bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex PCR for Differential Identification of Broad Tapeworms (Cestoda:Diphyllobothrium) Infecting Humans
Authors: Wicht Barbara , Yanagida Tetsuya , Scholz Tomáš , Ito Akira , Jiménez Juan A. , Brabec Jan 
Published: July 2010

ABSTRACTThe specific identification of broad tapeworms (genusDiphyllobothrium) infecting humans is very difficult to perform by morphological observation. Molecular analysis by PCR and sequencing represents the only reliable tool to date to identify these parasites to the species level. Due to the recent spread of human diphyllobothriosis in several countries, a correct diagnosis has become crucial to better understand the distribution and the life cycle of human-infecting species as well as to prevent the introduction of parasites to disease-free water systems. Nevertheless, PCR and sequencing, although highly precise, are too complicated, long, and expensive to be employed in medical laboratories for routine diagnostics. In the present study we optimized a cheap and rapid molecular test for the differential identification of the most commonDiphyllobothriumspecies infecting humans (D. latum,D. dendriticum,D. nihonkaiense, andD. pacificum), based on a multiplex PCR with the cytochromecoxidase subunit 1 gene of mitochondrial DNA.
Real-Time PCR Assay Provides Reliable Assessment of Intrapartum Carriage of Group B
Streptococcus
Authors: Alfa Michelle J. , Sepehri Shadi , De Gagne Pat , Helawa Michael , Sandhu Gunwat , Harding Godfrey K. M. 
Published: July 2010

ABSTRACT

The objective of this study was to determine the reliability of the real-time PCR assay for determining the group B
Streptococcus
(GBS) status of women in labor. In this prospective study we compared the results of culture and PCR testing of vaginal and rectal samples collected by nursing staff when women were in labor. Patients' charts were also reviewed to obtain relevant information about pregnancy risk factors. Our results demonstrated a sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 90.5%, 96.1%, 86.4%, and 97.4%, respectively, for rapid PCR. Of the 196 women evaluated, 29 (14.8%) presented with unknown GBS status, 11 (37.9%) of whom received unnecessary intrapartum antibiotics. The rapid real-time PCR test was robust and was able to reliably detect the presence of GBS in women in labor within 1 h of specimen submission to the laboratory. We recommend that the rapid PCR test be targeted to women who present in labor with unknown GBS status. In cases where the laboratory does not offer 24-h availability of testing, sample collection followed by PCR testing the next morning is still valuable and provides reliable results 24 to 48 h faster than culture and will aid appropriate decision-making regarding continuing or stopping antibiotics for neonates of women with unknown GBS status.
Chlamydophila psittaci
Zoonotic Risk Assessment in a Chicken and Turkey Slaughterhouse
Authors: Dickx V. , Geens T. , Deschuyffeleer T. , Tyberghien L. , Harkinezhad T. , Beeckman D. S. A. , Braeckman L. , Vanrompay D. 
Published: July 2010

ABSTRACT

Chlamydophila psittaci
causes respiratory disease in poultry and can be transmitted to humans. We conducted a
C. psittaci
zoonotic risk assessment study of a chicken and turkey slaughterhouse. Eighty-five percent of the slaughtered chicken flocks tested positive by PCR and culture. Genotype D was discovered. Fifty-seven percent of the slaughtered turkey flocks tested positive by PCR and culture. Genotype D was present. For the chicken slaughterhouse employees, 7.5% and 6% tested positive for
C. psittaci
by PCR and culture, respectively. In the turkey slaughterhouse, 87% and 61% of the employees tested positive by PCR and culture, respectively. All genotyped human samples contained genotype D. Using stationary bioaerosol monitoring by means of an MAS-100 ecosampler and ChlamyTrap collection medium, chlamydial DNA, and viable organisms were detected in both the chicken and turkey slaughterhouses. Positive air samples were most frequently found in the animal reception area and evisceration room. Zoonotic transmissions were very common, especially from processed turkeys. Accurate diagnostic monitoring and reporting of
C. psittaci
infections should be promoted in poultry workers.
Coxiella burnetii
Infection of a Steller Sea Lion (
Eumetopias jubatus
) Found in Washington State
Authors: Kersh Gilbert J. , Lambourn Dyanna M. , Self Joshua S. , Akmajian Adrianne M. , Stanton James B. , Baszler Timothy V. , Raverty Stephen A. , Massung Robert F. 
Published: July 2010

ABSTRACT

A pregnant sea lion stranded in the State of Washington was found to have placentitis caused by a unique strain of
Coxiella burnetii
. This is the first description of coxiellosis in a sea lion and suggests that exposure to sea lions may be a risk factor for contracting Q fever.
Frequency of Detection of Upper Respiratory Tract Viruses in Patients Tested for Pandemic H1N1/09 Viral Infection
Authors: Nisii Carla , Meschi Silvia , Selleri Marina , Bordi Licia , Castilletti Concetta , Valli Maria Beatrice , Lalle Eleonora , Lauria Francesco Nicola , Piselli Pierluca , Lanini Simone , Ippolito Giuseppe , Di Caro Antonino , Capobianchi Maria Rosaria 
Published: July 2010

ABSTRACT
Molecular testing of 270 consecutive nasopharyngeal swab samples taken in May and June 2009 and 274 samples from patients hospitalized between July and December 2009 showed similar findings of respiratory viruses, with influenza A pandemic virus H1N1/09 being the most represented, followed by human parainfluenza virus type 3 and rhinoviruses. Statistical analyses suggested virus cocirculation in the absence of viral interference.
False-Positive Transcription-Mediated Amplification Assay Detection of West Nile Virus in Blood from a Patient with Viremia Caused by an Usutu Virus Infection
Authors: Gaibani Paolo , Pierro Anna Maria , Cavrini Francesca , Rossini Giada , Landini Maria Paola , Sambri Vittorio 
Published: July 2010

ABSTRACT
Detection of West Nile virus (WNV) by nucleic acid amplification technology (NAAT) is used widely to screen blood and organ donations in areas where WNV is endemic. We report a false-positive result of a WNV transcription-mediated amplification assay (TMA) in a patient with viremia that was caused by Usutu virus, a mosquito-borne flavivirus.
Adaptation of Pandemic H1N1 Influenza Viruses in Mice
Authors: Ilyushina Natalia A. , Khalenkov Alexey M. , Seiler Jon P. , Forrest Heather L. , Bovin Nicolai V. , Marjuki Henju , Barman Subrata , Webster Robert G. , Webby Richard J. 
Published: July 2010

ABSTRACT
The molecular mechanism by which pandemic 2009 influenza A viruses were able to sufficiently adapt to humans is largely unknown. Subsequent human infections with novel H1N1 influenza viruses prompted an investigation of the molecular determinants of the host range and pathogenicity of pandemic influenza viruses in mammals. To address this problem, we assessed the genetic basis for increased virulence of A/CA/04/09 (H1N1) and A/TN/1-560/09 (H1N1) isolates, which are not lethal for mice, in a new mammalian host by promoting their mouse adaptation. The resulting mouse lung-adapted variants showed significantly enhanced growth characteristics in eggs, extended extrapulmonary tissue tropism, and pathogenicity in mice. All mouse-adapted viruses except A/TN/1-560/09-MA2 grew faster and to higher titers in cells than the original strains. We found that 10 amino acid changes in the ribonucleoprotein (RNP) complex (PB2 E158G/A, PA L295P, NP D101G, and NP H289Y) and hemagglutinin (HA) glycoprotein (K119N, G155E, S183P, R221K, and D222G) controlled enhanced mouse virulence of pandemic isolates. HA mutations acquired during adaptation affected viral receptor specificity by enhancing binding to α2,3 together with decreasing binding to α2,6 sialyl receptors. PB2 E158G/A and PA L295P amino acid substitutions were responsible for the significant enhancement of transcription and replication activity of the mouse-adapted H1N1 variants. Taken together, our findings suggest that changes optimizing receptor specificity and interaction of viral polymerase components with host cellular factors are the major mechanisms that contribute to the optimal competitive advantage of pandemic influenza viruses in mice. These modulators of virulence, therefore, may have been the driving components of early evolution, which paved the way for novel 2009 viruses in mammals.
Gene Expression Differences in Lungs of Mice during Secondary Immune Responses to Respiratory Syncytial Virus Infection
Authors: Schuurhof Annemieke , Bont Louis , Pennings Jeroen L. A. , Hodemaekers Hennie M. , Wester Piet W. , Buisman Annemarie , de Rond Lia C. G. H. , Widjojoatmodjo Myra N. , Luytjes Willem , Kimpen Jan L. L. , Janssen Riny 
Published: July 2010

ABSTRACTVaccine-induced immunity has been shown to alter the course of a respiratory syncytial virus (RSV) infection both in murine models and in humans. To elucidate which mechanisms underlie the effect of vaccine-induced immunity on the course of RSV infection, transcription profiles in the lungs of RSV-infected mice were examined by microarray analysis. Three models were used: RSV reinfection as a model for natural immunity, RSV challenge after formalin-inactivated RSV vaccination as a model for vaccine-enhanced disease, and RSV challenge following vaccination with recombinant RSV virus lacking the G gene (ΔG-RSV) as a model for vaccine-induced immunity. Gene transcription profiles, histopathology, and viral loads were analyzed at 1, 2, and 5 days after RSV challenge. On the first 2 days after challenge, all mice displayed an expression pattern in the lung similar of that found in primary infection, showing a strong innate immune response. On day 5 after RSV reinfection or after challenge following ΔG-RSV vaccination, the innate immune response was waning. In contrast, in mice with vaccine-enhanced disease, the innate immune response 5 days after RSV challenge was still present even though viral replication was diminished. In addition, only in this group was Th2 gene expression induced. These findings support a hypothesis that vaccine-enhanced disease is mediated by prolonged innate immune responses and Th2 polarization in the absence of viral replication.
Nonintegrating Foamy Virus Vectors
Authors: Deyle David R. , Li Yi , Olson Erik M. , Russell David W. 
Published: July 2010

ABSTRACT

Foamy viruses (FVs), or spumaviruses, are integrating retroviruses that have been developed as vectors. Here we generated nonintegrating foamy virus (NIFV) vectors by introducing point mutations into the highly conserved DD35E catalytic core motif of the foamy virus integrase sequence. NIFV vectors produced high-titer stocks, transduced dividing cells, and did not integrate. Cells infected with NIFV vectors contained episomal vector genomes that consisted of linear, 1-long-terminal-repeat (1-LTR), and 2-LTR circular DNAs. These episomes expressed transgenes, were stable, and became progressively diluted in the dividing cell population. 1-LTR circles but not 2-LTR circles were found in all vector stocks prior to infection. Residual integration of NIFV vectors occurred at a frequency 4 logs lower than that of integrase-proficient FV vectors. Cre recombinase expressed from a NIFV vector mediated excision of both an integrated, floxed FV vector and a gene-targeted
neo
expression cassette, demonstrating the utility of these episomal vectors. The broad host range and large packaging capacity of NIFV vectors should make them useful for a variety of applications requiring transient gene expression.
Reduced Fitness in Cell Culture of HIV-1 with Nonnucleoside Reverse Transcriptase Inhibitor-Resistant Mutations Correlates with Relative Levels of Reverse Transcriptase Content and RNase H Activity in Virions
Authors: Wang Jiong , Bambara Robert A. , Demeter Lisa M. , Dykes Carrie 
Published: July 2010

ABSTRACT
Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are important components of multidrug therapy for HIV-1. Understanding the effect of NNRTI-resistant mutants on virus replication and reverse transcriptase (RT) function is valuable for the development of extended-spectrum NNRTIs. We measured the fitness of six NNRTI-resistant mutants, the K103N, V106A, Y181C, G190A, G190S, and P236L viruses, using a flow cytometry-based cell culture assay. K103N and Y181C viruses had fitness similar to that of the wild type while V106A, G190A, G190S, and P236L viruses had reduced fitness. We also determined the biochemical correlates of fitness by measuring the RNase H and polymerization activities of recombinant mutant RTs and virion-associated RTs. The RNase H activities of recombinant and virion-associated RTs correlated with the relative fitness for each mutant. K103N and Y181C mutants had normal RNase H activity; V106A, G190A, and G190S mutants had moderate reductions in activity; and the P236L mutant had substantially reduced activity. With the exception of the P236L mutant, reduced fitness correlates with low virion-associated polymerization efficiency and reduced RT content. Reduced polymerase function in virions derived from low RT content rather than an intrinsic polymerization defect in each RT protein. In conclusion, severe defects in RNase H activity alone, exemplified by the P236L mutant, appear sufficient to cause a substantial reduction in fitness. For the other NNRTI mutants, reductions in RT content decreased both polymerization and RNase H activity in virions. RNase H reduction was compounded by intrinsic RNase H defects in the mutant RTs.
Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua
Authors: Yozwiak Nathan L. , Skewes-Cox Peter , Gordon Aubree , Saborio Saira , Kuan Guillermina , Balmaseda Angel , Ganem Don , Harris Eva , DeRisi Joseph L. 
Published: July 2010

ABSTRACT

Enteroviruses (
Picornaviridae
family) are a common cause of human illness worldwide and are associated with diverse clinical syndromes, including asymptomatic infection, respiratory illness, gastroenteritis, and meningitis. In this study, we report the identification and complete genome sequence of a novel enterovirus isolated from a case of acute respiratory illness in a Nicaraguan child. Unbiased deep sequencing of nucleic acids from a nose and throat swab sample enabled rapid recovery of the full-genome sequence. Phylogenetic analysis revealed that human enterovirus 109 (EV109) is most closely related to serotypes of human enterovirus species C (HEV-C) in all genomic regions except the 5′ untranslated region (5′ UTR). Bootstrap analysis indicates that the 5′ UTR of EV109 is likely the product of an interspecies recombination event between ancestral members of the HEV-A and HEV-C groups. Overall, the EV109 coding region shares 67 to 72% nucleotide sequence identity with its nearest relatives. EV109 isolates were detected in 5/310 (1.6%) of nose and throat swab samples collected from children in a pediatric cohort study of influenza-like illness in Managua, Nicaragua, between June 2007 and June 2008. Further experimentation is required to more fully characterize the pathogenic role, disease associations, and global distribution of EV109.
A Short N-Terminal Peptide Motif on Flavivirus Nonstructural Protein NS1 Modulates Cellular Targeting and Immune Recognition
Authors: Youn Soonjeon , Cho Hyelim , Fremont Daved H. , Diamond Michael S. 
Published: July 2010

ABSTRACTFlavivirus NS1 is a versatile nonstructural glycoprotein, with intracellular NS1 functioning as an essential cofactor for viral replication and cell surface and secreted NS1 antagonizing complement activation. Even though NS1 has multiple functions that contribute to virulence, the genetic determinants that regulate the spatial distribution of NS1 in cells among different flaviviruses remain uncharacterized. Here, by creating a panel of West Nile virus-dengue virus (WNV-DENV) NS1 chimeras and site-specific mutants, we identified a novel, short peptide motif immediately C-terminal to the signal sequence cleavage position that regulates its transit time through the endoplasmic reticulum and differentially directs NS1 for secretion or plasma membrane expression. Exchange of two amino acids within this motif reciprocally changed the cellular targeting pattern of DENV or WNV NS1. For WNV, this substitution also modulated infectivity and antibody-induced phagocytosis of infected cells. Analysis of a mutant lacking all three conserved N-linked glycosylation sites revealed an independent requirement of N-linked glycans for secretion but not for plasma membrane expression of WNV NS1. Collectively, our experiments define the requirements for cellular targeting of NS1, with implications for the protective host responses, immune antagonism, and association with the host cell sorting machinery. These studies also suggest a link between the effects of NS1 on viral replication and the levels of secreted or cell surface NS1.
Identification of a Critical T(Q/D/E)x
5
ADx
2
(I/L) Motif from Primate Lentivirus Vif Proteins That Regulate APOBEC3G and APOBEC3F Neutralizing Activity
Authors: Dang Ying , Wang Xiaojun , York Ian A. , Zheng Yong-Hui 
Published: July 2010

ABSTRACT

Primate lentiviruses are unique in that they produce several accessory proteins to help in the establishment of productive viral infection. The major function of these proteins is to clear host resistance factors that inhibit viral replication. Vif is one of these proteins. It functions as an adaptor that binds to the cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) and bridges them to a cullin 5 (Cul5) and elongin (Elo) B/C E3 ubiquitin ligase complex for proteasomal degradation. So far, 11 discontinuous domains in Vif have been identified that regulate this degradation process. Here we report another domain, T(Q/D/E)x
5
ADx
2
(I/L), which is located at residues 96 to 107 in the human immunodeficiency virus type 1 (HIV-1) Vif protein. This domain is conserved not only in all HIV-1 subtypes but also in other primate lentiviruses, including HIV-2 and simian immunodeficiency virus (SIV), which infects rhesus macaques (SIVmac) and African green monkeys (SIVagm). Mutations of the critical residues in this motif seriously disrupted Vif's neutralizing activity toward both A3G and A3F. This motif regulates Vif interaction not only with A3G and A3F but also with Cul5. When this motif was inactivated in the HIV-1 genome, Vif failed to exclude A3G and A3F from virions, resulting in abortive HIV replication in nonpermissive human T cells. Thus, T(Q/D/E)x
5
ADx
2
(I/L) is a critical functional motif that directly supports the adaptor function of Vif and is an attractive target for inhibition of Vif function.
Mutational and Metal Binding Analysis of the Endonuclease Domain of the Influenza Virus Polymerase PA Subunit
Authors: Crépin Thibaut , Dias Alexandre , Palencia Andrés , Swale Christopher , Cusack Stephen , Ruigrok Rob W. H. 
Published: July 2010

ABSTRACT

Influenza virus polymerase initiates the biosynthesis of its own mRNAs with capped 10- to 13-nucleotide fragments cleaved from cellular (pre-)mRNAs. Two activities are required for this cap-snatching activity: specific binding of the cap structure and an endonuclease activity. Recent work has shown that the cap-binding site is situated in the central part of the PB2 subunit and that the endonuclease activity is situated in the N-terminal domain of the PA subunit (PA-Nter). The influenza endonuclease is a member of the PD-(D/E)XK family of nucleases that use divalent metal ions for nucleic acid cleavage. Here we analyze the metal binding and endonuclease activities of eight PA-Nter single-point mutants. We show by calorimetry that the wild-type active site binds two Mn
2+
ions and has a 500-fold higher affinity for manganese than for magnesium ions. The endonuclease activity of the isolated mutant domains are compared with the cap-dependent transcription activities of identical mutations in trimeric recombinant polymerases previously described by other groups. Mutations that inactivate the endonuclease activity in the isolated PA-Nter knock out the transcription but not replication activity in the recombinant polymerase. We confirm the importance of a number of active-site residues and identify some residues that may be involved in the positioning of the RNA substrate in the active site. Our results validate the use of the isolated endonuclease domain in a drug-design process for new anti-influenza virus compounds.
De L'Influence Du Ganglion Sus-Oesophagien Sur Les Fonctions Du Pied De L'Escargot (Helix Pomatia Linné) 1)
Authors: Postma N. 
Published: July 2010

AbstractEn opposition aux resultats obtenus précédemment nous avons constaté que le ganglion sus-oesophagien de l'Helix pomatia Linné a une influence evidente sur le tonus du muscle pedieu. La seule presence du ganglion n'a pas d'influence: l'ablation du cerveau ne modifie pas la tonicite. Le ganglion cerebral agit sur le pied de l'escargot en modifiant la tonicite dans le sens positif ou dans le sens negatif, c'est-a-dire en augmentant ou en diminuant le myotonus. Selon 1'etat fonctionnel ou d'activite du ganglion nous distinguons quatre phases d'activite. En commençant a observer 1'activite a son minimum et en passant par ces phases progressives, nous pouvons noter successivement: i. Freinage du centre sous-oesophagien inhibiteur; 2. Moderation du centre excitateur dans le ganglion pédieu; 3. Stimulation du centre sub-oesophageal tonolytique; 4. Renforcement du centre accelerateurdans le ganglion pédieu, et deux phases de compensation, etats d'equilibre, l'un entre i et 2,1'autre entre 3 et 4. Les phases I et 4 causent un accroissement du tonus, tandis qu'une baisse du tonus est produite par les phases 2 et 3. L'effet de la derniere est accompagnee par un d6écalage de la contractilite. On peut augmenter 1'activite du ganglion au moyen d'im-pressions proprioceptives suscitées par l'allongement lui-meme ou par l'intermédiaire d'influx exteroceptifs, causes par 1'application de chlorure de sodium au ganglion (excitation permanente). L'activite cephalique peut etre supprimée si l'on applique du chlorure de cocaine au cerveau. Concernant le tonus musculair nous concluons qu'il est base sur une contracture qui probablement joue un role comme fonc- tion de calage a regard d'un lot tetanique de la tonicite. Chez l'Helix neanmoins la contracture a la priorite si un tetanos se produit.
Deux nouvelles attributions au Maître des Madones joufflues
Authors: Martens Didier 
Published: July 2010

AbstractThe Master of the Madonnas with the Chubby (cheeks is a Bruges painter from the early sixteenth century who was strongly influenced by Gerard David. Some ten works were attributed to this master on stylistic grounds in 2000. Two further attributions- both of a Madonna and Child - are proposed in this article. The paintings in question are a panel in the Groennigemuseum in Bruges (inv. no. O.GRO. 1358.1, fig. 1), which is derived from a composition, the Lisbon Madonna, by Memling, and a tondo (fig. 2) that was on view at the TEFAF in Maastricht in March of 2001.