bluuebunny/crossref_metadata_2025 huggingface dataset:
Antifungal Therapy in an Athymic Murine Model of Chromoblastomycosis by
Fonsecaea pedrosoi
Authors: Calvo Enrique , Pastor F. Javier , Mayayo Emilio , Hernández Pilar , Guarro Josep
Published: May 2011

We have compared the efficacy of terbinafine (TRB) and itraconazole (ITZ), the recommended drugs for the treatment of chromoblastomycosis, with that of posaconazole (PSC) and voriconazole (VRC) in athymic mice infected with the fungus
Fonsecaea pedrosoi
. Three weeks after challenge, mice were treated for 4 months with PSC at 10 or 20 mg/kg of body weight/day, with VRC at 10 or 20 mg/kg/day, with ITZ at 25 or 50 mg/kg/day, or with TRB at 150 or 250 mg/kg/day. The progress of the infection was evaluated by measuring the size of the lesions, by histopathological studies, and by cultures of the excised tissue. The two doses of PSC followed by the highest doses of ITZ and TRB showed the best results while VRC did not show efficacy. PSC could be an alternative in the treatment of chromoblastomycosis.
Switch from Enfuvirtide to Raltegravir Lowers Plasma Concentrations of Darunavir and Tipranavir: a Pharmacokinetic Substudy of the EASIER-ANRS 138 Trial
Authors: Goldwirt Lauriane , Braun Joséphine , de Castro Nathalie , Charreau Isabelle , Barrail-Tran Aurélie , Delaugerre Constance , Raffi François , Lascoux-Combe Caroline , Aboulker Jean-Pierre , Taburet Anne-Marie , Molina Jean-Michel
Published: May 2011

We compared tipranavir and darunavir concentrations measured at steady state in 20 human immunodeficiency virus (HIV)-infected patients enrolled in the EASIER-ANRS 138 clinical trial who switched from enfuvirtide to raltegravir while maintaining the same background regimen. The geometric mean ratios of the observed predose concentration (Ctrough), maximum concentration of drug observed in plasma (Cmax), and area under the plasma concentration-time curve (AUC) before (day 0) and after (week 24) the switch were 0.49, 0.76, and 0.67 and 0.82, 0.68, and 0.64 for tipranavir and darunavir, respectively. The virologic consequences of these drug interactions have yet to be determined.
Early MyD88-Dependent Induction of Interleukin-17A Expression during Salmonella Colitis
Authors: Keestra A. Marijke , Godinez Ivan , Xavier Mariana N. , Winter Maria G. , Winter Sebastian E. , Tsolis Renée M. , Bäumler Andreas J.
Published: May 2011

The development of T helper 17 (T
H
17) cells is a well-established adaptive mechanism for the production of interleukin-17A (IL-17A), a cytokine involved in neutrophil recruitment. However, pathways contributing to mucosal expression of IL-17A during the initial phase of a bacterial infection have received less attention. Here we used the mouse colitis model of
Salmonella enterica
serotype Typhimurium infection to investigate the contribution of myeloid differentiation primary response protein 88 (MyD88) to inflammation and mucosal IL-17A expression. Expression of IL-23 in the cecal mucosa during
S.
Typhimurium colitis was dependent on the presence of MyD88. Furthermore, initial expression of IL-17A at 24 h after
S.
Typhimurium infection was dependent on MyD88 and the receptor for IL-1β. IL-23 and IL-1β synergized in inducing expression of IL-17A in splenic T cells
in vitro
. In the intestinal mucosa, IL-17A was produced by three distinct T cell populations, including δγ T cells, T
H
17 cells, and CD4
−
CD8
−
T cells. The absence of IL-1β signaling or IL-17 signaling reduced CXC chemokine expression but did not alter the overall severity of pathological lesions in the cecal mucosa. In contrast, cecal pathology and neutrophil recruitment were markedly reduced in Myd88-deficient mice during the initial phases of
S.
Typhimurium infection. Collectively, these data demonstrate that MyD88-dependent mechanisms, including an initial expression of IL-17A, are important for orchestrating early inflammatory responses during
S.
Typhimurium colitis.
Sphingolipid Degradation by Leishmania major Is Required for Its Resistance to Acidic pH in the Mammalian Host
Authors: Xu Wei , Xin Lijun , Soong Lynn , Zhang Kai
Published: May 2011

Leishmaniaparasites alternate between flagellated promastigotes in sand flies and nonflagellated amastigotes in mammals, causing a spectrum of serious diseases. To survive, they must resist the harsh conditions in phagocytes (including acidic pH, elevated temperature, and increased oxidative/nitrosative stress) and evade the immune response. Recent studies have highlighted the importance of sphingolipid (SL) metabolism inLeishmaniavirulence. In particular, we have generated aLeishmania majoriscl−mutant which is deficient in SL degradation but grows normally as promastigotes in culture. Importantly,iscl−mutants cannot induce pathology in either immunocompetent or immunodeficient mice yet are able to persist at low levels. In this study, we investigated how the degradation of SLs might contribute toLeishmaniainfection. First, unlike wild-type (WT)L. major,iscl−mutants do not trigger polarized T cell responses in mice. Second, like WT parasites,iscl−mutants possess the ability to downregulate macrophage activation by suppressing the production of interleukin-12 (IL-12) and nitric oxide. Third, during the stationary phase,iscl−promastigotes were extremely vulnerable to acidic pH but not to other adverse conditions, such as elevated temperature and oxidative/nitrosative stress. In addition, inhibition of phagosomal acidification significantly improvediscl−survival in murine macrophages. Together, these findings indicate that SL degradation byLeishmaniais essential for its adaption to the acidic environment in phagolysosomes but is not required for the suppression of host cell activation. Finally, our studies withiscl−mutant-infected mice suggest that having viable, persistent parasites is not sufficient to provide immunity against virulentLeishmaniachallenge.
Spontaneous Phthiocerol Dimycocerosate-Deficient Variants of Mycobacterium tuberculosis Are Susceptible to Gamma Interferon-Mediated Immunity
Authors: Kirksey Meghan A. , Tischler Anna D. , Siméone Roxane , Hisert Katherine B. , Uplekar Swapna , Guilhot Christophe , McKinney John D.
Published: May 2011

Onset of the adaptive immune response in mice infected with
Mycobacterium tuberculosis
is accompanied by slowing of bacterial replication and establishment of a chronic infection. Stabilization of bacterial numbers during the chronic phase of infection is dependent on the activity of the gamma interferon (IFN-γ)-inducible nitric oxide synthase (NOS2). Previously, we described a differential signature-tagged mutagenesis screen designed to identify
M. tuberculosis
“counterimmune” mechanisms and reported the isolation of three mutants in the H37Rv strain background containing transposon insertions in the
rv0072
,
rv0405
, and
rv2958c
genes. These mutants were impaired for replication and virulence in NOS2
−/−
mice but were growth-proficient and virulent in IFN-γ
−/−
mice, suggesting that the disrupted genes were required for bacterial resistance to an IFN-γ-dependent immune mechanism other than NOS2. Here, we report that the attenuation of these strains is attributable to an underlying transposon-independent deficiency in biosynthesis of phthiocerol dimycocerosate (PDIM), a cell wall lipid that is required for full virulence in mice. We performed whole-genome resequencing of a PDIM-deficient clone and identified a spontaneous point mutation in the putative polyketide synthase PpsD that results in a G44C amino acid substitution. We demonstrate by complementation with the wild-type
ppsD
gene and reversion of the
ppsD
gene to the wild-type sequence that the
ppsD
(G44C) point mutation is responsible for PDIM deficiency, virulence attenuation in NOS2
−/−
and wild-type C57BL/6 mice, and a growth advantage
in vitro
in liquid culture. We conclude that PDIM biosynthesis is required for
M. tuberculosis
resistance to an IFN-γ-mediated immune response that is independent of NOS2.
Genomic and Surface Proteomic Analysis of the Canine Pathogen Staphylococcus pseudintermedius Reveals Proteins That Mediate Adherence to the Extracellular Matrix
Authors: Bannoehr Jeanette , Ben Zakour Nouri L. , Reglinski Mark , Inglis Neil F. , Prabhakaran Sabitha , Fossum Even , Smith David G. , Wilson Gillian J. , Cartwright Robyn A. , Haas Juergen , Hook Magnus , van den Broek Adri H. M. , Thoday Keith L. , Fitzgerald J. Ross
Published: May 2011

Cell wall-associated (CWA) proteins made by Gram-positive pathogens play a fundamental role in pathogenesis.Staphylococcus pseudintermediusis a major animal pathogen responsible for the canine skin disease bacterial pyoderma. Here, we describe the bioinformatic analysis of the family of 18 predicted CWA proteins encoded in the genome ofS. pseudintermediusstrain ED99 and determine their distribution among a phylogenetically diverse panel ofS. pseudintermediusclinical isolates and closely related species of theStaphylococcus intermediusgroup. In parallel, we employed a proteomic approach to identify proteins presented on the surface of strain ED99in vitro, revealing a total of 60 surface-localized proteins in one or more phases of growth, including 6 of the 18 genome-predicted CWA proteins. Based on these analyses, we selected two CWA proteins (SpsD and SpsL) encoded by all strains examined and investigated their capacity to mediate adherence to extracellular matrix proteins. We discovered that SpsD and SpsL mediated binding of a heterologous host,Lactococcus lactis, to fibrinogen and fibronectin and that SpsD mediated binding to cytokeratin 10, a major constituent of mammalian skin. Of note, the interaction with fibrinogen was host-species dependent, suggestive of a role for SpsD and SpsL in the host tropism ofS. pseudintermedius. Finally, we identified IgG specific for SpsD and SpsL in sera from dogs with bacterial pyoderma, implying that both proteins are expressed during infection. The combined genomic and proteomic approach employed in the current study has revealed novel host-pathogen interactions which represent candidate therapeutic targets for the control of bacterial pyoderma.
Bacillus cereus G9241 Makes Anthrax Toxin and Capsule like Highly Virulent B. anthracis Ames but Behaves like Attenuated Toxigenic Nonencapsulated B. anthracis Sterne in Rabbits and Mice
Authors: Wilson Melissa K. , Vergis James M. , Alem Farhang , Palmer John R. , Keane-Myers Andrea M. , Brahmbhatt Trupti N. , Ventura Christy L. , O'Brien Alison D.
Published: May 2011

Bacillus cereus
G9241 was isolated from a welder with a pulmonary anthrax-like illness. The organism contains two megaplasmids, pBCXO1 and pBC218. These plasmids are analogous to the
Bacillus anthracis
Ames plasmids pXO1 and pXO2 that encode anthrax toxins and capsule, respectively. Here we evaluated the virulence of
B. cereus
G9241 as well as the contributions of pBCXO1 and pBC218 to virulence.
B. cereus
G9241 was avirulent in New Zealand rabbits after subcutaneous inoculation and attenuated 100-fold compared to the published 50% lethal dose (LD
50
) values for
B. anthracis
Ames after aerosol inoculation. A/J and C57BL/6J mice were comparably susceptible to
B. cereus
G9241 by both subcutaneous and intranasal routes of infection. However, the LD
50
s for
B. cereus
G9241 in both mouse strains were markedly higher than those reported for
B. anthracis
Ames and more like those of the toxigenic but nonencapsulated
B. anthracis
Sterne. Furthermore,
B. cereus
G9241 spores could germinate and disseminate after intranasal inoculation into A/J mice, as indicated by the presence of vegetative cells in the spleen and blood of animals 48 h after infection. Lastly,
B. cereus
G9241 derivatives cured of one or both megaplasmids were highly attenuated in A/J mice. We conclude that the presence of the toxin- and capsule-encoding plasmids pBCXO1 and pBC218 in
B. cereus
G9241 alone is insufficient to render the strain as virulent as
B. anthracis
Ames. However, like
B. anthracis
, full virulence of
B. cereus
G9241 for mice requires the presence of both plasmids.
Suppressed Induction of Proinflammatory Cytokines by a Unique Metabolite Produced by Vibrio cholerae O1 El Tor Biotype in Cultured Host Cells
Authors: Bari Wasimul , Song Yoon-Jae , Yoon Sang Sun
Published: May 2011

Vibrio choleraeO1 has two biotypes, El Tor and Classical, and the latter is now presumed to be extinct in nature. Under carbohydrate-rich growth conditions, El Tor biotype strains produce the neutral fermentation end product 2,3-butanediol (2,3-BD), which prevents accumulation of organic acids from mixed acid fermentation and thus avoids a lethal decrease in the medium pH, while the Classical biotype strains fail to do the same. In this study, we investigated the inhibitory effect of 2,3-BD on the production of two proinflammatory biomarkers, intreleukin-8 (IL-8) and tumor necrosis factor alpha (TNF-α), in human intestinal epithelial HT29 and alveolar epithelial A549 cells. Cell-free culture supernatants of El Tor strain N16961 grown in LB supplemented with 1% glucose induced a negligible amount of IL-8 or TNF-α, while the Classical O395 strain induced much higher levels of these proinflammatory cytokines. On the other hand, three mutant strains constructed from the N16961 strain with defects in the constitutive 2,3-BD pathway were also able to induce high levels of cytokines. When HT29 and A549 cells were treated with bacterial flagella, known proinflammatory cytokine inducers, and chemically synthesized 2,3-BD at various concentrations, a dose-dependent decrease in IL-8 and TNF-α production was observed, demonstrating the suppressive effect of 2,3-BD on the production of proinflammatory cytokines in epithelial cells. Upon cotreatment with extraneous 2,3-BD, elevated levels of IκBα, the inhibitor of the NF-κB pathway, were detected in both HT29 and A549 cells. Furthermore, treatments containing 2,3-BD elicited lower levels of NF-κB-responsive luciferase activity, demonstrating that the reduced cytokine production is likely through the inhibition of the NF-κB pathway. These results reveal a novel and potential role of 2,3-BD as an immune modulator that might have conferred a superior pathogenic potential of the El Tor over the Classical biotype.
Helicobacter pylori AlpA and AlpB Bind Host Laminin and Influence Gastric Inflammation in Gerbils
Authors: Senkovich Olga A. , Yin Jun , Ekshyyan Viktoriya , Conant Carolyn , Traylor James , Adegboyega Patrick , McGee David J. , Rhoads Robert E. , Slepenkov Sergey , Testerman Traci L.
Published: May 2011

Helicobacter pylori
persistently colonizes humans, causing gastritis, ulcers, and gastric cancer. Adherence to the gastric epithelium has been shown to enhance inflammation, yet only a few
H. pylori
adhesins have been paired with targets in host tissue. The
alpAB
locus has been reported to encode adhesins involved in adherence to human gastric tissue. We report that abrogation of
H. pylori
AlpA and AlpB reduces binding of
H. pylori
to laminin while expression of plasmid-borne
alpA
or
alpB
confers laminin-binding ability to
Escherichia coli
. An
H. pylori
strain lacking only AlpB is also deficient in laminin binding. Thus, we conclude that both AlpA and AlpB contribute to
H. pylori
laminin binding. Contrary to expectations, the
H. pylori
SS1 mutant deficient in AlpA and AlpB causes more severe inflammation than the isogenic wild-type strain in gerbils. Identification of laminin as the target of AlpA and AlpB will facilitate future investigations of host-pathogen interactions occurring during
H. pylori
infection.
LOX-1 Deletion Improves Neutrophil Responses, Enhances Bacterial Clearance, and Reduces Lung Injury in a Murine Polymicrobial Sepsis Model
Authors: Wu Zhuang , Sawamura Tatsuya , Kurdowska Anna K. , Ji Hong-Long , Idell Steven , Fu Jian
Published: May 2011

Inflammatory tissue injury and immunosuppression are the major causes of death in sepsis. Novel therapeutic targets that can prevent excessive inflammation and improve immune responses during sepsis could be critical for treatment of this devastating disease. LOX-1 (lectin-like oxidized low-density lipoprotein receptor-1), a membrane protein expressed in endothelial cells, has been known to mediate vascular inflammation. In the present study, we demonstrated that LOX-1 deletion markedly improved the survival rate in a murine model of polymicrobial sepsis. Wild-type (LOX-1+/+) and LOX-1 knockout (LOX-1−/−) mice were subjected to cecal ligation and puncture (CLP) to induce sepsis. LOX-1 deletion significantly reduced systemic inflammation and inflammatory lung injury during sepsis, together with decreased production of proinflammatory cytokines and reduced lung edema formation. Furthermore, LOX-1 deletion improved host immune responses after the induction of sepsis, as indicated by enhanced bacterial clearance. Interestingly, we were able to demonstrate that LOX-1 is expressed in neutrophils. LOX-1 deletion prevented neutrophil overreaction and increased neutrophil recruitment to infection sites after sepsis induction, contributing at least partly to increased immune responses in LOX-1 knockout mice. Our study results indicate that LOX-1 is an important mediator of inflammation and neutrophil dysfunction in sepsis.
Glycogen Synthase Kinase 3 Activation Is Important for Anthrax Edema Toxin-Induced Dendritic Cell Maturation and Anthrax Toxin Receptor 2 Expression in Macrophages
Authors: Larabee Jason L. , Maldonado-Arocho Francisco J. , Pacheco Sergio , France Bryan , DeGiusti Kevin , Shakir Salika M. , Bradley Kenneth A. , Ballard Jimmy D.
Published: May 2011

Anthrax edema toxin (ET) is one of two binary toxins produced by
Bacillus anthracis
that contributes to the virulence of this pathogen. ET is an adenylate cyclase that generates high levels of cyclic AMP (cAMP), causing alterations in multiple host cell signaling pathways. We previously demonstrated that ET increases cell surface expression of the anthrax toxin receptors (ANTXR) in monocyte-derived cells and promotes dendritic cell (DC) migration toward the lymph node-homing chemokine MIP-3β. In this work, we sought to determine if glycogen synthase kinase 3 (GSK-3) is important for ET-induced modulation of macrophage and DC function. We demonstrate that inhibition of GSK-3 dampens ET-induced maturation and migration processes of monocyte-derived dendritic cells (MDDCs). Additional studies reveal that the ET-induced expression of ANTXR in macrophages was decreased when GSK-3 activity was disrupted with chemical inhibitors or with small interfering RNA (siRNA) targeting GSK-3. Further examination of the ET induction of ANTXR revealed that a dominant negative form of CREB could block the ET induction of ANTXR, suggesting that CREB or a related family member was involved in the upregulation of ANTXR. Because CREB and GSK-3 activity appeared to be important for ET-induced ANTXR expression, the impact of GSK-3 on ET-induced CREB activity was examined in RAW 264.7 cells possessing a CRE-luciferase reporter. As with ANTXR expression, the ET induction of the CRE reporter was decreased by reducing GSK-3 activity. These studies not only provide insight into host pathways targeted by ET but also shed light on interactions between GSK-3 and CREB pathways in host immune cells.
Expression of Anaplasma marginale Ankyrin Repeat-Containing Proteins during Infection of the Mammalian Host and Tick Vector
Authors: Ramabu Solomon S. , Schneider David A. , Brayton Kelly A. , Ueti Massaro W. , Graça Telmo , Futse James E. , Noh Susan M. , Baszler Timothy V. , Palmer Guy H.
Published: May 2011

Transmission of tick-borne pathogens requires transition between distinct host environments with infection and replication in host-specific cell types.
Anaplasma marginale
illustrates this transition: in the mammalian host, the bacterium infects and replicates in mature (nonnucleated) erythrocytes, while in the tick vector, replication occurs in nucleated epithelial cells. We hypothesized that proteins containing ankyrin motifs would be expressed by
A. marginale
only in tick cells and would traffic to the infected host cell nucleus.
A. marginale
encodes three proteins containing ankyrin motifs, an AnkA orthologue (the AM705 protein), AnkB (the AM926 protein), and AnkC (the AM638 protein). All three
A. marginale
Anks were confirmed to be expressed during intracellular infection: AnkA is expressed at significantly higher levels in erythrocytes, AnkB is expressed equally by both infected erythrocytes and tick cells, and AnkC is expressed exclusively in tick cells. There was no evidence of any of the Ank proteins trafficking to the nucleus. Thus, the hypothesis that ankyrin-containing motifs were predictive of cell type expression and nuclear localization was rejected. In contrast, AnkA orthologues in the closely related
A. phagocytophilum
and
Ehrlichia chaffeensis
have been shown to localize to the host cell nucleus. This difference, together with the lack of a nuclear localization signal in any of the AnkA orthologues, suggests that trafficking may be mediated by a separate transporter rather than by endogenous signals. Selection for divergence in Ank function among
Anaplasma
and
Ehrlichia
spp. is supported by both locus and allelic analyses of genes encoding orthologous proteins and their ankyrin motif compositions.
Klebsiella pneumoniae Yersiniabactin Promotes Respiratory Tract Infection through Evasion of Lipocalin 2
Authors: Bachman Michael A. , Oyler Jennifer E. , Burns Samuel H. , Caza Mélissa , Lépine François , Dozois Charles M. , Weiser Jeffrey N.
Published: May 2011

Klebsiella pneumoniae
is a pathogen of increasing concern because of multidrug resistance, especially due to
K. pneumoniae
carbapenemases (KPCs).
K. pneumoniae
must acquire iron to replicate, and it utilizes iron-scavenging siderophores, such as enterobactin (Ent). The innate immune protein lipocalin 2 (Lcn2) is able to specifically bind Ent and disrupt iron acquisition. To determine whether
K. pneumoniae
must produce Lcn2-resistant siderophores to cause disease, we examined siderophore production by clinical isolates (
n
= 129) from respiratory, urine, blood, and stool samples and by defined siderophore mutants through genotyping and liquid chromatography-mass spectrometry. Three categories of
K. pneumoniae
isolates were identified: enterobactin positive (Ent
+
) (81%), enterobactin and yersiniabactin positive (Ent
+
Ybt
+
) (17%), and enterobactin and salmochelin (glycosylated Ent) positive (Ent
+
gly-Ent
+
) with or without Ybt (2%). Ent
+
Ybt
+
strains were significantly overrepresented among respiratory tract isolates (
P
= 0.0068) and β-lactam-resistant isolates (
P
= 0.0019), including the epidemic KPC-producing clone multilocus sequence type 258 (ST258). In
ex vivo
growth assays, gly-Ent but not Ybt allowed evasion of Lcn2 in human serum, whereas siderophores were dispensable for growth in human urine. In a murine pneumonia model, an Ent
+
strain was an opportunistic pathogen that was completely inhibited by Lcn2 but caused severe, disseminated disease in
Lcn2
−/−
mice. In contrast, an Ent
+
Ybt
+
strain was a frank respiratory pathogen, causing pneumonia despite Lcn2. However, Lcn2 retained partial protection against disseminated disease. In summary, Ybt is a virulence factor that is prevalent among KPC-producing
K. pneumoniae
isolates and promotes respiratory tract infections through evasion of Lcn2.
The Borrelia burgdorferi Integrin Ligand P66 Affects Gene Expression by Human Cells in Culture
Authors: LaFrance Michelle E. , Pierce Jessica V. , Antonara Syliani , Coburn Jenifer
Published: May 2011

Borrelia burgdorferi, an agent of Lyme disease, establishes persistent infection in immunocompetent animals and humans. Although the infection in humans can be cleared by antibiotic therapy, persistence in reservoir animals is necessary for the maintenance of the bacterium in the natural reservoir host⇔tick vector infectious cycle.B. burgdorferibinds to β1- and β3-chain integrins, and the P66 outer membrane protein is responsible for at least some of the integrin binding activity of the spirochete. Because integrins are transmembrane, bidirectional signaling molecules, integrin binding may alter the nature of the host response to the bacteria. We used isogenicB. burgdorferip66+andΔp66strains to analyze the responses of cultured human cells to P66-integrin interaction during infection. Microarray results suggest that the response differs according to the cell type, infection time, and experimental conditions. Clusters of genes in functionally related categories that showed significant changes included proteins involved in cell-extracellular matrix interactions, actin dynamics, stress response, and immune responses. Integrin binding by P66 may therefore helpB. burgdorferiestablish infection by facilitating tissue invasion and modulating the activation of the immune system to other components of the bacteria, e.g., lipoproteins. These results provide insight into howB. burgdorferiis able to establish infection in immunocompetent hosts.
Development of soybean aphid genomic SSR markers using next generation sequencing
Authors: Jun Tae-Hwan , Michel Andrew P. , Mian M.A. Rouf
Published: May 2011

Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Aphis glycines Matsumura) has become the most damaging insect pest of soybean ( Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.
Isolation and characterization of resistance gene analogues from Psilanthus species that represent wild relatives of cultivated coffee endemic to India
Authors: Hendre Prasad S. , Bhat Prasanna R. , Krishnakumar V. , Aggarwal Ramesh K.
Published: May 2011

Biotic or abiotic stress can cause considerable damage to crop plants that can be managed by building disease resistance in the cultivated gene pool through breeding for disease resistance genes (R-genes). R-genes, conferring resistance to diverse pathogens or pests share a high level of similarity at the DNA and protein levels in different plant species. This property of R-genes has been successfully employed to isolate putative resistance gene analogues (RGAs) using a PCR-based approach from new plant sources. Using a similar approach, in the present study, we have successfully amplified putative RGAs having nucleotide-binding-site leucine-rich repeats (NBS-LRR-type RGAs) from seven different sources: two cultivated coffee species ( Coffea arabica L. and Coffea canephora Pierre ex. A. Froehner), four related taxa endemic to India (wild tree coffee species: Psilanthus bengalensis (Roem. & Schuttles) J.-F. Leroy, Psilanthus khasiana , Psilanthus travencorensis (Wight & Arn.) J.-F. Leroy, Psilanthus weightiana (Wall. ex Wight & Arn.) J.-F. Leroy), and a cDNA pool originally prepared from light- and drought-stressed Coffea arabica L. leaves. The total PCR amplicons obtained using NBS-LRR-specific primers from each source were cloned and transformed to construct seven independent libraries, from which 434 randomly picked clones were sequenced. In silico analysis of the sequenced clones revealed 27 sequences that contained characteristic RGA motifs, of which 24 had complete uninterrupted open reading frames. Comparisons of these with published RGAs showed several of these to be novel RGA sequences. Interestingly, most of such novel RGAs belonged to the related wild Psilanthus species. The data thus suggest the potential of the secondary gene pool as possible untapped donors of resistance genes to the present day cultivated species of coffee.
Quantitative evolution of transposable and satellite DNA sequences in Picea species
Authors: Sarri V. , Ceccarelli M. , Cionini P.G.
Published: May 2011

Clones containing tandemly arranged repeats belonging to two distinct sequence families, (i) PAG004P22F (2F) and PAG004E03C (3C) or (ii) Ty3/gypsy- (8R; PAG004B08R) and Ty1/copia-like sequences (9R; PAG007F19R), were selected from a randomly sheared total genomic DNA library of Picea abies . The inserts were used as probes in dot-blot hybridizations to genomic DNA of P. abies, Picea orientalis , Picea pungens , and Picea pungens var. glauca. All these entities are diploid and share the same chromosome number (2n = 24), but the genome sizes differ largely. The redundancy (copy number per 1C DNA) of sequences related to each probe varied greatly between the genomes. No significant correlation was found between the genome size and the copy number of sequences in any family. The quantitative ratios varied greatly (in each genome) between the two families of satellite DNA, between the sequences that represented copia or gypsy retrotransposons, and between tandemly arranged sequences and retroelements as a whole, suggesting that there is no common factor that controls the quantitative evolution of repeats belonging to different sequence families during speciation in Picea.
Postsynthetic modification of an imine-based microporous organic network
Authors: Kerneghan Phillip A. , Halperin Shira D. , Bryce David L. , Maly Kenneth E.
Published: May 2011

A highly cross-linked microporous organic network with imine linkers was prepared by condensation of tetrakis(4-aminophenyl)methane with terephthaldehyde. Gas adsorption studies indicate that the material exhibits permanent microporosity, and guest exchange experiments demonstrate that small molecules can diffuse into the network. Postsynthetic modification of this microporous network was achieved by treatment with borane in THF, which reduced the imine groups to the corresponding amines as shown by IR and 13C CP-MAS solid-state NMR spectroscopy. The resulting material showed enhanced resistance to acidic hydrolysis compared with the imine precursor, and retained its ability to absorb guest molecules. The amine network was amenable to further postsynthetic modifications. Specifically, acetylation of this network using acetic anhydride was demonstrated.
Sensing hazardous metal ions using a fluoroionophore calix[4]arene species containing two 8-oxyquinoline groups
Authors: Bagatin Izilda A. , Araki Koiti , Toma Henrique E.
Published: May 2011

The interaction of a calix[4]arene-based species containing two 8-oxyquinoline chromophore pendants with hazardous metal ions has been investigated using optical absorption and fluorimetric techniques. In the presence of Hg2+, Cd2+, and Pb2+ ions, there is only a small decrease of the calixarene absorption band at 283 nm. The main changes are associated with the absorption band of the 8-oxyquinoline group at 315 nm, undergoing a systematic bathochromic shift to above 350 nm. In addition, a systematic decrease of the oxyquinoline emission at λem = 392 nm (λexc = 315 nm) has been observed. These observations are consistent with the coordination of the metal ions to the quinoline groups attached to the calixarene ligand, providing a useful fluoroinophore species for analytical purposes.
Antibiotic-inspired zinc oxide with morphology-dependent photocatalytic activity
Authors: Gao Shuyan , Jia Xiaoxia , Li Zhengdao , Chen Yanli , Jiang Kai
Published: May 2011

ZnO materials with different morphologies (hexahedron, coneflowerlike, cauliflowerlike, and nanorods) have been synthesized via a bioinspired method, which is effective and facile for the controlled synthesis of ZnO. Zinc acetate and ammonia were used as growth precursors, and ampicillin was used as the morphology-directing agent. X-ray diffraction (XRD) data showed that the obtained ZnO with different morphologies displayed different crystal growth habits. Photodegradation of Orange G was used as a model reaction to test the photocatalytic activity of ZnO samples. Different morphologies exhibited different activities to Orange G degradation. The cauliflowerlike ZnO sample showed the best photocatalytic performance compared with the others. The influence of the morphology-directing agent and pH on the morphology of ZnO samples and the effect of the morphologies on the photocatalytic activity are tentatively discussed.
NaZSM-5-catalyzed dimethyl carbonate synthesis via the transesterification of ethylene carbonate with methanol
Authors: Yang Zhen-Zhen , Dou Xiao-Yong , Wu Fang , He Liang-Nian
Published: May 2011

NaZSM-5 zeolite was found to be an efficient heterogeneous catalyst for the synthesis of dimethyl carbonate (DMC), which can serve as a building block, an additive to fuel oil, and an electrolyte in batteries, via the transesterification of ethylene carbonate (EC) with methanol. Notably, 77% DMC yield and 97% selectivity were achieved under mild reaction conditions. Furthermore, the effects of various reaction parameters such as catalyst loading, reaction time, and methanol/EC molar ratio on the catalytic performance were investigated in detail. This protocol was found to be applicable to a variety of alcohols, producing the corresponding dialkyl carbonates with moderate yields and selectivities. Moreover, the catalyst can be recovered by simple filtration with retention of catalytic activity; a stable crystal configuration and a slight alteration of its superficial structure were observed by X-ray diffraction and BET measurements.
Copper and chromium oxide nanocomposite catalysts for simultaneous elimination of CO and oxygenate VOCs in toxic gas emissions
Authors: Tsoncheva Tanya , Ivanov Krasimir , Dimitrov Dimitar
Published: May 2011

Copper and chromium oxide nanocomposite materials with different Cu/Cr ratios were prepared by impregnation of a conventional silica support with toluene solutions of the corresponding acetylacetonate precursors and characterized by X-ray diffraction, Fourier transform infrared spectroscopy, UV–vis spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed reduction–thermogravimetric methods. Their catalytic behaviour in the total oxidation of CO and different oxygenate VOCs (methanol, dimethyl ether, and ethyl acetate) was tested. The relation between the phase composition and catalytic properties of the materials was also analyzed. It was established that materials with a 1:2 CuO/Cr2O3 molar ratio exhibit high catalytic activity for dimethyl ether oxidation, those with 2:1 and 1:1 ratios are suitable for CO and methanol oxidation, respectively, and both of the latter, but at much higher temperatures, are good for ethyl acetate elimination. A catalyst with an optimal composition of 1:1 (mol/mol) CuO/Cr2O3, working in a reactor with three temperature zones of 490–500 K, 570–580 K, and 620–630 K, is proposed for the effective simultaneous elimination of CO, methanol, ethyl acetate, and dimethyl ether in toxic emissions.
Modeling of 13C NMR chemical shifts of benzene derivatives using the RC–PC–ANN method: A comparative study of original molecular descriptors and multivariate image analysis descriptors
Authors: Garkani-Nejad Zahra , Poshteh-Shirani Marziyeh
Published: May 2011

The primary goal of a quantitative structure–property relationship study is to identify a set of structurally based numerical descriptors that can be mathematically linked to a property of interest. In this work, two main groups of descriptors have been used to predict 13C NMR chemical shifts of ipso, ortho, meta, and para positions in a series of 113 monosubstituted benzenes. First, two groups of descriptors — original molecular descriptors (constitutional, topological, electronic, and geometrical) and multivariate image analysis (MIA) descriptors — were calculated. Then, calculated descriptors were subjected to principal component analysis and the most significant principal components were extracted. Finally, more correlated principal components were used as inputs of artificial neural networks. The results obtained using the rank correlation–principal component–artificial neural network (RC–PC–ANN) modeling method show high ability to predict 13C NMR chemical shifts. Also, comparison of the results indicates that MIA descriptors show better ability to predict 13C NMR chemical shifts than the original molecular descriptors.
CLASSIFICATION OF EXTENSIONS OF A𝕋-ALGEBRAS
Authors: WEI CHANGGUO
Published: May 2011

We classify certain extensions of A𝕋-algebras using the six-term exact sequence in K-theory together with the Elliott invariants of the ideal and quotient. We also give certain necessary and sufficient conditions for such extension algebras being A𝕋-algebras.
COMBINATORIAL ASPECTS OF ORTHOGONAL GROUP INTEGRALS
Authors: BANICA TEODOR , SCHLENKER JEAN-MARC
Published: May 2011

We study the integrals of type [Formula: see text], depending on a matrix a ∈ Mp × q(ℕ), whose exact computation is an open problem. Our results are as follows: (1) an extension of the "elementary expansion" formula from the case a ∈ M2 × q(2ℕ) to the general case a ∈ Mp × q(ℕ), (2) the construction of the "best algebraic normalization" of I(a), in the case a ∈ M2 × q(ℕ), (3) an explicit formula for I(a), for diagonal matrices a ∈ M3 × 3(ℕ), (4) a modeling result in the case a ∈ M1 × 2(ℕ), in relation with the Euler–Rodrigues formula. Most proofs use various combinatorial techniques.
CIRCLE ACTION AND SOME VANISHING RESULTS ON MANIFOLDS
Authors: LI PING , LIU KEFENG
Published: May 2011

Kawakubo and Uchida showed that, if a closed oriented 4k-dimensional manifold M admits a semi-free circle action such that the dimension of the fixed point set is less than 2k, then the signature of M vanishes. In this note, by using G-signature theorem and the rigidity of the signature operator, we generalize this result to more general circle actions. Combining the same idea with the remarkable Witten–Taubes–Bott rigidity theorem, we explore more vanishing results on spin manifolds admitting such circle actions. Our results are closely related to some earlier results of Conner–Floyd, Landweber–Stong and Hirzebruch–Slodowy.
(t, s)-RACKS AND THEIR LINK INVARIANTS
Authors: CENICEROS JESSICA , NELSON SAM
Published: May 2011

A (t, s)-rack is a rack structure defined on a module over the ring [Formula: see text]. We identify necessary and sufficient conditions for two (t, s)-racks to be isomorphic. We define enhancements of the rack counting invariant using the structure of (t, s)-racks and give some computations and examples. As an application, we use these enhanced invariants to obtain obstructions to knot ordering.
DECOMPOSITION OF STOCHASTIC FLOWS WITH AUTOMORPHISM OF SUBBUNDLES COMPONENT
Authors: CATUOGNO PEDRO J. , DA SILVA FABIANO B. , RUFFINO PAULO R.
Published: May 2011

We show that given a G-structure P on a differential manifold M, if the group G(M) of automorphisms of P is large enough, then there exists the quotient of a stochastic flows φt by G(M), in the sense that φt = ξt ◦ ρt where ξt ∈ G(M), the remainder ρt has derivative which is vertical, transversal to the fibres of P. This geometrical context generalises previous results where M is a Riemannian manifold and φt is decomposed with an isometric component, see [12] and [15], which in our context corresponds to the particular case of an SO(n) -structure on M.
Embedding nonground logic programs into autoepistemic logic for knowledge-base combination
Authors: Bruijn Jos De , Eiter Thomas , Polleres Axel , Tompits Hans
Published: May 2011

In the context of the Semantic Web, several approaches for combining ontologies, given in terms of theories of classical first-order logic and rule bases, have been proposed. They either cast rules into classical logic or limit the interaction between rules and ontologies. Autoepistemic logic (AEL) is an attractive formalism which allows overcoming these limitations by serving as a uniform host language to embed ontologies and nonmonotonic logic programs into it. For the latter, so far only the propositional setting has been considered. In this article, we present three embeddings of normal and three embeddings of disjunctive nonground logic programs under the stable model semantics into first-order AEL. While all embeddings correspond with respect to objective ground atoms, differences arise when considering nonatomic formulas and combinations with first-order theories. We compare the embeddings with respect to stable expansions and autoepistemic consequences, considering the embeddings by themselves, as well as combinations with classical theories. Our results reveal differences and correspondences of the embeddings, and provide useful guidance in the choice of a particular embedding for knowledge combination.
Proposition algebra
Authors: Bergstra Jan A. , Ponse Alban
Published: May 2011

Sequential propositional logic deviates from conventional propositional logic by taking into account that during the sequential evaluation of a propositional statement, atomic propositions may yield different Boolean values at repeated occurrences. We introduce “free valuations” to capture this dynamics of a propositional statement's environment. The resulting logic is phrased as an equationally specified algebra rather than in the form of proof rules, and is named “proposition algebra.” It is strictly more general than Boolean algebra to the extent that the classical connectives fail to be expressively complete in the sequential case. The four axioms for free valuation congruence are then combined with other axioms in order define a few more valuation congruences that gradually identify more propositional statements, up to static valuation congruence (which is the setting of conventional propositional logic).

Proposition algebra is developed in a fashion similar to the process algebra ACP and the program algebra PGA, via an algebraic specification which has a meaningful initial algebra for which a range of coarser congruences are considered important as well. In addition, infinite objects (i.e., propositional statements, processes and programs respectively) are dealt with by means of an inverse limit construction which allows the transfer of knowledge concerning finite objects to facts about infinite ones while reducing all facts about infinite objects to an infinity of facts about finite ones in return.
DieCast
Authors: Gupta Diwaker , Vishwanath Kashi Venkatesh , McNett Marvin , Vahdat Amin , Yocum Ken , Snoeren Alex , Voelker Geoffrey M.
Published: May 2011

Large-scale network services can consist of tens of thousands of machines running thousands of unique software configurations spread across hundreds of physical networks. Testing such services for complex performance problems and configuration errors remains a difficult problem. Existing testing techniques, such as simulation or running smaller instances of a service, have limitations in predicting overall service behavior at such scales.

Testing large services should ideally be done at the same scale and configuration as the target deployment, which can be technically and economically infeasible. We present
DieCast
, an approach to scaling network services in which we multiplex all of the nodes in a given service configuration as virtual machines across a much smaller number of physical machines in a test harness. We show how to accurately scale CPU, network, and disk to provide the illusion that each VM matches a machine in the original service in terms of both available computing resources and communication behavior. We present the architecture and evaluation of a system we built to support such experimentation and discuss its limitations. We show that for a variety of services---including a commercial high-performance cluster-based file system---and resource utilization levels,
DieCast
matches the behavior of the original service while using a fraction of the physical resources.
Management of Multilevel, Multiclient Cache Hierarchies with Application Hints
Authors: Yadgar Gala , Factor Michael , Li Kai , Schuster Assaf
Published: May 2011

Multilevel caching, common in many storage configurations, introduces new challenges to traditional cache management: data must be kept in the appropriate cache and replication avoided across the various cache levels. Additional challenges are introduced when the lower levels of the hierarchy are shared by multiple clients. Sharing can have both positive and negative effects. While data fetched by one client can be used by another client without incurring additional delays, clients competing for cache buffers can evict each other’s blocks and interfere with exclusive caching schemes.

We present a global noncentralized, dynamic and informed management policy for multiple levels of cache, accessed by multiple clients. Our algorithm,
MC
2
, combines local, per client management with a global, system-wide scheme, to emphasize the positive effects of sharing and reduce the negative ones. Our local management scheme,
Karma
, uses readily available information about the client’s future access profile to save the most valuable blocks, and to choose the best replacement policy for them. The global scheme uses the same information to divide the shared cache space between clients, and to manage this space. Exclusive caching is maintained for nonshared data and is disabled when sharing is identified.

Previous studies have partially addressed these challenges through minor changes to the storage interface. We show that all these challenges can in fact be addressed by combining minor interface changes with smart allocation and replacement policies. We show the superiority of our approach through comparison to existing solutions, including LRU, ARC, MultiQ, LRU-SP, and Demote, as well as a lower bound on optimal I/O response times. Our simulation results demonstrate better cache performance than all other solutions and up to 87% better performance than LRU on representative workloads.
A cloud based software testing paradigm for mobile applications
Authors: Baride Srikanth , Dutta Kamlesh
Published: May 2011

The testing of applications for mobile computing devices is cumbersome due to the bounded computational resources that these devices have and diversity in mobile environments. There are many different types of emulators that have been proposed and used nowadays for this purpose. But these emulators typically cannot emulate: actual network speed and availability, actual device specific content-rendering speed, memory limitation, cache size, CPU speed, and stack size. These emulators are designed for specific platforms, which lack testing of applications on heterogeneous mobile platforms. Cloud Computing has a potential to overcome these challenges by taking up contemporary progress in parallel and distributed systems, virtualization, and software services. Cloud computing empowers us to have adaptable and on-demand network access to a common group of configurable computing resources. In this article, we introduce a cloudbased model that provides solutions to aforesaid challenges. Our model sets up a mobile environment, actual device and platform on the cloud resources for a given system configuration. It also provides software testing services to execute numerous tests automatically according to a given application.