bluuebunny/crossref_metadata_2025_split huggingface dataset:
Major Histocompatibility Complex Class II Molecule-Human Immunodeficiency Virus Peptide Analysis Using a Microarray Chip
Authors: Gaseitsiwe Simani , Valentini Davide , Ahmed Raija , Mahdavifar Shahnaz , Magalhaes Isabelle , Zerweck Johannes , Schutkowski Mike , Gautherot Emmanuel , Montero Felix , Ehrnst Anneka , Reilly Marie , Maeurer Markus 
Published: February 2009

ABSTRACTIdentification of major histocompatibility complex (MHC) class II binding peptides is a crucial step in rational vaccine design and immune monitoring. We designed a novel MHC class II molecule-peptide microarray binding assay and evaluated 346 peptides from already identified human immunodeficiency virus (HIV) epitopes and an additional set (n= 206) of 20-mer peptides, overlapping by 15 amino acid residues, from HIV type 1B (HIV-1B) gp160 and Nef as a paradigm. Peptides were attached via the N-terminal part to a linker that covalently binds to the epoxy glass slide. The 552 peptides were printed in triplicate on a single peptide microarray chip and tested for stable formation of MHC class II molecule-peptide complexes using recombinant soluble DRB1*0101(DR1), DRB1*1501(DR2), and DRB1*0401(DR4) molecules. Cluster analysis revealed unique patterns of peptide binding to all three, two, or a single MHC class II molecule. MHC class II binding peptides reside within previously described immunogenic regions of HIV gp160 and Nef, yet we could also identify new MHC class II binding peptides from gp160 and Nef. Peptide microarray chips allow the comprehensive and simultaneous screening of a high number of candidate peptide epitopes for MHC class II binding, guided by subsequent quality data extraction and binding pattern cluster analysis.
Seroepidemiological Study after a Long-Distance Industrial Outbreak of Legionnaires' Disease
Authors: Wedege E. , Bergdal T. , Bolstad K. , Caugant D. A. , Efskind J. , Heier H. E. , Kanestrøm A. , Strand B. H. , Aaberge I. S. 
Published: February 2009

ABSTRACT

Following a long-distance outbreak of Legionnaires' disease from an industrial air scrubber in Norway in 2005, a seroepidemiological study measuring levels of immunoglobulin G (IgG) and IgM antibodies to
Legionella pneumophila
was performed with a polyvalent enzyme-linked immunosorbent assay. One year after the outbreak, IgG levels in employees (
n
= 213) at the industrial plant harboring the scrubber and in blood donors (
n
= 398) from the outbreak county were low but significantly higher (
P
≤ 0.002) than those in blood donors (
n
= 406) from a nonexposed county. No differences in IgM levels among the three groups were found after adjustment for gender and age. Home addresses of the seroresponders in the exposed county clustered to the city of the outbreak, in contrast to the scattering of addresses of the seroresponding donors in the nonexposed county. Factory employees who operated at an open biological treatment plant had significantly higher IgG and IgM levels (
P
≤ 0.034) than those working >200 m away. Most of the healthy seroresponders among the factory employees worked near this exposure source. Immunoblotting showed that IgG and IgM antibodies in 82.1% of all seroresponders were directed to the lipopolysaccharide of the
L. pneumophila
serogroup 1 outbreak strain. In conclusion, 1 year after the long-distance industrial outbreak a small increase in IgG levels of the exposed population was observed. The open biological treatment plant within the industrial premises, however, constituted a short-distance exposure source of
L. pneumophila
for factory employees working nearby.
Hog1 Mitogen-Activated Protein Kinase (MAPK) Interrupts Signal Transduction between the Kss1 MAPK and the Tec1 Transcription Factor To Maintain Pathway Specificity
Authors: Shock Teresa R. , Thompson James , Yates John R. , Madhani Hiten D. 
Published: February 2009

ABSTRACT

In
Saccharomyces cerevisiae
, the mating, filamentous growth (FG), and high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) signaling pathways share components and yet mediate distinct responses to different extracellular signals. Cross talk is suppressed between the mating and FG pathways because mating signaling induces the destruction of the FG transcription factor Tec1. We show here that HOG pathway activation results in phosphorylation of the FG MAPK, Kss1, and the MAPKK, Ste7. However, FG transcription is not activated because HOG signaling prevents the activation of Tec1. In contrast to the mating pathway, we find that the mechanism involves the inhibition of DNA binding by Tec1 rather than its destruction. We also find that nuclear accumulation of Tec1 is not affected by HOG signaling. Inhibition by Hog1 is apparently indirect since it does not require any of the consensus S/TP MAPK phosphorylation sites on Tec1, its DNA-binding partner Ste12, or the associated regulators Dig1 or Dig2. It also does not require the consensus MAPK sites of the Ste11 activator Ste50, in contrast to a recent proposal for a role for negative feedback in specificity. Our results demonstrate that HOG signaling interrupts the FG pathway signal transduction between the phosphorylation of Kss1 and the activation of DNA binding by Tec1.
The 3′-to-5′ Exoribonuclease (Encoded by HP1248) ofHelicobacter pyloriRegulates Motility and Apoptosis-Inducing Genes
Authors: Tsao Ming-Yang , Lin Tzu-Lung , Hsieh Pei-Fang , Wang Jin-Town 
Published: February 2009

ABSTRACTThe human gastric pathogenHelicobacter pylorihas many virulence factors involved in pathogenesis, but the mechanisms regulating these virulence factors are not yet fully understood. In this study, we cloned HP1248, which is similar in sequence toEscherichia coli vacB, which was previously shown to be associated with the expression of virulence inShigellaand enteroinvasiveE. coli. E. coli vacBencodes RNase R. RNase R is involved in the posttranscriptional regulation of mRNA stability. By global transcriptional microarray profiling of anH. pyloriHP1248 deletion mutant, we defined six virulence-related genes which were posttranscriptionally downregulated by HP1248, including the motility-related genes HP1192 andflaB, the chemotaxis-related genecheY, and the apoptosis-inducing genes HP0175,cagA, andgtt. In this study, recombinant HP1248 protein expressed inE. colishowed 3′-to-5′ exoribonuclease activity. Motility and apoptosis induction were increased in theH. pyloriHP1248 deletion mutant. We also showed that HP1192 is associated withH. pylorimotility, possibly through HP1248 regulation. Further, we suggested and studied the possible mechanisms of this specific regulation of virulent genes by HP1248. In addition, the expression level of HP1248 mRNA changed dramatically in response to a variety of altered environmental conditions, including pH and temperature. Hence, HP1248 inH. pyloriseems to play a role in environmental sensing and in regulation of virulent phenotypes, such as motility and host apoptosis induction.
Constitutive Mutations in theEscherichia coliAraC Protein
Authors: Dirla Stephanie , Chien John Yeh-Heng , Schleif Robert 
Published: February 2009

ABSTRACTTheEscherichia coliAraC protein represses and induces thearaBADoperon in response to the absence or presence ofl-arabinose. Constitutive mutations in the AraC gene no longer require the presence ofl-arabinose to convert AraC from its repressing to its inducing state. Such mutations were isolated directly by virtue of their constitutivity or by their resistance to the nonmetabolizable arabinose analog,d-fucose. The majority of the constitutive mutations lie within the same residues of the N-terminal regulatory arm of AraC. Two, however, were found in the core of the dimerization domain. As predicted by the light switch mechanism of AraC, constitutive mutations increase the susceptibility of the N-terminal arms to digestion by trypsin or chymotrypsin, suggesting that these mutations weaken or disrupt the arm structure required for repression by AraC. Fluorescence, circular dichroism, and cysteine reactivity measurements show that the constitutive mutations in the core of the dimerization domain lead to a weakening of the support for the arms and reduce the stability of the minus-arabinose arm structure. These mutations also weaken the interaction between the two-helix bundle and the β-barrel subdomains of the dimerization domain and reduce the structural stability of the β-barrels.
The
Escherichia coli
Common Pilus and the Bundle-Forming Pilus Act in Concert during the Formation of Localized Adherence by Enteropathogenic
E. coli
Authors: Saldaña Zeus , Erdem Ayşen L. , Schüller Stephanie , Okeke Iruka N. , Lucas Mark , Sivananthan Arunon , Phillips Alan D. , Kaper James B. , Puente José L. , Girón Jorge A. 
Published: February 2009

ABSTRACT

Although the bundle-forming pilus (BFP) of enteropathogenic
Escherichia coli
(EPEC) mediates microcolony formation on epithelial cells, the adherence of BFP-deficient mutants is significantly abrogated, but the mutants are still adherent due to the presence of intimin and possibly other adhesins. In this study we investigated the contribution of the recently described
E
.
coli
common pilus (ECP) to the overall adherence properties of EPEC. We found that ECP and BFP structures can be simultaneously observed in the course (between zero time and 7 h during infection) of formation of localized adherence on cultured epithelial cells. These two pilus types colocalized at different levels of the microcolony topology, tethering the adhering bacteria. No evidence of BFP disappearance was found after prolonged infection. When expressed from a plasmid present in nonadherent
E. coli
HB101, ECP rendered this organism highly adherent at levels comparable to those of HB101 expressing the BFP. Purified ECP bound in a dose-dependent manner to epithelial cells, and the binding was blocked with anti-ECP antibodies, confirming that the pili possess adhesin properties. An ECP mutant showed only a modest reduction in adherence to cultured cells due to background expression levels of BFP and intimin. However, isogenic mutants not expressing EspA or BFP were significantly less adherent when the
ecpA
gene was also deleted. Furthermore, a Δ
espA
Δ
ecpA
double mutant (unable to translocate Tir and to establish intimate adhesion) was at least 10-fold less adherent than the Δ
espA
and Δ
ecpA
single mutants, even in the presence of BFP. A Δ
bfp
Δ
espA
Δ
ecpA
triple mutant showed the least adherence compared to the wild type and all the isogenic mutant strains tested, suggesting that ECP plays a synergistic role in adherence. Our data indicate that ECP is an accessory factor that, in association with BFP and other adhesins, contributes to the multifactorial complex interaction of EPEC with host epithelial cells.
Identification and Characterization of Catabolicpara-Nitrophenol 4-Monooxygenase andpara-Benzoquinone Reductase fromPseudomonassp. Strain WBC-3
Authors: Zhang Jun-Jie , Liu Hong , Xiao Yi , Zhang Xian-En , Zhou Ning-Yi 
Published: February 2009

ABSTRACTPseudomonassp. strain WBC-3 utilizespara-nitrophenol (PNP) as a sole source of carbon, nitrogen, and energy. In order to identify the genes involved in this utilization, we cloned and sequenced a 12.7-kb fragment containing a conserved region of NAD(P)H:quinone oxidoreductase genes. Of the products of the 13 open reading frames deduced from this fragment, PnpA shares 24% identity to the large component of a 3-hydroxyphenylacetate hydroxylase fromPseudomonas putidaU and PnpB is 58% identical to an NAD(P)H:quinone oxidoreductase fromEscherichia coli. Both PnpA and PnpB were purified to homogeneity as His-tagged proteins, and they were considered to be a monomer and a dimer, respectively, as determined by gel filtration. PnpA is a flavin adenine dinucleotide-dependent single-component PNP 4-monooxygenase that converts PNP topara-benzoquinone in the presence of NADPH. PnpB is a flavin mononucleotide-and NADPH-dependentp-benzoquinone reductase that catalyzes the reduction ofp-benzoquinone to hydroquinone. PnpB could enhance PnpA activity, and genetic analyses indicated that bothpnpAandpnpBplay essential roles in PNP mineralization in strain WBC-3. Furthermore, thepnpCDEFgene cluster next topnpABshares significant similarities with and has the same organization as a gene cluster responsible for hydroquinone degradation (hapCDEF) inPseudomonas fluorescensACB (M. J. Moonen, N. M. Kamerbeek, A. H. Westphal, S. A. Boeren, D. B. Janssen, M. W. Fraaije, and W. J. van Berkel, J. Bacteriol.190:5190-5198, 2008), suggesting that the genes involved in PNP degradation are physically linked.
σSControls Multiple Pathways Associated with Intracellular Multiplication ofLegionella pneumophila
Authors: Hovel-Miner Galadriel , Pampou Sergey , Faucher Sebastien P. , Clarke Margaret , Morozova Irina , Morozov Pavel , Russo James J. , Shuman Howard A. , Kalachikov Sergey 
Published: February 2009

ABSTRACTLegionella pneumophilais the causative agent of the severe and potentially fatal pneumonia Legionnaires' disease.L. pneumophilais able to replicate within macrophages and protozoa by establishing a replicative compartment in a process that requires the Icm/Dot type IVB secretion system. The signals and regulatory pathways required forLegionellainfection and intracellular replication are poorly understood. Mutation of therpoSgene, which encodes σS, does not affect growth in rich medium but severely decreasesL. pneumophilaintracellular multiplication within protozoan hosts. To gain insight into the intracellular multiplication defect of anrpoSmutant, we examined its pattern of gene expression during exponential and postexponential growth. We found that σSaffects distinct groups of genes that contribute toLegionellaintracellular multiplication. We demonstrate thatrpoSmutants have a functional Icm/Dot system yet are defective for the expression of many genes encoding Icm/Dot-translocated substrates. We also show that σSaffects the transcription of thecpxRandpmrAgenes, which encode two-component response regulators that directly affect the transcription of Icm/Dot substrates. Our characterization of theL. pneumophilasmall RNAcsrBhomologs,rsmYandrsmZ, introduces a link between σSand the posttranscriptional regulator CsrA. We analyzed the network of σS-controlled genes by mutational analysis of transcriptional regulators affected by σS. One of these, encoding theL. pneumophilaarginine repressor homolog gene,argR, is required for maximal intracellular growth in amoebae. These data show that σSis a key regulator of multiple pathways required forL. pneumophilaintracellular multiplication.
Differential Expression of
sigH
Paralogs during Growth and under Different Stress Conditions in
Mycobacterium smegmatis
Authors: Singh Anirudh K. , Singh Bhupendra N. 
Published: February 2009

ABSTRACT

SigH regulates a transcriptional network that responds to heat and oxidative stress in mycobacteria. Seven
sigH
paralogs are reported to exist in the
Mycobacterium smegmatis
genome. A comprehensive real-time reverse transcriptase PCR analysis during different stages of growth and upon exposure to various stress conditions and antimycobacterial compounds showed differential expression of
sigH
paralogs during stationary phase and severalfold increases in the levels of transcription of
sigH1
,
sigH4
,
sigH5
,
sigH6
, and
sigH7
under specific stress conditions.
Borrelia burgdorferi bba74Is Expressed Exclusively during Tick Feeding and Is Regulated by Both Arthropod- and Mammalian Host-Specific Signals
Authors: Mulay Vishwaroop B. , Caimano Melissa J. , Iyer Radha , Dunham-Ems Star , Liveris Dionysios , Petzke Mary M. , Schwartz Ira , Radolf Justin D. 
Published: February 2009

ABSTRACTAlthough BBA74 initially was described as a 28-kDa virulence-associated outer-membrane-spanning protein with porin-like function, subsequent studies revealed that it is periplasmic and downregulated in mammalian host-adapted spirochetes. To further elucidate the role of this protein in theBorrelia burgdorferitick-mammal cycle, we conducted a thorough examination of its expression profile in comparison with the profiles of three well-characterized, differentially expressed borrelial genes (ospA,ospC, andospE) and their proteins. In vitro, transcripts forbba74were expressed at 23°C and further enhanced by a temperature shift (37°C), whereas BBA74 protein diminished at elevated temperatures; in contrast, neither transcript nor protein was expressed by spirochetes grown in dialysis membrane chambers (DMCs). Primer extension of wild-typeB. burgdorferigrown in vitro, in conjunction with expression analysis of DMC-cultivated wild-type andrpoSmutant spirochetes, revealed that, likeospA,bba74is transcribed by σ70and is subject to RpoS-mediated repression within the mammalian host. A series of experiments utilizing wild-type andrpoSmutant spirochetes was conducted to determine the transcriptional and translational profiles ofbba74during the tick-mouse cycle. Results from these studies revealed (i) thatbba74is transcribed by σ70exclusively during the larval and nymphal blood meals and (ii) that transcription ofbba74is bracketed by RpoS-independent and -dependent forms of repression that are induced by arthropod- and mammalian host-specific signals, respectively. Although loss of BBA74 does not impair the ability ofB. burgdorferito complete its infectious life cycle, the temporal compartmentalization of this gene's transcription suggests that BBA74 facilitates fitness of the spirochete within a narrow window of its tick phase. A reexamination of the paradigm for reciprocal regulation ofospAandospC, performed herein, revealed that the heterogeneous expression of OspA and OspC displayed by spirochete populations during the nymphal blood meal results from the intricate sequence of transcriptional and translational changes that ensue asB. burgdorferitransitions between its arthropod vector and mammalian host.
Utility of Multilocus Variable-Number Tandem-Repeat Analysis as a Molecular Tool for Phylogenetic Analysis ofShigella sonnei
Authors: Chiou Chien-Shun , Watanabe Haruo , Wang You-Wun , Wang Wan-Ling , Terajima Jun , Thong Kwai-Lin , Phung Dac Cam , Tung Sheng Kai 
Published: February 2009

ABSTRACTA panel of 916 isolates, including 703 closely related IST1 isolates, were characterized by inter-IS1spacer typing (IST), pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to evaluate the utility of MLVA as a molecular tool for the phylogenetic analysis ofShigella sonnei. The global phylogenetic patterns determined by IST, PFGE, and MLVA were concordant. MLVA was carried out using 26 VNTR loci with a range of degrees of variability. MLVA data for the 703 IST1 isolates revealed that diversification among the closely related isolates was attributed mainly to four highly variable loci. The phylogenetic pattern for the closely related isolates determined using MLVA profiles of 8 highly variable loci was in agreement with that determined using the 26-locus profiles. A clustering analysis using the profiles of 18 loci with limited variability established clear phylogenetic relationships among IST clonal groups. Accordingly, MLVA is a useful tool for the phylogenetic analysis ofS. sonnei. Combined VNTR loci with higher variability are useful markers for resolving closely related isolates, whereas combined loci with lower variability are suitable for establishing clear phylogenetic relationships between strains or clones that have evolved over a longer timescale.
Bloodstream Infections Due to
Trichosporon
spp.: Species Distribution,
Trichosporon asahii
Genotypes Determined on the Basis of Ribosomal DNA Intergenic Spacer 1 Sequencing, and Antifungal Susceptibility Testing
Authors: Chagas-Neto Thomas C. , Chaves Guilherme M. , Melo Analy S. A. , Colombo Arnaldo L. 
Published: February 2009

ABSTRACT

The reevaluation of the genus
Trichosporon
has led to the replacement of the old taxon
Trichosporon beigelii
by six new species. Sequencing of the ribosomal DNA (rDNA) intergenic spacer 1 (IGS1) is currently mandatory for accurate
Trichosporon
identification, but it is not usually performed in routine laboratories. Here we describe
Trichosporon
species distribution and prevalence of
Trichosporon asahii
genotypes based on rDNA IGS1 sequencing as well as antifungal susceptibility profiles of 22 isolates recovered from blood cultures. The clinical isolates were identified as follows: 15
T. asahii
isolates, five
Trichosporon asteroides
isolates, one
Trichosporon coremiiforme
isolate, and one
Trichosporon dermatis
isolate. We found a great diversity of different species causing trichosporonemia, including a high frequency of isolation of
T. asteroides
from blood cultures that is lower than that of
T. asahii
only. Regarding
T. asahii
genotyping, we found that the majority of our isolates belonged to genotype 1 (86.7%). We report the first
T. asahii
isolate belonging to genotype 4 in South America. Almost 50% of all
T. asahii
isolates exhibited amphotericin B MICs of ≥2 μg/ml. Caspofungin MICs obtained for all the
Trichosporon
sp. isolates tested were consistently high (MICs ≥ 2 μg/ml). Most isolates (87%) had high MICs for 5-flucytosine, but all of them were susceptible to triazoles, markedly to voriconazole (all MICs ≤ 0.06 μg/ml).
Neuraminidase Stalk Length and Additional Glycosylation of the Hemagglutinin Influence the Virulence of Influenza H5N1 Viruses for Mice
Authors: Matsuoka Yumiko , Swayne David E. , Thomas Colleen , Rameix-Welti Marie-Anne , Naffakh Nadia , Warnes Christine , Altholtz Melanie , Donis Ruben , Subbarao Kanta 
Published: February 2009

ABSTRACT
Following circulation of avian influenza H5 and H7 viruses in poultry, the hemagglutinin (HA) can acquire additional glycosylation sites, and the neuraminidase (NA) stalk becomes shorter. We investigated whether these features play a role in the pathogenesis of infection in mammalian hosts. From 1996 to 2007, H5N1 viruses with a short NA stalk have become widespread in several avian species. Compared to viruses with a long-stalk NA, viruses with a short-stalk NA showed a decreased capacity to elute from red blood cells and an increased virulence in mice, but not in chickens. The presence of additional HA glycosylation sites had less of an effect on virulence than did NA stalk length. The short-stalk NA of H5N1 viruses circulating in Asia may contribute to virulence in humans.