bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are Putative Periodontal Pathogens Reliable Diagnostic Markers?
Authors: Riep Birgit , Edesi-Neuß Lilian , Claessen Friderike , Skarabis Horst , Ehmke Benjamin , Flemmig Thomas F. , Bernimoulin Jean-Pierre , Göbel Ulf B. , Moter Annette 
Published: April 2009

ABSTRACT

Periodontitis is one of the most common chronic inflammatory diseases. A number of putative bacterial pathogens have been associated with the disease and are used as diagnostic markers. In the present study, we compared the prevalence of oral bacterial species in the subgingival biofilm of generalized aggressive periodontitis (GAP) (
n
= 44) and chronic periodontitis (CP) (
n
= 46) patients with that of a periodontitis-resistant control group (PR) (
n
= 21). The control group consisted of subjects at least 65 years of age with only minimal or no periodontitis and no history of periodontal treatment. A total of 555 samples from 111 subjects were included in this study. The samples were analyzed by PCR of 16S rRNA gene fragments and subsequent dot blot hybridization using oligonucleotide probes specific for
Aggregatibacter
(
Actinobacillus) actinomycetemcomitans
,
Porphyromonas gingivalis
,
Prevotella intermedia
,
Tannerella forsythia
, a
Treponema denticola
-like phylogroup (Treponema phylogroup II),
Treponema lecithinolyticum
,
Campylobacter rectus
,
Fusobacterium
spp., and
Fusobacterium nucleatum
, as well as
Capnocytophaga ochracea
. Our data confirm a high prevalence of the putative periodontal pathogens
P. gingivalis
,
P. intermedia
, and
T. forsythia
in the periodontitis groups. However, these species were also frequently detected in the PR group. For most of the species tested, the prevalence was more associated with increased probing depth than with the subject group.
T. lecithinolyticum
was the only periodontopathogenic species showing significant differences both between GAP and CP patients and between GAP patients and PR subjects.
C. ochracea
was associated with the PR subjects, regardless of the probing depth. These results indicate that
T. lecithinolyticum
may be a diagnostic marker for GAP and
C. ochracea
for periodontal health. They also suggest that current presumptions of the association of specific bacteria with periodontal health and disease require further evaluation.
Phenotypic and Molecular Characterization of Clinical Isolates of
Mycobacterium elephantis
from Human Specimens
Authors: Turenne Christine , Chedore Pamela , Wolfe Joyce , Jamieson Frances , May Kevin , Kabani Amin 
Published: April 2009

ABSTRACT

Eleven strains of a rapidly growing mycobacterium were isolated from patient specimens originating from various regions of the province of Ontario, Canada, over a 2-year period. Unique high-performance liquid chromatography (HPLC) and PCR-restriction enzyme pattern analysis (PRA) profiles initially suggested a new
Mycobacterium
species, while sequencing of the 16S rRNA gene revealed a sequence match with
Mycobacterium
sp. strain MCRO 17 (GenBank accession no.
X93028
), an isolate determined to be unique which is to date uncharacterized, and also a close similarity to
M
.
elephantis
(GenBank accession no.
AJ010747
), with six base pair variations. A complete biochemical profile of these isolates revealed a species of mycobacteria with phenotypic characteristics similar to those of
M
.
flavescens
. HPLC, PRA, and 16S rRNA sequencing of strain
M
.
elephantis
DSM 44368
T
and result comparisons with the clinical isolates revealed that these strains were in fact
M
.
elephantis
, a newly described species isolated from an elephant. All strains were isolated from human samples, 10 from sputum and 1 from an axillary lymph node.
Development of Infectious Clones for Virulent and Avirulent Pichinde Viruses: a Model Virus To Study Arenavirus-Induced Hemorrhagic Fevers
Authors: Lan Shuiyun , McLay Schelde Lisa , Wang Jialong , Kumar Naveen , Ly Hinh , Liang Yuying 
Published: April 2009

ABSTRACT
Several arenaviruses can cause hemorrhagic fever diseases (VHFs) in humans, the pathogenic mechanism of which is poorly understood due to their virulent nature and the lack of molecular clones. A safe, convenient, and economical small animal model of arenavirus hemorrhagic fever is based on guinea pigs infected by the arenavirus Pichinde (PICV). PICV does not cause disease in humans, but an adapted strain of PICV (P18) causes a disease in guinea pigs that mimics arenavirus hemorrhagic fever in humans in many aspects, while a low-passaged strain (P2) remains avirulent in infected animals. In order to identify the virulence determinants within the PICV genome, we developed the molecular clones for both the avirulent P2 and virulent P18 viruses. Recombinant viruses were generated by transfecting plasmids that contain the antigenomic L and S RNA segments of PICV under the control of the T7 promoter into BSRT7-5 cells, which constitutively express T7 RNA polymerase. By analyzing viral growth kinetics in vitro and virulence in vivo, we show that the recombinant viruses accurately recapitulate the replication and virulence natures of their respective parental viruses. Both parental and recombinant virulent viruses led to high levels of viremia and titers in different organs of the infected animals, whereas the avirulent viruses were effectively controlled and cleared by the hosts. These novel infectious clones for the PICV provide essential tools to identify the virulence factors that are responsible for the severe VHF-like disease in infected animals.
The Respiratory Syncytial Virus M2-1 Protein Forms Tetramers and Interacts with RNA and P in a Competitive Manner
Authors: Tran Thi-Lan , Castagné Nathalie , Dubosclard Virginie , Noinville Sylvie , Koch Emmanuelle , Moudjou Mohammed , Henry Céline , Bernard Julie , Yeo Robert Paul , Eléouët Jean-François 
Published: April 2009

ABSTRACT

The respiratory syncytial virus (RSV) M2-1 protein is an essential cofactor of the viral RNA polymerase complex and functions as a transcriptional processivity and antitermination factor. M2-1, which exists in a phosphorylated or unphosphorylated form in infected cells, is an RNA-binding protein that also interacts with some of the other components of the viral polymerase complex. It contains a CCCH motif, a putative zinc-binding domain that is essential for M2-1 function, at the N terminus. To gain insight into its structural organization, M2-1 was produced as a recombinant protein in
Escherichia coli
and purified to >95% homogeneity by using a glutathione
S
-transferase (GST) tag. The GST-M2-1 fusion proteins were copurified with bacterial RNA, which could be eliminated by a high-salt wash. Circular dichroism analysis showed that M2-1 is largely α-helical. Chemical cross-linking, dynamic light scattering, sedimentation velocity, and electron microscopy analyses led to the conclusion that M2-1 forms a 5.4S tetramer of 89 kDa and ∼7.6 nm in diameter at micromolar concentrations. By using a series of deletion mutants, the oligomerization domain of M2-1 was mapped to a putative α-helix consisting of amino acid residues 32 to 63. When tested in an RSV minigenome replicon system using a luciferase gene as a reporter, an M2-1 deletion mutant lacking this region showed a significant reduction in RNA transcription compared to wild-type M2-1, indicating that M2-1 oligomerization is essential for the activity of the protein. We also show that the region encompassing amino acid residues 59 to 178 binds to P and RNA in a competitive manner that is independent of the phosphorylation status of M2-1.
Lymphocyte and Antibody Responses Reduce Enterovirus 71 Lethality in Mice by Decreasing Tissue Viral Loads
Authors: Lin Yu-Wen , Chang Kung-Chao , Kao Chia-Min , Chang Shih-Ping , Tung Yuk-Ying , Chen Shun-Hua 
Published: April 2009

ABSTRACT
Enterovirus 71 (EV71) infects the central nervous system and causes death and long-term neurological sequelae in hundreds of thousands of young children, but its pathogenesis remains elusive. Immunopathological mechanisms have been suspected to contribute to the pathogenesis of neurological symptoms, so anti-inflammatory agents have been used to treat patients with neurological symptoms. The present study was therefore designed to investigate the functions of lymphocyte and antibody responses in EV71 infection using a mouse model. Immunohistochemical staining analysis revealed virus and three types of lymphocytes, B cells, CD4 T cells, and CD8 T cells, in the spinal cord of an EV71-infected patient who died. A study of mice showed that the levels of virus and lymphocytes in brains and antibody titers in sera were elevated during the time when the mice succumbed to death in a phenomenon analogous to that observed in patients. Further studies demonstrated that after infection, the disease severity, mortality, and tissue viral loads of mice deficient in B, CD4 T, or CD8 T cells were significantly higher than those of wild-type mice. In addition, treatment with a virus-specific antibody, but not a control antibody, before or after infection significantly reduced the disease severity, mortality, and tissue viral loads of mice deficient in B cells. Our results show that both lymphocyte and antibody responses protect mice from EV71 infection. Our study suggests the use of vaccines and virus-specific antibodies to control fatal outbreaks and raises caution over the use of corticosteroids to treat EV71-infected patients with neurological symptoms.
Human Parainfluenza Virus Infection of the Airway Epithelium: Viral Hemagglutinin-Neuraminidase Regulates Fusion Protein Activation and Modulates Infectivity
Authors: Palermo Laura M. , Porotto Matteo , Yokoyama Christine C. , Palmer Samantha G. , Mungall Bruce A. , Greengard Olga , Niewiesk Stefan , Moscona Anne 
Published: April 2009

ABSTRACT
Three discrete activities of the paramyxovirus hemagglutinin-neuraminidase (HN) protein, receptor binding, receptor cleaving (neuraminidase), and triggering of the fusion protein, each affect the promotion of viral fusion and entry. For human parainfluenza virus type 3 (HPIV3), the effects of specific mutations that alter these functions of the receptor-binding protein have been well characterized using cultured monolayer cells, which have identified steps that are potentially relevant to pathogenesis. In the present study, proposed mechanisms that are relevant to pathogenesis were tested in natural host cell cultures, a model of the human airway epithelium (HAE) in which primary HAE cells are cultured at an air-liquid interface and retain functional properties. Infection of HAE cells with wild-type HPIV3 and variant viruses closely reflects that seen in an animal model, the cotton rat, suggesting that HAE cells provide an ideal system for assessing the interplay of host cell and viral factors in pathogenesis and for screening for inhibitory molecules that would be effective in vivo. Both HN′s receptor avidity and the function and timing of F activation by HN require a critical balance for the establishment of ongoing infection in the HAE, and these HN functions independently modulate the production of active virions. Alterations in HN′s F-triggering function lead to the release of noninfectious viral particles and a failure of the virus to spread. The finding that the dysregulation of F triggering prohibits successful infection in HAE cells suggests that antiviral strategies targeted to HN′s F-triggering activity may have promise in vivo.
Activated Ras/MEK Inhibits the Antiviral Response of Alpha Interferon by Reducing STAT2 Levels
Authors: Christian Sherri L. , Collier Thaddeus W. , Zu Dong , Licursi Maria , Hough Chris M. , Hirasawa Kensuke 
Published: April 2009

ABSTRACT
The ability of interferon (IFN) to induce the expression of antiviral genes, and therefore suppress viral infection, is dependent on the activity of cellular suppressors. The Ras/MEK pathway is one of these cellular suppressors, since the activation of Ras/MEK permits viral replication in the presence of alpha IFN (IFN-α). Here, we have investigated the mechanism by which activated Ras/MEK inhibits the IFN-α response. We found that the induction of antiviral proteins in response to IFN-α was impaired in Ras-transformed NIH 3T3 (RasV12) cells. The inhibition of the Ras/MEK pathway restored the IFN-mediated induction of antiviral genes, indicating that activated Ras interrupts the IFN pathway upstream of antiviral gene transcription. Indeed, the IFN-induced phosphorylation of signal transducer and activator of transcription 1 (STAT1) and STAT2 was inhibited in RasV12 cells compared to that of vector control cells. In addition, we found that the total amount of STAT2 was reduced in RasV12 cells. To determine if the impaired IFN-α response can be rescued by restoring the overall level of STAT2, we overexpressed STAT2 in RasV12 cells. The IFN-α-induced phosphorylation of STAT1 and STAT2, as well as the expression of antiviral protein, were restored, and IFN-induced antiviral protection was partially restored. Moreover, we demonstrated that the downregulation of STAT2 levels by Ras/MEK was mediated at the transcriptional level. Thus, the activation of the Ras/MEK pathway reduces the amount of STAT2 available for propagating the IFN signal, resulting in the impairment of the IFN-α-induced antiviral response.
Viral Entry through CXCR4 Is a Pathogenic Factor and Therapeutic Target in Human Immunodeficiency Virus Type 1 Disease
Authors: Schramm Birgit , Penn Michael L. , Speck Roberto F. , Chan Stephen Y. , De Clercq Erik , Schols Dominique , Connor Ruth I. , Goldsmith Mark A. 
Published: April 2009

ABSTRACT

The chemokine receptors CCR5 and CXCR4 function as the principal coreceptors for human immunodeficiency virus type 1 (HIV-1). Coreceptor function has also been demonstrated for a variety of related receptors in vitro. The relative contributions of CCR5, CXCR4, and other putative coreceptors to HIV-1 disease in vivo have yet to be defined. In this study, we used sequential primary isolates and recombinant strains of HIV-1 to demonstrate that CXCR4-using (X4) viruses emerging in association with disease progression are highly pathogenic in ex vivo lymphoid tissues compared to CXCR4-independent viruses. Furthermore, synthetic receptor antagonists that specifically block CXCR4-mediated entry dramatically suppressed the depletion of CD4
+
T cells by recombinant and clinically derived X4 HIV-1 isolates. Moreover, in vitro specificity for the additional coreceptors CCR3, CCR8, BOB, and Bonzo did not augment cytopathicity or diminish sensitivity toward CXCR4 antagonists in lymphoid tissues. These data provide strong evidence to support the concept that adaptation to CXCR4 specificity in vivo accelerates HIV-1 disease progression. Thus, therapeutic intervention targeting the interaction of HIV-1 gp120 with CXCR4 may be highly valuable for suppressing the pathogenic effects of late-stage viruses.
E1B 55-Kilodalton Oncoproteins of Adenovirus Types 5 and 12 Inactivate and Relocalize p53, but Not p51 or p73, and Cooperate with E4orf6 Proteins To Destabilize p53
Authors: Wienzek Sandra , Roth Judith , Dobbelstein Matthias 
Published: April 2009

ABSTRACT
The p53 tumor suppressor protein represents a target for viral and cellular oncoproteins, including adenovirus gene products. Recently, it was discovered that several proteins with structural and functional homologies to p53 exist in human cells. Two of them were termed p51 and p73. We have shown previously that the E1B 55-kDa protein (E1B-55 kDa) of adenovirus type 5 (Ad5) binds and inactivates p53 but not p73. Further, p53 is rapidly degraded in the presence of E1B-55 kDa and the E4orf6 protein of this virus. Here, it is demonstrated that p51 does not detectably associate with E1B-55 kDa. While p53 is relocalized to the cytoplasm by E1B-55 kDa, p51's location is unaffected. Finally, p51 retains its full transcriptional activity in the presence of E1B-55 kDa. Apparently, p51 does not represent a target of Ad5 E1B-55 kDa, suggesting that the functions of p51 are distinct from p53-like tumor suppression. E1B-55 kDa from highly oncogenic adenovirus type 12 (Ad12) was previously shown to surpass the oncogenic activity of Ad5 E1B-55 kDa in various assay systems, raising the possibility that Ad12 E1B-55 kDa might target a broader range of p53-like proteins. However, we show here that Ad12 E1B-55 kDa also inhibits p53's transcriptional activity without measurably affecting p73 or p51. Moderate inhibition of p51's transcriptional activity was observed in the presence of the E4orf6 proteins from Ad5 and Ad12. p53 and Ad12-E1B-55 kDa colocalize in the nucleus and also in cytoplasmic clusters when transiently coexpressed. Finally, E1B-55 kDa and E4orf6 of Ad12 mediate rapid degradation of p53 with an efficiency comparable to that of the Ad5 proteins in human and rodent cells. Our results suggest that E1B-55 kDa of either virus type has similar effects on p53 but does not affect p73 and p51.
Initial Events in Infectious Salmon Anemia Virus Infection: Evidence for the Requirement of a Low-pH Step
Authors: Eliassen Trygve Meum , Frøystad Marianne Kristin , Dannevig Birgit Helene , Jankowska Monika , Brech Andreas , Falk Knut , Romøren Kristine , Gjøen Tor 
Published: April 2009

ABSTRACT

We have investigated the initial steps in the interaction between infectious salmon anemia virus (ISAV) and cultured cells from Atlantic salmon (SHK-1 cell line). Using radioactively or fluorescently labelled viral particles we have studied the binding and fusion kinetics and the effect of pH on binding, uptake, and fusion of ISAV to SHK-1 cells and liposomes. As pH in the medium was reduced from 7.5 to 4.5, the association of virus to the cells was nearly doubled. The same effect of pH was observed when fusion between ISAV and liposomes was analyzed. In addition, the binding of ISAV to intact SHK-1 cells and to cell membrane proteins blotted onto filters was neuraminidase sensitive. However, the increased binding induced by low pH was not neuraminidase sensitive, probably reflecting activation of a fusion peptide at low pH. By using confocal fluorescence microscopy, the increased fusion of fluorescently labelled ISAV with the plasma membrane due to low pH could be demonstrated. When vacuolar pH in the cells was raised during inoculation with chloroquine or ammonium chloride, both electron and confocal microscopy showed accumulation of ISAV in endosomes and lysosomes. Production of infectious virus could be increased by lowering the extracellular pH during infection. Furthermore, chloroquine present during virus inoculation also caused a reduction in the synthesis of viral proteins in ISAV-infected cells as well as in the production of infective virus. These results indicate that ISAV binds to sialic acid residues on the cell surface and that the fusion between virus and cell membrane takes place in the acid environment of endosomes. This provides further evidence for a high degree of similarity between ISAV and influenza virus and extends the basis for the classification of this virus as a member of the
Orthomyxoviridae
family.
Measles Virus Induces Functional TRAIL Production by Human Dendritic Cells
Authors: Vidalain Pierre-Olivier , Azocar Olga , Lamouille Barbara , Astier Anne , Rabourdin-Combe Chantal , Servet-Delprat Christine 
Published: April 2009

ABSTRACTMeasles virus infection induces a profound immunosuppression that can lead to serious secondary infections. Here we demonstrate that measles virus induces tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) mRNA and protein expression in human monocyte-derived dendritic cells. Moreover, measles virus-infected dendritic cells are shown to be cytotoxic via the TRAIL pathway.
Competitive STDP-Based Spike Pattern Learning
Authors: Masquelier Timothée , Guyonneau Rudy , Thorpe Simon J. 
Published: April 2009

Recently it has been shown that a repeating arbitrary spatiotemporal spike pattern hidden in equally dense distracter spike trains can be robustly detected and learned by a single neuron equipped with spike-timing-dependent plasticity (STDP) (Masquelier, Guyonneau, & Thorpe, 2008). To be precise, the neuron becomes selective to successive coincidences of the pattern. Here we extend this scheme to a more realistic scenario with multiple repeating patterns and multiple STDP neurons “listening” to the incoming spike trains. These “listening” neurons are in competition: as soon as one fires, it strongly inhibits the others through lateral connections (one-winner-take-all mechanism). This tends to prevent the neurons from learning the same (parts of the) repeating patterns, as shown in simulations. Instead, the population self-organizes, trying to cover the different patterns or coding one pattern by the successive firings of several neurons, and a powerful distributed coding scheme emerges. Taken together, these results illustrate how the brain could easily encode and decode information in the spike times, a theory referred to as temporal coding, and how STDP could play a key role by detecting repeating patterns and generating selective response to them.
The Atmospheric Boundary Layer during Swell: A Field Study and Interpretation of the Turbulent Kinetic Energy Budget for High Wave Ages
Authors: Högström U. , Smedman A. , Sahleé E. , Drennan W. M. , Kahma K. K. , Pettersson H. , Zhang F. 
Published: April 2009

Abstract
Analysis of the turbulent kinetic energy (TKE) budget for five slightly unstable cases with swell has been performed based on measurements of mechanical production, buoyancy production, turbulent transport, and dissipation at five levels over the sea, from 2.5 to 26 m. The time rate of change and advection of TKE were found to be small, so the TKE residual is interpreted as an estimate of the pressure transport term (Tp). In two cases with high wave age, the Tp term is a gain at all heights. For three cases with smaller wave age, Tp is a loss in the TKE budget below 5–10 m and a gain for greater heights, where the decrease is exponential, thus showing the combined effects of swell waves and a range of waves traveling slower than the wind. The TKE budget for a case with growing sea but similar wind speed and stability as some of the swell cases has Tp close to zero at all heights. It is shown that the observed characteristic wind profile with either a low-level maximum in the 5–10-m range or a distinct “knee” at that height is an effect of the Tp term.