi Shinichiro
Published: March 2013

Acquired resistance to EGF receptor (EGFR) tyrosine kinase inhibitor (TKI) is a critical problem in the treatment of lung cancer. Although several mechanisms have been shown to be responsible for acquired resistance, all mechanisms have not been uncovered. In this study, we investigated the molecular and cellular profiles of the acquired resistant cells to EGFR-TKI in EGFR-mutant lung cancers. Four EGFR-mutant cell lines were exposed to gefitinib by stepwise escalation and high-concentration exposure methods, and resistant sublines to gefitinib were established. The molecular profiles and cellular phenotypes of these resistant sublines were characterized. Although previously reported, alterations including secondary EGFR T790M mutation, MET amplification, and appearance of epithelial-to-mesenchymal transition (EMT) features were observed, these 2 drug-exposure methods revealed different resistance mechanisms. The resistant cells with EMT features exhibited downregulation of miRNA-200c by DNA methylation. Furthermore, the HCC827-derived subline characterized by the high-concentration exposure method exhibited not only EMT features but also stem cell–like properties, including aldehyde dehydrogenase isoform 1 (ALDH1A1) overexpression, increase of side-population, and self-renewal capability. Resistant sublines with stem cell–like properties were resistant to conventional chemotherapeutic agents but equally sensitive to histone deacetylase and proteasome inhibitors, compared with their parental cells. ALDH1A1 was upregulated in clinical samples with acquired resistance to gefitinib. In conclusion, our study indicates that the manner of EGFR-TKI exposure influences the mechanism of acquired resistance and the appearance of stem cell–like property with EGFR-TKI treatment. Cancer Res; 73(10); 3051–61. ©2013 AACR.