bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of an Outer Membrane Protein ofSalmonella entericaSerovar Typhimurium That Confers Protection against Typhoid
Authors: Hamid Nowsheen , Jain S. K. 
Published: July 2008

ABSTRACTTyphoid caused bySalmonella entericaserovar Typhi remains a major health concern worldwide. The emergence of multidrug-resistant strains ofSalmonellawith increased virulence, communicability, and survivability leading to increased morbidity and mortality has further complicated its management. Currently available vaccines for typhoid have less-than-desired efficacy and certain unacceptable side effects, making it pertinent to search for new immunogens suitable for vaccine formulation. The outer membrane proteins (OMPs) ofSalmonellahave been considered possible candidates for conferring protection against typhoid. OMPs interface the cell with the environment, thus representing important virulence factors with a significant role in the pathobiology of gram-negative bacteria and bacterial adaptation. An OMP ofSalmonella entericaserovar Typhimurium with an apparent molecular mass of 49 kDa that is highly immunogenic, evokes humoral and cell-mediated immune responses, and confers 100% protection to immunized rats against challenge with very high doses (up to 100 times the 50% lethal dose) ofSalmonella entericaserovar Typhimurium has been identified. Further, very efficient clearance of bacteria from the reticuloendothelial systems of immunized animals was seen. This protein is recognized by the antibodies present in serum of typhoid patients. When sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel-eluted protein was further analyzed by high-performance liquid chromatography (HPLC) and two-dimensional electrophoresis, two polypeptides with the same molecular weight were resolved. These have different isoelectric points and gave two peaks with different retention times in reverse-phase HPLC. However, only one of the two bands interacted with patient serum. The immunogenicity studies (enzyme-linked immunosorbent assay and delayed-type hypersensitivity [DTH]) indicated that the immunoreactive protein evoked a strong immune response in rats. The N-terminal sequencing and analysis of the homology of this protein with sequences in the protein database ofSalmonellaresulted in a match with the N-terminal sequences of a protein inSalmonella entericaserovar Typhi (CT18 and Ty2 strains). The homology search further revealed it to be a hypothetical protein, whose gene had unidentified open reading frames inSalmonellaserovar Typhi encoding 447 amino acid residues, corresponding to a molecular mass of 49 kDa. The nucleotide sequence of the encoding gene was deduced, and the gene was amplified by PCR using appropriate primers. An amplified 1.3-kb band was purified and sequenced to confirm its identity. These OMPs provide promising targets for the development of a candidate vaccine against typhoid.
Molecular Method for Discrimination between
Francisella tularensis
and
Francisella
-Like Endosymbionts
Authors: Escudero Raquel , Toledo A. , Gil Horacio , Kovácsová Katarina , Rodríguez-Vargas Manuela , Jado Isabel , García-Amil Cristina , Lobo Bruno , Bhide Mangesh , Anda Pedro 
Published: July 2008

ABSTRACT

Environmental studies on the distribution of
Francisella
spp. are hampered by the frequency of
Francisella
-like endosymbionts that can produce a misleading positive result. A new, efficient molecular method for detection of
Francisella tularensis
and its discrimination from
Francisella
-like endosymbionts, as well as two variants associated with human disease (unusual
F. tularensis
strain FnSp1 and
F. tularensis
subsp.
novicida
-like strain 3523), is described. The method is highly specific and sensitive, detecting up to one plasmid copy or 10 genome equivalents.
Analysis of Integrated Virological and Epidemiological Reports of Norovirus Outbreaks Collected within the Foodborne Viruses in Europe Network from 1 July 2001 to 30 June 2006
Authors: Kroneman A. , Verhoef L. , Harris J. , Vennema H. , Duizer E. , van Duynhoven Y. , Gray J. , Iturriza M. , Böttiger B. , Falkenhorst G. , Johnsen C. , von Bonsdorff C.-H. , Maunula L. , Kuusi M. , Pothier P. , Gallay A. , Schreier E. , Höhne M. , Koch J. , Szücs G. , Reuter G. , Krisztalovics K. , Lynch M. , McKeown P. , Foley B. , Coughlan S. , Ruggeri F. M. , Di Bartolo I. , Vainio K. , Isakbaeva E. , Poljsak-Prijatelj M. , Grom A. Hocevar , Mijovski J. Zimsek , Bosch A. , Buesa J. , Fauquier A. Sanchez , Hernandéz-Pezzi G. , Hedlund K.-O. , Koopmans M. 
Published: July 2008

ABSTRACTThe Foodborne Viruses in Europe network has developed integrated epidemiological and virological outbreak reporting with aggregation and sharing of data through a joint database. We analyzed data from reported outbreaks of norovirus (NoV)-caused gastroenteritis from 13 European countries (July 2001 to July 2006) for trends in time and indications of different epidemiology of genotypes and variants. Of the 13 countries participating in this surveillance network, 11 were capable of collecting integrated epidemiological and virological surveillance data and 10 countries reported outbreaks throughout the entire period. Large differences in the numbers and rates of reported outbreaks per country were observed, reflecting the differences in the focus and coverage of national surveillance systems. GII.4 strains predominated throughout the 5-year surveillance period, but the proportion of outbreaks associated with GII.4 rose remarkably during years in which NoV activity was particularly high. Spring and summer peaks indicated the emergence of genetically distinct variants within GII.4 across Europe and were followed by increased NoV activity during the 2002-2003 and 2004-2005 winter seasons. GII.4 viruses predominated in health care settings and in person-to-person transmission. The consecutive emergence of new GII.4 variants is highly indicative of immune-driven selection. Their predominance in health care settings suggests properties that facilitate transmission in settings with a high concentration of people such as higher virus loads in excreta or a higher incidence of vomiting. Understanding the mechanisms driving the changes in epidemiology and clinical impact of these rapidly evolving RNA viruses is essential to design effective intervention and prevention measures.
Detection of 11 Common Viral and Bacterial Pathogens Causing Community-Acquired Pneumonia or Sepsis in Asymptomatic Patients by Using a Multiplex Reverse Transcription-PCR Assay with Manual (Enzyme Hybridization) or Automated (Electronic Microarray) Detection
Authors: Kumar Swati , Wang Lihua , Fan Jiang , Kraft Andrea , Bose Michael E. , Tiwari Sagarika , Van Dyke Meredith , Haigis Robert , Luo Tingquo , Ghosh Madhushree , Tang Huong , Haghnia Marjan , Mather Elizabeth L. , Weisburg William G. , Henrickson Kelly J. 
Published: July 2008

ABSTRACT

Community-acquired pneumonia (CAP) and sepsis are important causes of morbidity and mortality. We describe the development of two molecular assays for the detection of 11 common viral and bacterial agents of CAP and sepsis: influenza virus A, influenza virus B, respiratory syncytial virus A (RSV A), RSV B,
Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, Legionella micdadei, Bordetella pertussis, Staphylococcus aureus
, and
Streptococcus pneumoniae
. Further, we report the prevalence of carriage of these pathogens in respiratory, skin, and serum specimens from 243 asymptomatic children and adults. The detection of pathogens was done using both a manual enzyme hybridization assay and an automated electronic microarray following reverse transcription and PCR amplification. The analytical sensitivities ranged between 0.01 and 100 50% tissue culture infective doses, cells, or CFU per ml for both detection methods. Analytical specificity testing demonstrated no significant cross-reactivity among 19 other common respiratory organisms. One hundred spiked “surrogate” clinical specimens were all correctly identified with 100% specificity (95% confidence interval, 100%). Overall, 28 (21.7%) of 129 nasopharyngeal specimens, 11 of 100 skin specimens, and 2 of 100 serum specimens from asymptomatic subjects tested positive for one or more pathogens, with
S. pneumoniae
and
S. aureus
giving 89% of the positive results. Our data suggest that asymptomatic carriage makes the use of molecular assays problematic for the detection of
S. pneumoniae
or
S. aureus
in upper respiratory tract secretions; however, the specimens tested showed virtually no carriage of the other nine viral and bacterial pathogens, and the detection of these pathogens should not be a significant diagnostic problem. In addition, slightly less sensitive molecular assays may have better correlation with clinical disease in the case of CAP.
Molecular Epidemiology of Human Enterovirus 71 in the United Kingdom from 1998 to 2006
Authors: Bible Jon M. , Iturriza-Gomara Miren , Megson Brian , Brown David , Pantelidis Panagiotis , Earl Pam , Bendig Justin , Tong C. Y. William 
Published: July 2008

ABSTRACT
The last decade witnessed a significant increase in epidemic activity of human enterovirus 71 (EV71) in the Western Pacific Region (WPR). In most European countries, this risk is unrecognized despite occasional cases of severe disease and two severe outbreaks in Eastern Europe 30 years ago. In this study we report the first examination of the molecular epidemiology of EV71 in the United Kingdom from 1998 to 2006. Genomic regions encoding the 1D coat protein (VP1) and 3D polymerase (Pol) from 32 EV71 isolates associated with neurological or cutaneous manifestations were sequenced. Phylogenetic analyses of VP1 and 3D Pol sequences identified genotype C as the dominant strain. Several United Kingdom isolates had genetic linkages with predated C1 or C2 strains from Europe and the WPR. Recombination events were not detected between United Kingdom strains. However, a previously published Taiwanese strain was identified as an intergenotypic recombinant. EV71 genotype C appears to have continuous circulation in the United Kingdom from 1998 to 2006 with repeated introductions of new strains replacing previous strains. It is necessary to continuously monitor the molecular evolution and recombination events of EV71.
Identities of
Arthrobacter
spp. and
Arthrobacter
-Like Bacteria Encountered in Human Clinical Specimens
Authors: Mages Irene S. , Frodl Reinhard , Bernard Kathryn A. , Funke Guido 
Published: July 2008

ABSTRACT

After the initial description of
Arthrobacter
spp. isolated from clinical specimens in the mid-1990s, very few further reports on
Arthrobacter
spp. have appeared in the clinical microbiology literature. The aim of the present study was to elucidate the distribution of
Arthrobacter
spp. and
Arthrobacter
-like bacteria encountered in clinical specimens by studying 50 consecutively isolated or received strains of large-colony-forming, whiteish-grayish, non-cheese-like-smelling, nonfermentative gram-positive rods by applying phenotypic methods as well as 16S rRNA gene sequencing. We observed a very heterogenous distribution, with the 50 strains belonging to 20 different taxa and each of 13 strains as a single representative of its particular taxon. Thirty-eight strains represented true
Arthrobacter
strains, 7 strains belonged to the genus
Brevibacterium
, 2 were
Microbacterium
species, and each of 3 single strains was a member of the rarely encountered genera
Pseudoclavibacter, Leucobacter
, and
Brachybacterium
, respectively.
A. cumminsii
(
n
= 14) and
A. oxydans
(
n
= 11) were the most frequently found species. The present report describes the first three
A. aurescens
strains isolated from human clinical specimens. Comprehensive antimicrobial susceptibility data are given for the 38
Arthrobacter
isolates.
Fatal-Stroke Syndrome Revealing Fungal Cerebral Vasculitis Due to
Arthrographis kalrae
in an Immunocompetent Patient
Authors: Pichon N. , Ajzenberg D. , Desnos-Ollivier M. , Clavel M. , Gantier J. C. , Labrousse F. 
Published: July 2008

ABSTRACT

We report an uncommon clinical presentation of a unique case of fatal invasive fungal cerebral vasculitis due to
Arthrographis kalrae
in a nonimmunocompromised host. The identity of the fungus was determined by morphological characteristics and by analysis of internal transcribed spacer 1 sequences and was confirmed by postmortem examination of the brain tissues. Establishing rapidly the link between the clinical syndromes and the fungal infection of the central nervous system is essential to improve the outcome. As our case has shown, it is more challenging to make a diagnosis of fungal infection when there are no risk factors of immunodeficiency and when the clinical presentation seems uncommon.
Phylogenetic Analysis of Viridans Group Streptococci Causing Endocarditis
Authors: Simmon Keith E. , Hall Lori , Woods Christopher W. , Marco Francesc , Miro Jose M. , Cabell Christopher , Hoen Bruno , Marin Mercedes , Utili Riccardo , Giannitsioti Efthymia , Doco-Lecompte Thanh , Bradley Suzanne , Mirrett Stanley , Tambic Arjana , Ryan Suzanne , Gordon David , Jones Phillip , Korman Tony , Wray Dannah , Reller L. Barth , Tripodi Marie-Francoise , Plesiat Patrick , Morris Arthur J. , Lang Selwyn , Murdoch David R. , Petti Cathy A. 
Published: July 2008

ABSTRACT
Identification of viridans group streptococci (VGS) to the species level is difficult because VGS exchange genetic material. We performed multilocus DNA target sequencing to assess phylogenetic concordance of VGS for a well-defined clinical syndrome. The hierarchy of sequence data was often discordant, underscoring the importance of establishing biological relevance for finer phylogenetic distinctions.
Poliovirus
cis
-Acting Replication Element-Dependent VPg Uridylylation Lowers the

K
m

of the Initiating Nucleoside Triphosphate for Viral RNA Replication
Authors: Steil Benjamin P. , Barton David J. 
Published: July 2008

ABSTRACT

Initiation of RNA synthesis by RNA-dependent RNA polymerases occurs when a phosphodiester bond is formed between the first two nucleotides in the 5′ terminus of product RNA. The concentration of initiating nucleoside triphosphates (NTPi) required for RNA synthesis is typically greater than the concentration of NTPs required for elongation. VPg, a small viral protein, is covalently attached to the 5′ end of picornavirus negative- and positive-strand RNAs. A
cis
-acting replication element (CRE) within picornavirus RNAs serves as a template for the uridylylation of VPg, resulting in the synthesis of VPgpUpU
OH
. Mutations within the CRE RNA structure prevent VPg uridylylation. While the tyrosine hydroxyl of VPg can prime negative-strand RNA synthesis in a CRE- and VPgpUpU
OH
-independent manner, CRE-dependent VPgpUpU
OH
synthesis is absolutely required for positive-strand RNA synthesis. As reported herein, low concentrations of UTP did not support negative-strand RNA synthesis when CRE-disrupting mutations prevented VPg uridylylation, whereas correspondingly low concentrations of CTP or GTP had no negative effects on the magnitude of CRE-independent negative-strand RNA synthesis. The experimental data indicate that CRE-dependent VPg uridylylation lowers the

K
m

of UTP required for viral RNA replication and that CRE-dependent VPgpUpU
OH
synthesis was required for efficient negative-strand RNA synthesis, especially when UTP concentrations were limiting. By lowering the concentration of UTP needed for the initiation of RNA replication, CRE-dependent VPg uridylylation provides a mechanism for a more robust initiation of RNA replication.
Control of Cytoplasmic Maturation Events by Cytomegalovirus Tegument Protein pp150
Authors: Tandon Ritesh , Mocarski Edward S. 
Published: July 2008

ABSTRACT

Cytomegalovirus replication depends upon a betaherpesvirus-conserved 150-kDa tegument phosphoprotein (pp150; encoded by UL32) that supports the final steps in virion maturation at cytoplasmic assembly compartments. Amino acid substitutions were introduced into conserved region 1 (CR1) and CR2 of pp150, affecting a region that may interact with nucleocapsids. Two independent CR2 point mutants (N201A and G207A) failed to support viral replication in evaluations by a transient complementation assay or after reconstruction into recombinant viruses. An assembly compartment-like cytoplasmic inclusion developed in UL32 mutant virus-infected cells that was similar to that of wild-type virus-infected cells. The cellular localization of the
trans
-Golgi marker Golgin-97 suggested differences in the organization of the assembly compartment compared to that of wild-type virus-infected cells. Replication-defective CR2 point mutants exhibited the same phenotype as that of a virus carrying a complete deletion of the UL32 open reading frame in these assays. Electron micrographs of fibroblasts at 3 or 5 days postinfection with a deletion mutant (ΔUL32) grown on UL32-complementing cells showed a similar number and morphology of capsids in the nucleus, but the cytoplasmic region associated with virion assembly appeared highly vesiculated and contained few recognizable nucleocapsids or complete virus particles. These data demonstrate that the principle role of pp150 is to retain nucleocapsid organization through secondary envelopment at the assembly compartment.
Inhibition of Human Immunodeficiency Virus Type 1 Assembly and Release by the Cholesterol-Binding Compound Amphotericin B Methyl Ester: Evidence for Vpu Dependence
Authors: Waheed Abdul A. , Ablan Sherimay D. , Soheilian Ferri , Nagashima Kunio , Ono Akira , Schaffner Carl P. , Freed Eric O. 
Published: July 2008

ABSTRACT

We investigated the mechanism by which the cholesterol-binding compound amphotericin B methyl ester (AME) inhibits human immunodeficiency virus type 1 (HIV-1) particle production. We observed no significant effect of AME on Gag binding to the plasma membrane, Gag association with lipid rafts, or Gag multimerization, indicating that the mechanism of inhibition by AME is distinct from that by cholesterol depletion. Electron microscopy analysis indicated that AME significantly disrupts virion morphology. Interestingly, we found that AME does not inhibit the release of Vpu-defective HIV-1 or Vpu
−
retroviruses such as murine leukemia virus and simian immunodeficiency virus. We demonstrated that the ability of Vpu to counter the activity of CD317/BST-2/tetherin is markedly reduced by AME. These results indicate that AME interferes with the anti-CD317/BST-2/tetherin function of Vpu.
Dynamic Histone H3 Acetylation and Methylation at Human Cytomegalovirus Promoters during Replication in Fibroblasts
Authors: Cuevas-Bennett Christian , Shenk Thomas 
Published: July 2008

ABSTRACT

Human cytomegalovirus DNA is packaged in virions without histones but associates with histones upon reaching the nucleus of an infected cell. Since transcription is modulated by the interplay of histone modifications, we used chromatin immunoprecipitation to detect acetylation and methylation of histone H3 at viral promoters at different times during the viral replication cycle. Histone H3 at immediate-early promoters is acetylated at the start of infection, while it is initially methylated at early and late promoters. Acetylation at immediate-early promoters is dynamic, with a high level of activating modifications at 3 and 6 h postinfection (hpi), followed by a marked reduction at 12 hpi. All viral promoters, as well as nonpromoter regions, are modified with activating acetylations at 24 to 72 hpi. The transient reduction in histone H3 acetylation at the major immediate-early promoter depends on the
cis
-repressive sequence to which the UL122-coded IE2 protein binds. A mutant virus lacking this element exhibited decreased IE2 binding at the major immediate-early promoter and failed to show reduced acetylation of histone H3 residing at this promoter at 12 hpi. Our results demonstrate that cytomegalovirus chromatin undergoes dynamic, promoter-specific histone modifications early in the infectious cycle, after which the entire chromosome becomes highly acetylated.
Gag-Specific CD4+T-Cell Frequency Is Inversely Correlated with Proviral Load and Directly Correlated with Immune Activation in Infection with Human Immunodeficiency Virus Type 2 (HIV-2) but Not HIV-1
Authors: Foxall Russell B. , Cortesão Catarina S. , Albuquerque Adriana S. , Soares Rui S. , Victorino Rui M. M. , Sousa Ana E. 
Published: July 2008

ABSTRACTHuman immunodeficiency virus type 2 (HIV-2) infection, unlike HIV-1 infection, is normally characterized by low rates of CD4 depletion and low-to-undetectable viremia. We found that the frequency of Gag-specific CD4+T cells featured positive correlations with the expression of markers of CD4 activation and a negative correlation with peripheral blood mononuclear cell-associated proviral load in infection with HIV-2, in contrast with HIV-1. Moreover, HIV-2-infected individuals exhibited a greater ability to respond to HIV-1 Gag peptides (heterologous responses). Our data suggest a potential link between HIV-2-specific CD4 responses, immune activation, and viral control, which may in turn relate to the better prognosis associated with HIV-2 infection.
A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Saunders Gary W. 
Published: July 2008

The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.